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

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

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

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

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

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.

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

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

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.

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMID: 28957656

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

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

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

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

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

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

Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017;33(16):2471–2478. PMID: 28407137

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

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

Fukaya T, Levine M. Transvection. Curr Biol. 2017;27(19):R1047-R1049. PMID: 29017034

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

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

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

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

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

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

Arey R, Murphy CT. Conserved regulators of cognitive aging: From worms to humans. Behav Brain Res. 2017;322(Pt B):299–310. PMCID: PMC5164975

Koch MD, Shaevitz JW. Introduction to Optical Tweezers. Methods Mol Biol. 2017;1486:3–24. PMID: 27844423

Lim B, Levine M, Yamazaki Y. Transcriptional Pre-patterning of Drosophila Gastrulation. Curr Biol. 2017;27(2):286–290. PMCID: PMC5471612

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

Przytycki PF, Singh M. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med. 2017;9(1):79. PMCID: PMC5574113

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

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

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

Klibaite U, Berman GJ, Cande JD, Stern DL, Shaevitz JW. An unsupervised method for quantifying the behavior of paired animals. Phys Biol. 2017;14(1):015006. PMCID: PMC5414632

Hong S, Zhou W, Fang B, Lu W, Loro E, Damle M, Ding G, Jager J, Zhang S, Zhang Y, Feng D, Chu Q, Dill BD, Molina H, Khurana TS, Rabinowitz JD, Lazar MA, Sun Z. Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion. Nat Med. 2017;23(2):223–234. PMCID: PMC5540654