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Recent Publications

February 2022

De-la-Peña C, León P, Sharkey TD. “Editorial: Chloroplast Biotechnology for Crop Improvement.” Front Plant Sci. February 2022.

Gatreddi S, Urdiain-Arraiza J, Desguin B, Hausinger RP, Hu J. “Structural and mutational characterization of a malate racemase from the LarA superfamily.” Biometals. February 2022.

Singh AK, Ducat DC. “Generation of Stable, Light-Driven Co-cultures of Cyanobacteria with Heterotrophic Microbes.” Methods Mol Biol. January 2022.

Xue S, Pattathil S, da Costa Sousa L, Ubanwa B, Dale B, Jones AD, Balan V. “Understanding the structure and composition of recalcitrant oligosaccharides in hydrolysate using high-throughput biotin-based glycome profiling and mass spectrometry.” Sci Rep. February 2022.

Poliner E, Busch AWU, Newton L, Kim YU, Clark R, Gonzalez-Martinez SC, Jeong BR, Montgomery BL, Farré EM. “Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica.” Plant Physiol. February 2022.

Teoh ST, Leimanis-Laurens ML, Comstock SS, Winters JW, Vandenbosch NL, Prokop JW, Bachmann AS, Lunt SY, Rajasekaran S. “Combined Plasma and Urinary Metabolomics Uncover Metabolic Perturbations Associated with Severe Respiratory Syncytial Viral Infection and Future Development of Asthma in Infant Patients.” Metabolites. February 2022.

Ding X, Zhang X, Paez-Valencia J, McLoughlin F, Reyes FC, Morohashi K, Grotewold E, Vierstra RD, Otegui MS. “Microautophagy Mediates Vacuolar Delivery of Storage Proteins in Maize Aleurone Cells.” Front. Plant Sci. February 2022.

Lei L, Burton ZF. “Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code.” Life. February 2022.

Lin YT, Takeuchi T, Youk B, Umen J, Sears BB, Benning C. “Chlamydomonas CHT7 Is Involved in Repressing DNA Replication and Mitotic Genes During Synchronous Growth.” G3 Genes|Genomes|Genetics. February 2022.

Sosnick TR, Gaffney KA, Guo R, Bridges MD, Chen D, MuhammedNazaar FS, Kim M, Yang Z, Schilmiller AL, Faruk NF, Peng X, Jones AD, Sun L, Hubbell WL, Hong H.“Conformational diversity and contraction of the denatured state ensemble of a helical membrane protein.” Biophysical Journal. February 2022.

Aljazi MB, Gao Y, Wu Y, He J. “SMYD5 is a histone H3-specific methyltransferase mediating mono-methylation of histone H3 lysine 36 and 37.” Biochemical and Biophysical Research Communications. April 2022.

Lundquist PK. “Tracking subplastidic localization of carotenoid metabolic enzymes with proteomics.” Methods in Enzymology. February 2022.

Gu W, Li F, Liu T, Gong S, Gao Q, Li J, Fang Z. “Recyclable, Self-Healing Solid Polymer Electrolytes by Soy Protein-Based Dynamic Network.” Advanced Science. February 2022.

Noyes K, Carlson C, de Lima J, Long TM, Schwarz CV, Stoltzfus JR, Cooper MM. “A Deep Look into Designing a Task and Coding Scheme through the Lens of Causal Mechanistic Reasoning.” Journal of Chemical Education. February 2022.

Dong H, Sousa LDC, Ubanwa B, Jones AD, Balan V. “A New Method to Overcome Carboxyamide Formation During AFEX Pretreatment of Lignocellulosic Biomass.” Front Chem. January 2022.

Sharma G, Song LF, Merz KM. “Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2.” J Chem Inf Model. February 2022.

Oh S, Kong Q, Montgomery BL. “Guard-cell phytochromes impact seedling photomorphogenesis and rosette leaf morphology.” MicroPubl Biol. January 2022.

Chin M, Suh SM, Fang Z, Hegg EL, Diao T. “Depolymerization of Lignin via a Microscopic Reverse Biosynthesis Pathway.” ACS Catalysis. February 2022.

Cholico GN, Nault R, Zacharewski TR. “Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver.” International Journal of Molecular Sciences. February 2022.

Wieloch T, Sharkey TD, Werner RA, Schleucher J. “Intramolecular carbon isotope signals reflect metabolite allocation in plants.” J Exp Bot. January 2022.

Mills RH,  […] Quinn RA, […] Gonzalez DJ. “Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.” Nat Microbiol. January 2022.

Gao Y, Duque-Wilckens N, Aljazi MB, Moeser AJ, Mias GI, Robison A,Zhang Y, He J. “Impaired KDM2B-mediated PRC1 recruitment to chromatin causes defective neural stem cell self-renewal and ASD/ID-like behaviors.” iScience. February 2022.

January 2022

Ntana F, Johnson SR, Hamberger B, Jensen B, Jørgensen HJL, Collinge DB. “Regulation of Tomato Specialised Metabolism after Establishment of Symbiosis with the Endophytic Fungus Serendipita indica.” Microorganisms. January 2022.

Gomez-Cano F, Chu YH, Cruz-Gomez M, Abdullah HM, Lee YS, Schnell DJ, Grotewold E. “Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses.” Plant J. January 2022.

Russell MM, Leimanis-Laurens ML, Bu S, Kinney GA, Teoh ST, McKee RL, Ferguson K, Winters JW, Lunt SY, Prokop JW, Rajasekaran S, Comstock SS. “Loss of Health Promoting Bacteria in the Gastrointestinal Microbiome of PICU Infants with Bronchiolitis: A Single-Center Feasibility Study.” Children (Basel). January 2022.

Nault R, Saha S, Bhattacharya S, Dodson J, Sinha S, Maiti T, Zacharewski T. “Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose–response study designs.” Nucleic Acids Research. January 2022.

Olenic S, Buchanan F, VanPortfliet J, Parrell D, Kroos L. “Conserved Proline Residues of Bacillus subtilis Intramembrane Metalloprotease SpoIVFB Are Important for Substrate Interaction and Cleavage.” J Bacteriol. January 2022.

Johnson KA, Krishnan A. “Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data.” Genome Biol. January 2022.

Petrescu DI, Dilbeck PL, Montgomery BL. “Environmental Tuning of Homologs of the Orange Carotenoid Protein-Encoding Gene in the Cyanobacterium Fremyella diplosiphon.” Front Microbiol. December 2021.

Hong H, Choi HK, Yoon TY. “Untangling the complexity of membrane protein folding.” Curr Opin Struct Biol. January 2022.

Gaffney KA, Guo R, Bridges MD, Muhammednazaar S, Chen D, Kim M, Yang Z, Schilmiller AL, Faruk NF, Peng X, Jones AD, Kim KH, Sun L, Hubbell WL, Sosnick TR, Hong H. “Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein.” Proc Natl Acad Sci U S A. January 2022.

Neofotis P, Temple J, Tessmer OL, Bibik J, Norris N, Pollner E, Lucker B, Weraduwage SM, Withrow A, Sears B, Mogos G, Frame M, Hall D, Weissman J, Kramer DM. “The induction of pyrenoid synthesis by hyperoxia and its implications for the natural diversity of photosynthetic responses in Chlamydomonas.” Elife. December 2021.

So M, Stiban J, Ciesielski GL, Hovde SL, Kaguni LS. “Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase.” Front Genet. December 2021.

Kanazawa A, Chattopadhyay A, Kuhlgert S, Tuitupou H, Maiti T, Kramer DM. “Light potentials of photosynthetic energy storage in the field: what limits the ability to use or dissipate rapidly increased light energy?” R Soc Open Sci. December 2021.

Wurster JI, Peterson RL, Brown CE, Penumutchu S, Guzior DV, Neugebauer K, Sano WH, Sebastian MM, Quinn RA, Belenky P. “Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis.” Cell Rep. December 2021.

Cameron CE, Arnold JJ, Kaguni LS. “Preface, Viral replication enzymes and their inhibitors, Part B.” Enzymes. December 2021.

December 2021

Wu HL, Hsu PY. “RiboPlotR: a visualization tool for periodic Ribo-seq reads.” Plant Methods. December 2021.

Attanayake G, Mao G, Walker KD. “Semibiocatalytic Approach toward Regioisomerically Enriched Ethyl Dimethylpyrazines Important in Flavor Industries.” J Agric Food Chem. December 2021.

Dixon T, Lotz SD, Dickson A. “Creating Maps of the Ligand Binding Landscape for Kinetics-Based Drug Discovery.” Methods Mol Biol. December 2021.

Schmitz RJ, Grotewold E, Stam M. “Review-Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.” The Plant Cell. December 2021.

Moore BM, Lee YS, Wang P, Azodi C, Grotewold E, Shiu SH. “Modeling temporal and hormonal regulation of plant transcriptional response to wounding.” Plant Cell. December 2021.

Witalka D, Lapidus LJ. “Measurement of Submillisecond Protein Folding Using Trp Fluorescence and Photochemical Oxidation.” Methods Mol Biol. November 2021.

Pan Y, Wang X, Li H, Ren J, Zhang Y, Jordahl D, Schuster I, Farmakes J, Hong H, Yang Z. “In situ monitoring of protein transfer into nanoscale channels.” Cell Reports Physical Science. September 2021.

Balan V, Novak D, Knudson W, Jones AD, Iñiguez-Franco FM, Auras R, Cho S, Rodgers A, Ubanwa B. “Nutritious mushroom protein crisp – healthy alternative to starchy snack.” Food Production, Processing and Nutrition. December 2021.

Sosinski LM, Hernandez CM, Neugebauer KA, Ghuneim L-AJ, Guzior DV, Castillo-Bahena A, Mielke J, Thomas R, McClelland M, Conrad D, Quinn RA. “A restructuring of microbiome niche space is associated with Elexacaftor-Tezacaftor-Ivacaftor therapy in the cystic fibrosis lung.” Journal of Cystic Fibrosis. November 2021.

November 2021

Alherech M, Omolabake S, Holland CM, Klinger GE, Hegg EL, Stahl SS. “From lignin to valuable aromatic chemicals: Lignin depolymerization and monomer separation via centrifugal partition chromatography.” ACS Central Science. October 2021.

Fling RR, Zacharewski TR. “Aryl hydrocarbon receptor (Ahr) activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (tcdd) dose-dependently shifts the gut microbiome consistent with the progression of non-alcoholic fatty liver disease.” International Journal of Molecular Sciences. November 2021.

Lou YR, Anthony TM, Fiesel PD, Arking RE, Christensen EM, Jones AD, Last RL. “It happened again: Convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato.” Sci Adv. November 2021.

Steele JFC, Kerfeld CA. “Bioenergetics theory and components: The shells of bacterial microcompartments.” Encyclopedia of Biological Chemistry: Third Edition. July 2021.

Lundquist PK, Susanto FA. “Lipids: Biogenesis of lipid droplets.” Encyclopedia of Biological Chemistry: Third Edition. July 2021.

Sharkey TD. “Photosynthesis: Photosynthetic carbon dioxide fixation.” Encyclopedia of Biological Chemistry: Third Edition. July 2021.

Ghosh Jha SG, […] Gomez-Cano F, […] Rhee SY, Plant Cell Atlas Consortium. "Vision, challenges and opportunities for a Plant Cell Atlas" Elife, September, 2021. 

Gavgani HN, Fawaz R, Ehyaei N, Walls D, Pawlowski K, Fulgos R, Park S, Assar Z, Ghanbarpour A, Geiger JH. “A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb.” Journal of Biological Chemistry. November 2021.

Han Y, Xu Y, Ye Q, Li J, Fang Z. “Marine Sponge-Inspired Organic–Inorganic Double-Network Strategy to Produce Magnesium Oxychloride Cement with Integrated Water Resistance and Compressive Strength.” ACS Sustainable Chem Eng. November 2021.

Zhou P, Enders TA, Myers ZA, Magnusson E, Crisp PA, Noshay J, Gomez-Cano F, Liang Z, Grotewold E, Greenham K, Springer N. “Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information.” Plant Cell. November 2021.

Hoang Y, Franklin JL, Dufour YS, Kroos L. “Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development.” Proc Natl Acad Sci U S A. November 2021.

Khan T, Kuznetsova V, Dominguez-Martin MA, Kerfeld CA, Polívka T. “UV Excitation of Carotenoid Binding Proteins OCP and HCP: Excited-State Dynamics and Product Formation.” ChemPhotoChem. November 2021.

Srikanta Dani KG, Pollastri S, Pinosio S, Reichelt M, Sharkey TD, Schnitzler JP, Loreto F. “Isoprene enhances leaf cytokinin metabolism and induces early senescence.” New Phytol. October 2021.

Reese KL, Fisher CL, Lane PD, Jaryenneh JD, Jones AD, Frank M, Lane TW. “Abiotic and Biotic Damage of Microalgae Generate Different Volatile Organic Compounds (VOCs) for Early Diagnosis of Algal Cultures for Biofuel Production.” Metabolites. October 2021.

Sugimoto K, Zager JJ, Aubin BS, Lange BM, Howe GA. “Flavonoid Deficiency Disrupts Redox Homeostasis and Terpenoid Biosynthesis in Glandular Trichomes of Tomato.” Plant Physiol. October 2021.

Aljazi MB, Gao Y, Wu Y, Mias GI, He J. “Histone H3K36me2-Specific Methyltransferase ASH1L Promotes MLL-AF9-Induced Leukemogenesis.” Front Oncol. October 2021.

October 2021

Jensen M, Tyryshkina A, Pizzo L, Smolen C, Das M, Huber E, Krishnan A, Girirajan S. “Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion.” Genome Med. October 2021.

Kryshtafovych A, […] Feig M, […] Zheng W. “Modeling SARS-CoV-2 proteins in the CASP-commons experiment.” Proteins: Structure, Function and Bioinformatics. October 2021.

Mellon M, Storti M, Vera-Vives AM, Kramer DM, Alboresi A, Morosinotto T. “Inactivation of mitochondrial complex I stimulates chloroplast ATPase in Physcomitrium patens.” Plant Physiol. October 2021.

Panwalkar P, […] Ogrodzinski MP, […] Lunt SY, […] Venneti S. “Targeting integrated epigenetic and metabolic pathways in lethal childhood PFA ependymomas.” Sci Transl Med. October 2021.

Lavell A, Smith M, Xu Y, Froehlich JE, De La Mora C, Benning C. “Proteins associated with the Arabidopsis thaliana plastid rhomboid like protein RBL10.” Plant J. September 2021.

Feig M. “Virtual Issue on Protein Crowding and Stability.” J Phys Chem B. September 2021.

Payankaulam S, Hickey SL, Arnosti DN. “Cell cycle expression of polarity genes features Rb targeting of Vang.” Cells Dev. September 2021.

Liu J, Cook R, Danhof L, Lopatto D, Stoltzfus JR, Benning C. “Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen.” Biochem Mol Biol Educ. September 2021.

Aykul S, Maust J, Martinez-Hackert E. “BMP-4 Extraction from Extracellular Matrix and Analysis of Heparin-Binding Properties.” Mol Biotechnol. September 2021.

Pei J, Song LF, Merz KM Jr. “FFENCODER-PL: Pair Wise Energy Descriptors for Protein-Ligand Pose Selection.” J Chem Theory Comput. September 2021.

Rankin JA, Chatterjee S, Tariq Z, Lagishetty S, Desguin B, Hu J, Hausinger RP. “The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis.” Proc Natl Acad Sci U S A. September 2021.

September 2021

Quinn RA, Hagiwara KA, Liu K, Goudarzi M, Pathmasiri W, Sumner LW, Metz TO. “Bridging the Gap between Analytical and Microbial Sciences in Microbiome Research.” mSystems. September 2021.

Babu VMP, Homiski C, Scotland MK, Chodavarapu S, Kaguni JM, Sutton MD. “Elevated levels of the E. coli nrdAB-encoded ribonucleotide reductase counteract the toxicity caused by an increased abundance of the β clamp.” J Bacteriol. Sep 2021.

Homiski C, Scotland MK, Babu VMP, Chodavarapu S, Maul RW, Kaguni JM, Sutton MD. “The mutant βE202K sliding clamp protein impairs DNA polymerase III replication activity.” J Bacteriol. September 2021.

Ciesielski GL, Kim S, de Bovi Pontes C, Kaguni LS. “Physical and Functional Interaction of Mitochondrial Single-Stranded DNA-Binding Protein and the Catalytic Subunit of DNA Polymerase Gamma.” Front Genet. September 2021.

Gao Y, Aljazi MB, Wu Y, He J. “Vorinostat, a histone deacetylase inhibitor, ameliorates the sociability and cognitive memory in an Ash1L-deletion-induced ASD/ID mouse model.” Neurosci Lett. September 2021.

Gonzalez-Esquer CR, Ferlez B, Weraduwage SM, Kirst H, Lantz AT, Turmo A, Sharkey TD, Kerfeld CA. “Validation of an insertion-engineered isoprene synthase as a strategy to functionalize terpene synthases.” RSC Advances. September 2021.

Proshlyakov DA, Farrugia MA, Proshlyakov YD, Hausinger RP. “Iron-containing ureases.” Coordination Chemistry Reviews. August 2021.

Vogt S, Ramzan R, Grossman LI, Singh KK, Ferguson-Miller S, Yoshikawa S, Lee I, Hüttemann M. “Mitochondrial respiration is controlled by Allostery, Subunit Composition and Phosphorylation Sites of Cytochrome c Oxidase: A trailblazer's tale - Bernhard Kadenbach.”Mitochondrion. Sep 2021.

Cai Y, Shi SQ, Fang Z, Li J. “Design, Development, and Outlook of Superwettability Membranes in Oil/Water Emulsions Separation” Advanced Materials Interfaces. August 2021.

Rivett ED, Heo L, Feig M, Hegg EL. “Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer.” Crit Rev Biochem Mol Biol. Aug 2021.

Sharma G, Merz KM. “Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter.” Biochemistry. Aug 2021.

Jiang L, […] Hovde S, Abisambra JF, Kuo MH, […] Wolozin B. “Interaction of tau with HNRNPA2B1 and N6-methyladenosine RNA mediates the progression of tauopathy.” Mol Cell. Aug 2021.

August 2021

Chai Q, Li S, Collins MK, Li R, Ahmad I, Johnson SF, Frabutt DA, Yang Z, Shen X, Sun L, Hu J, Hultquist JF, Peterlin BM, Zheng YH. “HIV-1 Nef interacts with the cyclin K/CDK13 complex to antagonize SERINC5 for optimal viral infectivity.” Cell Rep. August 2021.

Abebe DA, van Bentum S, Suzuki M, Ando S, Takahashi H, Miyashita S. “Plant death caused by inefficient induction of antiviral R-gene-mediated resistance may function as a suicidal population resistance mechanism.” Commun Biol. August 2021.

Jayaraman ST, Kocot JT, Esfahani SH, Wangler NJ, Uyar A, Mechref Y, Trippier PC, Abbruscato TJ, Dickson A, Aihara H, Ostrov DA, Karamyan VT. “Identification and characterization of two structurally related dipeptides that enhance catalytic efficiency of neurolysin.” J Pharmacol Exp Ther. August 2021.

Uyar A, Dickson A. “Perturbation of ACE2 Structural Ensembles by SARS-CoV-2 Spike Protein Binding.” J Chem Theory Comput. August 2021.

Aykul S, Maust J, Thamilselvan V, Floer M, Martinez-Hackert E. “Smad2/3 activation regulates smad1/5/8 signaling via a negative feedback loop to inhibit 3t3-l1 adipogenesis.” International Journal of Molecular Sciences. August 2021.

Chan C, Foster ST, Cacace MJ, Sandum CT, Wright PT, Volmert B, Yang W, Aguirre A, Li W, Wright NT. “Repositioned Drugs for COVID-19—the Impact on Multiple Organs.” SN Comprehensive Clinical Medicine. August 2021.

Coletta RD, Lavell AA, Garvin DF. “A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon.” IS-MPMI. August 2021.

Naughton KJ, Treviño RE, Moore PJ, Wertz AE, Dickson JA, Shafaat HS. “In Vivo Assembly of a Genetically Encoded Artificial Metalloenzyme for Hydrogen Production.” ACS Synth Biol. August 2021.

Cholico GN, Fling RR, Zacharewski NA, Fader KA, Nault R, Zacharewski TR.  “Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation”.  Scientific Reports. August 2021.

Lea-Smith DJ, Summerfield TC, Ducat DC, Lu X, McCormick AJ, Purton S. “Editorial: Exploring the Growing Role of Cyanobacteria in Industrial Biotechnology and Sustainability.” Front Microbiol. July 2021.

Uhl JD, Sripathi KN, Meir E, Merrill J, Urban-Lurain M,  Haudek, KC. Automated Writing Assessments Measure Undergraduate Learning after Completion of a Computer-Based Cellular Respiration Tutorial. CBE—Life Sciences Education. June 2021.

Wei Y, Jiang S, Li X, Li J, Dong Y, Shi SQ, Li J, Fang Z. “‘Green’ Flexible Electronics: Biodegradable and Mechanically Strong Soy Protein-Based Nanocomposite Films for Human Motion Monitoring.” ACS Appl. Mater. Interfaces. July 2021.

July 2021

Martinez BL, Kararo AT, Parent KN, Underwood SM, Matz RL. “Creating and testing an activity with interdisciplinary connections: Entropy to osmosis.” Chemistry Education Research and Practice. July 2021.

Gregory LM, McClain AM, Kramer DM, Pardo JD, Smith KE, Tessmer OL, Walker BJ, Ziccardi LG, Sharkey TD. “The triose phosphate utilization limitation of photosynthetic rate: out of global models but important for leaf models.” Plant Cell Environ. July 2021.

Broadwater D, Medeiros HCD, Lunt RR, Lunt SY. “Current Advances in Photoactive Agents for Cancer Imaging and Therapy.” Annu Rev Biomed Eng. July 2021.

Ostrowska N, Feig M, Trylska J. “Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex.” Biophys J. July 2021.

Kailasam S, Peiter E. “A path toward concurrent biofortification and cadmium mitigation in plant-based foods.” New Phytologist. June 2021.

Sakkos JK, Hernandez-Ortiz S, Osteryoung KW, Ducat DC. “Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria.” ACS Synth Biol. July 2021.

Muratov EN, Amaro R, Andrade CH, Brown N, Ekins S, Fourches D, Isayev O, Kozakov D, Medina-Franco JL, Merz KM, Oprea TI, Poroikov V, Schneider G, Todd MH, Varnek A, Winkler DA, Zakharov AV, Cherkasov A, Tropsha A. “A critical overview of computational approaches employed for COVID-19 drug discovery.” Chem Soc Rev. 2021 July 2021.

Kasahara K, Re S, Nawrocki G, Oshima H, Mishima-Tsumagari C, Miyata-Yabuki Y, Kukimoto-Niino M, Yu I, Shirouzu M, Feig M, Sugita Y. “Reduced efficacy of a Src kinase inhibitor in crowded protein solution.” Nature Communications. July 2021.

Sharkey TD. “Pentose Phosphate Pathway Reactions in Photosynthesizing Cells.” Cells. June 2021.

Kirst H, Kerfeld CA. “Clues to the function of bacterial microcompartments from ancillary genes.” Biochem Soc Trans. June 2021.

Heo L, Janson G, Feig M. “Physics-Based Protein Structure Refinement in the Era of Artificial Intelligence.” Proteins. June 2021.

Espinoza-Corral R, Herrera-Tequia A, Lundquist PK. “Insights into topology and membrane interaction characteristics of plastoglobule-localized AtFBN1a and AtLOX2.” Plant Signal Behav. June 2021.

Donyapour N, Dickson A. “Predicting partition coefficients for the SAMPL7 physical property challenge using the ClassicalGSG method.” J Comput Aided Mol Des. June 2021.

Hiser C, Montgomery BL, Ferguson‑Miller S “Minireview: TSPO protein binding partners in bacteria, animals, and plants."  Journal of Bioenergetics and Biomembranes.  July 2021.

June 2021

Green AI, Parent KN, Underwood SM, Matz RL. “Connecting Ideas across Courses: Relating Energy, Bonds and How ATP Hydrolysis Powers a Molecular Motor.” American Biology Teacher. Volume 83 May 2021.

Ntana F, Bhat WW, Johnson SR, Jørgensen HJL, Collinge DB, Jensen B, Hamberger B. “A Sesquiterpene Synthase from the Endophytic Fungus Serendipita indica Catalyzes Formation of Viridiflorol.” Biomolecules. June 2021.

Guzior DV, Quinn RA. “Review: microbial transformations of human bile acids.” Microbiome. June 2021.

Sutter M, Melnicki MR, Schulz F, Woyke T, Kerfeld CA. “A catalog of the diversity and ubiquity of bacterial microcompartments.” Nature Communications. June 2021.

Gao Y, Duque-Wilckens N, Aljazi MB, Wu Y, Moeser AJ, Mias GI, Robison AJ, He J. “Loss of histone methyltransferase ASH1L in the developing mouse brain causes autistic-like behaviors.” Commun Biol. June 2021.

Li M, Svoboda V, Davis G, Kramer D, Kunz HH, Kirchhoff H. “Impact of ion fluxes across thylakoid membranes on photosynthetic electron transport and photoprotection.” Nature Plants. June 2021.

Hermanas TM, Subramanian S, Dann CE, Stewart GC.  “Spore-Associated Proteins Involved in c-di-GMP Synthesis and Degradation of Bacillus anthracis.” Journal of Bacteriology. June 2021

Melnicki MR, Sutter M, Kerfeld CA. “Evolutionary relationships among shell proteins of carboxysomes and metabolosomes.” Current Opinion in Microbiology.  June 2021.

Manathunga M, Jin C, Cruzeiro VWD, Miao Y, Mu D, Arumugam K, Keipert K, Aktulga HM, Merz KM Jr, Götz AW. “Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program.” J Chem Theory Comput. June 2021.

Sosa Alfaro V, Campeciño J, Tracy M, Elliott SJ, Hegg EL, Lehnert N. “Elucidating Electron Storage and Distribution within the Pentaheme Scaffold of Cytochrome c Nitrite Reductase (NrfA).” Biochemistry. June 2021.

Dos Santos Oliveira J, Lavell AA, Essus VA, Souza G, Nunes GHP, Benício E, Guimarães AJ, Parent KN, Cortines JR. “Structure and physiology of giant DNA viruses.” Current Opinion in Virology. May 2021.

O'Hagan D, Kruger RE, Gu G, Ralston A. “Efficient generation of endogenous protein reporters for mouse development.” Development. May 2021.

Asija K, Sutter M, Kerfeld CA. “A Survey of Bacterial Microcompartment Distribution in the Human Microbiome.” Frontiers in Microbiology. May 2021.

May 2021

Samart K, Tuyishime P, Krishnan A, Ravi J. “Reconciling multiple connectivity scores for drug repurposing.” Briefings in Bioinformatics. May 2021.

Lei L, Burton ZF. “Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria.” Front Mol Biosci. May 2021.

Lei L, Burton ZF. “Evolution of the genetic code.” Transcription. May 2021.

Shivaiah K-K, Lundquist P. “Omics of Plastoglobule Lipid Droplets from the “Resurrection Plant” Eragrostis nindensis.” The FASEB Journal. May 2021.

Borges RM, […] Merz KM, […] Renslow RS. “Quantum Chemistry Calculations for Metabolomics.” Chemical Reviews. May 2021.

Jagadish SVK, Way DA, Sharkey TD. “Scaling plant responses to high temperature from cell to ecosystem.” Plant Cell Environ. May 2021.

Corral RE, Lundquist P. “ABC1K proteins of Arabidopsis Plastoglobules regulate thylakoid membrane remodeling in chloroplasts.” The FASEB Journal. May 2021.

Fortin J, Wang K-W, Liu M, Kuo M-H. “Small Molecule Inhibitors of Hyperphosphorylated Tau Aggregation and Cytotoxicity.” The FASEB Journal. May 2021.

Feroz, H.a, […] Kerfeld, CA, […] Kumar, M. “Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin.” Biochimica et Biophysica Acta - Biomembranes. August 2021.

Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. “Highlighting membrane protein structure and function: A celebration of the Protein Data Bank.” Journal of Biological Chemistry. January 2021.

Cinelli MA, Jones DA. “Review - Alkaloids of the Genus Datura: Review of a Rich Resource for Natural Product Discovery.” Molecules. April 2021.

Rabbo MA, Khodour Y, Kaguni LS, Stiban J. “Review - Sphingolipid lysosomal storage diseases: from bench to bedside.” Lipids in Health and Disease. May 2021.

Ralston CY, Kerfeld CA. “Integrated Structural Studies for Elucidating Carotenoid-Protein Interactions.” Adv Exp Med Biol. May 2021.

Santos-Merino M, Singh AK, Ducat DC. “Sink engineering in photosynthetic microbes.” Cyanobacteria Biotechnology. April 2021.

Felczak MM, Bowers RM, Woyke T, TerAvest MA. “Zymomonas diversity and potential for biofuel production.” Biotechnol Biofuels. May 2021.

Cruzeiro V, Manathunga M, Merz KM, Götz AW. “Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK.” Chem Inf Model. April 2021.

Feroz H, […] Gaudana S,  […] Kerfeld CA, […] Kumar M. “Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin.” Biochim Biophys Acta Biomembr. April 2021.

Lee YS, Herrera-Tequia A, Silwal J, Geiger JH, Grotewold E. “A hydrophobic residue stabilizes dimers of regulatory ACT-like domains in plant basic helix-loop-helix transcription factors.” J Biol Chem. April 2021.

Strubbe-Rivera JO, Chen J, West BA, Parent KN, Wei G-W, Bazil JN. “Modeling the Effects of Calcium Overload on Mitochondrial Ultrastructural Remodeling.” Appl Sci. March 2021.

Kong Q, Singh SK, Mantyla JJ, Pattanaik S, Guo L, Yuan L, Benning C, Ma W. “TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR4 Interacts with WRINKLED1 to Mediate Seed Oil Biosynthesis.” Plant Physiol. October 2020.

Little M, […] Quinn RA, […] Roach TNF. “Three-Dimensional Molecular Cartography of the Caribbean Reef-Building Coral Orbicella faveolata.” Frontiers in Marine Science. Volume 8. April 2021.

Chan C, Foster ST, Chan KG, Cacace MJ, Ladd SL, Sandum CT, Wright PT, Volmert B, Yang W, Aguirre A, Li W, Wright NT. “Repositioned Drugs for COVID-19—the Impact on Multiple Organs.” SN Comprehensive Clinical Medicine. April 2021.

April 2021

Yin X, Busch FA, Struik PC, Sharkey TD. “Review-Evolution of a biochemical model of steady-state photosynthesis.” Plant Cell Environ. Volume 44. April 2021.

Montgomery BM. “My most memorable mentors? Plants.” Nature. Volume 592. April 2021.

Gupta R, Leimanis ML, Adams M, Bachmann AS, Uhl KL, Bupp CP, Hartog NL, Kort EJ, Olivero R, Comstock SS, Sanfilippo DJ, Lunt SY, Prokop JW, Rajasekaran S. “Balancing Precision vs. Cohort Transcriptomic Analysis of Acute and Recovery Phase of Viral Bronchiolitis.” Am J Physiol Lung Cell Mol Physiol. Volume 320. April 2021.

Landis JB, Miller CM, Broz AK, Bennett AA, Carrasquilla-Garcia N, Cook DR, Last RL, Bedinger PA, Moghe GD. “Migration through a major Andean ecogeographic disruption as a driver of genetic and phenotypic diversity in a wild tomato species.” Mol Biol Evol. Volume 38. April 2021.

Montgomery BL. “Planting Equity: Using What We Know to Cultivate Growth as a Plant Biology Community.” Plant Cell. Volume 32. Nov 2020.

Santos-Merino M, Torrado A, Davis GA, Röttig A, Bibby TS, Kramer DM, Ducat DC. “Improved photosynthetic capacity and photosystem I oxidation via heterologous metabolism engineering in cyanobacteria.” Proc Natl Acad Sci U S A. Volume 118. March 2021.

Raicu A-M, Bird KM, Arnosti DN. “Tête-à-tête with CtBP dimers.” Structure. Volume 29. April 2021.

Pizzo L, Lasser M, Yusuff T, Jensen M, Ingraham P, Huber E, Singh MD, Monahan C, Iyer J, Desai I, Karthikeyan S, Gould DJ, Yennawar S, Weiner AT, Pounraja VK, Krishnan A, Rolls MM, Lowery LA, Girirajan S. “Functional assessment of the "two-hit" model for neurodevelopmental defects in Drosophila and X. laevis.” PLoS Genet. Apr 2021.

Donyapour N, Hirn M, Dickson A. “ClassicalGSG: Prediction of log P using classical molecular force fields and geometric scattering for graphs.” J Comput Chem. Volume 42. Mar 2021.

Santiago JP, Soltani A, Bresson MM, Preiser AL, Lowry DB, Sharkey TD. “Contrasting anther glucose 6-phosphate dehydrogenase activities between two bean varieties suggest an important role in reproductive heat tolerance.” Plant Cell Environ. March 2021.

Espinoza-Corral R, Schwenkert S, Lundquist PK. “Molecular changes of Arabidopsis thaliana plastoglobules facilitate thylakoid membrane remodeling under high light stress.” Plant J. Volume 105. March 2021.

Liu R, Krishnan A. “PecanPy: a fast, efficient, and parallelized Python implementation of node2vec.” Bioinformatics. March 2021.

Tanemura KA, Das S, Merz KM. “AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations.” J Chem Inf Model. Mar 2021.

Mondisa JL, Packard BWL, Montgomery BL. “Understanding what STEM mentoring ecosystems need to thrive: A STEM-ME framework.” Mentoring & Tutoring: Partnership in Learning. Volume 28. March 2021.

Cook R, Lupette J, Benning C. “Review-The Role of Chloroplast Membrane Lipid Metabolism in Plant Environmental Responses.” Cells. March 2021.

March 2021

Doore SM, Subramanian S, Tefft NM, Morona R, TerAvest MA Parent KN. “Large metabolic rewiring from small genomic changes between strains of Shigella flexneri.” J Bacteriol. Volume 203. March 2021.

Jagadish SVK, Way DA, Sharkey TD. “Plant heat stress: concepts directing future research.” Plant Cell Environ. Volume 44. March 2021.

Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. “Highlighting membrane protein structure and function: A celebration of the Protein Data Bank.” J Biol Chem. Mar 2021.

Diepenbrock CH, Ilut DC, Magallanes-Lundback M, Kandianis CB, Lipka AE, Bradbury PJ, Holland JB, Hamilton JP, Wooldridge E, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mateos-Hernandez M, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D. “Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain.” Plant Cell. Volume 32. December 2020.

Deng X, Xin Y, Miller CL, Hamelberg D, Kirberger M, Moremen KW, Hu J, Yang JJ. “Structural Mechanism of Cooperative Regulation of Calcium-Sensing Receptor-Mediated Cellular Signaling.” Curr Opin Physiol. October 2020.

Zheng M, Domanskyi S, Piermarocchi C, Mias G. “Visibility graph based temporal community detection with applications in biological time series.” Scientific Reports. March 2021.

Jurgelewicz A, Dornbos P, Warren M, Nault R, Arkatkar A, Lin H, Threadgill DW, Zacharewski T, LaPres JJ. “Genetics-Based Approach to Identify Novel Genes Regulated by the Aryl Hydrocarbon Receptor (AHR) in Mice Liver.” Toxicol Sci. Volume 180. March 2021.

Santos-Merino M, Torrado A, Davis GA, Röttig A, Bibby TS, Kramer DM, Ducat DD. “Improved photosynthetic capacity and photosystem I oxidation via heterologous metabolism engineering in cyanobacteria.” PNAS. Volume 118. March 2021.

Brose J, Lau KH, Dang TTT, Hamilton JP,  Martins LdV,  Hamberger B,  Hamberger B,  Jiang J,  O'Connor SE, Buell CR. “The Mitragyna speciosa (Kratom) Genome: A resource for data-mining potent pharmaceuticals that impact human health.” G3. Volume 11. March 2021.

Williams TM, Bleau J, Allen ML, Seamans GS, Cannon B, Fontaine N, Halane M, Koopman R, Makunga NP, Moroenyane I, Soto T, Montgomery BL, [Black Botanists Week Committee]. “Growing a Community: The Inaugural #Blackbotanistsweek Recap and Looking Forward.” Taxon. Volume 70. February 2021.

Xu Y, Fu X, Sharkey TD, Shachar-Hill Y, Walker BJ. "The metabolic origins of non-photorespiratory CO2 release during photosynthesis: A metabolic flux analysis.”  Plant Physiol. Volume 185. Feb 2021. Online ahead of print.

Musa MM, Vieille C, Phillips RS. “Secondary Alcohol Dehydrogenases from Thermoanaerobacter pseudoethanolicus and Thermoanaerobacter brockii as Robust Catalysts.” ChemBioChem. Volume 22. Feb 2021. Online ahead of print.


Roach TNF, Dilworth J, Martin Hernandez C, Jones DA, Quinn RA, Drury C. “Metabolomic signatures of coral bleaching history.” Nat Ecol Evol. Volume 5. February 2021.

Heo L, Arbour CF, Janson G, Feig M. “Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.” J Chem Theory Comput. Volume 17. February 2021. Online ahead of print.

Lawson HD, Walton SP,  Christina Chan C. “Metal–Organic Frameworks for Drug Delivery: A Design Perspective.” ACS Appl. Mater. Interfaces. February 2021.

Christov CZ, Chaturvedi SS, Ramanan R, Hu J, Hausinger RP. “Atomic and electronic structure determinants distinguish between ethylene formation and L-arginine hydroxylation reaction mechanisms in the ethylene-forming enzyme.” ACS Catalysis. February 2021.

Osei-Bonsu I, McClain AM, Walker BJ, Sharkey TD, Kramer DM. “The roles of photorespiration and alternative electron acceptors in the responses of photosynthesis to elevated temperatures in cowpea.” Plant Cell Environ. Feb 8. 2021. Online ahead of print.

Sengupta  A, Li Z, Song LF, Li P, Merz KM. “Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.” J Chem Inf Model. Feb 2021.

Ely KS,…Sharkey TD,…Yang, D. “A reporting format for leaf-level gas exchange data and metadata.” Ecological Informatics. Volume 61, March 2021.

Manhas N*, Duong QV*, Lee P, Richardson JD, Robertson JD, Moxley MA, Bazil JN (*contributed equally). “Computationally modeling mammalian succinate dehydrogenase kinetics identifies the origins and primary determinants of ROS production.” Journal of Biological Chemistry. Volume 295. November 2020.

Fedeson DT, Ducat DF. “Symbiotic Interactions of Phototrophic Microbes: Engineering Synthetic Consortia for Biotechnology.” Role of Microbial Communities for Sustainability. January 2021.

Dutagaci B, Nawrocki G, Goodluck J, Ashkarran AA, Hoogstraten CG, Lapidus LJ, Feig M. “Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments.” Elife. January 2021. Online ahead of print.

Vocelle D, Chesniak OM, Smith MR, Chan C, Walton SP. “Kinetic analysis of the intracellular processing of siRNAs by confocal microscopy.” Microscopy. Volume 69. December 2020.

Burrows CJ, …, Merz KM, …, Laskin J. “Confronting Racism in Chemistry Journals.” ACS Biomater Sci Eng. July 2020.

Moyne O, …, Quinn RA, …, Gouëllec AL. “Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance, Virulence and Clinical Outcome in Cystic Fibrosis Chronic Infections.” Metabolites. Volume 11. January 2021.


Mias G, Singh VV, Rogers L, Xue S, Zheng M, Domanskyi S, Kanada M, Piermarocchi C, He J. “Longitudinal saliva omics responses to immune perturbation: a case study.” Scientific Reports. Volume 11. January 2021.

Strubbe-Rivera JO, Schrad JR, Pavlov EV, Conway JF, Parent KN, Bazil JN. “The mitochondrial permeability transition phenomenon elucidated by cryo-EM reveals the genuine impact of calcium overload on mitochondrial structure and function.” Scientific Reports. Volume 11. January 2021.

Yuan Z, Klinger GE, Nikafshar S, Cui Y, Fang Z, …,Hegg EL. “Effective Biomass Fractionation through Oxygen-Enhanced Alkaline–Oxidative Pretreatment.” ACS Sustainable Chem. Eng. Volume 9. January 2021.

Uhl, JD, Sripathi, KN, Saldanha, JN, Moscarella, RA, Merrill, J, Urban-Lurain, M & Haudek, KC. “Introductory biology undergraduate students' mixed ideas about genetic information flow.” Biochem Mol Biol Educ. December 2020.

Zhou F, Last RL, Pichersky E. “Degradation of salicylic acid to catechol in Solanaceae by SA 1-hydroxylase.” Plant Physiology. Volume 185. January 2021.

Kuliyev E, Zhang C, Sui D, Hu J. “Zinc transporter mutations linked to Acrodermatitis enteropathica disrupt function and cause mistrafficking.” Journal of Biological Chemistry. Volume 296. January 2021.

Sugimoto N, Engelgau P, Jones AD, Beaudry R. “Citramalate synthase yields a biosynthetic pathway for isoleucine and straight- and branched-chain ester formation in ripening apple fruit.” PNAS. Volume 118. January 2021.

Rahimabad PK, Anthony TM, Daniel Jones AD, Eslamimehr S, Mukherjee N, Ewart S, Holloway JW, Arshad H, Commodore S, Karmaus W. “Nicotine and Its Downstream Metabolites in Maternal and Cord Sera: Biomarkers of Prenatal Smoking Exposure Associated with Offspring DNA Methylation.” International Journal of Environmental Research and Public Health. Volume 17. January 2021.

Monson RK, Weraduwage SM, Rosenkranz M, Schnitzler J-P, Sharkey TD. “Leaf isoprene emission as a trait that mediates the growth-defense tradeoff in the face of climate stress.” Oecologia. January 2021.

Warren MR, Radulescu  A, Dornbos  P, Cuomo  D, Zumwalt S, Bueso-Mendoza D, Nitcher M, LaPres JJ, Threadgill DW. “Peanut butter as an alternative dose delivery method to prevent strain-dependent orogastric gavage-induced stress in mouse teratogenicity studies.” J Pharmacol Toxicol Methods. Volume 106. December 2020.

Merz KM Jr, Amaro R, Cournia Z, Rarey M, Soares T, Tropsha A, Wahab HA, Wang R. “Editorial: Method and Data Sharing and Reproducibility of Scientific Results.” J Chem Inf Model. Volume 60. December 2020.

Merz KM Jr, De Fabritiis G, Wei GW. “Generative Models for Molecular Design.” J Chem Inf Model. Volume 60. December 2020.

Nunes-Alves A, Mazzolari A, Merz KM Jr. “What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling.” J Chem Inf Model. Volume 60. December 2020.

Preiser AL, Banerjee,A, Weise SE, Renna L, Brandizzi F, Sharkey TD. “Phosphoglucoisomerase Is an Important Regulatory Enzyme in Partitioning Carbon out of the Calvin-Benson Cycle.” Frontiers in Plant Science. Volume 11. December 2020.

Teoh S, Leimanis M, Andersen N, Sanfilippo D, Rajasekaran S, Lunt S. “Advancing Our Understanding of Infant Bronchiolitis Using Plasma and Urine Metabolomics.” Critical Care Medicine. Volume 49. January 2021.

Montgomery BL. “Make equity essential to expedite change in academia.” Nat Microbiol. Volume 6. January 2021.

Voss PG, Haudek KC, Patterson RJ, Wang JL. “Complementation of splicing activity by a galectin-3-u1 snrnp complex on beads.” Journal of Visualized Experiments. Volume 2020.

Lotz SD, Dickson A. “Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling.” ACS Omega. Volume 5. December 2020.

Shee PK, Yan H, Walker KD. “Intermolecular Amine Transfer to Enantioenriched trans-3-Phenylglycidates by an α/β-Aminomutase to Access Both anti-Phenylserine Isomers.” ACS Catalysis. Volume 10. December 2020.

Rinaldi G, Pranzini E, Van Elsen J, …, Lunt SY, Thomas G.P.Grünewald TGP, Fendt SM. “In Vivo Evidence for Serine Biosynthesis-Defined Sensitivity of Lung Metastasis, but Not of Primary Breast Tumors, to mTORC1 Inhibition.” Molecular Cell. Volume 80. December 2020.

Pan J, Hu Y, Wang H, Guo Q, Chen Y, Howe GA, Yu D. “Molecular mechanism underlying the synergetic effect of jasmonate on abscisic acid signaling during seed germination in arabidopsis.” Plant Cell. Volume 32. December 2020.

Takeuchi T, Lin YT, Fekaris N, Umen J, Sears BB, Benning C. “Modulation of CHT7 complexes during light/dark- And nitrogen-mediated life cycle transitions of chlamydomonas.” Plant Physiology. Volume 184. December 2020.

Moore BM, Wang P, Fan P, Lee A, Leong B, Lou YR, Schenck CA, Sugimoto K, Last R, Lehti-Shiu MD, Barry CS, Shiu SH. “Within- and cross-species predictions of plant specialized metabolism genes using transfer learning”. In Silico Plants. December 2020

Oliver J, Fan M, McKinley B, Zemelis-Durfee S, Brandizzi F, Wilkerson C, Mullet JE. “The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor.” Plant Journal. Volume 104. December 2020.

Ghuneim L-AJ, Distaso MA, Chernikova TN, Bargiela R, Lunev EA, Korzhenkov AA, Toshchakov SV, Rojo D, Barbas C, Ferrer M, Golyshina OV, Golyshin PN, Jones DL “Utilization of low molecular weight organic compounds by the filterable fraction of a lotic microbiome.” FEMS Microbiology Ecology. Volume 96. December 2020.


Gomez-Cano F, Carey L, Lucas K, Navarrete TG, Mukundi M, Lundback S, Schnell D, Grotewold E. “CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa.” Database. Volume 2020. December 2020

Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E. “Pre-termination Transcription Complex: Structure and Function.” Mol Cell. Volume 80. December 2020. Online ahead of print.

Hu J. “Towards unzipping the ZIP metal transporters: structure, evolution, and implications on drug discovery against cancer.” FEBS J. Volume 287. Dec 2020. Online ahead of print.

de Los Campo G, Pook T, Gonzalez-Reymundez A, Simianer H, Mias G, Vazquez AI. “ANOVA-HD: Analysis of variance when both input and output layers are high-dimensional.” PLoS One. Dec 2020.

Singh S, Kailasam S, Lo JC, Yeh KC. “Histone H3 lysine4 trimethylation‐regulated GRF11 expression is essential for the iron deficiency response in Arabidopsis thaliana” New Phytologist. Volume 228. December 2020.

Shee PK, Yan H, Walker KD.“Intermolecular amine transfer to enantioenriched trans-3-phenylglycidates by an α/β-aminomutase to access both anti-phenylserine isomers” ACS Catalysis. Volume 10. December 2020.

González de Cózar JM, Carretero-Junquera M, Ciesielski GL, Miettinen SM, Varjosalo M, Kaguni LS, Dufour E, Jacobs HT. “A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1.” Journal of Biochemistry. Volume 168. November 2020.

Lapidus LJ. “The road less traveled in protein folding: evidence for multiple pathways (Review)” Current Opinion in Structural Biology. Volume 66. February 2021.

Jung J, Kobayashi C, Kasahara K, Tan C, Kuroda A, Minami K, Ishiduki S, Nishiki T, Inoue H, Ishikawa Y, Feig M, Sugita Y. “New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems.” J Comput Chem. Volume 41. November 2020.

Dixon T, Uyar A, Ferguson-Miller S, Dickson A. “Membrane-mediated ligand unbinding of the PK-11195 ligand from TSPO.” Biophys J. Volume 119. November 2020.


Aksenov AA, […] Quinn RA,  […] Veselkov K. “Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.” Nat Biotechnol. Volume 38. November 2020.

Nayfach S, […] Kerfeld S,  […] IMG/M Data Consortium. “A genomic catalog of Earth’s microbiomes.” Nat Biotechnol. Volume 38. November 2020

Parry G, […] Last RL, […] The Multinational Arabidopsis Steering Committee. “Current status of the multinational Arabidopsis community.” Plant Direct. Volume 4. July 2020.

Mitra A, Raicu AM, Hickey SL, Pile LA, Arnosti DA. “Soft repression: Subtle transcriptional regulation with global impact.” Bioessays. Volume 42. November 2020.

Lybbert AC, Williams JL, Raghuvanshi R, Jones AD, Quinn RA. “Mining Public Mass Spectrometry Data to Characterize the Diversity and Ubiquity of P. aeruginosa Specialized Metabolites.” Metabolites. Volume 10. November 2020.

Rahnamoun A, Kaymak MC, Manathunga M, Götz AW, Duin A, Merz KM, Aktulga HM. “ReaxFF/AMBER-A Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations.” J Chem Theory Comput. Volume 16. Nov 2020. Online ahead of print.

Vrbanac A, Patras KA, Jarmusch AK, Mills RH, Shing SR, Quinn RA, Vargas F, Gonzalez DJ, Dorrestein PC, Knight R, Nizet V. “Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic.” mSystems. Volume 5. November 2020.

McCracken J, Casey TM, Hausinger RP. “1H-HYSCORE Reveals Structural Details at the Fe(II) Active Site of Taurine:2-Oxoglutarate Dioxygenase.” Applied Magnetic Resonance. Volume 51. October 2020.

Edwards M, Johnson MDL, Fernandez RW, Montgomery BL, Adelaja A, Akingbade T. Mentoring to Foster a Diverse Future. Cell. Volume 183. October 2020.

Ogrodzinski MP, Teoh ST, Lunt SY. “Targeting subtype-specific metabolic preferences in nucleotide biosynthesis inhibits tumor growth in a breast cancer model.” Cancer Res. Volume 80. November 2020. Online ahead of print.

Montgomery BL. “Lessons from Microbes: What Can We Learn about Equity from Unculturable Bacteria?” mSphere. October 2020.

Nath A, Oak A, Chen KY, Li I, Splichal RC, Portis J, Foster S, Walton SP, Chan C. “Palmitate-induced IRE1-XBP1-ZEB signaling represses desmoplakin expression and promotes cancer cell migration.” Mol Cancer Res. October 2020. Online ahead of print.

Li P, Merz KM. “Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program.” Structural Genomics. October 2020.

Jiang N, Dillon FM, Silva A, Gomez-Cano L, Grotewold E. “Rhamnose in plants - from biosynthesis to diverse functions.” Plant Science. Volume 302. January 2021. Online ahead of print.

Watts JR, Ralston A. “Universal assembly instructions for the placenta.” Nature. Volume 586 (News and Commentary). October 2020.

Aljazi MB, Gao Y, Wu Y, Mias GI, He J. “Cell Signaling Coordinates Global PRC2 Recruitment and Developmental Gene Expression in Murine Embryonic Stem Cells.” iScience. Volume 23. November 2020.

Brock MT, Rubin MJ, DellaPenna D, Weinig C. “A nested association mapping panel in arabidopsis thaliana for mapping and characterizing genetic architecture.” G3: Genes, Genomes, Genetics. Volume 10. October 2020.

Bao Y, Magallenes-Lundback M, Deason N, DellaPenna D. “High throughput profiling of tocochromanols in leaves and seeds of Arabidopsis and Maize.” Plant Methods. Volume 16. September 2020.

Martinez-Hackert E, Sundan A, Holien T. “Receptor binding competition: A paradigm for regulating TGF-β family action.” Cytokine Growth Factor Rev. Volume 55. Oct 2020.

Desguin B, Urdiain-Arraiza J, Da Costa M, Fellner M, Hu J, Hausinger RP, Desmet T, Hols P, Soumillion P. “Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.” Sci Rep. October 2020.

October 2020

Zhao W, Korobskiy D, Chandrasekharan S, Merz KM, Chacko G. “Converging Interests: Chemoinformatics, History, and Bibliometrics.” J. Chem. Inf. Model. Volume 60. October 2020.

Lybrand DB, Anthony TM, Jones AD, Last RL. “An Integrated Analytical Approach Reveals Trichome Acylsugar Metabolite Diversity in the Wild Tomato Solanum pennellii.” Metabolites. Volume 10. Oct 2020.

Mancuso CA, Canfield JL, Singla D, Krishnan A. “A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes.” Nucleic Acids Res. Volume 48. October 2020. Online ahead of print.

Subramanian S, Parent KN, Doore, SM. “Ecology, Structure, and Evolution of Shigella Phages.” Annual Review of Virology. Volume 7, 2020.

Yu X, Bao Y. “Phylogenetics of Molecular Regulators Contributing to Plant Stress Tolerance.” Diversity. Volume 12. October 2020.

Liu M, Dexheimer T, Sui D, Hovde S, Deng X, Kwok R, Bochar DA, Kuo MH. “Hyperphosphorylated tau aggregation and cytotoxicity modulators screen identified prescription drugs linked to Alzheimer's disease and cognitive functions.” Scientific Reports. Volume 10. October 2020.

Roussey NM, Dickson A. “Enhanced Jarzynski free energy calculations using weighted ensemble.” J Chem Phys. Volume 153. October 2020.

Doore S, Subramanian S, Parent K. “Structural Analysis of the Shigella Virus Sf14 Capsid.” Microscopy and Microanalysis 2020 Proceedings. July 2020.

Zhai X, Haudek KC, Shi L, Nehm RH, Urban‐Lurain M. “From substitution to redefinition: A framework of machine learning‐based science assessment.” J Res Sci Teach. Volume 57. October 2020.

Jarmusch AK, Wang M, […] Quinn R, […] Dorrestein PC. “ReDU: a framework to find and reanalyze public mass spectrometry data.” Nature Methods. Volume 17. August 2020.

Louis-Félix Nothias, Daniel Petras, […] Quinn R, […] Dorrestein PC. “Feature-based molecular networking in the GNPS analysis environment.” Nature Methods. Volume 17. August 2020.

Dominguez-Martin MA, Hammel M, Gupta S, Lechno-Yossef S, Sutter M, Rosenberg DJ, Chen Y, Petzold CP, Ralston CY, Polívka T, Kerfeld CA. “Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP.” Scientific Reports. September 2020.

Orlando B, Li Y, Liao M. “Snapshots of Endotoxin Extraction from the Gram-Negative Inner Membrane.” Microscopy and Microanalysis 2020 Proceedings. August 2020.

September 2020

Dong S, Subramanian S, Parent KN, Chen M. “Promotion of CTL epitope presentation by a nanoparticle with environment-responsive stability and phagolysosomal escape capacity.” J Control Release.  Volume 328.  September 2020. Online ahead of print.

Guo R, Cang Z, Yao J, Kim M, Deans E, Wei G, Kang S-G, Hong, H.  “Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme.”  Proceedings of the National Academy of Sciences of the United States of America. Volume 117. September 2020.

Das S, Edison AS, Merz KM.  “Metabolite Structure Assignment Using in Silico NMR Techniques.” Analytical Chemistry.  Volume 92. August 2020.

Mukerjee S, Gonzalez-Reymundez A, Lunt  SY, Vazquez AI. “DNA Methylation and Gene Expression with Clinical Covariates Explain Variation in Aggressiveness and Survival of Pancreatic Cancer Patients.” Cancer Investigation.  Volume 38.  September 2020.

Meier M, Liu Y, Lay-Pruitt KS, Takahashi H, von Wirén N.  “Auxin-mediated root branching is determined by the form of available nitrogen.”  Nature Plants.  Volume 6. September 2020.

Allred ZDR, Farias AJ, Kararo AT, Parent KN, Matz RL, Underwood SM. “Students' use of chemistry core ideas to explain the structure and stability of DNA.” Biochem Mol Biol Educ. Volume 48. Sep 2020. Online ahead of print.

Hausinger RP.  “Hydrogenase” Biochemistry of Nickel. Volume 12. September 2020.

Miller GP, Bhat WW, Lanier ER, Johnson SR, Mathieu DT, Hamberger B. “The biosynthesis of the anti-microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all-cis prenyl intermediate.”  Plant Journal.  Aug 2020. Online ahead of print.

Santiago JP, Ward JM, Sharkey TD. “Phaseolus vulgaris SUT1.1 is a high affinity sucrose-proton co-transporter.” Plant Direct. Volume 4. August 2020.

Campeciño J, Lagishetty S, Wawrzak Z, Alfaro VS, Lehnert N, Reguera G, Hu J, Hegg EL. “Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass.” J Biol Chem. Volume 295. August 2020.

Guo R, Cang Z,  Yao, J  Kim M, Deans E,  Wei G, Kang SG, Hong H. “Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme.” Proc Natl Acad Sci USA. Volume 117. August 2020.

Lau KH, Bhat WW, Hamilton JP, Wood JC,  Vaillancourt B,  Wiegert-Rininger K, Newton L, Hamberger B, Holmes D, Hamberger B, Buell CR. “Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids” DNA Research. Volume 27. June 2020.

Small S, Arnosti D. “Transcriptional Enhancers in Drosophila.” Genetics. Volume 216. September 2020.

Hao Liu, Luo Z, Lin, YW, Merz KM, Zheng Z. “Receptor-Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method.” Journal of Chemical Theory and Computation. Volume 16. June 2020.

August 2020

Song LF, Merz KM. “Evolution of Alchemical Free Energy Methods in Drug Discovery.”  J. Chem. Inf. Model.  Volume 60. August 2020.

Sharkey T, Preiser A, Weraduwage S, Gog L. “Source of 12C in Calvin Benson cycle intermediates and isoprene emitted from plant leaves fed with 13CO2.”  Biochem J.  Volume 477. August 2020.

Teoh ST, Ogrodzinski MP, Lunt SY.  “UDP-glucose 6-dehydrogenase knockout impairs migration and decreases in vivo metastatic ability of breast cancer cells.” Cancer Letters. Volume 492.  July 2020. Online ahead of print.

Miller GP, Waheed Bhat W, Lanier ER, Johnson SR, Mathieu DT, Hamberger B. “The biosynthesis of the anti‐microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all‐cis prenyl intermediate.” The Plant Journal. Volume 103. August 2020.

Liu M, Sui D, Dexheimer T, Hovde S, Deng X, Wang XW, Lin HL, Chien HT, Kweon HK, Kuo NS, Ayoub CA, Jimenez-Harrison D, Andrews PC, Kwok R, Bochar DA, Kuret J, Fortin J, Tsay YG, Kuo MH. “Hyperphosphorylation Renders Tau Prone to Aggregate and to Cause Cell Death.” Molecular Neurobiology. Volume 57.  August 2020. Online ahead of print.

Veziroglu E, Mias G. “Characterizing Extracellular Vesicles and Their Diverse RNA Contents.” Frontiers in Genetics. Volume 11. July 2020.

Teoh ST, Ogrodzinski MP, Lunt SY. “UDP-glucose 6-dehydrogenase knockout impairs migration and decreases in vivo metastatic ability of breast cancer cells.” Cancer Lett. August 2020. Online ahead of print.

Splichal RC, Gredell, Vogel E, Malefyt A, Comiskey G, Smith M, Chan C, Walton P. “Modulating Polymer-siRNA Binding Does Not Promote Polyplex-Mediated Silencing.” Nucleic Acid Ther. July 2020. Online ahead of print.

Nevarez JL, Turmo A, Hu J ,Hausinger RP. “Biological Pincer Complexes.” ChemCatChem. Volume 12. May 2020.

Koenig AM, Benning C, Hoffmann-Benning S.“Lipid trafficking and signaling in plants”. Lipid Signaling and Metabolism. Chapter 2. 2020.

Hamberger B, Yuen MM, Buschiazzo E, Cullis C, Yuen A, Ritland C, Bohlmann J, Hamberger B.“An Intact, But Dormant LTR Retrotransposon Defines a Moderately Sized Family in White Spruce (Picea glauca).” The Spruce Genome. Pages 51-63. August 2020.

Cang Z, Munch E, Wei GW. “Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis.” J Appl. and Comput. Topology. Volume 4.  August 2020.

Hoogstraten CG, Terrazas M, Aviñó A, White NA, Sumita M.  “Dynamics-Function Analysis in Catalytic RNA Using NMR Spin Relaxation and Conformationally Restricted Nucleotides.”  Methods Mol Biol. Pages 183-202.  July 2020.

Kariagina A, Lunt SY, McCormick J. “Genomic and metabolomic analysis of step-wise malignant transformation in human skin fibroblasts.” Carcinogenesis.  Volume 41.  July 2020.

“Metabolomic profiling of mouse mammary tumor-derived cell lines reveals targeted therapy options for cancer subtypes.”  Ogrodzinski MP, Teoh ST, Lunt SY. Cellular Oncology. July 2020.  Online ahead of print.

Hoffmann-Benning S. “Beyond Membranes: The Evolution of Plant Lipid Signaling.” Molecular Plant. Volume 13. July 2020.

Xu G, Takahashi H. “Improving nitrogen use efficiency: from cells to plant systems.”  J Exp Bot. Volume 71. July 2020.

Lay-Pruitt KS, Takahashi H. “Integrating N signals and root growth: the role of nitrate transceptor NRT1.1 in auxin-mediated lateral root development.” J Exp Bot. Volume 71. July 2020.

Liu Y, Jia Z, Li X, Wang Z, Chen F, Mi G, Forde B, Takahashi H, Yuan L. “Involvement of a truncated MADS-box transcription factor ZmTMM1 in root nitrate foraging.” J Exp Bot. Volume 71. July 2020.

July 2020

Scott KM, Harmer TL, Gemmell BJ, Kramer AM, Sutter M, Kerfeld CA, Barber KS, Bari S, Boling JW, Campbell CP, Gallard-Gongora JF, Jackson JK, Lobos A, Mounger JM, Radulovic PW, Sanson JM, Schmid S, Takieddine C, Warlick KF, Whittaker R.  “Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters.”  FEMS Microbiol Lett. Volume 367. July 2020.

Alseekh S, Ofner I, Liu Z, Osorio S, Vallarino J, Last RL, Zamir D, Tohge T, Fernie, AR.  “Quantitative trait loci analysis of seed-specialized metabolites reveals seed-specific flavonols and differential regulation of glycoalkaloid content in tomato”.  Plant Journal.  Volume 103.  July 2020.

Lundquist P, Shivaiah KK, Espinoza-Corral R. “Lipid droplets throughout the evolutionary tree.”  Progress in Lipid Research.  Volume 78. April 2020.

Sahrmann P, Donnan P, Merz K, Mansoorabadi S, Goodwin D.  “MRP.py: A Parameterizer of Post-Translationally Modified Residues.”  J Chem Inf Model.  July 2020. Online ahead of print.

Lybrand DB, Xu H, Last RL, Pichersky E. “How Plants Synthesize Pyrethrins: Safe and Biodegradable Insecticides.” Trends in Plant Science.  Volume 25. July 2020.

Klinger GE, Zhou Y, Hao P, Robbins J, Aquilina JM, Jackson JE, Hegg EL. “Nucleophilic Thiols Reductively Cleave Ether Linkages in Lignin Model Polymers and Lignin.”  ChemSusChem.  July 2020. Online ahead of print.

Scott KM, Harmer TL, Gemmell BJ, Kramer AM, Sutter M, Kerfeld CA, Barber KS, Bari S, Boling JW, Campbell CP. “Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters.” FEMS Microbiology Letters. June 2020.

Sharkey TD. Emerging research in plant photosynthesis. Emerg Top Life Sci. June 23 2020.

Lupette J, Benning C. “Human health benefits of very-long-chain polyunsaturated fatty acids from microalgae”. Biochimie. May 2020.

Mazzolari A, Nunes-Alves A, Wahab HA, Amaro RE, Cournia Z, and Merz KM. “Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry.”  Journal of Chemical Information and Modeling. July 5th, 2020.

November 2019

Young E, Sakkos JK, Huang J, Wright JK, Kachel B, Fuentes-Cabrera M, Kerfeld CA, Ducat DC. “Visualizing in vivo dynamics of designer nanoscaffolds.” Nano Lett. (2019) Nov 20. doi: 10.1021/acs.nanolett.9b03651

Nawrocki G, Im W, Sugita Y, Feig M. “Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending.” Proc Natl Acad Sci U S A. (2019) Nov 18. doi: 10.1073/pnas.1910771116

Rogers LRK, Verlinde M, Mias GI. “Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease.” PLoS One. (2019) Nov 15;14(11):e0224750. doi: 10.1371/journal.pone.0224750

Josyula N, Andersen ME, Kaminski NE, Dere E, Zacharewski TR, Bhattacharya S. “Gene co-regulation and co-expression in the aryl hydrocarbon receptor-mediated transcriptional regulatory network in the mouse liver.” Arch Toxicol. (2019) Nov 14. doi: 10.1007/s00204-019-02620-5

Kuznetsova V, Dominguez-Martin MA, Bao H, Gupta S, Sutter M, Kloz M, Rebarz M, Přeček M, Chen Y, Petzold CJ, Ralston CY, Kerfeld CA, Polívka T. “Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix.” Biochim Biophys Acta Bioenerg. (2019) Nov 14;148120. doi: 10.1016/j.bbabio.2019.148120

Vocelle D, Chan C, Walton SP. “Endocytosis Controls Small Interfering RNA Efficiency: Implications for Small Interfering RNA Delivery Vehicle Design and Cell-Specific Targeting.” Nucleic Acid Ther. (2019) Nov 12. doi: 10.1089/nat.2019.0804

Rogers LRK, de los Campos G, Mias GI. “Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination.” Front. Immunol. (2019) Nov 7;10:2616. doi: 10.3389/fimmu.2019.02616

Heo L, Feig M. “High-Accuracy Protein Structures by Combining Machine-Learning with Physics-Based Refinement.” Proteins. (2019) Nov 6. doi: 10.1002/prot.25847

Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. “Learning representations of microbe-metabolite interactions.” Nat Methods. (2019) Nov 4. doi: 10.1038/s41592-019-0616-3

Dornbos P, Jurgelewicz A, Fader KA, Williams K, Zacharewski TR, LaPres JJ. “Characterizing the Role of HMG-CoA Reductase in Aryl Hydrocarbon Receptor-Mediated Liver Injury in C57BL/6 Mice.” Sci Rep. (2019) Nov 1;9(1):15828. doi: 10.1038/s41598-019-52001-2

Ocotober 2019

Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. “Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.” Genome Biol. (2019) Oct 31;20(1):226. doi: 10.1186/s13059-019-1834-9

Broadwater D, Bates M, Jayaram M, Young M, He J, Raithel AL, Hamann TW, Zhang W, Borhan B, Lunt RR, Lunt SY. “Modulating cellular cytotoxicity and phototoxicity of fluorescent organic salts through counterion pairing.” Sci Rep. (2019) Oct 25;9(1):15288. doi: 10.1038/s41598-019-51593-z

Madsen CS, TerAvest MA. “NADH dehydrogenases Nuo and Nqr1 contribute to extracellular electron transfer by Shewanella oneidensis MR-1 in bioelectrochemical systems.” Sci Rep. (2019) Oct 18;9(1):14959. doi: 10.1038/s41598-019-51452-x

Sharkey TD. “Is triose phosphate utilization important for understanding photosynthesis?” J Exp Bot. (2019) Oct 17;. doi: 10.1093/jxb/erz393

Schenck CA, Last RL. “Location, Location! Cellular relocalization primes specialized metabolic diversification.” FEBS J. (2019) Oct 17;. doi: 10.1111/febs.15097

Ghanbarpour A, Pinger C, Esmatpour Salmani R, Assar Z, Santos EM, Nosrati M, Pawlowski K, Spence D, Vasileiou C, Jin X, Borhan B, Geiger JH. “Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches.” J Am Chem Soc. (2019) Oct 16;. doi: 10.1021/jacs.9b04664

McClain AM, Sharkey TD. “Building a better equation for electron transport estimated from chlorophyll fluorescence: Accounting for non-photosynthetic light absorption.” New Phytol. (2019) Oct 12;. doi: 10.1111/nph.16255

Collins FL, Rios-Arce ND, Schepper JD, Jones AD, Schaefer L, Britton RA, McCabe LR, Parameswaran N. “Beneficial effects of Lactobacillus reuteri 6475 on bone density in male mice is dependent on lymphocytes.” Sci Rep. (2019) Oct 11;9(1):14708. doi: 10.1038/s41598-019-51293-8

Kirst H, Kerfeld CA. “Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering.” BMC Biol. (2019) Oct 10;17(1):79. doi: 10.1186/s12915-019-0691-z

Asirvatham-Jeyaraj N, Jones AD, Burnett R, Fink GD. “Brain Prostaglandin D2 Increases Neurogenic Pressor Activity and Mean Arterial Pressure in Angiotensin II-Salt Hypertensive Rats.” Hypertension. (2019) Oct 7;HYPERTENSIONAHA11913175. doi: 10.1161/HYPERTENSIONAHA.119.13175

Gooding S, Olechnowicz SWZ, Morris EV, Armitage AE, Arezes J, Frost J, Repapi E, Edwards JR, Ashley N, Waugh C, Gray N, Martinez-Hackert E, Lim PJ, Pasricha SR, Knowles H, Mead AJ, Ramasamy K, Drakesmith H, Edwards CM. “Transcriptomic profiling of the myeloma bone-lining niche reveals BMP signalling inhibition to improve bone disease.” Nat Commun. (2019) Oct 4;10(1):4533. doi: 10.1038/s41467-019-12296-1

Jasiński M, Miszkiewicz J, Feig M, Trylska J. “Thermal Stability of Peptide Nucleic Acid Complexes.” J Phys Chem B. (2019) Oct 3;123(39):8168-8177. doi: 10.1021/acs.jpcb.9b05168

September 2019

Felczak MM, Jacobson TB, Ong WK, Amador-Noguez D, TerAvest MA. “Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4.” Front Microbiol. (2019) Sep 27;10:2270. doi: 10.3389/fmicb.2019.02270

Scharlau M, Geren L, Zhen EY, Ma L, Rajagukguk R, Ferguson-Miller S, Durham B, Millett F. “Definition of the Interaction Domain and Electron Transfer Route between Cytochrome c and Cytochrome Oxidase.” Biochemistry. (2019) Sep 26. doi: 10.1021/acs.biochem.9b00646

Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. “Niche partitioning of a pathogenic microbiome driven by chemical gradients.” Sci Adv. (2018) Sep 26;4(9):eaau1908. doi: 10.1126/sciadv.aau1908

Reese KL, Fisher CL, Lane PD, Jaryenneh JD, Moorman MW, Jones AD, Frank M, Lane TW. “Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes.” Sci Rep. (2019) Sep 25;9(1):13866. doi: 10.1038/s41598-019-50125-z

Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. “Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.” mSystems. (2019) Sep 24;4:(5). doi: 10.1128/mSystems.00375-19

Doore SM, Schrad JR, Perrett HR, Schrad KP, Dean WF, Parent KN. “A cornucopia of Shigella phages from the Cornhusker State” Virology (2019) Sep 16;538:45-52. doi: 10.1016/j.virol.2019.09.007

Lechno-Yossef S, Rohnke BA, Belza ACO, Melnicki MR, Montgomery BL, Kerfeld CA. “Cyanobacterial Carboxysomes Contain a Unique Rubisco-Activase-Like protein.” New Phytol. (2019) Sep 13. doi: 10.1111/nph.16195

Ostrowska N, Feig M, Trylska J. “Modeling Crowded Environment in Molecular Simulations.” Front Mol Biosci. (2019) Sep 11;6:86. doi: 10.3389/fmolb.2019.00086

Fisher N, Bricker TM, Kramer DM. “Regulation of photosynthetic cyclic electron flow pathways by adenylate status in higher plant chloroplasts.” Biochim Biophys Acta Bioenerg. (2019) Sep 11;1860(11):148081. doi: 10.1016/j.bbabio.2019.148081

Sutter M, Laughlin TG, Sloan NB, Serwas D, Davies KM, Kerfeld CA. “Structure of a synthetic beta-carboxysome shell.” Plant Physiol. (2019) Sep 9. doi: 10.1104/pp.19.00885

Bhalla A, Cai CM, Xu F, Singh SK, Bansal N, Phongpreecha T, Dutta T, Foster CE, Kumar R, Simmons BA, Singh S, Wyman CE, Hegg EL, Hodge DB. “Performance of three delignifying pretreatments on hardwoods: hydrolysis yields, comprehensive mass balances, and lignin properties.” Biotechnol Biofuels. (2019) Sep 9;12:213. doi: 10.1186/s13068-019-1546-0

August 2019

Roushangar R, Mias GI. “Multi-study reanalysis of 2,213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures.” Sci Rep. (2019) Aug 27;9(1):12413. doi: 10.1038/s41598-019-48872-0

Baek S, Liu C, Gou K, Kim J, Gharahi H, Chan C. “Utilization of the Theory of Small on Large Deformation for Studying Mechanosensitive Cellular Behaviors.” J Elast. (2019) Aug;136(2):137-157.

Li W, Lybrand DB, Zhou F, Last RL, Pichersky E. “Pyrethrin biosynthesis: The cytochrome P450 oxidoreducatse CYP82Q3 converts jasmolone to pyrethrolone.” Plant Physiol. (2019) Aug 26. doi: 10.1104/pp.19.00499

Frum T, Watts JL, Ralston A. “TEAD4/YAP1/WWTR1 prevent the premature onset of pluripotency prior to the 16-cell stage.” Development. (2019) Aug 23. doi: 10.1242/dev.179861

Frum T, Ralston A. “Visualizing HIPPO Signaling Components in Mouse Early Embryonic Development.” Methods Mol Biol. (2019) Aug; 1893:335-352. doi: 10.1007/978-1-4939-8910-2_25

Mouawad R, Prasad J, Thorley D, Himadewi P, Kadiyala D, Wilson N, Kapranov P, Arnosti DN. “Diversification of retinoblastoma protein function associated with cis and trans adaptations.” Mol Biol Evol. (2019) Aug 16. doi: 10.1093/molbev/msz187

Klinger GE, Zhou Y, Hao P, Robbins J, Aquilina JM, Jackson JE, Hegg EL. “Biomimetic Reductive Cleavage of Keto Aryl Ether Bonds by Small Molecule Thiols.” ChemSusChem. (2019) Aug 16. doi: 10.1002/cssc.201901742

Raghuvanshi R, Grayson AG, Schena I, Amanze O, Suwintono K, Quinn RA. “Microbial Transformations of Organically Fermented Foods.” Metabolites. (2019) Aug 10;9:(8). doi: 10.3390/metabo9080165

Yuan Z, Singh SK, Bals B, Hodge DB, Hegg EL. “Integrated Two-Stage Alkaline–Oxidative Pretreatment of Hybrid Poplar. Part 2: Impact of Cu-Catalyzed Alkaline Hydrogen Peroxide Pretreatment Conditions on Process Performance and Economics.” Ind. Eng. Chem. Res. (2019) Aug 5. doi: 10.1021/acs.iecr.9b00901

Milutinovic M, Lindsey BE 3rd, Wijeratne A, Hernandez JM, Grotewold N, Fernández V, Grotewold E, Brkljacic J. “Arabidopsis EMSY-like (EML) histone readers are necessary for post-fertilization seed development, but prevent fertilization-independent seed formation.” Plant Sci. (2019) Aug;285:99-109. doi: 10.1016/j.plantsci.2019.04.007

July 2019

Springer N, de León N, Grotewold E. “Challenges of Translating Gene Regulatory Information into Agronomic Improvements.” Trends Plant Sci. (2019) Jul 31. doi: 10.1016/j.tplants.2019.07.004

Liu J, Lu Y, Hua W, Last RL. “A New Light on Photosystem II Maintenance in Oxygenic Photosynthesis.” Front Plant Sci. (2019) July 31;10:975. doi: 10.3389/fpls.2019.00975

Lantz AT, Allman J, Weraduwage SM, Sharkey TD. “Isoprene: New insights into the control of emission and mediation of stress tolerance by gene expression.” Plant Cell Environ. (2019) Jul 27. doi: 10.1111/pce.13629

Rennhack JP, To B, Swiatnicki M, Dulak C, Ogrodzinski MP, Zhang Y, Li C, Bylett E, Ross C, Szczepanek K, Hanrahan W, Jayatissa M, Lunt SY, Hunter K, Andrechek ER. “Integrated analyses of murine breast cancer models reveal critical parallels with human disease.” Nat Commun. (2019) Jul 22;10(1):3261. doi: 10.1038/s41467-019-11236-3

Du ZY, Zienkiewicz K, Vande Pol N, Ostrom NE, Benning C, Bonito GM. “Algal-fungal symbiosis leads to photosynthetic mycelium.” Elife. (2019) Jul 16. doi: 10.7554/eLife.47815

Peng J, Lu J, Hoh D, Dina AS, Shang X, Kramer DM, Chen J. “Identifying Emerging Phenomenon in Long Temporal Phenotyping Experiments.” Bioinformatics. (2019) Jul 15. doi: 10.1093/bioinformatics/btz559

Feig M, Sugita Y. “Whole-Cell Models and Simulations in Molecular Detail.” Annu Rev Cell Dev Biol. (2019) Jul 12. doi: 10.1146/annurev-cellbio-100617-062542

Shee KS, Ratnayake ND, Walter T, Goethe O, Onyeozili EN, Walker KD. “Exploring the Scope of an α/β-Aminomutase for the Amination of Cinnamate Epoxides to Arylserines and Arylisoserines” ACS Catal. (2019) July 9. doi: 10.1021/acscatal.9b01557

Kariagina A, Lunt SY, McCormick JJ. “Genomic and Metabolomic Analysis of Step-Wise Malignant Transformation in Human Skin Fibroblasts.” Carcinogenesis. (2019) Jul 4. doi: 10.1093/carcin/bgz126

Pei J, Zheng Z, Kim H, Song LF, Walworth S, Merz MR, Merz KM Jr. “Random Forest Refinement of Pairwise Potentials for Protein-Ligand Decoy Detection.” J Chem Inf Model. (2019) Jul 2. doi: 10.1021/acs.jcim.9b00356

Nguyen DD, Wei GW. “AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening.” J Chem Inf Model. (2019) Jul 1. doi: 10.1021/acs.jcim.9b00334

June 2019

Donyapour N, Roussey NM, Dickson A. “REVO: Resampling of ensembles by variation optimization.” J Chem Phys. (2019) Jun 28;150(24):244112. doi: 10.1063/1.5100521

Weise SE, Liu T, Childs KL, Preiser AL, Katulski HM, Perrin-Porzondek C, Sharkey TD. “Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope.” Front Plant Sci. (2019) Jun 27;10:827. doi: 10.3389/fpls.2019.00827

Wu HL, Song G, Walley JW, Hsu PY. “The tomato translational landscape revealed by transcriptome assembly and ribosome profiling.” Plant Physiol. (2019) Jun 27. doi: 10.1104/pp.19.00541

Tefft NM, TerAvest MA. “Reversing an Extracellular Electron Transfer Pathway for Electrode-Driven Acetoin Reduction.” ACS Synth Biol. (2019) Jun 21. doi: 10.1021/acssynbio.8b00498

Liu Y, Hickey DP, Minteer SD, Dickson A, Calabrese Barton S. “Markov-State Transition Path Analysis of Electrostatic Channeling.” J Phys Chem C Nanomater Interfaces. (2019) Jun 20;123(24):15284-15292. doi: 10.1021/acs.jpcc.9b02844

Heo L, Arbour CF, Feig M. “Driven to near-experimental accuracy by refinement via molecular dynamics simulations.” Proteins. (2019) Jun 14;. doi: 10.1002/prot.25759

Singh SK, Savoy AW, Yuan Z, Luo H, Stahl SS, Hegg EL, Hodge DB. “Integrated Two-Stage Alkaline-Oxidative Pretreatment of Hybrid Poplar. Part 1: Impact of Alkaline Pre-Extraction Conditions on Process Performance and Lignin Properties.” Ind. Eng. Chem. Res. (2019) Jun 5. doi: 10.1021/acs.iecr.9b01124

Zhang T, Kuliyev E, Sui D, Hu J. “The Histidine-rich Loop in the Extracellular Domain of ZIP4 Binds Zinc and Plays a Role in Zinc Transport.” Biochem J. (2019) Jun 4. doi: 10.1042/BCJ20190108

Chen B, Zhang G, Li P, Yang J, Guo L, Benning C, Wang X, Zhao J. “Multiple GmWRI1s are redundantly involved in seed filling and nodulation by regulating plastidic glycolysis, lipid biosynthesis, and hormone signaling in soybean (Glycine max).” Plant Biotechnol J. (2019) Jun 3. doi: 10.1111/pbi.13183

May 2019

Jones AD, Boundy-Mills KL, Barla GF, Kumar S, Ubanwa B, Balan V. “Microbial Lipid Alternatives to Plant Lipids.” Methods Mol Biol. (2019) May 31;1995:1-32. doi: 10.1007/978-1-4939-9484-7_1

Dalgıç E, Konu Ö, Öz ZS, Chan C. “Lower connectivity of tumor coexpression networks is not specific to cancer.” In Silico Biol. (2019) May 30;13(1-2):41-53. doi: 10.3233/ISB-190472

Li L, Lavell A, Meng X, Berkowitz O, Selinski J, van de Meene A, Carrie C, Benning C, Whelan J, De Clercq I, Wang Y. “Arabidopsis DGD1 SUPPRESSOR 1 is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis.” Plant Cell. (2019) May 22;. doi: 10.1105/tpc.18.00885

Chu F, Mason KE, Anex DS, Jones AD, Hart BR. “Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification.” Sci Rep. (2019) May 21;9(1):7641. doi: 10.1038/s41598-019-44007-7

Angart PA, Adu-Berchie K, Carlson RJ, Vocelle DB, Chan C, Walton SP. “Relative Quantification of siRNA Strand Loading into Ago2 for Design of Highly Active siRNAs.” Methods Mol Biol. (2019) May 17;1974:41-56. doi: 10.1007/978-1-4939-9220-1_4

Preiser AL, Fisher N, Banerjee A, Sharkey TD. “Plastidic glucose-6-phosphate dehydrogenase is regulated to maintain activity in the light.” Biochem J. (2019) May 15;. doi: 10.1042/BCJ20190234

Santiago JP, Sharkey TD. “Pollen development at high temperature and role of carbon and nitrogen metabolites.” Plant Cell Environ. (2019) May 11;. doi: 10.1111/pce.13576

Salminen TS, Cannino G, Oliveira MT, Lillsunde P, Jacobs HT, Kaguni LS. “Lethal Interaction of Nuclear and Mitochondrial Genotypes in Drosophila melanogaster.” G3 (Bethesda). (2019) May 10. doi: 10.1534/g3.119.400315

Oh S, Montgomery BL. “Roles of CpcF and CpcG1 in Peroxiredoxin-Mediated Oxidative Stress Responses and Cellular Fitness in the Cyanobacterium Synechocystis sp. PCC 6803.” Front Microbiol. (2019) May 9;10:1059. doi: 10.3389/fmicb.2019.01059

Wang K, Durrett TP, Benning C. “Functional diversity of glycerolipid acylhydrolases in plant metabolism and physiology.” Prog Lipid Res. (2019) May 9;75:100987. doi: 10.1016/j.plipres.2019.100987

Last RL. “Put on Your Sunscreen: The Birth of Arabidopsis Abiotic Stress Genetics.” Plant Cell. (2019) May 8;. doi: 10.1105/tpc.19.00341

Ferlez B, Sutter M, Kerfeld CA. “A designed bacterial microcompartment shell with tunable composition and precision cargo loading.” Metab Eng. (2019) May 7. doi: 10.1016/j.ymben.2019.04.011

Lavell A, Froehlich JE, Baylis O, Rotondo A, Benning C. “A Predicted Plastid Rhomboid Protease Affects Phosphatidic Acid Metabolism in Arabidopsis thaliana.” Plant J. (2019) May 7. doi: 10.1111/tpj.14377

Kim Y, Opron K, Burton ZF. “A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code.” Life (Basel). (2019) May 4;9:(2). doi: 10.3390/life9020037

Höhner R, Correa Galvis V, Strand DD, Voelkner C, Kraemer M, Messer M, Dinc F, Sjuts I, Bölter B, Kramer DM, Armbruster U, Kunz HH. “Photosynthesis in Arabidopsis thaliana is unaffected by the function of the vacuolar K+ channel TPK3.” Plant Physiol. (2019) May 3. doi: 10.1104/pp.19.00255

Howe GA. “Auspicious Beginnings for the Defense Hormone Jasmonate.” Plant Cell. (2019) May 2;. doi: 10.1105/tpc.19.00333

April 2019

Oh S, Montgomery BL. “Mesophyll-specific phytochromes impact chlorophyll light-harvesting complexes (LHCs) and non-photochemical quenching.” Plant Signal Behav. (2019) Apr 30;1-10. doi: 10.1080/15592324.2019.1609857

Fader KA, Nault R, Doskey CM, Fling RR, Zacharewski TR. “2,3,7,8-Tetrachlorodibenzo-p-dioxin abolishes circadian regulation of hepatic metabolic activity in mice.” Sci Rep. (2019) Apr 24;9(1):6514. doi: 10.1038/s41598-019-42760-3

Soltani A, Weraduwage SM, Sharkey TD, Lowry DB. “Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships.” BMC Genomics. (2019) Apr 24;20(1):312. doi: 10.1186/s12864-019-5669-2

Brooks LR, Mias GI. “Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease” Front. Neurosci. (2019) Apr 24;13:392. doi: 10.3389/fnins.2019.00392

Yang Y, Gunasekara M, Muhammednazaar S, Li Z, Hong H. “Proteolysis mediated by the membrane-integrated ATP-dependent protease FtsH has a unique nonlinear dependence on ATP hydrolysis rates.” Protein Sci. (2019) Apr 22;. doi: 10.1002/pro.3629

Fan P, Leong BJ, Last RL. “Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae.” Curr Opin Plant Biol. (2019) Apr 19;49:8-16. link

Dong W, Wang Y, Takahashi H. “CLE-CLAVATA1 Signaling Pathway Modulates Lateral Root Development under Sulfur Deficiency.” Plants (Basel). (2019) Apr 18;8:(4). doi: 10.3390/plants8040103

Cobián Güemes AG, Lim YW, Quinn RA, Conrad DJ, Benler S, Maughan H, Edwards R, Brettin T, Cantú VA, Cuevas D, Hamidi R, Dorrestein P, Rohwer F. “Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.” MBio. (2019) Apr 16;10:(2). doi: 10.1128/mBio.00431-19

Gupta S, Sutter M, Remesh SG, Dominguez-Martin MA, Bao H, Feng XA, Chan LG, Petzold CJ, Kerfeld CA, Ralston CY. “X-ray radiolytic labeling reveals the molecular basis of orange carotenoid protein photoprotection and its interactions with fluorescence recovery protein.” J Biol Chem. (2019) Apr 12;. doi: 10.1074/jbc.RA119.007592

Cerrón F, de Lorenzo S, Lemishko KM, Ciesielski GL, Kaguni LS, Cao FJ, Ibarra B. “Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis.” Nucleic Acids Res. (2019) Apr 10. doi: 10.1093/nar/gkz249

Chen J, Kuhn LA. “Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation.” J Mol Graph Model. (2019) Apr 9;90:59-76. doi: 10.1016/j.jmgm.2019.04.003

Leong BJ, Lybrand DB, Lou YR, Fan P, Schilmiller AL, Last RL. “Evolution of metabolic novelty: A trichome-expressed invertase creates specialized metabolic diversity in wild tomato.” Sci Adv. (2019) Apr;5(4):eaaw3754. doi: 10.1126/sciadv.aaw3754

Newcomer RL, Schrad JR, Gilcrease EB, Casjens SR, Feig M, Teschke CM, Alexandrescu AT, Parent KN. “The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy.” Elife. (2019) Apr 4;. doi: 10.7554/eLife.45345

Picchioni D, Antolin-Fontes A, Camacho N, Schmitz C, Pons-Pons A, Rodríguez-Escribà M, Machallekidou A, Güler MN, Siatra P, Carretero-Junquera M, Serrano A, Hovde SL, Knobel PA, Novoa EM, Solà-Vilarrubias M, Kaguni LS, Stracker TH, Ribas de Pouplana L. “Mitochondrial Protein Synthesis and mtDNA Levels Coordinated through an Aminoacyl-tRNA Synthetase Subunit.” Cell Rep. (2019) Apr 2;27(1):40-47.e5. doi: 10.1016/j.celrep.2019.03.022

Cho H, Stanzione F, Oak A, Kim GH, Yerneni S, Qi L, Sum AK, Chan C. “Intrinsic Structural Features of the Human IRE1α Transmembrane Domain Sense Membrane Lipid Saturation.” Cell Rep. (2019) Apr 2;27(1):307-320.e5. doi: 10.1016/j.celrep.2019.03.017

March 2019

Nguyen DD, Wei GW. “DG-GL: Differential geometry-based geometric learning of molecular datasets.” Int J Numer Method Biomed Eng. (2019) Mar;35(3):e3179. doi: 10.1002/cnm.3179

Sutter M, McGuire S, Ferlez B, Kerfeld CA. “Structural Characterization of a Synthetic Tandem-Domain Bacterial Microcompartment Shell Protein Capable of Forming Icosahedral Shell Assemblies.” ACS Synth Biol. (2019) Mar 27. doi: 10.1021/acssynbio.9b00011

Takahashi H. “Sulfate transport systems in plants: functional diversity and molecular mechanisms underlying regulatory coordination.” J Exp Bot. (2019) Mar 25;. doi: 10.1093/jxb/erz132

Saha S, Patra P, Igoshin O, Kroos L. “Systematic analysis of the Myxococcus xanthus developmental gene regulatory network supports posttranslational regulation of FruA by C-signaling.” Mol Microbiol. (2019) Mar 20;. doi: 10.1111/mmi.14249

Dominguez-Martin MA, Kerfeld CA. “Engineering the orange carotenoid protein for applications in synthetic biology.” Curr Opin Struct Biol. (2019) Mar 19;57:110-117. doi: 10.1016/j.sbi.2019.01.023

Li J, Weraduwage SM, Peiser AL, Tietz S, Weise SE, Strand DD, Froehlich JE, Kramer DM, Hu J, Sharkey TD. “A Cytosolic Bypass and G6P Shunt in Plants Lacking Peroxisomal Hydroxypyruvate Reductase.” Plant Physiol. (2019) Mar 18;. doi: 10.1104/pp.19.00256

Dominguez-Martin MA, Polívka T, Sutter M, Ferlez B, Lechno-Yossef S, Montgomery BL, Kerfeld CA. “Structural and spectroscopic characterization of HCP2.” Biochim Biophys Acta Bioenerg. (2019) Mar 14. doi: 10.1016/j.bbabio.2019.03.004

McClain AM, Sharkey TD. “Triose phosphate utilization and beyond: from photosynthesis to end product synthesis.” J Exp Bot. (2019) Mar 13;. doi: 10.1093/jxb/erz058

Baseggio M, Murray M, Magallanes-Lundback M, Kaczmar N, Chamness J, Buckler ES, Smith ME, DellaPenna D, Tracy WF, Gore MA. “Genome-Wide Association and Genomic Prediction Models of Tocochromanols in Fresh Sweet Corn Kernels.” Plant Genome. (2019) Mar;12:(1). doi: 10.3835/plantgenome2018.06.0038

Johnson SR, Bhat WW, Sadre R, Miller GP, Garcia AS, Hamberger B. “Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution.” New Phytol. (2019) Mar 7;. doi: 10.1111/nph.15778

February 2019

Santos-Merino M, Singh AK, Ducat DC. “New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering.” Front Bioeng Biotechnol. (2019) Feb 27;7:33. doi: 10.3389/fbioe.2019.00033

Thompson R, Casali C, Chan C. “Forskolin and IBMX Induce Neural Transdifferentiation of MSCs Through Downregulation of the NRSF.” Sci Rep. (2019) Feb 27;9(1):2969. doi: 10.1038/s41598-019-39544-0

Bai N, Roder H, Dickson A, Karanicolas J. “Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities.” Sci Rep. (2019) Feb 25;9(1):2650. doi: 10.1038/s41598-018-37072-x

Warakanont J, Li-Beisson Y, Benning C. “LIP4 Is Involved in Triacylglycerol Degradation in Chlamydomonas reinhardtii.” Plant Cell Physiol. (2019) Feb 22;. doi: 10.1093/pcp/pcz037

Sadre R, Kuo P, Chen J, Yang Y, Banerjee A, Benning C, Hamberger B. “Cytosolic lipid droplets as engineered organelles for production and accumulation of terpenoid biomaterials in leaves.” Nat Commun. (2019) Feb 20;10(1):853. doi: 10.1038/s41467-019-08515-4

Zuo Z, Weraduwage SM, Lantz AT, Sanchez LM, Weise SE, Wang J, Childs K, Sharkey TD. “Isoprene Acts as a Signaling Molecule in Gene Networks Important for Stress Responses and Plant Growth.” Plant Physiol. (2019) Feb 13. doi: 10.1104/pp.18.01391

Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC. “Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome.” Microbiome. (2019) Feb 13;7(1):23. doi: 10.1186/s40168-019-0636-3

Greber BJ, Sutter M, Kerfeld CA. “The Plasticity of Molecular Interactions Governs Bacterial Microcompartment Shell Assembly.” Structure. (2019) Feb 12;. doi: 10.1016/j.str.2019.01.017

Pei J, Zheng Z, Merz KM. “Random Forest Refinement of the KECSA2 Knowledge-based Scoring Function for Protein Decoy Detection.” J Chem Inf Model. (2019) Feb 6. doi: 10.1021/acs.jcim.8b00734

Howe GA, Yoshida Y. “Evolutionary Origin of JAZ Proteins and Jasmonate Signaling.” Mol Plant. (2019) Feb 4;12(2):153-155. doi: 10.1016/j.molp.2019.01.015

Jones MA, Morohashi K, Grotewold E, Harmer SL. “Arabidopsis JMJD5/JMJ30 Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable Temperature Compensation.” Front Plant Sci. (2019) Feb 1;10:57. doi: 10.3389/fpls.2019.00057

Kirberger SE, Ycas PD, Johnson JA, Chen C, Ciccone MF, Woo RWL, Urick AK, Zahid H, Shi K, Aihara H, McAllister SD, Kashani-Sabet M, Shi J, Dickson A, Dos Santos CO, Pomerantz WCK. “Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor.” Org Biomol Chem. (2019) Feb 1. doi: 10.1039/c8ob02599a

January 2019

Hausinger RP. “New metal cofactors and recent metallocofactor insights.” Curr Opin Struct Biol. (2019) Jan 31;59:1-8. doi: 10.1016/j.sbi.2018.12.008

Zhao D, Hamilton JP, Bhat WW, Johnson SR, Godden GT, Kinser TJ, Boachon B, Dudareva N, Soltis DE, Soltis PS, Hamberger B, Buell CR. “A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways.” Gigascience. (2019) Jan 30. doi: 10.1093/gigascience/giz005

Nguyen DD, Wei GW. “DG-GL: Differential geometry based geometric learning of molecular datasets.” Int J Numer Method Biomed Eng. (2019) Jan 28;e3179. doi: 10.1002/cnm.3179

Lavell AA, Benning C. “Cellular Organization and Regulation of Plant Glycerolipid Metabolism.” Plant Cell Physiol. (2019) Jan 25. doi: 10.1093/pcp/pcz016

Moore BM, Wang P, Fan P, Leong B, Schenck CA, Lloyd JP, Lehti-Shiu MD, Last RL, Pichersky E, Shiu SH. “Robust predictions of specialized metabolism genes through machine learning.” Proc Natl Acad Sci U S A. 2019 Jan 23. pii: 201817074. doi: 10.1073/pnas.1817074116

Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG. “A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.” Cell Syst. (2019) Jan 14;. doi: 10.1016/j.cels.2018.12.010

Ferlez B, Sutter M, Kerfeld CA. “Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles.” MBio. (2019) Jan 8;10:(1). doi: 10.1128/mBio.02327-18

Yu I, Feig M, Sugita Y. “High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations.” J Phys Conf Ser. (2018) Jan. doi: 10.1088/1742-6596/1036/1/012009

Feig M, Nawrocki G, Yu I, Wang PH, Sugita Y. “Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments.” J Phys Conf Ser. (2018) Jan. doi: 10.1088/1742-6596/1036/1/012010

Nawrocki G, Karaboga A, Sugita Y, Feig M. “Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments.” Phys Chem Chem Phys. (2019) Jan 2;21(2):876-883. doi: 10.1039/c8cp06142d

December 2018

Ren T, Weraduwage SM, Sharkey TD. “Prospects for enhancing leaf photosynthetic capacity by manipulating mesophyll cells morphology.” J Exp Bot. (2018) Dec 27. doi: 10.1093/jxb/ery448

Cocuron JC, Casas MI, Yang F, Grotewold E, Alonso AP. “Beyond the wall: High-throughput quantification of plant soluble and cell-wall bound phenolics by liquid chromatography tandem mass spectrometry.” J Chromatogr A. (2018) Dec 26. doi: 10.1016/j.chroma.2018.12.059

Opron K, Burton ZF. “Ribosome Structure, Function, and Early Evolution.” Int J Mol Sci. (2018) Dec 21;20:(1). doi: 10.3390/ijms20010040

Thompson R, Chan C. “NRSF and Its Epigenetic Effectors: New Treatments for Neurological Disease.” Brain Sci. (2018) Dec 19;8:(12). doi: 10.3390/brainsci8120226

Brocke S, Degen A, MacKerell AD, Dutagaci B, Feig M. “Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning.” J Chem Inf Model. (2018) Dec 12. doi: 10.1021/acs.jcim.8b00648

Bedewitz MA, Jones AD, D'Auria JC, Barry CS. “Tropinone synthesis via an atypical polyketide synthase and P450-mediated cyclization.” Nat Commun. (2018) Dec 11;9(1):5281. doi: 10.1038/s41467-018-07671-3

Frum T, Murphy TM, Ralston A. “HIPPO signaling resolves embryonic cell fate conflicts during establishment of pluripotency in vivo.” Elife. (2018) Dec 11. doi: 10.7554/eLife.42298

Heo L, Feig M. “Experimental accuracy in protein structure refinement via molecular dynamics simulations.” Proc Natl Acad Sci U S A. (2018) Dec 10. doi: 10.1073/pnas.1811364115

Yildirim A, Brenner N, Sutherland R, Feig M. “Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.” BMC Biophys. (2018) Dec 7;11:8. doi: 10.1186/s13628-018-0048-y

Lay KS, Takahashi H. “Nutrient-Responsive Small Signaling Peptides and Their Influence on the Root System Architecture.” Int J Mol Sci. (2018) Dec 7;19:(12). doi: 10.3390/ijms19123927

MacCready JS, Hakim P, Young EJ, Hu L, Liu J, Osteryoung KW, Vecchiarelli AG, Ducat DC. “Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria.” Elife. (2018) Dec 6. doi: 10.7554/eLife.39723

November 2018

Johnson SR, Bhat WW, Bibik J, Turmo A, Hamberger B, Genomics Consortium EM, Hamberger B. “A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae).” J Biol Chem. (2018) Nov 29. doi: 10.1074/jbc.RA118.006025

Banerjee A, Arnesen JA, Moser D, Motsa BB, Johnson SR, Hamberger B. “Engineering modular diterpene biosynthetic pathways in Physcomitrella patens.” Planta. (2018) Nov 23. doi: 10.1007/s00425-018-3053-0

Kamba PF, Dickson DA, White NA, Ekstrom JL, Koslowsky DJ, Hoogstraten CG. “The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein.” Sci Rep. (2018) Nov 19;8(1):16989. doi: 10.1038/s41598-018-34377-9

Chacón KN, Perkins J, Mathe Z, Alwan K, Ho EN, Ucisik MN, Merz KM, Blackburn NJ. “Trapping intermediates in metal transfer reactions of the CusCBAF export pump of Escherichia coli.” Commun Biol. (2018) Nov 14;1:192. doi: 10.1038/s42003-018-0181-9

Gaffney KA, Hong H. “The rhomboid protease GlpG has weak interaction energies in its active site hydrogen bond network.” J Gen Physiol. (2018) Nov 12;. doi: 10.1085/jgp.201812047

Aykul S, Martinez-Hackert E. “High-Throughput, Biosensor-Based Approach to Examine Bone Morphogenetic Protein (BMP)-Receptor Interactions.” Methods Mol Biol. (2019) Nov 10;1891:37-49. doi: 10.1007/978-1-4939-8904-1_5

Yu L, He J, Wang L, Yi H. “Inflammatory profiles revealed the dysregulation of cytokines in adult patients of HFMD.” Int J Infect Dis. (2018) Nov 10;. doi: 10.1016/j.ijid.2018.11.001

Sengupta A, Seitz A, Merz KM Jr. “Simulating the Chelate Effect.” J Am Chem Soc. (2018) Nov 6. doi: 10.1021/jacs.8b09371

Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, Burton RL, Saechao C, Sloan NB, Cheng X, Chan LG, Petzold CJ, Fuentes-Cabrera M, Ralston CY, Kerfeld CA. “Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.” Plant Physiol. (2018) Nov 2;. doi: 10.1104/pp.18.01190

October 2018

Kovinich N, Wang Y, Adegboye J, Chanoca AA, Otegui MS, Durkin P, Grotewold E. “Arabidopsis MATE45 antagonizes local abscisic acid signaling to mediate development and abiotic stress responses.” Plant Direct. (2018) Oct;2(10):e00087. doi: 10.1002/pld3.87

Sharkey TD. “Discovery of the canonical Calvin-Benson cycle.” Photosynth Res. (2018) Oct 29. doi: 10.1007/s11120-018-0600-2

Li J, Tietz S, Cruz JA, Strand DD, Xu Y, Chen J, Kramer DM, Hu J. “Photometric screens identified Arabidopsis peroxisome proteins that impact photosynthesis under dynamic light conditions.” Plant J. (2018) Oct 23. doi: 10.1111/tpj.14134

Hagen A, Plegaria JS, Sloan N, Ferlez B, Aussignargues C, Kerfeld CA. “In vitro assembly of diverse bacterial microcompartment shell architectures.” Nano Lett. (2018) Oct 22. doi: 10.1021/acs.nanolett.8b02991

Guo Q, Yoshida Y, Major IT, Wang K, Sugimoto K, Kapali G, Havko NE, Benning C, Howe GA. “JAZ repressors of metabolic defense promote growth and reproductive fitness in Arabidopsis.” Proc Natl Acad Sci U S A. (2018) Oct 22. doi: 10.1073/pnas.1811828115

Dornbos P, Warren M, Crawford RB, Kaminski N, Threadgill DW, LaPres JJ. “Characterizing Serpinb2 as a modulator of TCDD-induced suppression of the B cell.” Chem Res Toxicol. (2018) Oct 19. doi: 10.1021/acs.chemrestox.8b00225

Kim Y, Kowiatek B, Opron K, Burton ZF. “Type-II tRNAs and Evolution of Translation Systems and the Genetic Code” Int. J. Mol. Sci. (2018) Oct 18;19(10):3275. doi: 10.3390/ijms19103275

Ogrodzinski MP, Teoh ST, Yu L, Broadwater D, Ensink E, Lunt SY. “Measuring the Nutrient Metabolism of Adherent Cells in Culture.” Methods Mol Biol. (2018) Oct 13;1862:37-52. doi: 10.1007/978-1-4939-8769-6_3

Bramer D, Wei GW. “Blind prediction of protein B-factor and flexibility.” J Chem Phys. (2018) Oct 7;149(13):134107. doi: 10.1063/1.5048469

Fellner M, Hausinger RP, Hu J. “A structural perspective on the PP-loop ATP pyrophosphatase family.” Crit Rev Biochem Mol Biol. (2018) Oct 3;1-16. doi: 10.1080/10409238.2018.1516728

Pande K, Donatelli JJ, Malmerberg E, Foucar L, Poon BK, Sutter M, Botha S, Basu S, Bruce Doak R, Dörner K, Epp SW, Englert L, Fromme R, Hartmann E, Hartmann R, Hauser G, Hattne J, Hosseinizadeh A, Kassemeyer S, Lomb L, Montero SFC, Menzel A, Rolles D, Rudenko A, Seibert MM, Sierra RG, Schwander P, Ourmazd A, Fromme P, Sauter NK, Bogan M, Bozek J, Bostedt C, Schlichting I, Kerfeld CA, Zwart PH. “Free-electron laser data for multiple-particle fluctuation scattering analysis.” Sci Data. (2018) Oct 2;5:180201. doi: 10.1038/sdata.2018.201

September 2018

Dickson A. “Mapping the Ligand Binding Landscape.” Biophys J. (2018) Sep 29. doi: 10.1016/j.bpj.2018.09.021

Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. “Niche partitioning of a pathogenic microbiome driven by chemical gradients.” Sci Adv. (2018) Sep;4(9):eaau1908. doi: 10.1126/sciadv.aau1908

Silva GFF, Silva EM, Correa JPO, Vicente MH, Jiang N, Notini MM, Junior AC, De Jesus FA, Castilho P, Carrera E, Lopes-Diaz I, Grotewold E, Peres LEP, Nogueira FTS. “Tomato floral induction and flower development are orchestrated by the interplay between gibberellin and two unrelated microRNA-controlled modules.” New Phytol. (2018) Sep 20. doi: 10.1111/nph.15492

Lienemann M, TerAvest MA, Pitkänen JP, Stuns I, Penttilä M, Ajo-Franklin CM, Jäntti J. “Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili.” Microb Biotechnol. (2018) Sep 17. doi: 10.1111/1751-7915.13309

Fan M, Herburger K, Jensen JK, Zemelis-Durfee S, Brandizzi F, Fry SC, Wilkerson CG. “A Trihelix Family Transcription Factor is Associated with Key Genes in Mixed-linkage Glucan Accumulation.” Plant Physiol. (2018) Sep 17. doi: 10.1104/pp.18.00978

Toyota M, Spencer D, Sawai-Toyota S, Jiaqi W, Zhang T, Koo AJ, Howe GA, Gilroy S. “Glutamate triggers long-distance, calcium-based plant defense signaling.” Science. (2018) Sep 14;361(6407):1112-1115. doi: 10.1126/science.aat7744

Pizzo L, Jensen M, Polyak A, Rosenfeld JA, Mannik K, Krishnan A, McCready E, Pichon O, Le Caignec C, Van Dijck A, Pope K, Voorhoeve E, Yoon J, Stankiewicz P, Cheung SW, Pazuchanics D, Huber E, Kumar V, Kember RL, Mari F, Curró A, Castiglia L, Galesi O, Avola E, Mattina T, Fichera M, Mandarà L, Vincent M, Nizon M, Mercier S, Bénéteau C, Blesson S, Martin-Coignard D, Mosca-Boidron AL, Caberg JH, Bucan M, Zeesman S, Nowaczyk MJM, Lefebvre M, Faivre L, Callier P, Skinner C, Keren B, Perrine C, Prontera P, Marle N, Renieri A, Reymond A, Kooy RF, Isidor B, Schwartz C, Romano C, Sistermans E, Amor DJ, Andrieux J, Girirajan S. “Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants.” Genet Med. (2018) Sep 7. doi: 10.1038/s41436-018-0266-3

Zheng Z, Pei J, Bansal N, Liu H, Song LF, Merz KM. “Generation of Pairwise Potentials Using Multi-Dimensional Data Mining.” J Chem Theory Comput. (2018) Sep 5. doi: 10.1021/acs.jctc.8b00516

Li M, Martinez S, Hausinger RP, Emerson JP. “Thermodynamics of iron(II) and substrate binding to the ethylene-forming enzyme.” Biochemistry. (2018) Sep 5. doi: 10.1021/acs.biochem.8b00730

Hoang Y, Kroos L. “Ultrasensitive response of developing Myxococcus xanthus to the addition of nutrient medium correlates with the level of MrpC.” J Bacteriol. (2018) Sep 4. doi: 10.1128/JB.00456-18

Herwaldt EJ, Rivett ED, White AJ, Hegg EL. “Cox15 interacts with the cytochrome bc1 dimer within respiratory supercomplexes as well as in the absence of cytochrome c oxidase.” J Biol Chem. (2018) Sep 4. doi: 10.1074/jbc.RA118.002496

Zhao R, Cang Z, Tong Y, Wei GW. “Protein pocket detection via convex hull surface evolution and associated Reeb graph.” Bioinformatics. (2018) Sep 1;34(17):i830-i837. doi: 10.1093/bioinformatics/bty598

Hurlock AK, Wang K, Takeuchi T, Horn PJ, Benning C. “In vivo lipid 'tag and track' approach shows acyl editing of plastid lipids and chloroplast import of phosphatidylglycerol precursors in Arabidopsis thaliana.” Plant J. (2018) Sep;95(6):1129-1139. doi: 10.1111/tpj.13999

August 2018

Righini S, Rodriguez EJ, Berosich C, Grotewold E, Casati P, Falcone Ferreyra ML. “Apigenin produced by maize flavone synthase I and II protects plants against UV-B-induced damage.” Plant Cell Environ. (2018) Aug 30. doi: 10.1111/pce.13428

Fellner M, Rankin JA, Desguin B, Hu J, Hausinger RP. “Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum.” Biochemistry. (2018) Aug 29. doi: 10.1021/acs.biochem.8b00601

Woodard J, Srivastava KR, Rahamim G, Grupi A, Hogan S, Witalka DJ, Nawrocki G, Haas E, Feig M, Lapidus LJ. “Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It.” Biophys J. (2018) Aug 27. doi: 10.1016/j.bpj.2018.08.023

Song LF, Bansal N, Zheng Z, Merz KM Jr. “Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.” J Comput Aided Mol Des. (2018) Aug 24. doi: 10.1007/s10822-018-0153-7

Dixon T, Lotz SD, Dickson A. “Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.” J Comput Aided Mol Des. (2018) Aug 23. doi: 10.1007/s10822-018-0149-3

Nguyen DD, Cang Z, Wu K, Wang M, Cao Y, Wei GW. “Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.” J Comput Aided Mol Des. (2018) Aug 16. doi: 10.1007/s10822-018-0146-6

Galtier d'Auriac I, Quinn RA, Maughan H, Nothias LF, Little M, Kapono CA, Cobian A, Reyes BT, Green K, Quistad SD, Leray M, Smith JE, Dorrestein PC, Rohwer F, Deheyn DD, Hartmann AC. “Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism.” Proc Biol Sci. (2018) Aug 15;285:(1884). doi: 10.1098/rspb.2018.1307

White NA, Sumita M, Marquez VE, Hoogstraten CG. “Coupling Between Conformational Dynamics and Catalytic Function at the Active Site of the Lead-Dependent Ribozyme.” RNA. (2018) Aug 15. doi: 10.1261/rna.067579.118

Shen X, Kou Q, Guo R, Yang Z, Chen D, Liu X, Hong H, Sun L. “Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry.” Anal Chem. (2018) Aug 13. doi: 10.1021/acs.analchem.8b02725

Zhang Q, van Wijk R, Zarza X, Shahbaz M, van Hooren M, Guardia A, Scuffi D, García-Mata C, Van den Ende W, Hoffmann-Benning S, Haring MA, Laxalt AM, Munnik T. “Knock-Down of Arabidopsis PLC5 Reduces Primary Root Growth and Secondary Root Formation While Overexpression Improves Drought Tolerance and Causes Stunted Root Hair Growth.” Plant Cell Physiol. (2018) Aug 9;. doi: 10.1093/pcp/pcy120

July 2018

Mejia-Guerra MK, Li W, Doseff AI, Grotewold E. “Genome-Wide TSS Identification in Maize.” Methods Mol Biol. (2018) Jul 25;1830:239-256. doi: 10.1007/978-1-4939-8657-6_14

Basson MD, Wang Q, Chaturvedi LS, More S, Vomhof-DeKrey EE, Al-Marsoummi S, Sun K, Kuhn LA, Kovalenko P, Kiupel M. “Schlafen 12 Interaction with SerpinB12 and Deubiquitylases Drives Human Enterocyte Differentiation.” Cell Physiol Biochem. (2018) Jul 25;48(3):1274-1290. doi: 10.1159/000492019

Hagen A, Sutter M, Sloan N, Kerfeld CA. “Programmed loading and rapid purification of engineered bacterial microcompartment shells.” Nat Commun. (2018) Jul 23;9(1):2881. doi: 10.1038/s41467-018-05162-z

Song G, Hsu PY, Walley JW. “Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling.” Proteomics. (2018) Jul 23;e1800220. doi: 10.1002/pmic.201800220

Feroz H, Ferlez B, Lefoulon C, Ren T, Baker CS, Gajewski JP, Lugar DJ, Gaudana SB, Butler PJ, Hühn J, Lamping M, Parak WJ, Hibberd JM, Kerfeld CA, Smirnoff N, Blatt MR, Golbeck JH, Kumar M. “Light-Driven Chloride Transport Kinetics of Halorhodopsin.” Biophys J. (2018) Jul 17;115(2):353-360. doi: 10.1016/j.bpj.2018.06.009

Deng X, Kuo MH. “Tripartite Chromatin Localization of Budding Yeast Shugoshin Involves Higher-Ordered Architecture of Mitotic Chromosomes.” G3 (Bethesda). (2018) Jul 12. doi: 10.1534/g3.118.200522

Hausinger RP, Desguin B, Fellner M, Rankin JA, Hu J. “Nickel-pincer nucleotide cofactor.” Curr Opin Chem Biol. (2018) Jul 9;47:18-23. doi: 10.1016/j.cbpa.2018.06.019

Kim Y, Benning N, Pham K, Baghdadi N, Caruso G, Colligan M, Grayson A, Hurley A, Ignatoski N, Mcclure S, Mckaig K, Neag E, Showers C, Tangalos A, Vanells J, Padmanabhan K, Burton ZF. “Homology threading to generate RNA polymerase structures.” Protein Expr Purif. (2018) Jul;147:13-16. doi: 10.1016/j.pep.2018.02.002

June 2018

Zeng X, Uyar A, Sui D, Donyapour N, Wu D, Dickson A, Hu J. “Structural Insights into Lethal Contractural Syndrome Type 3 (LCCS3) Caused by a Missense Mutation of PIP5Kγ.” Biochem J. (2018) Jun 29;. doi: 10.1042/BCJ20180326

Haslun JA, Ostrom NE, Hegg EL, Ostrom PH. “Estimation of Isotope Variation of N2O during Denitrification by Pseudomonas aureofaciens and Pseudomonas chlororaphis: Implications for N2O Source Apportionment.” Biogeosciences. (2018) Jun 27. 15:3873-3882. doi: 10.5194/bg-15-3873-2018

Du ZY, Alvaro J, Hyden B, Zienkiewicz K, Benning N, Zienkiewicz A, Bonito G, Benning C. “Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata.” Biotechnol Biofuels. (2018) Jun 22;11:174. doi: 10.1186/s13068-018-1172-2

Brooks LRK, Mias GI. “Streptococcus pneumoniae's Virulence and Host Immunity: Aging, Diagnostics, and Prevention.” Frontiers in Immunology (2018) Jun 22; doi: 10.3389/fimmu.2018.01366

Yuan Z, Li G, Hegg EL. “Enhancement of sugar recovery and ethanol production from wheat straw through alkaline pre-extraction followed by steam pretreatment.” Bioresour Technol. (2018) Jun 21;266:194-202. doi: 10.1016/j.biortech.2018.06.065

Li M, Henderson KL, Martinez S, Hausinger RP, Emerson JP. “The Irving-Williams series and the 2-His-1-carboxylate facial triad: a thermodynamic study of Mn2+, Fe2+, and Co2+ binding to taurine/α-ketoglutarate dioxygenase (TauD).” J Biol Inorg Chem. (2018) Jun 19;. doi: 10.1007/s00775-018-1574-4

Chanoca A, Burkel B, Grotewold E, Eliceiri KW, Otegui MS. “Imaging Vacuolar Anthocyanins with Fluorescence Lifetime Microscopy (FLIM).” Methods Mol Biol. (2018) Jun 19;1789:131-141. doi: 10.1007/978-1-4939-7856-4_10

Hurlock AK, Wang K, Takeuchi T, Horn PJ, Benning C. “In Vivo Lipid "Tag and Track" Approach Shows Acyl Editing of Plastid Lipids and Chloroplast Import of Phosphatidylglycerol Precursors in Arabidopsis thaliana.” Plant J. (2018) Jun 19;. doi: 10.1111/tpj.13999

Hackenberg C, Hakanpää J, Cai F, Antonyuk S, Eigner C, Meissner S, Laitaoja M, Jänis J, Kerfeld CA, Dittmann E, Lamzin VS. “Structural and functional insights into the unique CBS-CP12 fusion protein family in cyanobacteria.” Proc Natl Acad Sci U S A. (2018) Jun 18;. doi: 10.1073/pnas.1806668115

Liu C, Kray J, Chan C. “Schwann Cells Enhance Penetration of Regenerated Axons into Three-Dimensional Microchannels.” Tissue Eng Regen Med. (2018) Jun;15(3):351-361. doi: 10.1007/s13770-018-0115-0

Midic U, Vincent KA, Wang K, Lokken A, Severance AL, Ralston A, Knott JG, Latham KE. “Novel key roles for Structural maintenance of chromosome flexible domain containing 1 (Smchd1) during preimplantation mouse development.” Mol Reprod Dev. (2018) Jun 13; doi: 10.1002/mrd.23001

Severin GB, Ramliden MS, Hawver LA, Wang K, Pell ME, Kieninger AK, Khataokar A, O'Hara BJ, Behrmann LV, Neiditch MB, Benning C, Waters CM, Ng WL. “Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae.” Proc Natl Acad Sci U S A. (2018) Jun 11. doi: 10.1073/pnas.1801233115

Desguin B, Fellner M, Riant O, Hu J, Hausinger R, Hols P, Soumillion P. “Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.” J Biol Chem. (2018) Jun 10. doi: 10.1074/jbc.RA118.003741

May 2018

Agostoni M, Logan-Jackson AR, Heinz ER, Severin GB, Bruger EL, Waters CM, Montgomery BL. “Homeostasis of Second Messenger Cyclic-di-AMP Is Critical for Cyanobacterial Fitness and Acclimation to Abiotic Stress.” Front Microbiol. (2018) May 29;9:1121. doi: 10.3389/fmicb.2018.01121

Teoh ST, Ogrodzinski MP, Ross C, Hunter KW, Lunt SY. “Sialic Acid Metabolism: A Key Player in Breast Cancer Metastasis Revealed by Metabolomics.” Front Oncol. (2018) May 28;8:174. doi: 10.3389/fonc.2018.00174

Wong AK, Krishnan A, Troyanskaya OG. “GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.” Nucleic Acids Res. (2018) May 25. doi: 10.1093/nar/gky408

Jasiński M, Feig M, Trylska J. “Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.” J Chem Theory Comput. (2018) May 23. doi: 10.1021/acs.jctc.8b00291

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. “Best practices for analysing microbiomes.” Nat Rev Microbiol. (2018) May 23. doi: 10.1038/s41579-018-0029-9

Buehl CJ, Kuo MH. “Critical roles of Shugoshin and histones as tension sensors during mitosis.” Curr Genet. (2018) May 23. doi: 10.1007/s00294-018-0846-4

Bhalla A, Fasahati P, Particka CA, Assad AE, Stoklosa RJ, Bansal N, Semaan R, Saffron CM, Hodge DB, Hegg EL. “Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline-oxidative pretreatment of hybrid poplar.” Biotechnol Biofuels. (2018) May 17. 11:143. doi: 10.1186/s13068-018-1124-x

Rangan AV, McGrouther CC, Kelsoe J, Schork N, Stahl E, Zhu Q, Krishnan A, Yao V, Troyanskaya O, Bilaloglu S, Raghavan P, Bergen S, Jureus A, Landen M. “A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.” PLoS Comput Biol. (2018) May 14;14(5):e1006105. doi: 10.1371/journal.pcbi.1006105

Attanayake G, Walter T, Walker KD. “Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define its Mutase and Lyase Activities.” Biochemistry. (2018) May 14. doi: 10.1021/acs.biochem.8b00269

Nault R, Doskey CM, Fader KA, Rockwell CE, Zacharewski TR. “Comparison of hepatic NRF2 and AHR binding in 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice demonstrates NRF2-independent PKM2 induction.” Mol Pharmacol. (2018) May 11. doi: 10.1124/mol.118.112144

Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH. “Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato.” Plant Cell. (2018) May 9. doi: 10.1105/tpc.18.00194

Pak D, Kim Y, Burton ZF. “Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code.” Transcription. (2018) May 4;1-36. doi: 10.1080/21541264.2018.1467718

Ye Y, Bian W, Fu F, Hu J, Liu H. “Selenoprotein S inhibits inflammation-induced vascular smooth muscle cell calcification.” J Biol Inorg Chem. (2018) May 2. doi: 10.1007/s00775-018-1563-7

Wang K, Guo Q, Froehlich JE, Hersh HL, Zienkiewicz A, Howe GA, Benning C. “Two Abscisic Acid-Responsive Plastid Lipase Genes Involved in Jasmonic Acid Biosynthesis in Arabidopsis thaliana.” Plant Cell. (2018) May;30(5):1006-1022. doi: 10.1105/tpc.18.00250

April 2018

Herr CQ, Hausinger RP. “Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases.” Trends Biochem Sci. (2018) Apr 27. doi: 10.1016/j.tibs.2018.04.002

Salim V, Jones AD, DellaPenna D. “Camptotheca acuminata 10-hydroxycamptothecin O-methyltransferase: an alkaloid biosynthetic enzyme coopted from flavonoid metabolism.” Plant J. (2018) Apr 22. doi: 10.1111/tpj.13936

Dutagaci B, Heo L, Feig M. “Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations.” Proteins. (2018) Apr 20. doi: 10.1002/prot.25508

Frum T, Ralston A. “AttrActin' Attention to Early Mouse Development.” Cell. (2018) Apr 19;173(3):544-545. doi: 10.1016/j.cell.2018.03.078

Wang K, Guo Q, Froehlich JE, Hersh HL, Zienkiewicz A, Howe GA, Benning C. “Two Abscisic Acid Responsive Plastid Lipase Genes Involved in Jasmonic Acid Biosynthesis in Arabidopsis thaliana.” Plant Cell. (2018) Apr 17. doi: 10.1105/tpc.18.00250

Fader KA, Nault R, Raehtz S, McCabe LR, Zacharewski TR. “2,3,7,8-Tetrachlorodibenzo-p-dioxin dose-dependently increases bone mass and decreases marrow adiposity in juvenile mice.” Toxicol Appl Pharmacol. (2018) Apr 16. doi: 10.1016/j.taap.2018.04.013

Ouma WZ, Pogacar K, Grotewold E. “Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties.” PLoS Comput Biol. (2018) Apr;14(4):e1006098. doi: 10.1371/journal.pcbi.1006098

Duhl KL, Tefft NM, TerAvest MA. “Shewanella oneidensis MR-1 utilizes both sodium- and proton-pumping NADH dehydrogenases during aerobic growth.” Appl Environ Microbiol. (2018) Apr 13. doi: 10.1128/AEM.00415-18

Schwarz EM, Tietz S, Froehlich JE. “Photosystem I-LHCII megacomplexes respond to high light and aging in plants.” Photosynth Res. (2018) Apr;136(1):107-124. doi: 10.1007/s11120-017-0447-y

Xu H, Lybrand D, Bennewitz S, Tissier A, Last RL, Pichersky E. “Production of trans-chrysanthemic acid, the monoterpene acid moiety of natural pyrethrin insecticides, in tomato fruit.” Metab Eng. (2018) Apr 9. doi: 10.1016/j.ymben.2018.04.004

Wu K, Zhao Z, Wang R, Wei GW. “TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility.” J Comput Chem. (2018) Apr 6. doi: 10.1002/jcc.25213

Hiser C, Liu J, Ferguson-Miller S. “The K-path entrance in cytochrome c oxidase is defined by mutation of E101 and controlled by an adjacent ligand binding domain.” Biochim Biophys Acta. (2018) Apr 4. doi: 10.1016/j.bbabio.2018.03.017

Im H, Rao V, Sridhar K, Bentley J, Mishra T, Chen R, Hall J, Graber A, Zhang Y, Li X, Mias GI, Snyder MP, Greenberg PL. “Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells.” Leuk Lymphoma. (2018) Apr 4;1-11. doi: 10.1080/10428194.2018.1452210

Eschweiler JD, Farrugia MA, Dixit SM, Hausinger RP, Ruotolo BT. “A Structural Model of the Urease Activation Complex Derived from Ion Mobility-Mass Spectrometry and Integrative Modeling.” Structure. (2018) Apr 3;26(4):599-606.e3. doi: 10.1016/j.str.2018.03.001

Bansal N, Zheng Z, Song LF, Pei J, Merz KM. “The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation.” J Am Chem Soc. (2018) Apr 2. doi: 10.1021/jacs.8b00743

Raschka S, More SK, Devadoss D, Zeng B, Kuhn LA, Basson MD. “Identification of potential small-molecule protein-protein inhibitors of cancer metastasis by 3D epitope-based computational screening.” J Physiol Pharmacol. (2018) Apr;69:(2). doi: 10.26402/jpp.2018.2.11

March 2018

Mias, G. “Mathematica for Bioinformatics.” Springer (2018) March ISBN: 978-3-319-72377-8

Raschka S, Scott AM, Huertas M, Li W, Kuhn LA. “Automated Inference of Chemical Discriminants of Biological Activity.” Methods Mol Biol. (2018) March 29;1762:307-338. doi: 10.1007/978-1-4939-7756-7_16

Guo Q, Major IT, Howe GA. “Resolution of growth-defense conflict: mechanistic insights from jasmonate signaling.” Curr Opin Plant Biol. (2018) Mar 16;44:72-81. doi: 10.1016/j.pbi.2018.02.009

Banerjee A, Hamberger B. “P450s controlling metabolic bifurcations in plant terpene specialized metabolism.” Phytochem Rev. (2018) 17(1):81-111. doi: 10.1007/s11101-017-9530-4

Heskes AM, Sundram TCM, Boughton BA, Jensen NB, Hansen NL, Crocoll C, Cozzi F, Rasmussen S, Hamberger B, Hamberger B, Staerk D, Møller BL, Pateraki I. “Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus.” Plant J. (2018) Mar;93(5):943-958. doi: 10.1111/tpj.13822

Xue S, Jones AD, Sousa L, Piotrowski J, Jin M, Sarks C, Dale BE, Balan V. “Water-soluble phenolic compounds produced from extractive ammonia pretreatment exerted binary inhibitory effects on yeast fermentation using synthetic hydrolysate.” PLoS One. (2018) Mar 15;13(3):e0194012. doi: 10.1371/journal.pone.0194012

Kaguni JM. “The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery.” Antibiotics (Basel). (2018) Mar 14;7:(1). doi: 10.3390/antibiotics7010023

Howe GA, Major IT, Koo AJ. “Modularity in Jasmonate Signaling for Multistress Resilience.” Annu Rev Plant Biol. (2018) Mar 14. doi: 10.1146/annurev-arplant-042817-040047

Poliner E, Takeuchi T, Du ZY, Benning C, Farré EM. “Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779.” ACS Synth Biol. (2018) Mar 14. doi: 10.1021/acssynbio.7b00362

Yang Y, Guo R, Gaffney K, Kim M, Muhammednazaar S, Tian W, Wang B, Liang J, Hong H. “Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-dependent Protease FtsH.” J Am Chem Soc. (2018) Mar 12. doi: 10.1021/jacs.8b00832

Scott KM, Williams J, Porter CMB, Russel S, Harmer TL, Paul JH, Antonen KM, Bridges MK, Camper GJ, Campla CK, Casella LG, Chase E, Conrad JW, Cruz MC, Dunlap DS, Duran L, Fahsbender EM, Goldsmith DB, Keeley RF, Kondoff MR, Kussy BI, Lane MK, Lawler S, Leigh BA, Lewis C, Lostal LM, Marking D, Mancera PA, McClenthan EC, McIntyre EA, Mine JA, Modi S, Moore BD, Morgan WA, Nelson KM, Nguyen KN, Ogburn N, Parrino DG, Pedapudi AD, Pelham RP, Preece AM, Rampersad EA, Richardson JC, Rodgers CM, Schaffer BL, Sheridan NE, Solone MR, Staley ZR, Tabuchi M, Waide RJ, Wanjugi PW, Young S, Clum A, Daum C, Huntemann M, Ivanova N, Kyrpides N, Mikhailova N, Palaniappan K, Pillay M, Reddy TBK, Shapiro N, Stamatis D, Varghese N, Woyke T, Boden R, Freyermuth SK, Kerfeld CA. “Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments.” Environ Microbiol. (2018) Mar 9. doi: 10.1111/1462-2920.14090

Poliner E, Farré EM, Benning C. “Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp.” Plant Cell Rep. (2018) Mar 6. doi: 10.1007/s00299-018-2270-0

Kerfeld CA, Aussignargues C, Zarzycki J, Cai F, Sutter M. “Bacterial microcompartments.” Nat Rev Microbiol. (2018) Mar 5. doi: 10.1038/nrmicro.2018.10

Ligaba-Osena A, Jones J, Donkor E, Chandrayan S, Pole F, Wu CH, Vieille C, Adams MWW, Hankoua BB. “Novel Bioengineered Cassava Expressing an Archaeal Starch Degradation System and a Bacterial ADP-Glucose Pyrophosphorylase for Starch Self-Digestibility and Yield Increase.” Front Plant Sci. (2018) 9:192. doi: 10.3389/fpls.2018.00192

February 2018

Genoni A, Bucinsky L, Claiser N, Contreras-Garcia J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa LJ, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. “Quantum Crystallography: Current Developments and Future Perspectives.” Chemistry. (2018) Feb 28. doi: 10.1002/chem.201705952

Rankin JA, Mauban RC, Fellner M, Desguin B, McCracken J, Hu J, Varganov SA, Hausinger RP. “The Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism.” Biochemistry. (2018) Feb 28. doi: 10.1021/acs.biochem.8b00100

Yildirim A, Feig M. “High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.” Nucleic Acids Res. (2018) Feb 26. doi: 10.1093/nar/gky141

Bohm K, Porwollik S, Chu W, Dover JA, Gilcrease EB, Casjens SR, McClelland M, Parent KN. “Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens.” Mol Microbiol. (2018) Feb 22. doi: 10.1111/mmi.13936

Jensen JK, Busse-Wicher M, Poulsen CP, Fangel JU, Smith PJ, Yang JY, Peña MJ, Dinesen MH, Martens HJ, Melkonian M, Wong GK, Moremen KW, Wilkerson CG, Scheller HV, Dupree P, Ulvskov P, Urbanowicz BR, Harholt J. “Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis.” New Phytol. (2018) Feb 20. doi: 10.1111/nph.15050

Dornbos P, LaPres JJ. “Incorporating population-level genetic variability within laboratory models in toxicology: From the individual to the population.” Toxicology. (2018) Feb 15;395:1-8. doi: 10.1016/j.tox.2017.12.007

Raschka S, Wolf AJ, Bemister-Buffington J, Kuhn LA. “Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.” J Comput Aided Mol Des. (2018) Feb 12. doi: 10.1007/s10822-018-0105-2

Kim Y, Benning N, Pham K, Baghdadi A, Caruso G, Colligan M, Grayson A, Hurley A, Ignatoski N, Mcclure S, Mckaig K, Neag E, Showers C, Tangalos A, Vanells J, Padmanabhan K, Burton ZF. “Homology threading to generate RNA polymerase structures.” Protein Expr Purif. (2018) Feb 11. doi: 10.1016/j.pep.2018.02.002

Ciesielski GL, Nadalutti CA, Oliveira MT, Jacobs HT, Griffith JD, Kaguni LS. “Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase.” Nucleic Acids Res. (2018) Feb 8. doi: 10.1093/nar/gky094

Bramer D, Wei GW. “Multiscale weighted colored graphs for protein flexibility and rigidity analysis.” J Chem Phys. (2018) Feb 7;148(5):054103. doi: 10.1063/1.5016562

Parent KN, Schrad JR, Cingolani G. “Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy.” Viruses. (2018) Feb 7;10:(2). doi: 10.3390/v10020067

Doore SM, Schrad JR, Dean WF, Dover JA, Parent KN. “Shigella phages isolated during a dysentery outbreak reveal uncommon structures and broad species diversity” J of Virology (2018) Feb 7. doi: 10.1128/JVI.02117-17

Du ZY, Lucker BF, Zienkiewicz K, Miller TE, Zienkiewicz A, Sears BB, Kramer DM, Benning C. “Galactoglycerolipid Lipase PGD1 Is Involved in Thylakoid Membrane Remodeling in Response to Adverse Environmental Conditions in Chlamydomonas.” Plant Cell. (2018) Feb 5. doi: 10.1105/tpc.17.00446

Fristedt R, Hu C, Wheatley N, Roy LM, Wachter RM, Savage L, Harbinson J, Kramer DM, Merchant SS, Yeates T, Croce R. “RAF2 is a Rubisco Assembly Factor in Arabidopsis thaliana.” Plant J. (2018) Feb 3;. doi: 10.1111/tpj.13849

Rohnke BA, Singh SP, Pattanaik B, Montgomery BL. “RcaE-Dependent Regulation of Carboxysome Structural Proteins Has a Central Role in Environmental Determination of Carboxysome Morphology and Abundance in Fremyella diplosiphon.” mSphere. (2018) Jan-Feb;3:(1). doi: 10.1128/mSphere.00617-17

January 2018

Wu K, Wei GW. “Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks.” J Chem Inf Model. (2018) Jan 31. doi: 10.1021/acs.jcim.7b00558

Raschka S, Scott AM, Liu N, Gunturu S, Huertas M, Li W, Kuhn LA. “Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control.” J Comput Aided Mol Des. (2018) Jan 30. doi: 10.1007/s10822-018-0100-7

Wei J, Zheng Y, Feng H, Qu H, Fan X, Yamaji N, Feng Ma J, Xu G, Takahashi H. “OsNRT2.4 encodes a dual-affinity nitrate transporter and functions in nitrate-regulated root growth and nitrate distribution in rice.” J Exp Bot. (2018) Jan 29. doi: 10.1093/jxb/erx486

Kim SJ, Zemelis-Durfee S, Jensen JK, Wilkerson CG, Keegstra K, Brandizzi F. “In the grass species Brachypodium distachyon, the production of mixed linkage (1,3;1,4)-Β-glucan (MLG) occurs in the Golgi apparatus.” Plant J. (2018) Jan 27. doi: 10.1111/tpj.13830

Pak D, Du N, Kim Y, Sun Y, Burton ZF. “Rooted tRNAomes and evolution of the genetic code.” Transcription. (2018) Jan 26;1-31. doi: 10.1080/21541264.2018.1429837

Liu D, Wang Q, Traverse CJ, Yang C, Young M, Kuttipillai PS, Lunt SY, Hamann TW, Lunt RR. “Impact of Ultrathin C60 on Perovskite Photovoltaic Devices.” ACS Nano. (2018) Jan 23;12(1):876-883. doi: 10.1021/acsnano.7b08561

Bhalla A, Bansal N, Pattathil S, Li M, Shen W, Particka CA, Karlen SD, Phongpreecha T, Semaan RR, Gonzales-Vigil E, Ralph J, Mansfield SD, Ding SY, Hodge DB, Hegg EL. ”Engineered Lignin in Poplar Biomass Facilitates Cu-Catalyzed Alkaline-Oxidative Pretreatment&lduo; ACS Sustainable Chemistry & Engineering (2018) Jan 22;6(3):2932-2941 doi: 10.1021/acssuschemeng.7b02067

Das A, Rahimi A, Ulbrich A, Alherech M, Motagamwala AH, Bhalla A, da Costa Sousa L, Balan V, Dumesic JA, Hegg EL, Dale BE, Ralph J, Coon JJ, Stahl SS. ”Lignin Conversion to Low-Molecular-Weight Aromatics via an Aerobic Oxidation-Hydrolysis Sequence: Comparison of Different Lignin Sources&dlquo; ACS Sustainable Chemistry & Engineering (2018) Jan 19;6(3):3367-3374 doi: 10.1021/acssuschemeng.7b03541

Wood RJ, Ormsby AR, Radwan M, Cox D, Sharma A, Vöpel T, Ebbinghaus S, Oliveberg M, Reid GE, Dickson A, Hatters DM. “A biosensor-based framework to measure latent proteostasis capacity.” Nat Commun. (2018) Jan 18;9(1):287. doi: 10.1038/s41467-017-02562-5

Gurchiek JK, Bao H, Domínguez-Martín MA, McGovern SE, Marquardt CE, Roscioli JD, Ghosh S, Kerfeld CA, Beck WF. “Fluorescence and Excited State Conformational Dynamics of the Orange Carotenoid Protein.” J Phys Chem B. (2018) Jan 18;. doi: 10.1021/acs.jpcb.7b09435

Howe GA. “Plant hormones: Metabolic end run to jasmonate.” Nat Chem Biol. (2018) Jan 16;14(2):109-110. doi: 10.1038/nchembio.2553

Watts J, Lokken A, Moauro A, Ralston A. “Capturing and Interconverting Embryonic Cell Fates in a Dish.” Curr Top Dev Biol. (2018) Jan 12. 128:181-202. doi: 10.1016/bs.ctdb.2017.11.008

Hodeib M, Ogrodzinski MP, Vergnes L, Reue K, Karlan BY, Lunt SY, Aspuria PP. “Metformin induces distinct bioenergetic and metabolic profiles in sensitive versus resistant high grade serous ovarian cancer and normal fallopian tube secretory epithelial cells.” Oncotarget. (2018) Jan 9;9(3):4044-4060. doi: 10.18632/oncotarget.23661

Hunter CT, Saunders JW, Magallanes-Lundback M, Christensen SA, Willett D, Stinard PS, Li QB, Lee K, DellaPenna D, Koch KE. “Maize w3 disrupts homogentisate solanesyl transferase (ZmHst) and reveals a plastoquinone-9 independent path for phytoene desaturation and tocopherol accumulation in kernels.” Plant J. (2018) Jan 8. doi: 10.1111/tpj.13821

Heskes AM, Sundram TCM, Boughton BA, Bjerg Jensen N, Hansen NL, Crocoll C, Cozzi F, Rasmussen S, Hamberger B, Hamberger B, Staerk D, Møller BL, Pateraki I. “Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus.” Plant J. (2018) Jan 8. doi: 10.1111/tpj.13822

Cang Z, Mu L, Wei GW. “Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening.” PLoS Comput Biol. (2018) Jan 8;14(1):e1005929. doi: 10.1371/journal.pcbi.1005929

Lotz SD, Dickson A. “Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions.” J Am Chem Soc. (2018) Jan 5;. doi: 10.1021/jacs.7b08572

December 2017

Hu, J., Wille, H., and Schmitt-Ulms, G. “The Evolutionary unZIPping of a Dimerization Motif-A Comparison of ZIP and PrP Architectures.” Pathogens. (2017) Dec 29;7(1):4. doi: 10.3390/pathogens7010004

Tsai CH, Uygun S, Roston R, Shiu SH, Benning C. “Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State in Chlamydomonas.” Plant Physiol. (2017) Dec 29;. doi: 10.1104/pp.17.01546

Oakley CG, Savage L, Lotz S, Rudd Larson G, Thomashow MF, Kramer DM, Schemske DW. “Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana.” J Exp Bot. (2017) Dec 28;. doi: 10.1093/jxb/erx437

Zhang Q, Wijk RV, Shahbaz M, Roels W, Schooten BV, Vermeer JEM, Zarza X, Guardia A, Scuffi D, García-Mata C, Laha D, Williams P, Willems LAJ, Ligterink W, Hoffmann-Benning S, Gillaspy G, Schaaf G, Haring MA, Laxalt AM, Munnik T. “Arabidopsis Phospholipase C3 is Involved in Lateral Root Initiation and ABA Responses in Seed Germination and Stomatal Closure.” Plant Cell Physiol. (2017) Dec 22. doi: 10.1093/pcp/pcx194

Buehl CJ, Deng X, Luo J, Buranasudja V, Hazbun T, Kuo MH. “A Failsafe for Sensing Chromatid Tension in Mitosis with the Histone H3 Tail in Saccharomyces cerevisiae.” Genetics. (2017) Dec 14;. doi: 10.1534/genetics.117.300606

Fan P, Miller AM, Liu X, Jones AD, Last RL. “Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity.” Nat Commun. (2017) Dec 12;8(1):2080. doi: 10.1038/s41467-017-02045-7

Uyar A, Karamyan VT, Dickson A. “Long-Range Changes in Neurolysin Dynamics Upon Inhibitor Binding.” J Chem Theory Comput. (2017) Dec 8;. doi: 10.1021/acs.jctc.7b00944

Huang D, Guo G, Yuan P, Ralston A, Sun L, Huss M, Mistri T, Pinello L, Ng HH, Yuan G, Ji J, Rossant J, Robson P, Han X. “The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation.” Sci Rep. (2017) Dec 7;7(1):17156. doi: 10.1038/s41598-017-16009-w

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM. “The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.” Plant Physiol. (2017) Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490

November 2017

Oh S, Montgomery BL. “Phytochromes: Where to Start?” Cell. (2017) Nov 30;171(6):1254-1256. doi: 10.1016/j.cell.2017.11.020

Nawrocki G, Wang PH, Yu I, Sugita Y, Feig M. “Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.” J Phys Chem B. (2017) Nov 30. doi: 10.1021/acs.jpcb.7b08785

Huot B, Castroverde CDM, Velásquez AC, Hubbard E, Pulman JA, Yao J, Childs KL, Tsuda K, Montgomery BL, He SY. “Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis.” Nat Commun. (2017) Nov 27;8(1):1808. doi: 10.1038/s41467-017-01674-2

Halder S, Parrell D, Whitten D, Feig M, Kroos L. “Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK.” Proc Natl Acad Sci U S A. (2017) Nov 27. doi: 10.1073/pnas.1711467114

Ralston A. “XEN and the Art of Stem Cell Maintenance: Molecular Mechanisms Maintaining Cell Fate and Self-Renewal in Extraembryonic Endoderm Stem (XEN) Cell Lines.” Adv Anat Embryol Cell Biol. (2017) Nov 25. 229:69-78. doi: 10.1007/978-3-319-63187-5_6

Dutagaci B, Feig M. “Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.” J Chem Inf Model. (2017) Nov 20. doi: 10.1021/acs.jcim.7b00510

Zeng B, Devadoss D, Wang S, Vomhof-DeKrey EE, Kuhn LA, Basson MD. “Inhibition of pressure-activated cancer cell adhesion by FAK-derived peptides.” Oncotarget. (2017) Nov 17;8(58):98051-98067. doi: 10.18632/oncotarget.20556

Yu Z, Li P, Merz KM. “The Extended Zinc AMBER Force Field (EZAFF).” J Chem Theory Comput. (2017) Nov 17. doi: 10.1021/acs.jctc.7b00773

Nagarajan S, Lapidus LJ. “Fluorescent Probe DCVJ Shows High Sensitivity for Characterization of Amyloid Β-Peptide Early in the Lag Phase.” Chembiochem. (2017) Nov 16;18(22):2205-2211. doi: 10.1002/cbic.201700387

Cang Z, Wei GW. “Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology.” Bioinformatics. (2017) Nov 15;33(22):3549-3557. doi: 10.1093/bioinformatics/btx460

Wang B, Wang C, Wu K, Wei GW. “Breaking the polar-nonpolar division in solvation free energy prediction.” J Comput Chem. (2017) Nov 11. doi: 10.1002/jcc.25107

Xu H, Moghe GD, Wiegert-Rininger K, Schilmiller AL, Barry CS, Last RL, Pichersky E. “Identification of dehydrogenases involved in the biosynthesis of the monoterpene moiety of pyrethrin.” Plant Physiol. (2017) Nov 9;. doi: 10.1104/pp.17.01330

Heo L, Feig M. “PREFMD: a web server for protein structure refinement via molecular dynamics simulations.” Bioinformatics. (2017) Nov 8;. doi: 10.1093/bioinformatics/btx726

October 2017

Müller TA, Struble SL, Meek K, Hausinger RP. “Characterization of human AlkB homolog 1 produced in mammalian cells and demonstration of mitochondrial dysfunction in ALKBH1-deficient cells.” Biochem Biophys Res Commun. (2017) Oct 30. doi: 10.1016/j.bbrc.2017.10.158

Diepenbrock CH, Kandianis CB, Lipka AE, Magallanes-Lundback M, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mesberg A, Bradbury PJ, Ilut DC, Mateos-Hernandez M, Hamilton J, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D. “Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain.” Plant Cell. (2017) Oct;29(10):2374-2392. doi: 10.1105/tpc.17.00475

Burns LA, Faver JC, Zheng Z, Marshall MS, Smith DGA, Vanommeslaeghe K, MacKerell AD Jr, Merz KM Jr, Sherrill CD. “The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.” J Chem Phys. (2017) Oct 28;147(16):161727. doi: 10.1063/1.5001028

Chen C, MacCready JS, Ducat DC, Osteryoung KW. “The Molecular Machinery of Chloroplast Division.” Plant Physiol. (2017) Oct 27. doi: 10.1104/pp.17.01272

Felczak MM, Chodavarapu S, Kaguni JM. “DnaC, the indispensable companion of DnaB helicase, controls the accessibility of DnaB helicase by primase.” J Biol Chem. (2017) Oct 25. doi: 10.1074/jbc.M117.807644

Thornburg CK, Walter T, Walker KD. “Biocatalysis of a Paclitaxel Analogue: Conversion of Baccatin III to N-Debenzoyl-N-(2-furoyl)paclitaxel and Characterization of an Amino Phenylpropanoyl CoA Transferase” Biochemistry (2017) Oct 25. doi: 10.1021/acs.biochem.7b00912

Weiss TL, Young EJ, Ducat DC. “A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate production.” Metab Eng. (2017) Oct 20. doi: 10.1016/j.ymben.2017.10.009

Lindsey BE 3rd, Rivero L, Calhoun CS, Grotewold E, Brkljacic J. “Standardized Method for High-throughput Sterilization of Arabidopsis Seeds.” J Vis Exp. (2017) Oct 17. doi: 10.3791/56587

Plegaria JS, Kerfeld CA. “Engineering nanoreactors using bacterial microcompartment architectures.” Curr Opin Biotechnol. (2017) Oct 13;51:1-7. doi: 10.1016/j.copbio.2017.09.005

Teoh ST, Lunt SY. “Metabolism in cancer metastasis: bioenergetics, biosynthesis, and beyond.” Wiley Interdiscip Rev Syst Biol Med. (2017) Oct 9. doi: 10.1002/wsbm.1406

Kar P, Feig M. “Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.” J Chem Theory Comput. (2017) Oct 9. doi: 10.1021/acs.jctc.7b00840

Heo L, Feig M. “What makes it difficult to refine protein models further via molecular dynamics simulations?” Proteins. (2017) Oct 4;. doi: 10.1002/prot.25393

Turmo A, Gonzalez-Esquer CR, Kerfeld CA. “Carboxysomes: metabolic modules for CO2 fixation.” FEMS Microbiol Lett. (2017) Oct 2;364:(18). doi: 10.1093/femsle/fnx176

September 2017

Plegaria JS, Sutter M, Ferlez B, Aussignargues C, Niklas J, Poluektov OG, Fromwiller C, TerAvest M, Utschig LM, Tiede DM, Kerfeld CA. “Structural and Functional Characterization of a Short-Chain Flavodoxin Associated with a Non-Canonical PDU Bacterial Microcompartment.” Biochemistry. (2017) Sep 28. doi: 10.1021/acs.biochem.7b00682

Kerfeld CA. “A bioarchitectonic approach to the modular engineering of metabolism.” Philos Trans R Soc Lond B Biol Sci. (2017) Sep 26;372:(1730). doi:10.1098/rstb.2016.0387

Davis GA, Rutherford AW, Kramer DM. “Hacking the thylakoid proton motive force for improved photosynthesis: modulating ion flux rates that control proton motive force partitioning into Δφ and ΔpH.” Philos Trans R Soc Lond B Biol Sci. (2017) Sep 26;372:(1730). doi:10.1098/rstb.2016.0381

Lapidus LJ. “Protein unfolding mechanisms and their effects on folding experiments.” F1000Res. (2017) Sep 22;6:1723. doi: 10.12688/f1000research.12070.1

Morales A, Yin X, Harbinson J, Driever SM, Molenaar J, Kramer DM, Struik P. “In silico analysis of the regulation of the photosynthetic electron transport chain in C3 plants.” Plant Physiol. (2017) Sep 18. doi: 10.1104/pp.17.00779

Nagarajan S, Lapidus LJ. “Fluorescent probe DCVJ shows high sensitivity for characterization of amyloid beta peptide early in the lag phase.” Chembiochem. (2017) Sep 11. doi: 10.1002/cbic.201700387

Liu J, Last RL. “A chloroplast thylakoid lumen protein is required for proper photosynthetic acclimation of plants under fluctuating light environments.” Proc Natl Acad Sci U S A. (2017) Sep 5. doi: 10.1073/pnas.1712206114

Lucker B, Schwartz E, Kuhlgert S, Ostendorf E, Kramer DM. “Spectroanalysis in Native Gels (SING): Rapid Spectral Analysis of Pigmented Thylakoid Membrane Complexes Separated By Clear Native PAGE.” Plant J. (2017) Sep 2. doi: 10.1111/tpj.13703

Zhao D, Hamilton JP, Pham GM, Crisovan E, Wiegert-Rininger K, Vaillancourt B, DellaPenna D, Buell CR. “De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin.” Gigascience. (2017) Sep 1;6(9):1-7. doi: 10.1093/gigascience/gix065

August 2017

Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, Wei G, Burton ZF. “Hinge action versus grip in translocation by RNA polymerase.” Transcription. (2017) Aug 30;e1330179. doi: 10.1080/21541264.2017.1330179

Moghe GD, Leong BJ, Hurney S, Jones AD, Last RL. “Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway.” Elife. (2017) Aug 30. doi: 10.7554/eLife.28468

Sharkey TD. “A dichotomy resolved: plant growth can control the rate of starch accumulation.” Plant Cell Environ. (2017) Aug 30. doi: 10.1111/pce.13059

Liu J, Hiser C, Ferguson-Miller S. “Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity.” Biochem Soc Trans. (2017) Aug 24. doi: 10.1042/BST20160138

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. “Improvements to the APBS biomolecular solvation software suite.” Protein Sci. (2017) Aug 24. doi: 10.1002/pro.3280

Leong BJ, Last RL. “Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism.” Curr Opin Struct Biol. (2017) Aug 16;47:105-112. doi: 10.1016/j.sbi.2017.07.005

Terbush AD, MacCready JS, Chen C, Ducat DC, Osteryoung KW. “Conserved Dynamics of Chloroplast Cytoskeletal FtsZ Proteins Across Photosynthetic Lineages.” Plant Physiol. (2017) Aug 16. doi:10.1104/pp.17.00558

Matsushima Y, Hirofuji Y, Aihara M, Yue S, Uchiumi T, Kaguni LS, Kang D. “Drosophila protease ClpXP specifically degrades DmLRPPRC1 controlling mitochondrial mRNA and translation.” Sci Rep. (2017) Aug 16;7(1):8315. doi:10.1038/s41598-017-08088-6

Kieffer-Kwon K, McAndrew M, Floer M, et al. “Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation” Molecular Cell. (2017) Aug 11;67:1-13. doi: 10.1016/j.molcel.2017.07.013

Pak D, Root-Bernstein R, Burton ZF. “tRNA structure and evolution and standardization to the three nucleotide genetic code.” Transcription. (2017) Aug 8;8(4):205-219. doi: 10.1080/21541264.2017.1318811

Chakraborty D, Benham V, Bullard B, Kearney T, Hsia HC, Gibbon D, Demireva EY, Lunt SY, Bernard JJ. “Fibroblast growth factor receptor is a mechanistic link between visceral adiposity and cancer.” Oncogene. (2017) Aug 7. doi: 10.1038/onc.2017.278

Fellner M, Desguin B, Hausinger RP, Hu J. “Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.” Proc Natl Acad Sci U S A. (2017) Aug 7. pii: 201704967. doi: 10.1073/pnas.1704967114

Martinez S, Fellner M, Herr CQ, Ritchie A, Hu J, Hausinger RP. “Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist.” J Am Chem Soc. (2017) Aug 5. doi: 10.1021/jacs.7b06186

Zhang T, Liu J, Fellner M, Zhang C, Sui D, Hu J. “Crystal structures of a ZIP zinc transporter reveal a binuclear metal center in the transport pathway.” Sci Adv. (2017) Aug;3(8):e1700344. doi: 10.1126/sciadv.1700344

Desguin B, Soumillion P, Hausinger RP, Hols P. “Unexpected complexity in the lactate racemization system of lactic acid bacteria.” FEMS Microbiol Rev. (2017) Aug 1;41(Supp_1):S71-S83. doi: 10.1093/femsre/fux021

Tietz S, Hall CC, Cruz JA, Kramer DM. “NPQ((T)) : a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem-II-associated antenna complexes.” Plant Cell Environ. (2017) Aug;40(8):1243-1255. doi: 10.1111/pce.12924

Feller A, Yuan L, Grotewold E. “The BIF Domain in Plant bHLH Proteins Is an ACT-Like Domain.” Plant Cell. (2017) Aug;29(8):1800-1802. doi: 10.1105/tpc.17.00356

July 2017

Young EJ, Burton R, Mahalik JP, Sumpter BG, Fuentes-Cabrera M, Kerfeld CA, Ducat DC. “Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications.” Front Microbiol. (2017) Jul 31;8:1441. doi: 10.3389/fmicb.2017.01441

Cang Z, Wei GW. “TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.” PLoS Comput Biol. (2017) Jul 27;13(7):e1005690. doi: 10.1371/journal.pcbi.1005690

Nguyen DD, Xiao T, Wang M, Wei GW. “Rigidity Strengthening: A Mechanism for Protein-Ligand Binding.” J Chem Inf Model. (2017) Jul 24;57(7):1715-1721. doi: 10.1021/acs.jcim.7b00226

Kohzuma K, Froehlich JE, Davis GA, Temple JA, Minhas D, Dhingra A, Cruz JA, Kramer DM. “The Role of Light-Dark Regulation of the Chloroplast ATP Synthase.” Front Plant Sci. (2017) Jul 24;8:1248. doi: 10.3389/fpls.2017.01248

Pickens CA, Vazquez AI, Jones AD, Fenton JI. “Obesity, adipokines, and C-peptide are associated with distinct plasma phospholipid profiles in adult males, an untargeted lipidomic approach.” Sci Rep. (2017) Jul 24;7(1):6335. doi: 10.1038/s41598-017-05785-0

Fader KA, Nault R, Zhang C, Kumagai K, Harkema JR, Zacharewski TR. “2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism.” Sci Rep. (2017) Jul 19;7(1):5921. doi: 10.1038/s41598-017-05656-8

Ogrodzinski MP, Bernard JJ, Lunt SY. “Deciphering metabolic rewiring in breast cancer subtypes.” Transl Res. (2017) Jul 15. pii: S1931-5244(17)30234-7. doi: 10.1016/j.trsl.2017.07.004

Cang Z, Wei GW. “Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology.” Bioinformatics. (2017) Jul 14. doi: 10.1093/bioinformatics/btx460

White NA, Hoogstraten CG. “Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.” Biophys Chem. (2017) Jul 8;228:62-68. doi: 10.1016/j.bpc.2017.07.001

Nadakuduti SS, Uebler JB, Liu X, Jones AD, Barry CS. “Characterization of trichome-expressed BAHDs in Petunia reveals distinct acylsugar assembly mechanisms.” Plant Physiol. (2017) Jul 12. pii: pp.00538.2017. doi: 10.1104/pp.17.00538

Bao H, Melnicki MR, Pawlowski EG, Sutter M, Agostoni M, Lechno-Yossef S, Cai F, Montgomery BL, Kerfeld CA. “Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria.” Nat Plants. (2017) Jul 10;3:17089. doi: 10.1038/nplants.2017.89

Wang K, Froehlich JE, Zienkiewicz A, Hersh HL, Benning C. “A Plastid Phosphatidylglycerol Lipase Contributes to the Export of Acyl Groups from Plastids for Seed Oil Biosynthesis.” Plant Cell. (2017) Jul 6. pii: tpc.00397.2017. doi: 10.1105/tpc.17.00397

Cang Z, Wei GW. “Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.” Int J Numer Method Biomed Eng. (2017) Jul 5. doi: 10.1002/cnm.2914

Parrell D, Zhang Y, Olenic S, Kroos L. “Bacillus subtilis Intramembrane Protease RasP Activity in Escherichia coli and in Vitro.” J Bacteriol. (2017) Jul 3. pii: JB.00381-17. doi: 10.1128/JB.00381-17

June 2017

Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. “Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.” J Phys Chem B. (2017) Jun 30. doi: 10.1021/acs.jpcb.7b03570

Major IT, Yoshida Y, Campos ML, Kapali G, Xin XF, Sugimoto K, de Oliveira Ferreira D, He SY, Howe GA. “Regulation of growth-defense balance by the JASMONATE ZIM-DOMAIN (JAZ)-MYC transcriptional module.” New Phytol. (2017) Jun 26. doi: 10.1111/nph.14638

Dutta S, Cruz JA, Imran SM, Chen J, Kramer DM, Osteryoung KW. “Variations in chloroplast movement and chlorophyll fluorescence among chloroplast division mutants under light stress.” J Exp Bot. (2017) Jun 22. doi: 10.1093/jxb/erx203

Kuhn MJ, Mavangira V, Gandy JC, Zhang C, Jones AD, Sordillo LM. “Differences in the Oxylipid Profiles of Bovine Milk and Plasma at Different Stages of Lactation.” J Agric Food Chem. (2017) Jun 21;65(24):4980-4988. doi: 10.1021/acs.jafc.7b01602

Martinez S, Hausinger RP. “Correction to Biochemical and Spectroscopic Characterization of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme from Pseudomonas syringae pv. phaseolicola PK2.” Biochemistry. (2017) Jun 20;56(24):3158. doi: 10.1021/acs.biochem.7b00502

Mukundi E, Gomez-Cano F, Ouma WZ, Grotewold E. “Design of Knowledge Bases for Plant Gene Regulatory Networks.” Methods Mol Biol. (2017) Jun 17;1629:207-223. doi: 10.1007/978-1-4939-7125-1_14

Forman V, Callari R, Folly C, Heider H, Hamberger B. “Production of Putative Diterpene Carboxylic Acid Intermediates of Triptolide in Yeast.” Molecules. (2017) Jun 13;22(6). pii: E981. doi: 10.3390/molecules22060981

Poliner E, Pulman JA, Zienkiewicz K, Childs K, Benning C, Farré EM. “A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long-chain polyunsaturated fatty acid production.” Plant Biotechnol J. (2017) Jun 12. doi: 10.1111/pbi.12772

de Bang TC, Lay KS, Scheible WR, Takahashi H. “Small peptide signaling pathways modulating macronutrient utilization in plants.” Curr Opin Plant Biol. (2017) Jun 2;39:31-39. doi: 10.1016/j.pbi.2017.05.005

May 2017

Strand DD, Fisher N, Kramer DM. “The higher plant plastid NAD(P)H dehydrogenase-like complex (NDH) is a high efficiency proton pump that increases ATP production by cyclic electron flow.” J Biol Chem. (2017) May 30. pii: jbc.M116.770792. doi: 10.1074/jbc.M116.770792

Mansfeld BN, Colle M, Kang Y, Jones AD, Grumet R. “Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici.” Hortic Res. (2017) May 24;4:17022. doi: 10.1038/hortres.2017.22

Yang Y, Zienkiewicz A, Lavell A, Benning C. “Co-evolution of Domain Interactions in the Chloroplast TGD1, 2, 3 Lipid Transfer Complex Specific to Brassicaceae and Poaceae Plants.” Plant Cell. (2017) May 19. pii: tpc.00182.2017. doi: 10.1105/tpc.17.00182

Xing A, Last RL. “A Regulatory Hierarchy of the Arabidopsis Branched-chain Amino Acid Metabolic Network.” Plant Cell. (2017) May 18. pii: tpc.00186.2017. doi: 10.1105/tpc.17.00186

Lechno-Yossef S, Melnicki MR, Bao H, Montgomery BL, Kerfeld CA. “Synthetic OCP Heterodimers are Photoactive and Recapitulate the Fusion of Two Primitive Carotenoproteins in the Evolution of Cyanobacterial Photoprotection.” Plant J. (2017) May 15. doi: 10.1111/tpj.13593

Kanazawa A, Ostendorf E, Kohzuma K, Hoh D, Strand DD, Sato-Cruz M, Savage L, Cruz JA, Fisher N, Froehlich JE, Kramer DM. “Chloroplast ATP Synthase Modulation of the Thylakoid Proton Motive Force: Implications for Photosystem I and Photosystem II Photoprotection.” Front Plant Sci. (2017) May 3;8:719. doi: 10.3389/fpls.2017.00719

Dutagaci B, Wittayanarakul K, Mori T, Feig M. “Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.” J Chem Theory Comput. (2017) May 11. doi: 10.1021/acs.jctc.7b00254

Morin JA, Cerrón F, Jarillo J, Beltran-Heredia E, Ciesielski GL, Arias-Gonzalez JR, Kaguni LS, Cao FJ, Ibarra B. “DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein.” Nucleic Acids Res. (2017) May 9. doi: 10.1093/nar/gkx395

Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen J, Zacharewski TR, Tiedje JM, Hashsham SA. “TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome.” FEMS Microbiol Ecol. (2017) May 4. doi: 10.1093/femsec/fix058

Yang Y, Xu L, Feng Z, Cruz JA, Savage LJ, Kramer DM, Chen J. “PhenoCurve: capturing dynamic phenotype-environment relationships using phenomics data.” Bioinformatics. (2017) May 1;33(9):1370-1378. doi: 10.1093/bioinformatics/btw673

Benning C. “Plant science from The Plant Journal Editors' perspective.” Plant J. (2017) May;90(4):625-627. doi: 10.1111/tpj.13565

April 2017

Liban TJ, Medina EM, Tripathi S, Sengupta S, Henry RW, Buchler NE, Rubin SM. “Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family.” Proc Natl Acad Sci U S A. (2017) Apr 24. pii: 201619170. doi: 10.1073/pnas.1619170114

Nurminen A, Farnum GA, Kaguni LS. “Pathogenicity in POLG syndromes: DNA polymerase gamma pathogenicity prediction server and database.” BBA Clin. (2017) Apr 18;7:147-156. doi: 10.1016/j.bbacli.2017.04.001

Dickson A, Tiwary P, Vashisth H. “Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review.” Curr Top Med Chem. (2017) Apr 14. doi: 10.2174/1568026617666170414142908

Montgomery BL. “Seeing new light: recent insights into the occurrence and regulation of chromatic acclimation in cyanobacteria.” Curr Opin Plant Biol. (2017) Apr 6;37:18-23. doi: 10.1016/j.pbi.2017.03.009

Bao H, Melnicki MR, Kerfeld CA. “Structure and functions of Orange Carotenoid Protein homologs in cyanobacteria.” Curr Opin Plant Biol. (2017) Apr 5;37:1-9. doi: 10.1016/j.pbi.2017.03.010

March 2017

Srivastava KR, Lapidus LJ. “Prion protein dynamics before aggregation.” Proc Natl Acad Sci U S A. (2017) Mar 20. pii: 201620400. doi: 10.1073/pnas.1620400114

Roushangar R, Mias GI. “MathIOmica-MSViewer: A Dynamic Viewer for Mass Spectrometry Files for Mathematica.” J Mass Spectrom. (2017) Mar 15. doi: 10.1002/jms.3928

Müller TA, Tobar MA, Perian MN, Hausinger RP. “Biochemical characterization of AP lyase and m(6)A demethylase activities of human AlkB homolog 1 (ALKBH1).” Biochemistry. (2017) Mar 14. doi: 10.1021/acs.biochem.7b00060

Pateraki I, Andersen-Ranberg J, Jensen NB, Wubshet SG, Heskes AM, Forman V, Hallström B, Hamberger B, Motawia MS, Olsen CE, Staerk D, Hansen J, Møller BL, Hamberger B. “Total biosynthesis of the cyclic AMP booster forskolin from Coleus forskohlii.” Elife. (2017) Mar 14;6. pii: e23001. doi: 10.7554/eLife.23001

González-Reymúndez A, de Los Campos G, Gutiérrez L, Lunt SY, Vazquez AI. “Prediction of years of life after diagnosis of breast cancer using omics and omic-by-treatment interactions.” Eur J Hum Genet. (2017) Mar 8. doi: 10.1038/ejhg.2017.12

Rajagopalan R, Kroos L. “The dev Operon Regulates the Timing of Sporulation during Myxococcus xanthus Development.” J Bacteriol. (2017) Mar 6. pii: JB.00788-16. doi: 10.1128/JB.00788-16

Hansen NL, Nissen JN, Hamberger B. “Two residues determine the product profile of the class II diterpene synthases TPS14 and TPS21 of Tripterygium wilfordii.” Phytochemistry. (2017) Mar 6. pii: S0031-9422(17)30093-6. doi: j.phytochem.2017.02.022

Walker RG, Czepnik M, Goebel EJ, McCoy JC, Vujic A, Cho M, Oh J, Aykul S, Walton KL, Schang G, Bernard DJ, Hinck AP, Harrison CA, Martinez-Hackert E, Wagers AJ, Lee RT, Thompson TB. “Structural basis for potency differences between GDF8 and GDF11.” BMC Biol. (2017) Mar 3;15(1):19. doi: 10.1186/s12915-017-0350-1

Jensen JK, Wilkerson CG. “Brachypodium as an experimental system for the study of stem parenchyma biology in grasses.” PLoS One. (2017) Mar 1;12(3):e0173095. doi: 10.1371/journal.pone.0173095

February 2017

Dickson A, Lotz SD. “Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.” Biophys J. (2017) Feb 28;112(4):620-629. doi: 10.1016/j.bpj.2017.01.006

Nault R, Fader KA, Lydic TA, Zacharewski TR. “Lipidomic evaluation of aryl hydrocarbon receptor-mediated hepatic steatosis in male and female mice by 2,3,7,8-tetrachlorodibenzo-p-dioxin.” Chem Res Toxicol. (2017) Feb 27. doi: 10.1021/acs.chemrestox.6b00430

Jordan A, Chandler J, MacCready JS, Huang J, Osteryoung KW, Ducat DC. “Engineering Cyanobacterial Cell Morphology for Enhanced Recovery and Processing of Biomass.” Appl Environ Microbiol. (2017) Feb 24. pii: AEM.00053-17. doi: 10.1128/AEM.00053-17

Wang B, Sexton RE, Feig M. “Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.” Biochim Biophys Acta. (2017) Feb 24. pii: S1874-9399(16)30280-2. doi: 10.1016/j.bbagrm.2017.02.008

Walker AR, Silvestrov P, Müller TA, Podolsky RH, Dyson G, Hausinger RP, Cisneros GA. “ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding.” PLoS Comput Biol. (2017) Feb 23;13(2):e1005345. doi: 10.1371/journal.pcbi.1005345

Busch AW, Montgomery BL. “Distinct light-, stress-, and nutrient-dependent regulation of three tryptophan-rich sensory protein (TSPO) genes in the cyanobacterium Fremyella diplosiphon.” Plant Signal Behav. (2017) Feb 21:0. doi: 10.1080/15592324.2017.1293221

Nguyen DD, Wang B, Wei GW. “Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.” J Comput Chem. (2017) Feb 16. doi: 10.1002/jcc.24757

Salminen TS, Oliveira MT, Cannino G, Lillsunde P, Jacobs HT, Kaguni LS. “Mitochondrial genotype modulates mtDNA copy number and organismal phenotype in Drosophila. Mitochondrion.” (2017) Feb 15. pii: S1567-7249(16)30075-7. doi: 10.1016/j.mito.2017.02.001

Henderson KL, Li M, Martinez S, Lewis EA, Hausinger RP, Emerson JP. “Global stability of an α-ketoglutarate-dependent dioxygenase (TauD) and its related complexes.” Biochim Biophys Acta. (2017) Feb 15. pii: S0304-4165(17)30066-1. doi: 10.1016/j.bbagen.2017.02.018

Ghosh B, Jones AD. “Profiling, characterization, and analysis of natural and synthetic acylsugars (sugar esters)” Analytical Methods. (2017) Feb 14; 9(6):892-905. doi: 10.1039/C6AY02944B

Schrad JR, Young EJ, Abrahão JS, Cortines JR, Parent KN. “Microscopic Characterization of the Brazilian Giant Samba Virus.” Viruses. (2017) Feb 14;9(2). pii: E30. doi: 10.3390/v9020030

Fader KA, Nault R, Kirby MP, Markous G, Matthews J, Zacharewski TR. “Convergence of hepcidin deficiency, systemic iron overloading, heme accumulation, and REV-ERBα/β activation in aryl hydrocarbon receptor-elicited hepatotoxicity.” Toxicol Appl Pharmacol. (2017) Feb 14. pii: S0041-008X(17)30064-9. doi: 10.1016/j.taap.2017.02.006

Kim JS, Nanfara MT, Chodavarapu S, Jin KS, Babu VM, Ghazy MA, Chung S, Kaguni JM, Sutton MD, Cho Y. “Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing.&rdqup; Nucleic Acids Res. (2017) Feb 7. doi: 10.1093/nar/gkx081

Dutagaci B, Sayadi M, Feig M. “Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.” J Comput Chem. (2017) Feb 4. doi: 10.1002/jcc.24691

Sharkey TD, Monson RK. “Isoprene research - 60 years later, the biology is still enigmatic.” Plant Cell Environ. (2017) Feb 4. doi: 10.1111/pce.12930

Fader KA, Zacharewski TR. “Beyond the Aryl Hydrocarbon Receptor: Pathway Interactions in the Hepatotoxicity of 2,3,7,8-Tetrachlorodibenzo-<i>p</i>-dioxin and Related Compounds.” Curr Opin Toxicol. (2017) Feb;2:36-41. doi: 10.1016/j.cotox.2017.01.010

Hansen NL, Heskes AM, Hamberger B, Olsen CE, Hallström BM, Andersen-Ranberg J, Hamberger B. “The terpene synthase gene family in Tripterygium wilfordii harbors a labdane-type diterpene synthase among the monoterpene synthase TPS-b subfamily.” Plant J. (2017) Feb;89(3):429-441. doi: 10.1111/tpj.13410

January 2017

Lokareddy RK, Sankhala RS, Roy A, Afonine PV, Motwani T, Teschke CM, Parent KN, Cingolani G. “Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation.” Nat Commun. (2017) Jan 30;8:14310. doi: 10.1038/ncomms14310

Zhang F, Ke J, Zhang L, Chen R, Sugimoto K, Howe GA, Xu HE, Zhou M, He SY, Melcher K. “Structural insights into alternative splicing-mediated desensitization of jasmonate signaling.” Proc Natl Acad Sci U S A. (2017) Jan 30. pii: 201616938. doi: 10.1073/pnas.1616938114

Aykul S, Parenti A, Chu KY, Reske J, Floer M, Ralston A, Martinez-Hackert E. “Biochemical and cellular analysis reveals ligand binding specificities, a molecular basis for ligand recognition, and membrane association dependent activities of Cripto-1 and Cryptic.” J Biol Chem. (2017) Jan 26. pii: jbc.M116.747501. doi: 10.1074/jbc.M116.747501

Hays SG, Yan LL, Silver PA, Ducat DC. “Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction.” J Biol Eng. (2017) Jan 23;11:4. doi: 10.1186/s13036-017-0048-5

Strand DD, Livingston AK, Satoh-Cruz M, Koepke T, Enlow HM, Fisher N, Froehlich JE, Cruz JA, Minhas D, Hixson KK, Kohzuma K, Lipton M, Dhingra A, Kramer DM. “Defects in the Expression of Chloroplast Proteins Leads to H(2)O(2) Accumulation and Activation of Cyclic Electron Flow around Photosystem I.” Front Plant Sci. (2017) Jan 13;7:2073. doi: 10.3389/fpls.2016.02073

Masukawa H, Sakurai H, Hausinger RP, Inoue K. “Increased heterocyst frequency by patN disruption in Anabaena leads to enhanced photobiological hydrogen production at high light intensity and high cell density.” Appl Microbiol Biotechnol. (2017) Jan 7. doi: 10.1007/s00253-016-8078-3

Liu B, Wang B, Zhao R, Tong Y, Wei GW. “ESES: Software for Eulerian solvent excluded surface.” J Comput Chem. (2017) Jan 4. doi: 10.1002/jcc.24682

Zienkiewicz K, Zienkiewicz A, Poliner E, Du ZY, Vollheyde K, Herrfurth C, Marmon S, Farré EM, Feussner I, Benning C. “ldqou;Nannochloropsis, a rich source of diacylglycerol acyltransferases for engineering of triacylglycerol content in different hosts.” Biotechnol Biofuels. (2017) Jan 3;10:8. doi: 10.1186/s13068-016-0686-8