Publications

1198 Publications

2016

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Teng X, Emmett MJ, Lazar MA, Goldberg E, Rabinowitz JD. Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis. ACS Chem Biol. 2016;. PMID: 27333189
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Ducker GS, Chen L, Morscher RJ, Ghergurovich JM, Esposito M, Teng X, Kang Y, Rabinowitz JD. Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway. Cell Metab. 2016;.
1.
Ron-Harel N, Santos D, Ghergurovich JM, Sage PT, Reddy A, Lovitch SB, Dephoure N, Satterstrom K, Sheffer M, Spinelli JB, Gygi S, Rabinowitz JD, Sharpe AH, Haigis MC. Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation. Cell Metab. 2016;24(1):104–17. PMID: 27411012
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Zhang X, Chamberlayne C, Kurimoto A, Frank N, Harbron E. Visible light photoswitching of conjugated polymer nanoparticle fluorescence. Chemical Communications. 2016;52:4144–4147.
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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
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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
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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

2015

1.
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
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Ducker GS, Rabinowitz JD. ZMP: a master regulator of one-carbon metabolism. Mol Cell. 2015;57(2):203–4.
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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
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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.
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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.
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Nadimpalli S, Persikov A V, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015;11(3):e1005011.
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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
1.
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.
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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
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Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus B, Helbing S, Moritz RFA, Glastad KM, Hunt BG, Goodisman MAD, Hauser F, Grimmelikhuijzen CJP, Pinheiro DG, Nunes FMF, Soares MPM, Tanaka Érica D, Simões ZLP, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C, Sinha S, Johnston S, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science. 2015;348(6239):1139–43. PMCID: PMC5471836
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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.
1.
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
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Tikhonov M, Leach RW, Wingreen NS. Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 2015;9(1):68–80.
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Lakhina V, Murphy CT. For longevity, perception is everything. Cell. 2015;160(5):807–9.
1.
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
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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.
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Lakhina V, Murphy CT. Genome Sequencing Fishes out Longevity Genes. Cell. 2015;163(6):1312–3. PMID: 26638067
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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
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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;.
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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
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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
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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
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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.
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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;.
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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.
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Farley EK, Olson KM, Zhang W, Brandt AJ, Rokhsar DS, Levine MS. Suboptimization of developmental enhancers. Science. 2015;350(6258):325–8.
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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.
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Mok WWK, Park JO, Rabinowitz JD, Brynildsen MP. RNA Futile Cycling in Model Persisters Derived from MazF Accumulation. MBio. 2015;6(6):e01588–15.
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DiLoreto R, Murphy CT. The cell biology of aging. Mol Biol Cell. 2015;26(25):4524–31. PMCID: PMC4678010
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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.
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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.
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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.
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Pritykin Y, Ghersi D, Singh M. Genome-Wide Detection and Analysis of Multifunctional Genes. PLoS Comput Biol. 2015;11(10):e1004467.
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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.
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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.
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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.
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Dolinski K, Troyanskaya OG. Implications of Big Data for cell biology. Mol Biol Cell. 2015;26(14):2575–8.
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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.