Publications

102 Publications
Applied Filters: First Letter Of Title: D Reset

D

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Tepper RG, Murphy CT, Bussemaker HJ. DAF-16 and PQM-1: partners in longevity. Aging (Albany NY). 2014;6(1):5–6.
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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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Ewald CY, Landis JN, Abate JP, Murphy CT, Blackwell K. Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity. Nature. 2015;519(7541):97–101. PMCID: PMC4352135
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Persikov A V, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res. 2014;42(1):97–108.
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Markstein M, Levine M. Decoding cis-regulatory DNAs in the Drosophila genome. Curr Opin Genet Dev. 2002;12(5):601–6.
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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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Swem LR, Swem DL, Wingreen NS, Bassler BL. Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi. Cell. 2008;134(3):461–73.
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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
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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
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Persikov A V, Rowland EF, Oakes BL, Singh M, Noyes MB. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res. 2014;42(3):1497–508.
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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
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Ju W, Greene CS, Eichinger F, Nair V, Hodgin JB, Bitzer M, Lee Y- suk, Zhu Q, Kehata M, Li M, Jiang S, Rastaldi MP, Cohen CD, Troyanskaya OG, Kretzler M. Defining cell-type specificity at the transcriptional level in human disease. Genome Res. 2013;23(11):1862–73.
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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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McAllister SR, Feng X-J, DiMaggio PA, Floudas CA, Rabinowitz JD, Rabitz H. Descriptor-free molecular discovery in large libraries by adaptive substituent reordering. Bioorg Med Chem Lett. 2008;18(22):5967–70.
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Robinson DG, Chen W, Storey JD, Gresham D. Design and analysis of Bar-seq experiments. G3 (Bethesda). 2014;4(1):11–8.
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Emberly EG, Wingreen NS, Tang C. Designability of alpha-helical proteins. Proc Natl Acad Sci U S A. 2002;99(17):11163–8.
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Huttenhower C, Mutungu T, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA. Detailing regulatory networks through large scale data integration. Bioinformatics. 2009;25(24):3267–74.
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Bothma JP, Levine M. Development: lights, camera, action--the Drosophila embryo goes live!. Curr Biol. 2013;23(21):R965–7.
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Goltsev Y, Rezende GL, Vranizan K, Lanzaro G, Valle D, Levine M. Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo. Dev Biol. 2009;330(2):462–70.
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Welte MA, Gross SP, Postner M, Block SM, Wieschaus EF. Developmental regulation of vesicle transport in Drosophila embryos: forces and kinetics. Cell. 1998;92(4):547–57.
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Käss S, Gregor T, Kersting B. Diels-Alder reactivity of binuclear complexes with calixarene-like structures. Angew Chem Int Ed Engl. 2005;45(1):101–4.
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Guan D, Xiong Y, Borck PC, Jang C, Doulias P-T, Papazyan R, Fang B, Jiang C, Zhang Y, Briggs ER, Hu W, Steger D, Ischiropoulos H, Rabinowitz JD, Lazar MA. Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes. Cell. 2018;174(4):831–842.e12. PMCID: PMC6086765
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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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Neumann S, Hansen CH, Wingreen NS, Sourjik V. Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis. EMBO J. 2010;29(20):3484–95.
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Zhao H, Langerød A, Ji Y, Nowels KW, Nesland JM, Tibshirani R, Bukholm IK, Kåresen R, Botstein D, Børresen-Dale A-L, Jeffrey SS. Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Mol Biol Cell. 2004;15(6):2523–36.
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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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Wang Y-C, Khan Z, Kaschube M, Wieschaus EF. Differential positioning of adherens junctions is associated with initiation of epithelial folding. Nature. 2012;484(7394):390–3.
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Mancini-Dinardo D, Steele SJS, Ingram RS, Tilghman SM. A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer. Hum Mol Genet. 2003;12(3):283–94.
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Gregor T, Bialek W, van Steveninck RR de R, Tank DW, Wieschaus EF. Diffusion and scaling during early embryonic pattern formation. Proc Natl Acad Sci U S A. 2005;102(51):18403–7.
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Tkačik G, Bialek W. Diffusion, dimensionality, and noise in transcriptional regulation. Phys Rev E Stat Nonlin Soft Matter Phys. 2009;79(5 Pt 1):051901.
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Stephens GJ, Johnson-Kerner B, Bialek W, Ryu WS. Dimensionality and dynamics in the behavior of C. elegans. PLoS Comput Biol. 2008;4(4):e1000028.
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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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Titchenell PM, Quinn WJ, Lu M, Chu Q, Lu W, Li C, Chen H, Monks BR, Chen J, Rabinowitz JD, Birnbaum MJ. Direct Hepatocyte Insulin Signaling Is Required for Lipogenesis but Is Dispensable for the Suppression of Glucose Production. Cell Metab. 2016;.
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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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Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM. Direct observation of base-pair stepping by RNA polymerase. Nature. 2005;438(7067):460–5.
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Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG. Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol. 2009;5(3):e1000322.
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Thutupalli S, Sun M, Bunyak F, Palaniappan K, Shaevitz JW. Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation. J R Soc Interface. 2015;12(109):20150049. PMCID: PMC4535398
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Myers CL, Chiriac C, Troyanskaya OG. Discovering biological networks from diverse functional genomic data. Methods Mol Biol. 2009;563:157–75.
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Xu Y-F, Lu W, Chen JC, Johnson SA, Gibney PA, Thomas DG, Brown G, May AL, Campagna S, Yakunin AF, Botstein D, Rabinowitz JD. Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase. ACS Chem Biol. 2018;13(10):3011–3020. PMCID: PMC6466636
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Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Discovery of biological networks from diverse functional genomic data. Genome Biol. 2005;6(13):R114.
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Pribyl M, Muratov CB, Shvartsman SY. Discrete models of autocrine cell communication in epithelial layers. Biophys J. 2003;84(6):3624–35.