Publications

1198 Publications

2019

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
1.
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
1.
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
1.
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
1.
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
1.
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
1.
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.
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.
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.
García-Cañaveras JC, Chen L, Rabinowitz JD. The Tumor Metabolic Microenvironment: Lessons from Lactate. Cancer Res. 2019;79(13):3155–3162. PMCID: PMC6606343
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
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.
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.
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
1.
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
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.
Liu Q, Johnson EM, Lam RK, Wang Q, Ye HB, Wilson EN, Minhas PS, Liu L, Swarovski MS, Tran S, Wang J, Mehta SS, Yang X, Rabinowitz JD, Yang SS, Shamloo M, Mueller C, James ML, Andreasson KI. Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity. Nat Immunol. 2019;20(8):1023–1034. PMID: 31263278
1.
Ron-Harel N, Ghergurovich JM, Notarangelo G, LaFleur MW, Tsubosaka Y, Sharpe AH, Rabinowitz JD, Haigis MC. T Cell Activation Depends on Extracellular Alanine. Cell Rep. 2019;28(12):3011–3021.e4. PMID: 31533027
1.
Park JO, Tanner LB, Wei MH, Khana DB, Jacobson TB, Zhang Z, Rubin SA, Li SH-J, Higgins MB, Stevenson DM, Amador-Noguez D, Rabinowitz JD. Near-equilibrium glycolysis supports metabolic homeostasis and energy yield. Nat Chem Biol. 2019;15(10):1001–1008. PMID: 31548693
1.
Dekhne AS, Shah K, Ducker GS, Katinas JM, Wong-Roushar J, Nayeen MJ, Doshi A, Ning C, Bao X, Frühauf J, Liu J, Wallace-Povirk A, O’Connor C, Dzinic SH, White K, Kushner J, Kim S, Hüttemann M, Polin L, Rabinowitz JD, Li J, Hou Z, Dann CE, Gangjee A, Matherly LH. Novel pyrrolo[3,2-d]pyrimidine compounds target mitochondrial and cytosolic one-carbon metabolism with broad-spectrum antitumor efficacy. Mol Cancer Ther. 2019;. PMID: 31289137
1.
Stine RR, Sakers AP, TeSlaa T, Kissig M, Stine ZE, Kwon CW, Cheng L, Lim H-W, Kaestner KH, Rabinowitz JD, Seale P. PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism. Cell Stem Cell. 2019;. PMID: 31564549
1.
Anikeeva P, Boyden E, Brangwynne C, Troyanskaya O, al. et. Voices in methods development. Nat Methods. 2019;16(10):945–951.
1.
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
1.
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
1.
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.
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
1.
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
1.
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
1.
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.
1.
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
1.
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
1.
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.
1.
Lanaspa MA, Andres-Hernando A, Orlicky DJ, Cicerchi C, Jang C, Li N, Milagres T, Kuwabara M, Wempe MF, Rabinowitz JD, Johnson RJ, Tolan DR. Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice. J Clin Invest. 2018;128(6):2226–2238. PMCID: PMC5983342
1.
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
1.
Browning SR, Browning BL, Zhou Y, Tucci S, Akey J. Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture. Cell. 2018;173(1):53–61.e9. PMCID: PMC5866234
1.
Miller RA, Shi Y, Lu W, Pirman DA, Jatkar A, Blatnik M, Wu H, Cárdenas C, Wan M, Foskett K, Park JO, Zhang Y, Holland WL, Rabinowitz JD, Birnbaum MJ. Targeting hepatic glutaminase activity to ameliorate hyperglycemia. Nat Med. 2018;24(4):518–524. PMCID: PMC6089616
1.
Yao V, Wong AK, Troyanskaya OG. Enabling Precision Medicine through Integrative Network Models. J Mol Biol. 2018;430(18 Pt A):2913–2923. PMID: 30003887
1.
Jin Y, Gittelman RM, Lu Y, Liu X, Li MD, Ling F, Akey J. Evolution of DNAase I hypersensitive sites in MHC regulatory regions of primates. Genetics. 2018;209(2):579–589.
1.
Liu L, Su X, Quinn WJ, Hui S, Krukenberg K, Frederick DW, Redpath P, Zhan L, Chellappa K, White E, Migaud M, Mitchison TJ, Baur JA, Rabinowitz JD. Quantitative Analysis of NAD Synthesis-Breakdown Fluxes. Cell Metab. 2018;27(5):1067–1080.e5. PMCID: PMC5932087
1.
Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG. An integrative tissue-network approach to identify and test human disease genes. Nat Biotechnol. 2018;. PMID: 30346941
1.
Wolf AB, Akey J. Outstanding questions in the study of archaic hominin admixture. PLoS Genet. 2018;14(5):e1007349. PMCID: PMC5978786
1.
Jang C, Chen L, Rabinowitz JD. Metabolomics and Isotope Tracing. Cell. 2018;173(4):822–837. PMCID: PMC6034115
1.
Lee Y- suk, Wong AK, Tadych A, Hartmann BM, Park CY, DeJesus VA, Ramos I, Zaslavsky E, Sealfon SC, Troyanskaya OG. Interpretation of an individual functional genomics experiment guided by massive public data. Nat Methods. 2018;15(12):1049–1052. PMID: 30478325