List of Faculty Publications
Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua
“Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate.”, Nature, vol. 579, no. 7800, pp. 586-591, 2020.
, “Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.”, Cell Syst, vol. 10, no. 2, pp. 193-203.e4, 2020.
, “Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.”, Nature, vol. 571, no. 7765, pp. 403-407, 2019.
, “Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.”, Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
, “Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice.”, Proc Natl Acad Sci U S A, vol. 115, no. 52, pp. 13347-13352, 2018.
, “Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes.”, Cell, vol. 174, no. 4, pp. 831-842.e12, 2018.
, “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.”, ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
, “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, vol. 8, no. 34, pp. 57121-57133, 2017.
, “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
, “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
, “Domain prediction with probabilistic directional context.”, Bioinformatics, vol. 33, no. 16, pp. 2471-2478, 2017.
, “Dynamic Control of dNTP Synthesis in Early Embryos.”, Dev Cell, vol. 42, no. 3, pp. 301-308.e3, 2017.
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“Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity.”, Nature, vol. 519, no. 7541, pp. 97-101, 2015.
, “Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation.”, J R Soc Interface, vol. 12, no. 109, p. 20150049, 2015.
, , “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
, “De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.”, Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
, “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
, “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
, “Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos.”, Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
, “Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression.”, Mol Biol Cell, vol. 24, no. 2, pp. 157-68, 2013.
, “Defining cell-type specificity at the transcriptional level in human disease.”, Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
, “Development: lights, camera, action--the Drosophila embryo goes live!”, Curr Biol, vol. 23, no. 21, pp. R965-7, 2013.
, “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
, “Distinct Rap1 activity states control the extent of epithelial invagination via α-catenin.”, Dev Cell, vol. 25, no. 3, pp. 299-309, 2013.
, “Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network.”, Proc Natl Acad Sci U S A, vol. 110, no. 17, pp. 6724-9, 2013.
, “Dynamic model for the coordination of two enhancers of broad by EGFR signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 44, pp. 17939-44, 2013.
, “Differential positioning of adherens junctions is associated with initiation of epithelial folding.”, Nature, vol. 484, no. 7394, pp. 390-3, 2012.
, “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
, “Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells.”, Phys Rev Lett, vol. 107, no. 15, p. 158101, 2011.
, “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
, “Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism.”, PLoS Pathog, vol. 7, no. 7, p. e1002124, 2011.
, “Does the potential for chaos constrain the embryonic cell-cycle oscillator?”, PLoS Comput Biol, vol. 7, no. 7, p. e1002109, 2011.
, “Dynamics of cooperativity in chemical sensing among cell-surface receptors.”, Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
, “Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis.”, EMBO J, vol. 29, no. 20, pp. 3484-95, 2010.
, “A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli.”, Proc Natl Acad Sci U S A, vol. 107, no. 40, pp. 17170-5, 2010.
, “Detailing regulatory networks through large scale data integration.”, Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
, “Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo.”, Dev Biol, vol. 330, no. 2, pp. 462-70, 2009.
, “Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines.”, Proc Natl Acad Sci U S A, vol. 106, no. 21, pp. 8701-6, 2009.
, “Diffusion, dimensionality, and noise in transcriptional regulation.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 79, no. 5 Pt 1, p. 051901, 2009.
, “Directing experimental biology: a case study in mitochondrial biogenesis.”, PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
, “Discovering biological networks from diverse functional genomic data.”, Methods Mol Biol, vol. 563, pp. 157-75, 2009.
, “Dynamics of the Dorsal morphogen gradient.”, Proc Natl Acad Sci U S A, vol. 106, no. 51, pp. 21707-12, 2009.
, “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
, “Descriptor-free molecular discovery in large libraries by adaptive substituent reordering.”, Bioorg Med Chem Lett, vol. 18, no. 22, pp. 5967-70, 2008.
, “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
, “Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase.”, Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
, “Diverse metabolic model parameters generate similar methionine cycle dynamics.”, J Theor Biol, vol. 251, no. 4, pp. 628-39, 2008.
, “A domino effect in antifolate drug action in Escherichia coli.”, Nat Chem Biol, vol. 4, no. 10, pp. 602-8, 2008.
, “Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.”, Development, vol. 135, no. 2, pp. 343-51, 2008.
, “Dual regulation by the Hunchback gradient in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 105, no. 8, pp. 2901-6, 2008.
, “Dynamics of maternal morphogen gradients in Drosophila.”, Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
, “Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition.”, J Am Chem Soc, vol. 129, no. 30, pp. 9294-5, 2007.
, “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
, “Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway.”, Dev Cell, vol. 10, no. 2, pp. 257-64, 2006.
, “Dynamics of the cellular metabolome during human cytomegalovirus infection.”, PLoS Pathog, vol. 2, no. 12, p. e132, 2006.
, “Diels-Alder reactivity of binuclear complexes with calixarene-like structures.”, Angew Chem Int Ed Engl, vol. 45, no. 1, pp. 101-4, 2005.
, “Diffusion and scaling during early embryonic pattern formation.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
, “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
, “Discovery of biological networks from diverse functional genomic data.”, Genome Biol, vol. 6, no. 13, p. R114, 2005.
, “A DNA microarray survey of gene expression in normal human tissues.”, Genome Biol, vol. 6, no. 3, p. R22, 2005.
, “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
, “Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.”, Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
, “Diverse and specific gene expression responses to stresses in cultured human cells.”, Mol Biol Cell, vol. 15, no. 5, pp. 2361-74, 2004.
, “Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.”, Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
, “A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer.”, Hum Mol Genet, vol. 12, no. 3, pp. 283-94, 2003.
, “Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease.”, Nat Genet, vol. 33 Suppl, pp. 228-37, 2003.
, “Discrete models of autocrine cell communication in epithelial layers.”, Biophys J, vol. 84, no. 6, pp. 3624-35, 2003.
, “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
, “Decoding cis-regulatory DNAs in the Drosophila genome.”, Curr Opin Genet Dev, vol. 12, no. 5, pp. 601-6, 2002.
, “Designability of alpha-helical proteins.”, Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
, “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
, “Diversity, topographic differentiation, and positional memory in human fibroblasts.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
, “Dorsal gradient networks in the Drosophila embryo.”, Dev Biol, vol. 246, no. 1, pp. 57-67, 2002.
, “Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development.”, Development, vol. 129, no. 7, pp. 1751-62, 2002.
, “Deletion of a nuclease-sensitive region between the Igf2 and H19 genes leads to Igf2 misregulation and increased adiposity.”, Hum Mol Genet, vol. 10, no. 8, pp. 807-14, 2001.
, “Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice.”, Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
, “Diversity of gene expression in adenocarcinoma of the lung.”, Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
, “The Dlk1 and Gtl2 genes are linked and reciprocally imprinted.”, Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
, “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
, “Dynein-mediated cargo transport in vivo. A switch controls travel distance.”, J Cell Biol, vol. 148, no. 5, pp. 945-56, 2000.
, “The Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation.”, Cell, vol. 96, no. 4, pp. 563-73, 1999.
, “Developmental regulation of vesicle transport in Drosophila embryos: forces and kinetics.”, Cell, vol. 92, no. 4, pp. 547-57, 1998.
, “A Drosophila homolog of the tumor suppressor gene adenomatous polyposis coli down-regulates beta-catenin but its zygotic expression is not essential for the regulation of Armadillo.”, Proc Natl Acad Sci U S A, vol. 94, no. 1, pp. 242-7, 1997.
, “Disruption of imprinting caused by deletion of the H19 gene region in mice.”, Nature, vol. 375, no. 6526, pp. 34-9, 1995.
, “DNA methylation: a phoenix rises.”, Proc Natl Acad Sci U S A, vol. 90, no. 19, pp. 8761-2, 1993.
, “The Drosophila cellularization gene nullo produces a blastoderm-specific transcript whose levels respond to the nucleocytoplasmic ratio.”, Genes Dev, vol. 6, no. 7, pp. 1255-68, 1992.
, “The Drosophila gastrulation gene concertina encodes a G alpha-like protein.”, Cell, vol. 64, no. 2, pp. 447-58, 1991.
, “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
, “Dominant maternal-effect mutations of Drosophila melanogaster causing the production of double-abdomen embryos.”, Genetics, vol. 112, no. 4, pp. 803-22, 1986.
, “Dosage requirements for runt in the segmentation of Drosophila embryos.”, Cell, vol. 45, no. 2, pp. 289-99, 1986.
, “The development and function of the female germ line in Drosophila melanogaster: a cell lineage study.”, Dev Biol, vol. 68, no. 1, pp. 29-46, 1979.
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