Publications

1198 Publications

2018

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.
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
1.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
Zhang X, Kurimoto A, Frank N, Harbron E. Controlling Photoswitching via pcFRET in Conjugated Polymer Nanoparticles. Journal of Physical Chemistry C. 2018;122:22728–22737.
1.
Chen H, Levo M, Barinov L, Fujioka M, Jaynes J, Gregor T. Dynamic interplay between enhancer-promoter topology and gene activity. Nature genetics. 2018;50(9):1296–1303. PMCID: PMC6119122
1.
Zoller B, Little S, Gregor T. Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. Cell. 2018;175(3):835–847.e25. PMCID: PMC6779125
1.
Horlbeck M, Xu A, Wang M, Bennett N, Park C, Bogdanoff D, Adamson B, Chow E, Kampmann M, Peterson T, Nakamura K, Fischbach M, Weissman J, Gilbert L. Mapping the Genetic Landscape of Human Cells. Cell. 2018;174(4):953–967.e22. PMCID: PMC6426455

2017

1.
Skinnider M, Dejong C, Franczak B, McNicholas P, Magarvey N. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. Journal of cheminformatics. 2017;9(1):46. PMCID: PMC5559407
1.
Pritykin Y, Brito T, Schüpbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA. 2017;23(7):1097–1109. PMCID: PMC5473144
1.
Choi J, Rajagopal A, Xu Y-F, Rabinowitz JD, O’Shea EK. A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae. PLoS One. 2017;12(5):e0176085. PMCID: PMC5435139
1.
Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMID: 28957656
1.
Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, Damle M, Fang B, Wang CC, Qian J, Lie N, Lanzillotta C, Rabinowitz JD, Sun Z. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol. 2017;. PMID: 28554803
1.
Rajeshkumar N V, Yabuuchi S, Pai SG, De Oliveira E, Kamphorst JJ, Rabinowitz JD, Tejero H, Al-Shahrour F, Hidalgo M, Maitra A, Dang C V. Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin. Clin Cancer Res. 2017;23(18):5639–5647. PMID: 28611197
1.
Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem. 2017;86:277–304. PMID: 28654323
1.
Song Y, Marmion RA, Park JO, Biswas D, Rabinowitz JD, Shvartsman SY. Dynamic Control of dNTP Synthesis in Early Embryos. Dev Cell. 2017;42(3):301–308.e3. PMCID: PMC5630127
1.
Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017;33(16):2471–2478. PMID: 28407137
1.
Dannenfelser R, Nome M, Tahiri A, Ursini-Siegel J, Vollan HKM, Haakensen VD, Helland Åslaug, Naume B, Caldas C, Børresen-Dale A-L, Kristensen VN, Troyanskaya OG. Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity. Oncotarget. 2017;8(34):57121–57133. PMCID: PMC5593630
1.
Oslund RC, Su X, Haugbro M, Kee J-M, Esposito M, David Y, Wang B, Ge E, Perlman DH, Kang Y, Muir TW, Rabinowitz JD. Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate. Nat Chem Biol. 2017;13(10):1081–1087. PMCID: PMC5605442
1.
Nirschl CJ, Suárez-Fariñas M, Izar B, Prakadan S, Dannenfelser R, Tirosh I, Liu Y, Zhu Q, Devi SP, Carroll SL, Chau D, Rezaee M, Kim T-G, Huang R, Fuentes-Duculan J, Song-Zhao GX, Gulati N, Lowes MA, King SL, Quintana FJ, Lee Y- suk, Krueger JG, Sarin KY, Yoon CH, Garraway L, Regev A, Shalek AK, Troyanskaya OG, Anandasabapathy N. IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment. Cell. 2017;170(1):127–141.e15. PMCID: PMC5569303
1.
Chen L, Ducker GS, Lu W, Teng X, Rabinowitz JD. An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate. Anal Bioanal Chem. 2017;. PMID: 28799108
1.
Zhang Y, Kurupati R, Liu L, Zhou XY, Zhang G, Hudaihed A, Filisio F, Giles-Davis W, Xu X, Karakousis GC, Schuchter LM, Xu W, Amaravadi R, Xiao M, Sadek N, Krepler C, Herlyn M, Freeman GJ, Rabinowitz JD, Ertl HCJ. Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy. Cancer Cell. 2017;32(3):377–391.e9. PMID: 28898698
1.
Fukaya T, Levine M. Transvection. Curr Biol. 2017;27(19):R1047-R1049. PMID: 29017034
1.
Clancy T, Dannenfelser R, Troyanskaya OG, Malmberg KJ, Hovig E, Kristensen V. Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery. Curr Pharm Des. 2017;. PMID: 28699527
1.
Zhang Z, Chen L, Liu L, Su X, Rabinowitz JD. Chemical Basis for Deuterium Labeling of Fat and NADPH. J Am Chem Soc. 2017;139(41):14368–14371. PMID: 28911221
1.
Fukaya T, Lim B, Levine M. Rapid Rates of Pol II Elongation in the Drosophila Embryo. Curr Biol. 2017;27(9):1387–1391. PMCID: PMC5665007
1.
Nofal M, Zhang K, Han S, Rabinowitz JD. mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein. Mol Cell. 2017;67(6):936–946.e5. PMCID: PMC5612669
1.
Arey R, Murphy CT. Conserved regulators of cognitive aging: From worms to humans. Behav Brain Res. 2017;322(Pt B):299–310. PMCID: PMC5164975
1.
Rogers WA, Goyal Y, Yamaya K, Shvartsman SY, Levine MS. Uncoupling neurogenic gene networks in the Drosophila embryo. Genes Dev. 2017;31(7):634–638. PMCID: PMC5411704
1.
Kim HI, Raffler J, Lu W, Lee J-J, Abbey D, Saleheen D, Rabinowitz JD, Bennett MJ, Hand NJ, Brown C, Rader DJ. Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport. Am J Hum Genet. 2017;101(4):489–502. PMCID: PMC5630162
1.
Koch MD, Shaevitz JW. Introduction to Optical Tweezers. Methods Mol Biol. 2017;1486:3–24. PMID: 27844423
1.
Lim B, Levine M, Yamazaki Y. Transcriptional Pre-patterning of Drosophila Gastrulation. Curr Biol. 2017;27(2):286–290. PMCID: PMC5471612
1.
Liu LX, Rowe GC, Yang S, Li J, Damilano F, Chan MC, Lu W, Jang C, Wada S, Morley M, Hesse M, Fleischmann BK, Rabinowitz J, Das S, Rosenzweig A, Arany Z. PDK4 Inhibits Cardiac Pyruvate Oxidation in Late Pregnancy. Circ Res. 2017;. PMID: 28928113
1.
Son HG, Seo M, Ham S, Hwang W, Lee D, An SWA, Artan M, Seo K, Kaletsky R, Arey R, Ryu Y, Ha CM, Kim YK, Murphy CT, Roh T-Y, Nam HG, Lee S-J V. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat Commun. 2017;8:14749. PMCID: PMC5347137
1.
Bartlett TM, Bratton BP, Duvshani A, Miguel A, Sheng Y, Martin NR, Nguyen JP, Persat A, Desmarais SM, VanNieuwenhze MS, Huang KC, Zhu J, Shaevitz JW, Gitai Z. A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis. Cell. 2017;168(1-2):172–185.e15. PMCID: PMC5287421
1.
Wooldridge AL, Bischof RJ, Liu H, Heinemann GK, Hunter DS, Giles LC, Simmons RA, Lien Y-C, Lu W, Rabinowitz JD, Kind KL, Owens JA, Clifton VL, Gatford KL. Late gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR. Am J Physiol Regul Integr Comp Physiol. 2017;:ajpregu.00549.2016. PMID: 28978515
1.
Shi C, Runnels AM, Murphy CT. Mating and male pheromone kill Caenorhabditis males through distinct mechanisms. Elife. 2017;6. PMCID: PMC5378475