Publications

1198 Publications

2022

1.
Kathe C, Skinnider M, Hutson T, Regazzi N, Gautier M, Demesmaeker R, Komi S, Ceto S, James N, Cho N, Baud L, Galan K, Matson K, Rowald A, Kim K, Wang R, Minassian K, Prior J, Asboth L, Barraud Q, Lacour S, Levine A, Wagner F, Bloch J, Squair J, Courtine G. The neurons that restore walking after paralysis. Nature. 2022;611(7936):540–547. PMCID: PMC9668750
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Olszewski K, Barsotti A, Feng X-J, Momcilovic M, Liu KG, Kim J-I, Morris K, Lamarque C, Gaffney J, Yu X, Patel JP, Rabinowitz JD, Shackelford DB, Poyurovsky M V. Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors. Cell Chem Biol. 2022;29(3):423–435.e10. PMID: 34715056
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Yang L, TeSlaa T, Ng S, Nofal M, Wang L, Lan T, Zeng X, Cowan AJ, McBride M, Lu W, Davidson S, Liang G, Oh TG, Downes M, Evans R, Von Hoff D, Guo JY, Han H, Rabinowitz JD. Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth. Med (N Y). 2022;3(2):119–136. PMCID: PMC9004683
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Wang L, Xing X, Zeng X, Jackson R, TeSlaa T, Al-Dalahmah O, Samarah LZ, Goodwin K, Yang L, McReynolds MR, Li X, Wolff JJ, Rabinowitz JD, Davidson SM. Spatially resolved isotope tracing reveals tissue metabolic activity. Nat Methods. 2022;19(2):223–230. PMID: 35132243
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Zhang X, Schwarz KN, Zhang L, Fassioli F, Fu B, Nguyen LQ, Knowles RR, Scholes GD. Interference of nuclear wavepackets in a pair of proton transfer reactions. Proceedings of the National Academy of Sciences [Internet]. Proceedings of the National Academy of Sciences; 2022;119. Referenced from doi.org: Interference of nuclear wavepackets in a pair of proton transfer reactions
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Zhang X, Geng K, Jiang D, Scholes GD. Exciton Diffusion and Annihilation in an sp2 Carbon-Conjugated Covalent Organic Framework. Journal of the American Chemical Society [Internet]. American Chemical Society (ACS); 2022;144:16423–16432. Referenced from doi.org: Exciton Diffusion and Annihilation in an sp2 Carbon-Conjugated Covalent Organic Framework
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Biswas S, Kim J, Zhang X, Scholes G. Coherent Two-Dimensional and Broadband Electronic Spectroscopies. Chemical Reviews. 2022;122:4257–4321.
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Zhang Z, Zamojski M, Smith G, Willis T, Yianni V, Mendelev N, Pincas H, Seenarine N, Amper M, Vasoya M, Cheng W, Zaslavsky E, Nair V, Turgeon J, Bernard D, Troyanskaya O, Andoniadou C, Sealfon S, Ruf-Zamojski F. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms. Cell reports. 2022;38(10):110467. PMCID: PMC8957708
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Nofal M, Wang T, Yang L, Jankowski C, Li S, Han S, Parsons L, Frese A, Gitai Z, Anthony T, Wühr M, Sabatini D, Rabinowitz J. GCN2 adapts protein synthesis to scavenging-dependent growth. Cell systems. 2022;13(2):158–172.e9. PMCID: PMC8961722
1.
Chacha P, Horie R, Kusakabe T, Sasakura Y, Singh M, Horie T, Levine M. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(4). PMCID: PMC8794889
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Batut P, Bing X, Sisco Z, Raimundo J, Levo M, Levine M. Genome organization controls transcriptional dynamics during development. Science (New York, N.Y.). 2022;375(6580):566–570. PMID: 35113722
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Weaver C, Patel A, Shvartsman S, Levine M, Treen N. ERK signaling dissolves ERF repression condensates in living embryos. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(9). PMCID: PMC8892517
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Levo M, Raimundo J, Bing X, Sisco Z, Batut P, Ryabichko S, Gregor T, Levine M. Transcriptional coupling of distant regulatory genes in living embryos. Nature. 2022;605(7911):754–760. PMCID: PMC9886134
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Creevy K, Akey J, Kaeberlein M, Promislow D, Consortium D. An open science study of ageing in companion dogs. Nature. 2022;602(7895):51–57. PMCID: PMC8940555
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Bray E, Zheng Z, Tolbert K, McCoy B, Consortium D, Kaeberlein M, Kerr K. Once-daily feeding is associated with better health in companion dogs: results from the Dog Aging Project. GeroScience. 2022;44(3):1779–1790. PMCID: PMC9213604

2021

1.
Skinnider M, Squair J, Kathe C, Anderson M, Gautier M, Matson K, Milano M, Hutson T, Barraud Q, Phillips A, Foster L, La Manno G, Levine A, Courtine G. Cell type prioritization in single-cell data. Nature biotechnology. 2021;39(1):30–34. PMCID: PMC7610525
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Skinnider M, Foster L. Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments. Nature methods. 2021;18(7):806–815. PMID: 34211188
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Squair J, Gautier M, Kathe C, Anderson M, James N, Hutson T, Hudelle R, Qaiser T, Matson K, Barraud Q, Levine A, La Manno G, Skinnider M, Courtine G. Confronting false discoveries in single-cell differential expression. Nature communications. 2021;12(1):5692. PMCID: PMC8479118
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Skinnider M, Scott N, Prudova A, Kerr C, Stoynov N, Stacey G, Chan Q, Rattray D, Gsponer J, Foster L. An atlas of protein-protein interactions across mouse tissues. Cell. 2021;184(15):4073–4089.e17. PMID: 34214469
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Goodwin M, Zhang X, Shekleton T, Kirr D, Hannon H, Harbron E. Amplifying the reactivity of BODIPY photoremovable protecting groups. Chemical Communications. 2021;57:10059–10062.
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Zhou J, Troyanskaya O. An analytical framework for interpretable and generalizable single-cell data analysis. Nature methods. 2021;18(11):1317–1321. PMCID: PMC8959118
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Wong A, Sealfon R, Theesfeld C, Troyanskaya O. Decoding disease: from genomes to networks to phenotypes. Nature reviews. Genetics. 2021;22(12):774–790. PMID: 34341555
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Munro D, Singh M. DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. Bioinformatics (Oxford, England). 2021;36(22-23):5322–5329. PMCID: PMC8016454
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Marmion R, Yang L, Goyal Y, Jindal G, Wetzel J, Singh M, Schüpbach T, Shvartsman S. Molecular mechanisms underlying cellular effects of human MEK1 mutations. Molecular biology of the cell. 2021;32(9):974–983. PMCID: PMC8108529
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Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic acids research. 2021;49(13):e78. PMCID: PMC8287948
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Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics (Oxford, England). 2021;37(Suppl_1):i133-i141. PMCID: PMC8275333
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Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella A, Shen Y, Cowan AJ, McReynolds M, Kennedy B, Lato A, Campagna S, Singh M, Rabinowitz J. Metabolite discovery through global annotation of untargeted metabolomics data. Nature methods. 2021;18(11):1377–1385. PMCID: PMC8733904
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King S, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS computational biology. 2021;17(11):e1009560. PMCID: PMC8601562
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Pritykin Y, van der Veeken J, Pine A, Zhong Y, Sahin M, Mazutis L, Pe’er D, Rudensky A, Leslie C. A unified atlas of CD8 T cell dysfunctional states in cancer and infection. Molecular cell. 2021;81(11):2477–2493.e10. PMCID: PMC8454502
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Treen N, Shimobayashi S, Eeftens J, Brangwynne C, Levine M. Properties of repression condensates in living Ciona embryos. Nature communications. 2021;12(1):1561. PMCID: PMC7946874
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Lemaire L, Cao C, Yoon P, Long J, Levine M. The hypothalamus predates the origin of vertebrates. Science advances. 2021;7(18). PMCID: PMC8081355
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Xu H, Zhen Q, Bai M, Fang L, Zhang Y, Li B, Ge H, Moon S, Chen W, Fu W, Xu Q, Zhou Y, Yu Y, Lin L, Yong L, Zhang T, Chen S, Liu S, Zhang H, Chen R, Cao L, Zhang Y, Zhang R, Yang H, Hu X, Akey J, Jin X, Sun L. Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals. Genome research. 2021;31(7):1150–8. PMCID: PMC8256863

2020

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Skinnider M, Johnston C, Gunabalasingam M, Merwin N, Kieliszek A, MacLellan R, Li H, Ranieri M, Webster A, Cao M, Pfeifle A, Spencer N, To H, Wallace D, Dejong C, Magarvey N. Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences. Nature communications. 2020;11(1):6058. PMCID: PMC7699628
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Gokhale S, Lu W, Zhu S, Liu Y, Hart RP, Rabinowitz JD, Xie P. Elevated Choline Kinase α-Mediated Choline Metabolism Supports the Prolonged Survival of TRAF3-Deficient B Lymphocytes. J Immunol. 2020;204(2):459–471. PMCID: PMC6946882
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Hermans D, Gautam S, García-Cañaveras JC, Gromer D, Mitra S, Spolski R, Li P, Christensen S, Nguyen R, Lin J-X, Oh J, Du N, Veenbergen S, Fioravanti J, Ebina-Shibuya R, Bleck C, Neckers LM, Rabinowitz JD, Gattinoni L, Leonard WJ. Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity. Proc Natl Acad Sci U S A. 2020;117(11):6047–6055. PMCID: PMC7084161
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Yang L, Canaveras JCG, Chen Z, Wang L, Liang L, Jang C, Mayr JA, Zhang Z, Ghergurovich JM, Zhan L, Joshi S, Hu Z, McReynolds MR, Su X, White E, Morscher RJ, Rabinowitz JD. Serine Catabolism Feeds NADH when Respiration Is Impaired. Cell Metab. 2020;31(4):809–821.e6. PMID: 32187526
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Zhao S, Jang C, Liu J, Uehara K, Gilbert M, Izzo L, Zeng X, Trefely S, Fernandez S, Carrer A, Miller KD, Schug ZT, Snyder NW, Gade TP, Titchenell PM, Rabinowitz JD, Wellen KE. Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate. Nature. 2020;579(7800):586–591. PMID: 32214246
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Li AM, Ducker GS, Li Y, Seoane JA, Xiao Y, Melemenides S, Zhou Y, Liu L, Vanharanta S, Graves EE, Rankin EB, Curtis C, Massague J, Rabinowitz JD, Thompson CB, Ye J. Metabolic profiling reveals a dependency of human metastatic breast cancer on mitochondrial serine and one-carbon unit metabolism. Mol. Cancer Res. 2020;18(4):599–611.
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Zhu Q, Tekpli X, Troyanskaya OG, Kristensen VN. Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations. Bioinformatics. 2020;36(4):994–999. PMCID: PMC7031777
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Menon R, Otto EA, Hoover P, Eddy S, Mariani L, Godfrey B, Berthier CC, Eichinger F, Subramanian L, Harder J, Ju W, Nair V, Larkina M, Naik AS, Luo J, Jain S, Sealfon R, Troyanskaya O, Hacohen N, Hodgin JB, Kretzler M, Kpmp KPMP, Network NSS. Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI Insight. 2020;5(6). PMID: 32107344
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Przytycki PF, Singh M. Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. Cell Syst. 2020;10(2):193–203.e4. PMID: 32078798
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Li X, Pritykin Y, Concepcion C, Lu Y, La Rocca G, Zhang M, King B, Cook P, Au Y, Popow O, Paulo J, Otis H, Mastroleo C, Ogrodowski P, Schreiner R, Haigis K, Betel D, Leslie C, Ventura A. High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. Molecular cell. 2020;79(1):167–179.e11. PMCID: PMC7446397
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Chen L, Wolf A, Fu W, Li L, Akey J. Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals. Cell. 2020;180(4):677–687.e16. PMID: 32004458
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Saad-Roy C, Arinaminpathy N, Wingreen N, Levin S, Akey J, Grenfell B. Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans. PLoS computational biology. 2020;16(6):e1007892. PMCID: PMC7316228

2019

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
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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
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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