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
“Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth.”, Med (N Y), vol. 3, no. 2, pp. 119-136, 2022.
, “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
, “Macrophage de novo NAD synthesis specifies immune function in aging and inflammation.”, Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
, “Macrophage de novo NAD synthesis specifies immune function in aging and inflammation.”, Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
, “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
, “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
, “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “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.
, “As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid.”, Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
, “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.
, “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.
, “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.
, “Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.”, Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.
, “Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.”, Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.
, “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.
, “Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain.”, J Neurochem, vol. 145, no. 5, pp. 362-373, 2018.
, “Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain.”, J Neurochem, vol. 145, no. 5, pp. 362-373, 2018.
, “Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate.”, Nat Chem Biol, vol. 13, no. 10, pp. 1081-1087, 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.
, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 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.
, “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
, “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
, “Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy.”, Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
, “Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport.”, Am J Hum Genet, vol. 101, no. 4, pp. 489-502, 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.
, “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.
, “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.
, “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.
, “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.
, “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
, “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
, “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
, “An unsupervised method for quantifying the behavior of paired animals.”, Phys Biol, vol. 14, no. 1, p. 015006, 2017.
, “The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.”, MBio, vol. 7, no. 2, pp. e02164-15, 2016.
, “The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators.”, Nature, vol. 529, no. 7584, pp. 92-6, 2016.
, “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
, “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
, “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
, “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
, “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.”, Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
, “Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera).”, Proc Natl Acad Sci U S A, vol. 113, no. 4, pp. 1020-5, 2016.
, “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
, “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
, “RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.”, Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 2015.
, “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
, “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
, “ZMP: a master regulator of one-carbon metabolism.”, Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
, “ZMP: a master regulator of one-carbon metabolism.”, Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
, “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
, “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
, “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
, “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.
, “Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS.”, Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
, “Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.”, Mol Cell, vol. 55, no. 6, pp. 916-30, 2014.
, “Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.”, Mol Cell, vol. 55, no. 6, pp. 916-30, 2014.
, “Global quantitative modeling of chromatin factor interactions.”, PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
, “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
, “Looping back to leap forward: transcription enters a new era.”, Cell, vol. 157, no. 1, pp. 13-25, 2014.
, “molBLOCKS: decomposing small molecule sets and uncovering enriched fragments.”, Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
, “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
, “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
, “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
, “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
, “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”, Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
, “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”, Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
, “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”, Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
, “Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.”, Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
, “Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.”, Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
, “Defining cell-type specificity at the transcriptional level in human disease.”, Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
, “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
, “An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”, Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
, “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.
, “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.
, “Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids.”, Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
, “Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids.”, Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
, “Kinetics of gene derepression by ERK signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
, “The mechanics of shape in prokaryotes.”, Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
, “Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”, PLoS One, vol. 8, no. 5, p. e63304, 2013.
, “Nucleotide degradation and ribose salvage in yeast.”, Mol Syst Biol, vol. 9, p. 665, 2013.
, “Nucleotide degradation and ribose salvage in yeast.”, Mol Syst Biol, vol. 9, p. 665, 2013.
, “Nucleotide degradation and ribose salvage in yeast.”, Mol Syst Biol, vol. 9, p. 665, 2013.
, “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
, “Phylogenetic portrait of the Saccharomyces cerevisiae functional genome.”, G3 (Bethesda), vol. 3, no. 8, pp. 1335-40, 2013.
, “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
, “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
, “Posttranslational control of Cdc25 degradation terminates Drosophila's early cell-cycle program.”, Curr Biol, vol. 23, no. 2, pp. 127-32, 2013.
, “Posttranslational control of Cdc25 degradation terminates Drosophila's early cell-cycle program.”, Curr Biol, vol. 23, no. 2, pp. 127-32, 2013.
, “Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.”, Genetics, vol. 195, no. 2, pp. 443-55, 2013.
, “Pyrimidine homeostasis is accomplished by directed overflow metabolism.”, Nature, vol. 500, no. 7461, pp. 237-41, 2013.
, “Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.”, J Vis Exp, no. 81, p. e51153, 2013.
, “Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.”, J Vis Exp, no. 81, p. e51153, 2013.
, “Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.”, J Vis Exp, no. 81, p. e51153, 2013.
, “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
, “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
, “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
, “Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.”, Science, vol. 337, no. 6093, pp. 470-3, 2012.
, “Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.”, Science, vol. 337, no. 6093, pp. 470-3, 2012.
, “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.
, “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.
, “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
, “An effective statistical evaluation of ChIPseq dataset similarity.”, Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
, “ELAV mediates 3' UTR extension in the Drosophila nervous system.”, Genes Dev, vol. 26, no. 20, pp. 2259-64, 2012.
, “ELAV mediates 3' UTR extension in the Drosophila nervous system.”, Genes Dev, vol. 26, no. 20, pp. 2259-64, 2012.
, “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
, “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
, “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
, “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
, “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
, “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
, “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
, “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
, “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
, “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
, “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
, “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
, “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
, “Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase.”, J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
, “Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase.”, J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
, “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.
, “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.
, “Identification of a rudimentary neural crest in a non-vertebrate chordate.”, Nature, vol. 492, no. 7427, pp. 104-7, 2012.
, “IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.”, Nucleic Acids Res, vol. 40, no. Web Server issue, pp. W484-90, 2012.
, “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
, “Introducing WIREs Developmental Biology.”, Wiley Interdiscip Rev Dev Biol, vol. 1, no. 1, pp. 1-2, 2012.
, “Introducing WIREs Developmental Biology.”, Wiley Interdiscip Rev Dev Biol, vol. 1, no. 1, pp. 1-2, 2012.
, “Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.”, Mol Cell Biol, vol. 32, no. 23, pp. 4861-76, 2012.
, “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.
, “Methods to detect selection on noncoding DNA.”, Methods Mol Biol, vol. 856, pp. 141-59, 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.
, “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.”, Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
, “Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.”, Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
, “Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.”, Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
, “Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.”, Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
, “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
, “RpoS proteolysis is controlled directly by ATP levels in Escherichia coli.”, Genes Dev, vol. 26, no. 6, pp. 548-53, 2012.
, “RpoS proteolysis is controlled directly by ATP levels in Escherichia coli.”, Genes Dev, vol. 26, no. 6, pp. 548-53, 2012.
, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
, “Short-term integration of Cdc25 dynamics controls mitotic entry during Drosophila gastrulation.”, Dev Cell, vol. 22, no. 4, pp. 763-74, 2012.
, “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
, “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
, “Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient.”, Curr Opin Genet Dev, vol. 22, no. 6, pp. 542-6, 2012.
, “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
, “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
, “Transcriptional repression via antilooping in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
, “Transcriptional repression via antilooping in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
, “Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase.”, Nat Chem Biol, vol. 8, no. 6, pp. 562-8, 2012.
, “Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase.”, Nat Chem Biol, vol. 8, no. 6, pp. 562-8, 2012.
, “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
, “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Accurate quantification of functional analogy among close homologs.”, PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
, “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
, “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 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.
, “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.
, “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
, “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
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