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Zhou J, Troyanskaya OG. Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. Nat Commun. 2016;7:10528.

Guo JY, Teng X, Laddha S V, Ma S, Van Nostrand SC, Yang Y, Khor S, Chan CS, Rabinowitz JD, White E. Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells. Genes Dev. 2016;30(15):1704–17. PMCID: PMC5002976

Zhang X, Chamberlayne C, Kurimoto A, Frank N, Harbron E. Visible light photoswitching of conjugated polymer nanoparticle fluorescence. Chemical Communications. 2016;52:4144–4147.

Horlbeck M, Gilbert L, Villalta J, Adamson B, Pak R, Chen Y, Fields A, Park C, Corn J, Kampmann M, Weissman J. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. eLife. 2016;5. PMCID: PMC5094855

Dixit A, Parnas O, Li B, Chen J, Fulco C, Jerby-Arnon L, Marjanovic N, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman T, Lander E, Weissman J, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016;167(7):1853–1866.e17. PMCID: PMC5181115

Adamson B, Norman T, Jost M, Cho M, Nuñez J, Chen Y, Villalta J, Gilbert L, Horlbeck M, Hein M, Pak R, Gray A, Gross C, Dixit A, Parnas O, Regev A, Weissman J. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016;167(7):1867–1882.e21. PMCID: PMC5315571

Skinnider M, Dejong C, Rees P, Johnston C, Li H, Webster A, Wyatt M, Magarvey N. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic acids research. 2015;43(20):9645–62. PMCID: PMC4787774

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;30(6):813–21.

Ewald CY, Landis JN, Abate JP, Murphy CT, Blackwell K. Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity. Nature. 2015;519(7541):97–101. PMCID: PMC4352135

Purdy JG, Shenk T, Rabinowitz JD. Fatty acid elongase 7 catalyzes lipidome remodeling essential for human cytomegalovirus replication. Cell Rep. 2015;10(8):1375–85.

Tikhonov M, Leach RW, Wingreen NS. Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 2015;9(1):68–80.

Lakhina V, Murphy CT. For longevity, perception is everything. Cell. 2015;160(5):807–9.

Hahm J-H, Kim S, DiLoreto R, Shi C, Lee S-J V, Murphy CT, Nam HG. C. elegans maximum velocity correlates with healthspan and is maintained in worms with an insulin receptor mutation. Nat Commun. 2015;6:8919. PMCID: PMC4656132

Bott AJ, Peng I-C, Fan Y, Faubert B, Zhao L, Li J, Neidler S, Sun Y, Jaber N, Krokowski D, Lu W, Pan J-A, Powers S, Rabinowitz J, Hatzoglou M, Murphy DJ, Jones R, Wu S, Girnun G, Zong W-X. Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation. Cell Metab. 2015;22(6):1068–77.

Lakhina V, Murphy CT. Genome Sequencing Fishes out Longevity Genes. Cell. 2015;163(6):1312–3. PMID: 26638067

Thutupalli S, Sun M, Bunyak F, Palaniappan K, Shaevitz JW. Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation. J R Soc Interface. 2015;12(109):20150049. PMCID: PMC4535398

Xu Y-F, Lu W, Rabinowitz JD. Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics. Anal Chem. 2015;87(4):2273–81.

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;.

Wang J, Kaletsky R, Silva M, Williams A, Haas LA, Androwski RJ, Landis JN, Patrick C, Rashid A, Santiago-Martinez D, Gravato-Nobre M, Hodgkin J, Hall DH, Murphy CT, Barr MM. Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis. Curr Biol. 2015;25(24):3232–8. PMCID: PMC4698341

Bratton BP, Shaevitz JW. Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System. PLoS One. 2015;10(8):e0134616. PMCID: PMC4536040

Morgenstein RM, Bratton BP, Nguyen JP, Ouzounov N, Shaevitz JW, Gitai Z. RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis. Proc Natl Acad Sci U S A. 2015;112(40):12510–5. PMCID: PMC4603514

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;12(3):211–4, 3 p following 214.

Oktaba K, Zhang W, Lotz TS, Jun DJ, Lemke SB, Ng SP, Esposito E, Levine M, Hilgers V. ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System. Mol Cell. 2015;57(2):341–8.

Farley EK, Olson KM, Zhang W, Brandt AJ, Rokhsar DS, Levine MS. Suboptimization of developmental enhancers. Science. 2015;350(6258):325–8.

Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, Hartmann BM, Albrecht RA, García-Sastre A, Kleinstein SH, Troyanskaya OG, Sealfon SC. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015;43(3):605–14.

Gibney PA, Schieler A, Chen JC, Rabinowitz JD, Botstein D. Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter. Proc Natl Acad Sci U S A. 2015;.

Mok WWK, Park JO, Rabinowitz JD, Brynildsen MP. RNA Futile Cycling in Model Persisters Derived from MazF Accumulation. MBio. 2015;6(6):e01588–15.

DiLoreto R, Murphy CT. The cell biology of aging. Mol Biol Cell. 2015;26(25):4524–31. PMCID: PMC4678010

Abitua PB, Gainous B, Kaczmarczyk AN, Winchell CJ, Hudson C, Kamata K, Nakagawa M, Tsuda M, Kusakabe TG, Levine M. The pre-vertebrate origins of neurogenic placodes. Nature. 2015;524(7566):462–5.

Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine M. Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo. Elife. 2015;4.

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;47(6):569–76.

Pritykin Y, Ghersi D, Singh M. Genome-Wide Detection and Analysis of Multifunctional Genes. PLoS Comput Biol. 2015;11(10):e1004467.

Ochoa A, Storey JD, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol. 2015;11(11):e1004509.

Rajeshkumar N V, Dutta P, Yabuuchi S, de Wilde RF, Martinez G V, Le A, Kamphorst JJ, Rabinowitz JD, Jain SK, Hidalgo M, Dang C V, Gillies RJ, Maitra A. Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function. Cancer Res. 2015;75(16):3355–64.

Tkačik G, Dubuis J, Petkova MD, Gregor T. Positional information, positional error, and readout precision in morphogenesis: a mathematical framework. Genetics. 2015;199(1):39–59.

Dolinski K, Troyanskaya OG. Implications of Big Data for cell biology. Mol Biol Cell. 2015;26(14):2575–8.

Lakhina V, Arey R, Kaletsky R, Kauffman A, Stein G, Keyes W, Xu D, Murphy CT. Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs. Neuron. 2015;85(2):330–45.

Ayroles J, Buchanan SM, O’Leary C, Skutt-Kakaria K, Grenier JK, Clark A, Hartl DL, de Bivort BL. Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proc Natl Acad Sci U S A. 2015;112(21):6706–11.

Ducker GS, Rabinowitz JD. ZMP: a master regulator of one-carbon metabolism. Mol Cell. 2015;57(2):203–4.

Zwarts L, Broeck LV, Cappuyns E, Ayroles J, Magwire MM, Vulsteke V, Clements J, Mackay TFC, Callaerts P. The genetic basis of natural variation in mushroom body size in Drosophila melanogaster. Nat Commun. 2015;6:10115. PMCID: PMC4682101

Buescher JM, Antoniewicz MR, Boros LG, Burgess SC, Brunengraber H, Clish CB, DeBerardinis RJ, Feron O, Frezza C, Ghesquiere B, Gottlieb E, Hiller K, Jones RG, Kamphorst JJ, Kibbey RG, Kimmelman AC, Locasale JW, Lunt SY, Maddocks OD, Malloy C, Metallo CM, Meuillet EJ, Munger J, Nöh K, Rabinowitz JD, Ralser M, Sauer U, Stephanopoulos G, St-Pierre J, Tennant DA, Wittmann C, Heiden MGV, Vazquez A, Vousden K, Young JD, Zamboni N, Fendt S-M. A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr Opin Biotechnol. 2015;34:189–201.

Nadimpalli S, Persikov A V, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015;11(3):e1005011.

Kocher SD, Tsuruda JM, Gibson JD, Emore CM, Arechavaleta-Velasco ME, Queller DC, Strassmann JE, Grozinger CM, Gribskov MR, San Miguel P, Westerman R, Hunt GJ. A Search for Parent-of-Origin Effects on Honey Bee Gene Expression. G3 (Bethesda). 2015;5(8):1657–62. PMCID: PMC4528322

Zhou J, Troyanskaya OG. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 2015;.

Kamphorst JJ, Nofal M, Commisso C, Hackett SR, Lu W, Grabocka E, Heiden MGV, Miller G, Drebin JA, Bar-Sagi D, Thompson CB, Rabinowitz JD. Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein. Cancer Res. 2015;75(3):544–53.

Persikov A V, Wetzel JL, Rowland EF, Oakes BL, Xu DJ, Singh M, Noyes MB. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res. 2015;43(3):1965–84.

Gainous B, Wagner E, Levine M. Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate. Dev Biol. 2015;.

Li S, Stone HA, Murphy CT. A microfluidic device and automatic counting system for the study of C. elegans reproductive aging. Lab Chip. 2015;15(2):524–31. PMCID: PMC4277648

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;.