Recent Publications

Selected Publications

Krishnan A, Zhang R, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG. “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.” Nat Neurosci. (2016) Aug 1;. doi: 10.1038/nn.4353

Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. “Understanding multicellular function and disease with human tissue-specific networks.” Nat Genet. (2015) Jun;47(6):569-76. doi: 10.1038/ng.3259

Park CY, Krishnan A, Zhu Q, Wong AK, Lee YS, Troyanskaya OG. “Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.” Bioinformatics. (2015) Apr 1;31(7):1093-101. doi: 10.1093/bioinformatics/btu786

Ambavaram MM, Basu S, Krishnan A, Ramegowda V, Batlang U, Rahman L, Baisakh N, Pereira A. “Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress.” Nat Commun. (2014) Oct 31;5:5302. doi: 10.1038/ncomms6302

Lee YS, Krishnan A, Zhu Q, Troyanskaya OG. “Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies.” Bioinformatics. (2013) Dec 1;29(23):3036-44. doi: 10.1093/bioinformatics/btt529

Ambavaram MM, Krishnan A, Trijatmiko KR, Pereira A. “Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice.” Plant Physiol. (2011) Feb;155(2):916-31. doi: 10.1104/pp.110.168641

Other Publications

Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG. “IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.” Nucleic Acids Res. (2015) Jul 1;43(W1):W128-33. doi: 10.1093/nar/gkv486

Goya J, Wong AK, Yao V, Krishnan A, Homilius M, Troyanskaya OG. “FNTM: a server for predicting functional networks of tissues in mouse.” Nucleic Acids Res. (2015) Jul 1;43(W1):W182-7. doi: 10.1093/nar/gkv443

Chikina MD, Gerald CP, Li X, Ge Y, Pincas H, Nair VD, Wong AK, Krishnan A, Troyanskaya OG, Raymond D, Saunders-Pullman R, Bressman SB, Yue Z, Sealfon SC. “Low-variance RNAs identify Parkinson's disease molecular signature in blood.” Mov Disord. (2015) May;30(6):813-21. doi: 10.1002/mds.26205

Zhu Q, Wong AK, Krishnan A, Aure MR, Tadych A, Zhang R, Corney DC, Greene CS, Bongo LA, Kristensen VN, Charikar M, Li K, Troyanskaya OG. “Targeted exploration and analysis of large cross-platform human transcriptomic compendia.” Nat Methods. (2015) Mar;12(3):211-4, 3 p following 214. doi: 10.1038/nmeth.3249

Ramegowda V, Basu S, Krishnan A, Pereira A. “Rice GROWTH UNDER DROUGHT KINASE is required for drought tolerance and grain yield under normal and drought stress conditions.” Plant Physiol. (2014) Nov;166(3):1634-45. doi: 10.1104/pp.114.248203

Poirel CL, Rahman A, Rodrigues RR, Krishnan A, Addesa JR, Murali TM. “Reconciling differential gene expression data with molecular interaction networks.” Bioinformatics. (2013) Mar 1;29(5):622-9. doi: 10.1093/bioinformatics/btt007

Kakumanu A, Ambavaram MM, Klumas C, Krishnan A, Batlang U, Myers E, Grene R, Pereira A. “Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq.” Plant Physiol. (2012) Oct;160(2):846-67. doi: 10.1104/pp.112.200444