Publications

Selected Peer-Reviewed Journal Articles

  1. Krishnan A†, Taroni JN, Greene CS†. (2016) Integrative networks illuminate biological factors underlying gene-disease associations. In Press at Current Genetic Medicine Reports doi:10.1101/062695.
  2. Krishnan A*, Zhang R*, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG. (2016) Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nature Neuroscience doi:10.1038/nn.4353. [* Co-first authors listed alphabetically.] [Web-interface: asd.princeton.edu]
  3. Greene C*, Krishnan A*, Wong AK*, Ricciotti E, Zelaya R, Himmelstein D, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman D, FitzGerald G, Dolinski K, Grosser T, Troyanskaya OG. (2015) Understanding multi-cellular function and disease with human tissue-specific gene interaction networks. Nature Genetics, 47:569-576. [* Co-first authors listed alphabetically.] [Web-interface: giant.princeton.edu]
  4. 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 (2015) Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nature Methods, 12:211-214. [Web-interface: seek.princeton.edu]
  5. Park C, Krishnan A, Zhu Q, Wong AK, Lee Y, Troyanskaya OG (2015). Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics, 31:1093-1101. [Web-interface: pathwaynet.princeton.edu]
  6. Ambavaram MM, Basu S, Krishnan A, Venkategowda R, Batlang U, Rahman L, Baisakh N, Pereira A (2014). Coordinate regulation of photosynthetic carbon metabolism for yield and environmental stress response in rice. Nature Communications, 5:5302.
  7. Lee Y, Krishnan A, Zhu Q, Troyanskaya OG (2013). Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinformatics, 29:3036-3044. [Web-interface: ursa.princeton.edu]
  8. Ambavaram MM*, Krishnan A*, Trijatmiko KR, Pereira A (2011) Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice. Plant Physiology, 155:916-931. [* Co-first authors listed alphabetically.]
  9. Harb A, Krishnan A, Pereira A. (2010) Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. Plant Physiology, 154:1254-1271.
  10. Krishnan A, Greco R, Pereira A (2009) Diversity of En/Spm transposons in maize and rice. Maydica, 53:181-187.
  11. Krishnan A, Guiderdoni E, An G, Hsing YC, Han C, Lee MC, Yu SM, Upadhyaya N, Ramachandran S, Zhang Q, Sundaresan V, Hirochika H, Leung H, Pereira A. (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiology, 149:165-170.
  12. Krishnan A, Greco R, Pereira A. (2008) Integrative approaches for mining transcriptional regulatory programs in Arabidopsis. Briefings in Functional Genomics and Proteomics, 7:264-274.

Other Peer-Reviewed Journal Papers

  1. Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG. (2015) IMP 2.0: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research, 43:W128-133.
  2. Goya J*, Wong AK*, Yao V*, Krishnan A, Homilius M, Troyanskaya OG. (2015) FNTM: a server for predicting Functional Networks of Tissues in Mouse. Nucleic Acids Research, 43:W182-W187.
  3. 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 (2015) Low variance RNAs identify Parkinson’s disease molecular signature in blood. Movement Disorders, 30:813-821.
  4. Batlang U, Ambavaram MMR, Krishnan A, Pereira A (2014). Drought responsive genes and their functional terms identified by GS FLX Pyro sequencing in maize. Maydica 59: 306-314.
  5. Venkategowda R, Basu S, Krishnan A, Pereira A (2014). Rice GROWTH UNDER DROUGHT KINASE is required for drought tolerance and grain yield under normal and drought stress conditions. Plant Physiology, 166:1634-1645.
  6. Poirel CL, Rahman A, Rodrigues RR, Krishnan A, Addesa JR, Murali TM (2013) Reconciling differential gene expression data with molecular interaction networks. Bioinformatics, 29:622-629.
  7. Xu X, Kumar N, Krishnan A, Kulkarni R (2013) Stochastic modeling of dwell-time distributions during transcriptional pausing and initiation. 52nd IEEE Conference on Decision and Control, 4068-4073.
  8. Kakumanu A, Ambavaram MM, Klumas C, Krishnan A, Batlang U, Myers E, Grene R, Pereira A (2012) Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiology, 160:846-867.
  9. Bassaganya-Riera J, Skoneczka J, Kingston DG, Krishnan A, Misyak S, Carter A, Pereira A, Guri AJ, Tumarkin R, Hontecillas R. (2009) Mechanisms of action and medicinal applications of abscisic acid. Current Medicinal Chemistry, 17:467-478.
  10. Karaba A, Dixit S, Greco R, Aharoni A, Trijatmiko KR, Marsch-Martinez N, Krishnan A, Nataraja KN, Udayakumar M, Pereira A. (2007) Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proc Natl Acad Sci USA, 104:15270-15275.

Book Chapters

  1. Mohapatra SK*, Krishnan A*. (2009) Microarray data analysis. Plant Reverse Genetics. The Humana Press Inc., Totowa NJ, USA.
  2. Krishnan A, Ambavaram MMR, Harb A, Batlang U, Wittich PE, Pereira A (2009) Genetic networks underlying plant abiotic stress responses. Genes for Plant Abiotic Stress. John Wiley & Sons, Inc., Ames IA, USA.