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.
, “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
, “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
, “Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.”, Nature, vol. 571, no. 7765, pp. 403-407, 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.
, “Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.”, Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
, “As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid.”, Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
, “Autophagy maintains tumour growth through circulating arginine.”, Nature, vol. 563, no. 7732, pp. 569-573, 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.
, “Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”, J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
, “Nicotinamide adenine dinucleotide is transported into mammalian mitochondria.”, Elife, vol. 7, 2018.
, “Outstanding questions in the study of archaic hominin admixture.”, PLoS Genet, vol. 14, no. 5, p. e1007349, 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.
, “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
, “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
, “Targeting hepatic glutaminase activity to ameliorate hyperglycemia.”, Nat Med, vol. 24, no. 4, pp. 518-524, 2018.
, “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 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.
, “Dynamic Control of dNTP Synthesis in Early Embryos.”, Dev Cell, vol. 42, no. 3, pp. 301-308.e3, 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.
, “IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.”, Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
, “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
, “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 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.
, “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 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.
, “Feeding the germline.”, Genes Dev, vol. 30, no. 3, pp. 249-50, 2016.
, “The Neuronal Kinesin UNC-104/KIF1A Is a Key Regulator of Synaptic Aging and Insulin Signaling-Regulated Memory.”, Curr Biol, vol. 26, no. 5, pp. 605-15, 2016.
, “Nodal and FGF coordinate ascidian neural tube morphogenesis.”, Development, vol. 143, no. 24, pp. 4665-4675, 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.
, “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 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.
, “Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
, “C. elegans maximum velocity correlates with healthspan and is maintained in worms with an insulin receptor mutation.”, Nat Commun, vol. 6, p. 8919, 2015.
, “The cell biology of aging.”, Mol Biol Cell, vol. 26, no. 25, pp. 4524-31, 2015.
, “Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis.”, Curr Biol, vol. 25, no. 24, pp. 3232-8, 2015.
, “Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity.”, Nature, vol. 519, no. 7541, pp. 97-101, 2015.
, “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
, “For longevity, perception is everything.”, Cell, vol. 160, no. 5, pp. 807-9, 2015.
, “The genetic basis of natural variation in mushroom body size in Drosophila melanogaster.”, Nat Commun, vol. 6, p. 10115, 2015.
, “Genome Sequencing Fishes out Longevity Genes.”, Cell, vol. 163, no. 6, pp. 1312-3, 2015.
, “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
, “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
, “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.
, “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 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.
, “Suboptimization of developmental enhancers.”, Science, vol. 350, no. 6258, pp. 325-8, 2015.
, “ZMP: a master regulator of one-carbon metabolism.”, Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
, “Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation.”, Nature, vol. 508, no. 7496, pp. 392-6, 2014.
, “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
, “The contraction of time and space in remote chromosomal interactions.”, Cell, vol. 158, no. 2, pp. 243-4, 2014.
, “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 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.
, “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.
, “Fly wing vein patterns have spatial reproducibility of a single cell.”, J R Soc Interface, vol. 11, no. 97, p. 20140443, 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.
, “On the GFP-based analysis of dynamic concentration profiles.”, Biophys J, vol. 106, no. 3, pp. L13-5, 2014.
, “Global quantitative modeling of chromatin factor interactions.”, PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
, “Lasker∼Koshland to genetics pioneer.”, Cell, vol. 158, no. 6, pp. 1230-2, 2014.
, “Looping back to leap forward: transcription enters a new era.”, Cell, vol. 157, no. 1, pp. 13-25, 2014.
, “Mating induces shrinking and death in Caenorhabditis mothers.”, Science, vol. 343, no. 6170, pp. 536-40, 2014.
, “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
, “Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.”, Development, vol. 141, no. 14, pp. 2895-900, 2014.
, “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
, “Retrospective. Walter Gehring (1939-2014).”, Science, vol. 345, no. 6194, p. 277, 2014.
, “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
, “Social interactions dominate speed control in poising natural flocks near criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
, “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
, “Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection.”, Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 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.
, “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.
, “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
, “ERK as a model for systems biology of enzyme kinetics in cells.”, Curr Biol, vol. 23, no. 21, pp. R972-9, 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.
, “Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.”, PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
, “Genetic incompatibilities are widespread within species.”, Nature, vol. 504, no. 7478, pp. 135-7, 2013.
, “Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia.”, Mol Syst Biol, vol. 9, p. 712, 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.
, “Kinetics of receptor occupancy during morphogen gradient formation.”, J Chem Phys, vol. 138, no. 24, p. 244105, 2013.
, “Microfluidic trap array for massively parallel imaging of Drosophila embryos.”, Nat Protoc, vol. 8, no. 4, pp. 721-36, 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.
, “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.
, “Precise developmental gene expression arises from globally stochastic transcriptional activity.”, Cell, vol. 154, no. 4, pp. 789-800, 2013.
, “Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning.”, Curr Biol, vol. 23, no. 21, pp. 2140-5, 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.
, “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
, “Three-dimensional epithelial morphogenesis in the developing Drosophila egg.”, Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
, “The Capicua repressor--a general sensor of RTK signaling in development and disease.”, J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 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.
, “EGFR-dependent network interactions that pattern Drosophila eggshell appendages.”, Development, vol. 139, no. 15, pp. 2814-20, 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.
, “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
, “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”, PLoS One, vol. 7, no. 3, p. e33528, 2012.
, “FGF signaling establishes the anterior border of the Ciona neural tube.”, Development, vol. 139, no. 13, pp. 2351-9, 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.
, “HOT DNAs: a novel class of developmental enhancers.”, Genes Dev, vol. 26, no. 9, pp. 873-6, 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.
, “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.
, “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.
, “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.
, “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
, “Pattern formation by graded and uniform signals in the early Drosophila embryo.”, Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
, “Precision of hunchback expression in the Drosophila embryo.”, Curr Biol, vol. 22, no. 23, pp. 2247-52, 2012.
, “Quantifying the Bicoid morphogen gradient in living fly embryos.”, Cold Spring Harb Protoc, vol. 2012, no. 4, pp. 398-406, 2012.
, “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 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.
, “Statistical mechanics for natural flocks of birds.”, Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 2012.
, “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 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.
, “Torso RTK controls Capicua degradation by changing its subcellular localization.”, Development, vol. 139, no. 21, pp. 3962-8, 2012.
, “Transcriptional interpretation of the EGF receptor signaling gradient.”, Proc Natl Acad Sci U S A, vol. 109, no. 5, pp. 1572-7, 2012.
, “Transcriptional repression via antilooping in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
, “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
, “Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis.”, Proc Natl Acad Sci U S A, vol. 109, no. 47, pp. 19298-303, 2012.
, “Accurate quantification of functional analogy among close homologs.”, PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
, “Caenorhabditis elegans reproductive aging: Regulation and underlying mechanisms.”, Genesis, vol. 49, no. 2, pp. 53-65, 2011.
, “Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles.”, PLoS Biol, vol. 9, no. 1, p. e1000584, 2011.
, “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
, “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 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.
, “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
, “EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan.”, EMBO J, vol. 30, no. 15, pp. 2990-3003, 2011.
, “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.
, “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.
, “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA.”, PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
, “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
, “Gene regulation by MAPK substrate competition.”, Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
, “Genome-sequencing anniversary. Fruits of genome sequences for biology.”, Science, vol. 331, no. 6020, p. 1025, 2011.
, “Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism.”, Anal Chem, vol. 83, no. 23, pp. 9114-22, 2011.
, “Measurement and perturbation of morphogen lifetime: effects on gradient shape.”, Biophys J, vol. 101, no. 8, pp. 1807-15, 2011.
, “A microfluidic array for large-scale ordering and orientation of embryos.”, Nat Methods, vol. 8, no. 2, pp. 171-6, 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.
, “Neural tube patterning by Ephrin, FGF and Notch signaling relays.”, Development, vol. 138, no. 24, pp. 5429-39, 2011.
, “Neural-specific elongation of 3' UTRs during Drosophila development.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
, “Neuronal subtype specification in the spinal cord of a protovertebrate.”, Development, vol. 138, no. 5, pp. 995-1004, 2011.
, “Pattern formation by a moving morphogen source.”, Phys Biol, vol. 8, no. 4, p. 045003, 2011.
, “Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis.”, Curr Opin Genet Dev, vol. 21, no. 6, pp. 719-25, 2011.
, “Paused RNA polymerase II as a developmental checkpoint.”, Cell, vol. 145, no. 4, pp. 502-11, 2011.
, “PILGRM: an interactive data-driven discovery platform for expert biologists.”, Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
, “The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.”, Mol Cell, vol. 42, no. 6, pp. 837-44, 2011.
, “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
, “Remodeling of the metabolome during early frog development.”, PLoS One, vol. 6, no. 2, p. e16881, 2011.
, “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.
, “The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo.”, Curr Biol, vol. 21, no. 18, pp. 1571-7, 2011.
, “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
, “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
, “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
, “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
, “Aging: miRacles of longevity?”, Curr Biol, vol. 20, no. 24, pp. R1076-8, 2010.
, “Approaching the molecular origins of collective dynamics in oscillating cell populations.”, Curr Opin Genet Dev, vol. 20, no. 6, pp. 574-80, 2010.
, “Autophagy and metabolism.”, Science, vol. 330, no. 6009, pp. 1344-8, 2010.
, “The Bicoid gradient is shaped independently of nuclei.”, Development, vol. 137, no. 17, pp. 2857-62, 2010.
, “BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.”, Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
, “Branched tricarboxylic acid metabolism in Plasmodium falciparum.”, Nature, vol. 466, no. 7307, pp. 774-8, 2010.
, “Cell cycle regulation via inter-nuclear communication during the early embryonic development of Drosophila melanogaster.”, Cell Cycle, vol. 9, no. 14, pp. 2908-10, 2010.
, “A compartmental model for the bicoid gradient.”, Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
, “Early chordate origins of the vertebrate second heart field.”, Science, vol. 329, no. 5991, pp. 565-8, 2010.
, “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
, “Functional genomics complements quantitative genetics in identifying disease-gene associations.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
, “The Gene Ontology in 2010: extensions and refinements.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 2010.
“Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
, “Insulin signaling and dietary restriction differentially influence the decline of learning and memory with age.”, PLoS Biol, vol. 8, no. 5, p. e1000372, 2010.
, “Integration of contractile forces during tissue invagination.”, J Cell Biol, vol. 188, no. 5, pp. 735-49, 2010.
, “Integration of diverse inputs in the regulation of Caenorhabditis elegans DAF-16/FOXO.”, Dev Dyn, vol. 239, no. 5, pp. 1405-12, 2010.
, “Integrative systems biology for data-driven knowledge discovery.”, Semin Nephrol, vol. 30, no. 5, pp. 443-54, 2010.
,