Publications

1198 Publications

2019

1.
Anikeeva P, Boyden E, Brangwynne C, Troyanskaya O, al. et. Voices in methods development. Nat Methods. 2019;16(10):945–951.
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Heist T, Fukaya T, Levine M. Large distances separate coregulated genes in living embryos. Proc Natl Acad Sci U S A. 2019;116(30):15062–15067. PMCID: PMC6660726
1.
Cao C, Lemaire LA, Wang W, Yoon PH, Choi YA, Parsons LR, Matese JC, Wang W, Levine M, Chen K. Comprehensive single-cell transcriptome lineages of a proto-vertebrate. Nature. 2019;571(7765):349–354. PMID: 31292549
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Kobren SN, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845
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Jang C, Hui S, Zeng X, Cowan AJ, Wang L, Chen L, Morscher RJ, Reyes J, Frezza C, Hwang HY, Imai A, Saito Y, Okamoto K, Vaspoli C, Kasprenski L, Zsido GA, Gorman JH, Gorman RC, Rabinowitz JD. Metabolite Exchange between Mammalian Organs Quantified in Pigs. Cell Metab. 2019;30(3):594–606.e3. PMCID: PMC6726553
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Neinast MD, Jang C, Hui S, Murashige DS, Chu Q, Morscher RJ, Li X, Zhan L, White E, Anthony T, Rabinowitz JD, Arany Z. Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids. Cell Metab. 2019;29(2):417–429.e4. PMCID: PMC6365191
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Jang C, Hui S, Zeng X, Cowan AJ, Wang L, Chen L, Morscher RJ, Reyes J, Frezza C, . Y. Hwang H, Imai A, Saito Y, Okamoto K, Vaspoli C, Kasprenski L, Zsido GA 2nd, Gorman JH 3rd, Gorman RC, Rabinowitz JD. Metabolite exchange between mammalian organs quantified in pigs. Cell Metab. 2019;30(3):594–606.
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Bailis W, Shyer JA, Zhao J, Canaveras JCG, Khazal FJA, Qu R, Steach HR, Bielecki P, Khan O, Jackson R, Kluger Y, Maher LJ, Rabinowitz J, Craft J, Flavell RA. Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function. Nature. 2019;571(7765):403–407. PMCID: PMC6939459
1.
Minhas PS, Liu L, Moon PK, Joshi AU, Dove C, Mhatre S, Contrepois K, Wang Q, Lee BA, Coronado M, Bernstein D, Snyder MP, Migaud M, Majeti R, Mochly-Rosen D, Rabinowitz JD, Andreasson KI. Macrophage de novo NAD synthesis specifies immune function in aging and inflammation. Nat Immunol. 2019;20(1):50–63. PMID: 30478397
1.
Tucci S, Akey J. The long walk to African genomics. Genome Biol. 2019;20(1):130. PMCID: PMC6598360
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Benson KK, Hu W, Weller AH, Bennett AH, Chen ER, Khetarpal SA, Yoshino S, Bone WP, Wang L, Rabinowitz JD, Voight BF, Soccio RE. Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene. Proc Natl Acad Sci U S A. 2019;116(46):23232–23242. PMCID: PMC6859347
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Stadlmeier M, Runtsch LS, Streshnev F, Wühr M, Carell T. A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry. Chembiochem. 2019;. PMID: 31593346
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Dinh H V, Suthers PF, Chan SHJ, Shen Y, Xiao T, Deewan A, Jagtap SS, Zhao H, Rao C V, Rabinowitz JD, Maranas CD. A comprehensive genome-scale model for IFO0880 accounting for functional genomics and phenotypic data. Metab Eng Commun. 2019;9:e00101. PMCID: PMC6838544
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Wang L, Xing X, Chen L, Yang L, Su X, Rabitz H, Lu W, Rabinowitz JD. Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics. Anal Chem. 2019;91(3):1838–1846. PMCID: PMC6501219
1.
Estrella MA, Du J, Chen L, Rath S, Prangley E, Chitrakar A, Aoki T, Schedl P, Rabinowitz J, Korennykh A. The metabolites NADP and NADPH are the targets of the circadian protein Nocturnin (Curled). Nat Commun. 2019;10(1):2367. PMCID: PMC6542800
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Rodriguez AE, Ducker GS, Billingham LK, Martinez CA, Mainolfi N, Suri V, Friedman A, Manfredi MG, Weinberg SE, Rabinowitz JD, Chandel NS. Serine Metabolism Supports Macrophage IL-1β Production. Cell Metab. 2019;29(4):1003–1011.e4. PMCID: PMC6447453
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Bradley PH, Gibney PA, Botstein D, Troyanskaya OG, Rabinowitz JD. Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. mSystems. 2019;4(1). PMCID: PMC6392091
1.
Chen L, Zhang Z, Hoshino A, Zheng HD, Morley M, Arany Z, Rabinowitz JD. NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism. Nat Metab. 2019;1:404–415. PMCID: PMC6489125
1.
Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O’Connor C, Luo J, Nair V, Cebrián C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M, Bank ER cDNA, Network NSS. Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight. 2019;4(1). PMCID: PMC6485369
1.
Wang W, Ishibashi J, Trefely S, Shao M, Cowan AJ, Sakers A, Lim H-W, O’Connor S, Doan MT, Cohen P, Baur JA, King T, Veech RL, Won K-J, Rabinowitz JD, Snyder NW, Gupta RK, Seale P. A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate. Cell Metab. 2019;30(1):174–189.e5. PMID: 31155495
1.
Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nat Genet. 2019;51(6):973–980. PMID: 31133750
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García-Cañaveras JC, Chen L, Rabinowitz JD. The Tumor Metabolic Microenvironment: Lessons from Lactate. Cancer Res. 2019;79(13):3155–3162. PMCID: PMC6606343
1.
Chen KM, Cofer EM, Zhou J, Troyanskaya OG. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16(4):315–318. PMID: 30923381
1.
Sargin D, Chottekalapanda RU, Perit KE, Yao V, Chu D, Sparks DW, Kalik S, Power SK, Troyanskaya OG, Schmidt EF, Greengard P, Lambe EK. Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons. Mol Psychiatry. 2019;. PMCID: PMC7031043
1.
Schober AF, Mathis AD, Ingle C, Park JO, Chen L, Rabinowitz JD, Junier I, Rivoire O, Reynolds KA. A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism. Cell Rep. 2019;27(11):3359–3370.e7. PMCID: PMC6625508
1.
Lee Y- suk, 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;8(2):152–162.e6. PMID: 30685436
1.
Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, Furlong EEM, Troyanskaya OG. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019;15(9):e1008382. PMCID: PMC6779412
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Song Y, Park JO, Tanner L, Nagano Y, Rabinowitz JD, Shvartsman SY. Energy budget of Drosophila embryogenesis. Curr Biol. 2019;29(12):R566-R567. PMID: 31211973
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Konopacki C, Pritykin Y, Rubtsov Y, Leslie C, Rudensky A. Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function. Nature immunology. 2019;20(2):232–242. PMCID: PMC7534899
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Brown C, Gudjonson H, Pritykin Y, Deep D, Lavallée V-P, Mendoza A, Fromme R, Mazutis L, Ariyan C, Leslie C, Pe’er D, Rudensky A. Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity. Cell. 2019;179(4):846–863.e24. PMCID: PMC6838684
1.
Petkova M, Tkačik G, Bialek W, Wieschaus E, Gregor T. Optimal Decoding of Cellular Identities in a Genetic Network. Cell. 2019;176(4):844–855.e15. PMCID: PMC6526179
1.
Chan M, Smith Z, Grosswendt S, Kretzmer H, Norman T, Adamson B, Jost M, Quinn J, Yang D, Jones M, Khodaverdian A, Yosef N, Meissner A, Weissman J. Molecular recording of mammalian embryogenesis. Nature. 2019;570(7759):77–82. PMCID: PMC7229772

2018

1.
Li SH-J, Li Z, Park JO, King CG, Rabinowitz JD, Wingreen NS, Gitai Z. Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions. Nat Microbiol. 2018;3(8):939–947. PMCID: PMC6278830
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Guan D, Xiong Y, Borck PC, Jang C, Doulias P-T, Papazyan R, Fang B, Jiang C, Zhang Y, Briggs ER, Hu W, Steger D, Ischiropoulos H, Rabinowitz JD, Lazar MA. Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes. Cell. 2018;174(4):831–842.e12. PMCID: PMC6086765
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Hui S, Rabinowitz JD. An unexpected trigger for calorie burning in brown fat. Nature. 2018;560(7716):38–39. PMID: 30061641
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Rangan A V, 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, Consortium BDWG of the PG. A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data. PLoS Comput Biol. 2018;14(5):e1006105. PMCID: PMC5997363
1.
Pavlova NN, Hui S, Ghergurovich JM, Fan J, Intlekofer AM, White RM, Rabinowitz JD, Thompson CB, Zhang J. As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid. Cell Metab. 2018;27(2):428–438.e5. PMCID: PMC5803449
1.
Xu Y-F, Lu W, Chen JC, Johnson SA, Gibney PA, Thomas DG, Brown G, May AL, Campagna S, Yakunin AF, Botstein D, Rabinowitz JD. Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase. ACS Chem Biol. 2018;13(10):3011–3020. PMCID: PMC6466636
1.
Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018;50(8):1171–1179. PMCID: PMC6094955
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Morscher RJ, Ducker GS, Li SH-J, Mayer JA, Gitai Z, Sperl W, Rabinowitz JD. Mitochondrial translation requires folate-dependent tRNA methylation. Nature. 2018;554(7690):128–132. PMCID: PMC6020024
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Poillet-Perez L, Xie X, Zhan L, Yang Y, Sharp DW, Hu ZS, Su X, Maganti A, Jiang C, Lu W, Zheng H, Bosenberg MW, Mehnert JM, Guo JY, Lattime E, Rabinowitz JD, White E. Autophagy maintains tumour growth through circulating arginine. Nature. 2018;563(7732):569–573. PMCID: PMC6287937
1.
Jabeen S, Zucknick M, Nome M, Dannenfelser R, Fleischer T, Kumar S, Lüders T, Gythfeldt H von der L, Troyanskaya O, Kyte JA, Børresen-Dale A-L, Naume B, Tekpli X, Engebraaten O, Kristensen V. Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab. Oncoimmunology. 2018;7(11):e1457598. PMCID: PMC6205029
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Jang C, Hui S, Lu W, Cowan AJ, Morscher RJ, Lee G, Liu W, Tesz GJ, Birnbaum MJ, Rabinowitz JD. The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids. Cell Metab. 2018;27(2):351–361.e3. PMCID: PMC6032988
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Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol. 2018;14(6):e1006290. PMCID: PMC6040777
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McKee SE, Zhang S, Chen L, Rabinowitz JD, Reyes TM. Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain. J Neurochem. 2018;145(5):362–373. PMCID: PMC6288810
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Wong AK, Krishnan A, Troyanskaya OG. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Research. 2018;46(W1):W65-W70.
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Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell. 2018;29(8):897–910. PMCID: PMC5896929
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Ron-Harel N, Notarangelo G, Ghergurovich JM, Paulo JA, Sage PT, Santos D, Satterstrom K, Gygi SP, Rabinowitz JD, Sharpe AH, Haigis MC. Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice. Proc Natl Acad Sci U S A. 2018;115(52):13347–13352. PMCID: PMC6310842
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Kaletsky R, Yao V, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genetics. 2018;14(8):e1007559.
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Menon R, Otto EA, Kokoruda A, Zhou J, Zhang Z, Yoon E, Chen Y-C, Troyanskaya O, Spence JR, Kretzler M, Cebrián C. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development. 2018;145(16). PMCID: PMC6124540