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
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“Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.”, Genetics, vol. 195, no. 2, pp. 443-55, 2013.
, “Saccharomyces genome database: underlying principles and organisation.”, Brief Bioinform, vol. 5, no. 1, pp. 9-22, 2004.
, “Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).”, Nucleic Acids Res, vol. 30, no. 1, pp. 69-72, 2002.
, “Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16144-9, 2002.
, “Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway.”, Cell Metab, 2016.
, “One-Carbon Metabolism in Health and Disease.”, Cell Metab, 2016.
, “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, vol. 114, no. 43, pp. 11404-11409, 2017.
, “ZMP: a master regulator of one-carbon metabolism.”, Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
, “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
, “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
, “Computational analysis of three-dimensional epithelial morphogenesis using vertex models.”, Phys Biol, vol. 11, no. 6, p. 066007, 2014.
, “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
, “Measurement and perturbation of morphogen lifetime: effects on gradient shape.”, Biophys J, vol. 101, no. 8, pp. 1807-15, 2011.
, “Solutions to the public goods dilemma in bacterial biofilms.”, Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
, “α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition.”, Nat Chem Biol, vol. 7, no. 12, pp. 894-901, 2011.
, “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
, “Automating the construction of gene ontologies.”, Nat Biotechnol, vol. 31, no. 1, pp. 34-5, 2013.
, “Orthology and functional conservation in eukaryotes.”, Annu Rev Genet, vol. 41, pp. 465-507, 2007.
, “Implications of Big Data for cell biology.”, Mol Biol Cell, vol. 26, no. 14, pp. 2575-8, 2015.
, “Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action.”, G3 (Bethesda), vol. 2, no. 8, pp. 943-59, 2012.
, “A comprehensive genome-scale model for IFO0880 accounting for functional genomics and phenotypic data.”, Metab Eng Commun, vol. 9, p. e00101, 2019.
, “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
, “The cell biology of aging.”, Mol Biol Cell, vol. 26, no. 25, pp. 4524-31, 2015.
, “SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”, Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
, “Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”, Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
, “Genome-scale identification of membrane-associated human mRNAs.”, PLoS Genet, vol. 2, no. 1, p. e11, 2006.
, “Simple biochemical pathways far from steady state can provide switchlike and integrated responses.”, Biophys J, vol. 107, no. 3, pp. L1-4, 2014.
, “Short-term integration of Cdc25 dynamics controls mitotic entry during Drosophila gastrulation.”, Dev Cell, vol. 22, no. 4, pp. 763-74, 2012.
, “Posttranslational control of Cdc25 degradation terminates Drosophila's early cell-cycle program.”, Curr Biol, vol. 23, no. 2, pp. 127-32, 2013.
, “Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle.”, Dev Biol, vol. 244, no. 2, pp. 385-95, 2002.
, “Analyzing gene regulation in ascidian embryos: new tools for new perspectives.”, Differentiation, vol. 70, no. 4-5, pp. 132-9, 2002.
, “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.
, “Spatial covariance reconstructive (SCORE) super-resolution fluorescence microscopy.”, PLoS One, vol. 9, no. 4, p. e94807, 2014.
, “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
, “Effect of aberration on height calibration in three-dimensional localization-based microscopy and particle tracking.”, Appl Opt, vol. 48, no. 10, pp. 1886-90, 2009.
, “Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells.”, Phys Rev Lett, vol. 107, no. 15, p. 158101, 2011.
, “Novel pyrrolo[3,2-d]pyrimidine compounds target mitochondrial and cytosolic one-carbon metabolism with broad-spectrum antitumor efficacy.”, Mol Cancer Ther, 2019.
, “Insect behaviour: arboreal ants build traps to capture prey.”, Nature, vol. 434, no. 7036, p. 973, 2005.
, “Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.”, PLoS Biol, vol. 5, no. 5, p. e117, 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.
, “An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology.”, PLoS Genet, vol. 10, no. 3, p. e1004225, 2014.
, “Cell and developmental biology--a shared past, an intertwined future.”, Dev Cell, vol. 1, no. 1, pp. 27-36, 2001.
, “Bringing classical embryology to C elegans gastrulation.”, Dev Cell, vol. 4, no. 1, pp. 6-8, 2003.
, “folded gastrulation, cell shape change and the control of myosin localization.”, Development, vol. 132, no. 18, pp. 4165-78, 2005.
, “Nicotinamide adenine dinucleotide is transported into mammalian mitochondria.”, Elife, vol. 7, 2018.
, “Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis.”, Development, vol. 132, no. 21, pp. 4811-8, 2005.
, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
, “Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis.”, Proc Natl Acad Sci U S A, vol. 100, no. 20, pp. 11469-73, 2003.
, “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.
, “Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 4 Pt 1, p. 041922, 2011.
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