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
“Maximally informative "stimulus energies" in the analysis of neural responses to natural signals.”, PLoS One, vol. 8, no. 11, p. e71959, 2013.
, “Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function.”, Cancer Res, vol. 75, no. 16, pp. 3355-64, 2015.
, “Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin.”, Clin Cancer Res, vol. 23, no. 18, pp. 5639-5647, 2017.
, “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
, “A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins.”, Am J Hypertens, vol. 16, no. 2, pp. 158-62, 2003.
, “A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.”, PLoS Comput Biol, vol. 14, no. 5, p. e1006105, 2018.
, “Coordinate regulation of downstream genes by extradenticle and the homeotic selector proteins.”, EMBO J, vol. 13, no. 15, pp. 3561-9, 1994.
, “extradenticle determines segmental identities throughout Drosophila development.”, Development, vol. 121, no. 11, pp. 3663-73, 1995.
, “extradenticle, a regulator of homeotic gene activity, is a homolog of the homeobox-containing human proto-oncogene pbx1.”, Cell, vol. 74, no. 6, pp. 1101-12, 1993.
, “Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.”, Science, vol. 337, no. 6093, pp. 470-3, 2012.
, “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
, “Characteristic phenotypes associated with ptsN-null mutants in Escherichia coli K-12 are absent in strains with functional ilvG.”, J Bacteriol, vol. 193, no. 18, pp. 4576-81, 2011.
, “Pyrimidine homeostasis is accomplished by directed overflow metabolism.”, Nature, vol. 500, no. 7461, pp. 237-41, 2013.
, “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
, “GeneXplorer: an interactive web application for microarray data visualization and analysis.”, BMC Bioinformatics, vol. 5, p. 141, 2004.
, “Quantitative models of developmental pattern formation.”, Dev Cell, vol. 11, no. 3, pp. 289-300, 2006.
, “Computational analysis of EGFR inhibition by Argos.”, Dev Biol, vol. 284, no. 2, pp. 523-35, 2005.
, “Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.”, J Biol, vol. 5, no. 4, p. 11, 2006.
, “Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.”, G3 (Bethesda), 2013.
, “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.
, “Spatial expression of the Drosophila segment polarity gene armadillo is posttranscriptionally regulated by wingless.”, Cell, vol. 63, no. 3, pp. 549-60, 1990.
, “The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO.”, PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
, “GIANT API: an application programming interface for functional genomics.”, Nucleic Acids Res, 2016.
, “subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling.”, Bioinformatics, vol. 30, no. 23, pp. 3424-6, 2014.
, “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
, “5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination.”, Mol Genet Metab, vol. 125, no. 1-2, pp. 118-126, 2018.
, “Serine Metabolism Supports Macrophage IL-1β Production.”, Cell Metab, vol. 29, no. 4, pp. 1003-1011.e4, 2019.
, “Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.”, Mol Biol Evol, vol. 31, no. 7, pp. 1750-66, 2014.
, “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
, “Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group.”, G3 (Bethesda), vol. 4, no. 12, pp. 2345-51, 2014.
, “T Cell Activation Depends on Extracellular Alanine.”, Cell Rep, vol. 28, no. 12, pp. 3011-3021.e4, 2019.
, “Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation.”, Cell Metab, vol. 24, no. 1, pp. 104-17, 2016.
, “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.
, “Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.”, Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
, “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
, “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.
, “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
, “Genetic map of the fused locus on mouse chromosome 17.”, Genomics, vol. 23, no. 1, pp. 178-84, 1994.
, “Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts.”, Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
, “Museum genomics: low-cost and high-accuracy genetic data from historical specimens.”, Mol Ecol Resour, vol. 11, no. 6, pp. 1082-92, 2011.
, “Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient.”, Curr Opin Genet Dev, vol. 22, no. 6, pp. 542-6, 2012.
, “Force generation by groups of migrating bacteria.”, Proc Natl Acad Sci U S A, vol. 114, no. 28, pp. 7266-7271, 2017.
, “Nutritional homeostasis in batch and steady-state culture of yeast.”, Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
, “Recurated protein interaction datasets.”, Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
, “Multiscale modeling of diffusion in the early Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 2010.
, “Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta.”, Proc Natl Acad Sci U S A, vol. 100, no. 8, pp. 4622-7, 2003.
, “Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons.”, Mol Psychiatry, 2019.
, “Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”, BMC Immunol, vol. 3, p. 5, 2002.
, “Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains.”, PLoS One, vol. 2, no. 3, p. e322, 2007.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Functional elements of the cytoskeleton in the early Drosophila embryo.”, Annu Rev Cell Biol, vol. 9, pp. 67-99, 1993.
, “Role of the zygotic genome in the restructuring of the actin cytoskeleton at the cycle-14 transition during Drosophila embryogenesis.”, Cold Spring Harb Symp Quant Biol, vol. 57, pp. 653-9, 1992.
, “bottleneck acts as a regulator of the microfilament network governing cellularization of the Drosophila embryo.”, Cell, vol. 75, no. 2, pp. 373-85, 1993.
, “Enhancer competition between H19 and Igf2 does not mediate their imprinting.”, Proc Natl Acad Sci U S A, vol. 96, no. 17, pp. 9733-8, 1999.
, “The Dlk1 and Gtl2 genes are linked and reciprocally imprinted.”, Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
, “Synergy, redundancy, and independence in population codes.”, J Neurosci, vol. 23, no. 37, pp. 11539-53, 2003.
, “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
, “Network information and connected correlations.”, Phys Rev Lett, vol. 91, no. 23, p. 238701, 2003.
, “Weak pairwise correlations imply strongly correlated network states in a neural population.”, Nature, vol. 440, no. 7087, pp. 1007-12, 2006.
, “A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism.”, Cell Rep, vol. 27, no. 11, pp. 3359-3370.e7, 2019.
, “How common is homoploid hybrid speciation?”, Evolution, vol. 68, no. 6, pp. 1553-60, 2014.
, “High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species.”, Elife, vol. 3, 2014.
, “An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”, Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
, “Germline autonomy of maternal-effect mutations altering the embryonic body pattern of Drosophila.”, Dev Biol, vol. 113, no. 2, pp. 443-8, 1986.
, “Probing for gene specificity in epithelial development.”, Int J Dev Biol, vol. 42, no. 3, pp. 249-55, 1998.
, “Female sterile mutations on the second chromosome of Drosophila melanogaster. I. Maternal effect mutations.”, Genetics, vol. 121, no. 1, pp. 101-17, 1989.
, “Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking oogenesis or altering egg morphology.”, Genetics, vol. 129, no. 4, pp. 1119-36, 1991.
, “GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.”, BMC Bioinformatics, vol. 7, p. 443, 2006.
, “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.”, Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
, “Pervasive natural selection in the Drosophila genome?”, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
, “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
, “Immunity regulatory DNAs share common organizational features in Drosophila.”, Mol Cell, vol. 13, no. 1, pp. 19-32, 2004.
, “Combining modeling and experiment to understand bacterial growth.”, Biophys J, vol. 104, no. 12, p. 2573, 2013.
, “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
, “Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function.”, J Opt Soc Am A Opt Image Sci Vis, vol. 24, no. 9, pp. 2622-7, 2007.
, “Spiroplasma swim by a processive change in body helicity.”, Cell, vol. 122, no. 6, pp. 941-5, 2005.
, “Curvature and torsion in growing actin networks.”, Phys Biol, vol. 5, no. 2, p. 026006, 2008.
, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
, “The structure and function of bacterial actin homologs.”, Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.
, “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
, “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
, “Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.”, Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
, “Neural decision boundaries for maximal information transmission.”, PLoS One, vol. 2, no. 7, p. e646, 2007.
, “Analyzing neural responses to natural signals: maximally informative dimensions.”, Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
, “The C. elegans TGF-beta Dauer pathway regulates longevity via insulin signaling.”, Curr Biol, vol. 17, no. 19, pp. 1635-45, 2007.
, “Mating induces shrinking and death in Caenorhabditis mothers.”, Science, vol. 343, no. 6170, pp. 536-40, 2014.
, “Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis.”, Genome Res, vol. 15, no. 12, pp. 1668-74, 2005.
, “Feeding the germline.”, Genes Dev, vol. 30, no. 3, pp. 249-50, 2016.
, “FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.”, Development, vol. 136, no. 1, pp. 23-8, 2009.
, “Mating and male pheromone kill Caenorhabditis males through distinct mechanisms.”, Elife, vol. 6, 2017.
, “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.
, “The temporal requirement for endothelin receptor-B signalling during neural crest development.”, Nature, vol. 402, no. 6761, pp. 496-501, 1999.
, “Mathematical models of morphogen gradients and their effects on gene expression.”, Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
, “Shooting from the hip: spatial control of signal release by intracellular waves.”, Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9087-9, 2002.
, “MAPK signaling in equations and embryos.”, Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
, “Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.”, Development, vol. 129, no. 11, pp. 2577-89, 2002.
, “Dynamics of maternal morphogen gradients in Drosophila.”, Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
, “A DNA microarray survey of gene expression in normal human tissues.”, Genome Biol, vol. 6, no. 3, p. R22, 2005.
, “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.
, “EGFR-dependent network interactions that pattern Drosophila eggshell appendages.”, Development, vol. 139, no. 15, pp. 2814-20, 2012.
, “Zygotic activity of the nullo locus is required to stabilize the actin-myosin network during cellularization in Drosophila.”, Development, vol. 110, no. 3, pp. 851-63, 1990.
, “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”, Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
, “Chemical sensing by nonequilibrium cooperative receptors.”, Phys Rev Lett, vol. 110, no. 24, p. 248102, 2013.
, “Chemical Sensing by Nonequilibrium Cooperative Receptors.”, Phys Rev Lett, vol. 110, no. 24, 2013.
, “Dynamics of cooperativity in chemical sensing among cell-surface receptors.”, Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
, “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.
, “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
, “Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.”, Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 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.
, “Information-based clustering.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
, “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
, “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
, “Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1.”, Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
, “Zygotically controlled F-actin establishes cortical compartments to stabilize furrows during Drosophila cellularization.”, J Cell Sci, vol. 121, no. Pt 11, pp. 1815-24, 2008.
, “Local actin-dependent endocytosis is zygotically controlled to initiate Drosophila cellularization.”, Dev Cell, vol. 14, no. 5, pp. 775-86, 2008.
, “RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans.”, Nat Commun, vol. 8, p. 14749, 2017.
, “From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization.”, PLoS Comput Biol, vol. 9, no. 2, p. e1002910, 2013.
, “Energy budget of Drosophila embryogenesis.”, Curr Biol, vol. 29, no. 12, pp. R566-R567, 2019.
, “How and when should interactome-derived clusters be used to predict functional modules and protein function?”, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
, “Dynamic Control of dNTP Synthesis in Early Embryos.”, Dev Cell, vol. 42, no. 3, pp. 301-308.e3, 2017.
, “Repeated observation of breast tumor subtypes in independent gene expression data sets.”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8418-23, 2003.
, “Turning to the cold.”, Nat Cell Biol, vol. 9, no. 9, pp. 1029-31, 2007.
, “Responding to chemical gradients: bacterial chemotaxis.”, Curr Opin Cell Biol, vol. 24, no. 2, pp. 262-8, 2012.
, “Role of alpha-fetoprotein regulatory elements in transcriptional activation in transient heterokaryons.”, Mol Cell Biol, vol. 10, no. 10, pp. 5047-54, 1990.
, “A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry.”, Chembiochem, 2019.
, “Dorsal gradient networks in the Drosophila embryo.”, Dev Biol, vol. 246, no. 1, pp. 57-67, 2002.
, “Whole-genome expression profiles identify gene batteries in Drosophila.”, Dev Cell, vol. 3, no. 4, pp. 464-5, 2002.
, “Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo.”, Dev Biol, vol. 280, no. 2, pp. 482-93, 2005.
, “Whole-genome analysis of Drosophila gastrulation.”, Curr Opin Genet Dev, vol. 14, no. 5, pp. 477-84, 2004.
, “Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo.”, Cell, vol. 111, no. 5, pp. 687-701, 2002.
, “Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset.”, Development, vol. 129, no. 14, pp. 3411-9, 2002.
, “pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos.”, Genes Dev, vol. 18, no. 6, pp. 687-99, 2004.
, “C. elegans positive olfactory associative memory is a molecularly conserved behavioral paradigm.”, Neurobiol Learn Mem, vol. 115, pp. 86-94, 2014.
, “The Intersection of Aging, Longevity Pathways, and Learning and Memory in C. elegans.”, Front Genet, vol. 3, p. 259, 2012.
, “Statistical mechanics of letters in words.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 81, no. 6 Pt 2, p. 066119, 2010.
, “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
, “Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7286-9, 2011.
, “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
, “Searching for simplicity in the analysis of neurons and behavior.”, Proc Natl Acad Sci U S A, vol. 108 Suppl 3, pp. 15565-71, 2011.
, “Statistical thermodynamics of natural images.”, Phys Rev Lett, vol. 110, no. 1, p. 018701, 2013.
, “How many clusters? An information-theoretic perspective.”, Neural Comput, vol. 16, no. 12, pp. 2483-506, 2004.
, “PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism.”, Cell Stem Cell, 2019.
, “Neuronal subtype specification in the spinal cord of a protovertebrate.”, Development, vol. 138, no. 5, pp. 995-1004, 2011.
, “Neural tube patterning by Ephrin, FGF and Notch signaling relays.”, Development, vol. 138, no. 24, pp. 5429-39, 2011.
, “Early chordate origins of the vertebrate second heart field.”, Science, vol. 329, no. 5991, pp. 565-8, 2010.
, “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
, “Influence of climate variability on whitefish (Coregonus lavaretus) year-class strength in a deep, warm monomictic lake.”, Oecologia, vol. 151, no. 3, pp. 521-9, 2007.
, “Metabolic control of methylation and acetylation.”, Curr Opin Chem Biol, vol. 30, pp. 52-60, 2016.
, “Metabolite Spectral Accuracy on Orbitraps.”, Anal Chem, vol. 89, no. 11, pp. 5940-5948, 2017.
, “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
, “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
, “Gastrulation in Drosophila: the formation of the ventral furrow and posterior midgut invaginations.”, Development, vol. 112, no. 3, pp. 775-89, 1991.
, “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.
, “Cell lineage and development in the larval epidermis of Drosophila melanogaster.”, Dev Biol, vol. 73, no. 2, pp. 256-71, 1979.
, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
, “Four Key Steps Control Glycolytic Flux in Mammalian Cells.”, Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
, “Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis.”, ACS Chem Biol, 2016.
, “Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi.”, Mol Syst Biol, vol. 7, p. 491, 2011.
, “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.
, “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
, “PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity.”, Cell, vol. 154, no. 3, pp. 676-90, 2013.
, “Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
, “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
, “Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.”, Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
, “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
, “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.
, “Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.”, ISME J, vol. 9, no. 1, pp. 68-80, 2015.
, “Lessons learned, promises kept: a biologist's eye view of the Genome Project.”, Genome Res, vol. 6, no. 9, pp. 773-80, 1996.
, “Parental imprinting of the H19 and Igf2 genes in the mouse.”, Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
, “Parental imprinting in the mouse.”, Harvey Lect, vol. 87, pp. 69-84, 1991.
, “It's all about the talent.”, Mol Biol Cell, vol. 21, no. 22, p. 3823, 2010.
, “DNA methylation: a phoenix rises.”, Proc Natl Acad Sci U S A, vol. 90, no. 19, pp. 8761-2, 1993.
, “Twists and turns: a scientific journey.”, Annu Rev Cell Dev Biol, vol. 30, pp. 1-21, 2014.
, “The sins of the fathers and mothers: genomic imprinting in mammalian development.”, Cell, vol. 96, no. 2, pp. 185-93, 1999.
, “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
, “Direct Hepatocyte Insulin Signaling Is Required for Lipogenesis but Is Dispensable for the Suppression of Glucose Production.”, Cell Metab, 2016.
, “Positional information, positional error, and readout precision in morphogenesis: a mathematical framework.”, Genetics, vol. 199, no. 1, pp. 39-59, 2015.
, “Information flow and optimization in transcriptional regulation.”, Proc Natl Acad Sci U S A, vol. 105, no. 34, pp. 12265-70, 2008.
, “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
, “Diffusion, dimensionality, and noise in transcriptional regulation.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 79, no. 5 Pt 1, p. 051901, 2009.
, “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
, “Optimizing information flow in small genetic networks. III. A self-interacting gene.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 85, no. 4 Pt 1, p. 041903, 2012.
, “Optimizing information flow in small genetic networks.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 3 Pt 1, p. 031920, 2009.
, “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
, “A nuclear escort for beta-catenin.”, Nat Cell Biol, vol. 6, no. 7, pp. 579-80, 2004.
, “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
, “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
, “Rethinking WNT signaling.”, Trends Genet, vol. 20, no. 4, pp. 177-81, 2004.
, “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
, “The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.”, Mol Biol Cell, vol. 15, no. 3, pp. 1254-61, 2004.
, “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.
, “Putting the 'bio' into bioinformatics.”, Genome Biol, vol. 6, no. 10, p. 351, 2005.
, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
, “Nonparametric methods for identifying differentially expressed genes in microarray data.”, Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
, “"Getting started in..": a series not to miss.”, PLoS Comput Biol, vol. 3, no. 10, p. 1841, 2007.
, “Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”, Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
, “A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 2003.
,