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
“Metabolic profiling reveals a dependency of human metastatic breast cancer on mitochondrial serine and one-carbon unit metabolism.”, Mol. Cancer Res., vol. 18, no. 4, pp. 599-611, 2020.
, “Macrophage de novo NAD synthesis specifies immune function in aging and inflammation.”, Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
, “Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons.”, Mol Psychiatry, 2019.
, “Metabolite Exchange between Mammalian Organs Quantified in Pigs.”, Cell Metab, vol. 30, no. 3, pp. 594-606.e3, 2019.
, “Metabolite exchange between mammalian organs quantified in pigs.”, Cell Metab., vol. 30, no. 3, pp. 594-606, 2019.
, “The metabolites NADP and NADPH are the targets of the circadian protein Nocturnin (Curled).”, Nat Commun, vol. 10, no. 1, p. 2367, 2019.
, “Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.”, mSystems, vol. 4, no. 1, 2019.
, “Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.”, Genome Res, vol. 28, no. 8, pp. 1169-1178, 2018.
, “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
, “Mitochondrial translation requires folate-dependent tRNA methylation.”, Nature, vol. 554, no. 7690, pp. 128-132, 2018.
, “Mating and male pheromone kill Caenorhabditis males through distinct mechanisms.”, Elife, vol. 6, 2017.
, “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
, “Metabolite Spectral Accuracy on Orbitraps.”, Anal Chem, vol. 89, no. 11, pp. 5940-5948, 2017.
, “mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein.”, Mol Cell, vol. 67, no. 6, pp. 936-946.e5, 2017.
, “Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage.”, Nat Chem Biol, vol. 12, no. 5, pp. 345-52, 2016.
, “Metabolic control of methylation and acetylation.”, Curr Opin Chem Biol, vol. 30, pp. 52-60, 2016.
, “Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.”, Elife, vol. 5, 2016.
, “Metabolite concentrations, fluxes and free energies imply efficient enzyme usage.”, Nat Chem Biol, 2016.
, “Mitochondria and Cancer.”, Mol Cell, vol. 61, no. 5, pp. 667-76, 2016.
, “Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation.”, Cell Metab, vol. 24, no. 1, pp. 104-17, 2016.
, “Mitosis-associated repression in development.”, Genes Dev, vol. 30, no. 13, pp. 1503-8, 2016.
, “MreB Orientation Correlates with Cell Diameter in Escherichia coli.”, Biophys J, vol. 111, no. 5, pp. 1035-43, 2016.
, “mTORC2 Responds to Glutamine Catabolite Levels to Modulate the Hexosamine Biosynthesis Enzyme GFAT1.”, Mol Cell, vol. 63, no. 5, pp. 811-26, 2016.
, “A microfluidic device and automatic counting system for the study of C. elegans reproductive aging.”, Lab Chip, vol. 15, no. 2, pp. 524-31, 2015.
, “Mapping the stereotyped behaviour of freely moving fruit flies.”, J R Soc Interface, vol. 11, no. 99, 2014.
, “Maternal origins of developmental reproducibility.”, Curr Biol, vol. 24, no. 11, pp. 1283-8, 2014.
, “Mating induces shrinking and death in Caenorhabditis mothers.”, Science, vol. 343, no. 6170, pp. 536-40, 2014.
, “A microfluidic device and automatic counting system for the study of C. elegans reproductive aging.”, Lab Chip, 2014.
, “molBLOCKS: decomposing small molecule sets and uncovering enriched fragments.”, Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
, “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
, “Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility.”, PLoS Comput Biol, vol. 10, no. 5, p. e1003619, 2014.
, “Maximally informative "stimulus energies" in the analysis of neural responses to natural signals.”, PLoS One, vol. 8, no. 11, p. e71959, 2013.
, “The mechanics of shape in prokaryotes.”, Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
, “Microfluidic trap array for massively parallel imaging of Drosophila embryos.”, Nat Protoc, vol. 8, no. 4, pp. 721-36, 2013.
, “Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster.”, Genome Res, vol. 22, no. 12, pp. 2507-19, 2012.
, “Mathematical models of morphogen gradients and their effects on gene expression.”, Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
, “Mechanisms of transcriptional precision in animal development.”, Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
, “Methods to detect selection on noncoding DNA.”, Methods Mol Biol, vol. 856, pp. 141-59, 2012.
, “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
, “Measurement and perturbation of morphogen lifetime: effects on gradient shape.”, Biophys J, vol. 101, no. 8, pp. 1807-15, 2011.
, “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.
, “Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria.”, Mol Microbiol, vol. 81, no. 2, pp. 340-53, 2011.
, “Metabolic cycling without cell division cycling in respiring yeast.”, Proc Natl Acad Sci U S A, vol. 108, no. 47, pp. 19090-5, 2011.
, “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
, “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
, “A microfluidic array for large-scale ordering and orientation of embryos.”, Nat Methods, vol. 8, no. 2, pp. 171-6, 2011.
, “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
, “Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 108, no. 33, pp. 13570-5, 2011.
, “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
, “Museum genomics: low-cost and high-accuracy genetic data from historical specimens.”, Mol Ecol Resour, vol. 11, no. 6, pp. 1082-92, 2011.
, “MAPK substrate competition integrates patterning signals in the Drosophila embryo.”, Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
, “Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.”, PLoS Comput Biol, vol. 6, no. 12, p. e1001034, 2010.
, “Mass spectrometry-based metabolomics of yeast.”, Methods Enzymol, vol. 470, pp. 393-426, 2010.
, “Maximum entropy models for antibody diversity.”, Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
, “Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.”, Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
, “Measuring the bending stiffness of bacterial cells using an optical trap.”, J Vis Exp, no. 38, 2010.
, “Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.”, Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
, “Metabolomic analysis and visualization engine for LC-MS data.”, Anal Chem, vol. 82, no. 23, pp. 9818-26, 2010.
, “Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer.”, Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
, “miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data.”, Genome Biol, vol. 11, no. 4, p. R39, 2010.
, “Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism.”, Phys Biol, vol. 7, no. 1, p. 016006, 2010.
, “Modelling the Bicoid gradient.”, Development, vol. 137, no. 14, pp. 2253-64, 2010.
, “Morphogen gradients: limits to signaling or limits to measurement?”, Curr Biol, vol. 20, no. 5, pp. R232-4, 2010.
, “Multiscale modeling of diffusion in the early Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 2010.
, “MAPK signaling in equations and embryos.”, Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
, “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
, “Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5347, 2009.
, “Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.”, Phys Rev Lett, vol. 103, no. 24, p. 248102, 2009.
, “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
, “A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.”, Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
, “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
, “Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein.”, Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
, “Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.”, Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
, “A method for detecting and correcting feature misidentification on expression microarrays.”, BMC Genomics, vol. 5, p. 64, 2004.
, “Min-protein oscillations in round bacteria.”, Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
, “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.”, Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
, “Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12963-8, 2002.
, “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
, “Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.”, Development, vol. 129, no. 11, pp. 2577-89, 2002.
, “Molecular characterisation of soft tissue tumours: a gene expression study.”, Lancet, vol. 359, no. 9314, pp. 1301-7, 2002.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
, “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
, “Molecular characterization of four induced alleles at the Ednrb locus.”, Proc Natl Acad Sci U S A, vol. 94, no. 24, pp. 13105-10, 1997.
, “Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene.”, Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
, “Maternal effect mutations of the sponge locus affect actin cytoskeletal rearrangements in Drosophila melanogaster embryos.”, J Cell Biol, vol. 119, no. 5, pp. 1205-18, 1992.
, “A mouse genomic library of yeast artificial chromosome clones.”, Mamm Genome, vol. 1, no. 1, p. 65, 1991.
, “Molecular analysis of odd-skipped, a zinc finger encoding segmentation gene with a novel pair-rule expression pattern.”, EMBO J, vol. 9, no. 11, pp. 3795-804, 1990.
, “Mutations in the Drosophila gene extradenticle affect the way specific homeo domain proteins regulate segmental identity.”, Genes Dev, vol. 4, no. 7, pp. 1209-23, 1990.
, “Molecular analysis of the armadillo locus: uniformly distributed transcripts and a protein with novel internal repeats are associated with a Drosophila segment polarity gene.”, Genes Dev, vol. 3, no. 1, pp. 96-113, 1989.
, “Mutations affecting segment number and polarity in Drosophila.”, Nature, vol. 287, no. 5785, pp. 795-801, 1980.
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