Publications

51 Publications
Applied Filters: First Letter Of Last Name: D Reset

D

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Daly KE, Huang KC, Wingreen NS, Mukhopadhyay R. Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria. Phys Rev E Stat Nonlin Soft Matter Phys. 2011;83(4 Pt 1):041922.
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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
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Davidson B, Shi W, Levine M. Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis. Development. 2005;132(21):4811–8.
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Davidson B, Levine M. Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis. Proc Natl Acad Sci U S A. 2003;100(20):11469–73.
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Davidson SM, Jonas O, Keibler MA, Hou HW, Luengo A, Mayers JR, Wyckoff J, Del Rosario AM, Whitman M, Chin CR, Condon KJ, Lammers A, Kellersberger KA, Stall BK, Stephanopoulos G, Bar-Sagi D, Han J, Rabinowitz JD, Cima MJ, Langer R, Heiden MGV. Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors. Nat Med. 2017;23(2):235–241. PMCID: PMC5407288
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Davila A, Liu L, Chellappa K, Redpath P, Nakamaru-Ogiso E, Paolella LM, Zhang Z, Migaud ME, Rabinowitz JD, Baur JA. Nicotinamide adenine dinucleotide is transported into mammalian mitochondria. Elife. 2018;7. PMCID: PMC6013257
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Dawes-Hoang RE, Parmar KM, Christiansen AE, Phelps CB, Brand AH, Wieschaus EF. folded gastrulation, cell shape change and the control of myosin localization. Development. 2005;132(18):4165–78.
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Dawes-Hoang RE, Zallen JA, Wieschaus EF. Bringing classical embryology to C elegans gastrulation. Dev Cell. 2003;4(1):6–8.
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Dawes-Hoang RE, Wieschaus EF. Cell and developmental biology--a shared past, an intertwined future. Dev Cell. 2001;1(1):27–36.
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de Abreu DAF, Caballero A, Fardel P, Stroustrup N, Chen Z, Lee K, Keyes WD, Nash ZM, López-Moyado IF, Vaggi F, Cornils A, Regenass M, Neagu A, Ostojic I, Liu C, Cho Y, Sifoglu D, Shen Y, Fontana W, Lu H, Csikasz-Nagy A, Murphy CT, Antebi A, Blanc E, Apfeld J, Zhang Y, Alcedo J, Ch’ng Q. An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology. PLoS Genet. 2014;10(3):e1004225.
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De Renzis S, Elemento O, Tavazoie S, Wieschaus EF. Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol. 2007;5(5):e117.
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De Renzis S, Yu J, Zinzen R, Wieschaus E. Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway. Dev Cell. 2006;10(2):257–64.
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Dejean A, Solano PJ, Ayroles J, Corbara B, Orivel J. Insect behaviour: arboreal ants build traps to capture prey. Nature. 2005;434(7036):973.
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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
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Deng Y, Sun M, Lin P-H, Ma J, Shaevitz JW. Spatial covariance reconstructive (SCORE) super-resolution fluorescence microscopy. PLoS One. 2014;9(4):e94807.
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Deng Y, Coen P, Sun M, Shaevitz JW. Efficient multiple object tracking using mutually repulsive active membranes. PLoS One. 2013;8(6):e65769.
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Deng Y, Sun M, Shaevitz JW. Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells. Phys Rev Lett. 2011;107(15):158101.
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Desai KH, Tan CS, Leek JT, Maier R V, Tompkins RG, Storey JD, Program I and the HR to IL-SCR. Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study. PLoS Med. 2011;8(9):e1001093.
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Di Gregorio A, Harland RM, Levine M, Casey ES. Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle. Dev Biol. 2002;244(2):385–95.
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Di Gregorio A, Levine M. Analyzing gene regulation in ascidian embryos: new tools for new perspectives. Differentiation. 2002;70(4-5):132–9.
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Di Talia S, She R, Blythe SA, Lu X, Zhang QF, Wieschaus EF. Posttranslational control of Cdc25 degradation terminates Drosophila’s early cell-cycle program. Curr Biol. 2013;23(2):127–32.
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Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry M, Botstein D, Brown PO, Alizadeh AA. SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 2003;31(1):219–23.
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Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D, Crabtree GR, Brown PO. Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci U S A. 2002;99(18):11796–801.
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Diehn M, Bhattacharya R, Botstein D, Brown PO. Genome-scale identification of membrane-associated human mRNAs. PLoS Genet. 2006;2(1):e11.
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DiLoreto R, Murphy CT. The cell biology of aging. Mol Biol Cell. 2015;26(25):4524–31. PMCID: PMC4678010
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DiMaggio PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA. Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformatics. 2008;9:458.
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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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Dixit A, Parnas O, Li B, Chen J, Fulco C, Jerby-Arnon L, Marjanovic N, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman T, Lander E, Weissman J, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016;167(7):1853–1866.e17. PMCID: PMC5181115
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Dolinski K, Botstein D. Orthology and functional conservation in eukaryotes. Annu Rev Genet. 2007;41:465–507.
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Dolinski K, Troyanskaya OG. Implications of Big Data for cell biology. Mol Biol Cell. 2015;26(14):2575–8.
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Dolinski K, Botstein D. Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res. 2005;15(12):1611–9.
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Dolinski K, Botstein D. Automating the construction of gene ontologies. Nat Biotechnol. 2013;31(1):34–5.
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Doucette CD, Schwab DJ, Wingreen NS, Rabinowitz JD. α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nat Chem Biol. 2011;7(12):894–901.
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Drescher K, Nadell CD, Stone HA, Wingreen NS, Bassler BL. Solutions to the public goods dilemma in bacterial biofilms. Curr Biol. 2014;24(1):50–5.
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Drocco JA, Grimm O, Tank DW, Wieschaus E. Measurement and perturbation of morphogen lifetime: effects on gradient shape. Biophys J. 2011;101(8):1807–15.
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Du X, Osterfield M, Shvartsman SY. Computational analysis of three-dimensional epithelial morphogenesis using vertex models. Phys Biol. 2014;11(6):066007.
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Dubuis J, Tkačik G, Wieschaus EF, Gregor T, Bialek W. Positional information, in bits. Proc Natl Acad Sci U S A. 2013;110(41):16301–8.
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Dubuis J, Samanta R, Gregor T. Accurate measurements of dynamics and reproducibility in small genetic networks. Mol Syst Biol. 2013;9:639.
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Ducker GS, Rabinowitz JD. ZMP: a master regulator of one-carbon metabolism. Mol Cell. 2015;57(2):203–4.
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Ducker GS, Chen L, Morscher RJ, Ghergurovich JM, Esposito M, Teng X, Kang Y, Rabinowitz JD. Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway. Cell Metab. 2016;.
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Ducker GS, Rabinowitz JD. One-Carbon Metabolism in Health and Disease. Cell Metab. 2016;. PMID: 27641100
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Ducker GS, Ghergurovich JM, Mainolfi N, Suri V, Jeong SK, Li SH-J, Friedman A, Manfredi MG, Gitai Z, Kim H, Rabinowitz JD. Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2017;114(43):11404–11409. PMCID: PMC5664509
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Dunham M, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2002;99(25):16144–9.
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Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry M. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004;5(1):9–22.
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Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry M. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002;30(1):69–72.