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
“Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors.”, Cell Chem Biol, vol. 29, no. 3, pp. 423-435.e10, 2022.
, “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.
, “Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate.”, Nature, vol. 579, no. 7800, pp. 586-591, 2020.
, “Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.”, Cell Syst, vol. 10, no. 2, pp. 193-203.e4, 2020.
, “Elevated Choline Kinase α-Mediated Choline Metabolism Supports the Prolonged Survival of TRAF3-Deficient B Lymphocytes.”, J Immunol, vol. 204, no. 2, pp. 459-471, 2020.
, “Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.”, Cell, vol. 180, no. 4, pp. 677-687.e16, 2020.
, “Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity.”, Proc Natl Acad Sci U S A, vol. 117, no. 11, pp. 6047-6055, 2020.
, “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.
, “Serine Catabolism Feeds NADH when Respiration Is Impaired.”, Cell Metab, vol. 31, no. 4, pp. 809-821.e6, 2020.
, “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
, “Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker.”, JCI Insight, vol. 5, no. 6, 2020.
, “Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.”, Bioinformatics, vol. 36, no. 4, pp. 994-999, 2020.
, “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry.”, Chembiochem, 2019.
, “A comprehensive genome-scale model for IFO0880 accounting for functional genomics and phenotypic data.”, Metab Eng Commun, vol. 9, p. e00101, 2019.
, “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
, “A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.”, Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
, “Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.”, Nature, vol. 571, no. 7765, pp. 403-407, 2019.
, “Energy budget of Drosophila embryogenesis.”, Curr Biol, vol. 29, no. 12, pp. R566-R567, 2019.
, “Large distances separate coregulated genes in living embryos.”, Proc Natl Acad Sci U S A, vol. 116, no. 30, pp. 15062-15067, 2019.
, “The long walk to African genomics.”, Genome Biol, vol. 20, no. 1, p. 130, 2019.
, “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, 2019.
, “Metabolite Exchange between Mammalian Organs Quantified in Pigs.”, Cell Metab, vol. 30, no. 3, pp. 594-606.e3, 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.
, “NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism.”, Nat Metab, vol. 1, pp. 404-415, 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.
, “Near-equilibrium glycolysis supports metabolic homeostasis and energy yield.”, Nat Chem Biol, vol. 15, no. 10, pp. 1001-1008, 2019.
, “Novel pyrrolo[3,2-d]pyrimidine compounds target mitochondrial and cytosolic one-carbon metabolism with broad-spectrum antitumor efficacy.”, Mol Cancer Ther, 2019.
, “Organoid single cell profiling identifies a transcriptional signature of glomerular disease.”, JCI Insight, vol. 4, no. 1, 2019.
, “Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics.”, Anal Chem, vol. 91, no. 3, pp. 1838-1846, 2019.
, “Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity.”, Nat Immunol, vol. 20, no. 8, pp. 1023-1034, 2019.
, “PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism.”, Cell Stem Cell, 2019.
, “A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate.”, Cell Metab, vol. 30, no. 1, pp. 174-189.e5, 2019.
, “Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids.”, Cell Metab, vol. 29, no. 2, pp. 417-429.e4, 2019.
, “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
, “Serine Metabolism Supports Macrophage IL-1β Production.”, Cell Metab, vol. 29, no. 4, pp. 1003-1011.e4, 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.
, “T Cell Activation Depends on Extracellular Alanine.”, Cell Rep, vol. 28, no. 12, pp. 3011-3021.e4, 2019.
, “The Tumor Metabolic Microenvironment: Lessons from Lactate.”, Cancer Res, vol. 79, no. 13, pp. 3155-3162, 2019.
, “A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism.”, Cell Rep, vol. 27, no. 11, pp. 3359-3370.e7, 2019.
, “Voices in methods development.”, Nat Methods, vol. 16, no. 10, pp. 945-951, 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.
, “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.
, “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 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.
, “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.
, “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.”, ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
, “Enabling Precision Medicine through Integrative Network Models.”, J Mol Biol, vol. 430, no. 18 Pt A, pp. 2913-2923, 2018.
, “Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.”, Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.
, “Evolution of DNAase I hypersensitive sites in MHC regulatory regions of primates.”, Genetics, vol. 209, no. 2, pp. 579-589, 2018.
, “Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia.”, Science, vol. 361, no. 6401, pp. 511-516, 2018.
, “Four Key Steps Control Glycolytic Flux in Mammalian Cells.”, Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
, “GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.”, Nucleic Acids Research, vol. 46, no. W1, pp. W65-W70, 2018.
, “An integrative tissue-network approach to identify and test human disease genes.”, Nat Biotechnol, 2018.
, “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
, “Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”, J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
, “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.
, “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.
, “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.
, “Quantitative Analysis of NAD Synthesis-Breakdown Fluxes.”, Cell Metab, vol. 27, no. 5, pp. 1067-1080.e5, 2018.
, “Ribosomes on the night shift.”, Science, vol. 360, no. 6390, pp. 710-711, 2018.
, “Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.”, Oncoimmunology, vol. 7, no. 11, p. e1457598, 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.
, “Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.”, PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
, “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
, “An unexpected trigger for calorie burning in brown fat.”, Nature, vol. 560, no. 7716, pp. 38-39, 2018.
, “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
, “Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.”, Curr Pharm Des, 2017.
, “Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate.”, Nat Chem Biol, vol. 13, no. 10, pp. 1081-1087, 2017.
, “Chemical Basis for Deuterium Labeling of Fat and NADPH.”, J Am Chem Soc, vol. 139, no. 41, pp. 14368-14371, 2017.
, “Conserved regulators of cognitive aging: From worms to humans.”, Behav Brain Res, vol. 322, no. Pt B, pp. 299-310, 2017.
, “Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.”, Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
, “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.
, “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
, “Domain prediction with probabilistic directional context.”, Bioinformatics, vol. 33, no. 16, pp. 2471-2478, 2017.
, “Dynamic Control of dNTP Synthesis in Early Embryos.”, Dev Cell, vol. 42, no. 3, pp. 301-308.e3, 2017.
, “The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane.”, PLoS One, vol. 12, no. 10, p. e0185810, 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.
, “Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors.”, Antioxid Redox Signal, 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.
, “Force generation by groups of migrating bacteria.”, Proc Natl Acad Sci U S A, vol. 114, no. 28, pp. 7266-7271, 2017.
, “Glucose feeds the TCA cycle via circulating lactate.”, Nature, vol. 551, no. 7678, pp. 115-118, 2017.
, “Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma.”, Proc Natl Acad Sci U S A, vol. 114, no. 43, pp. 11404-11409, 2017.
, “IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.”, Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
, “Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle.”, Mol Cell Endocrinol, 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.
, “Introduction to Optical Tweezers.”, Methods Mol Biol, vol. 1486, pp. 3-24, 2017.
, “Late gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR.”, Am J Physiol Regul Integr Comp Physiol, p. ajpregu.00549.2016, 2017.
, “An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate.”, Anal Bioanal Chem, 2017.
, “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.
, “Network-Based Coverage of Mutational Profiles Reveals Cancer Genes.”, Cell Syst, vol. 5, no. 3, pp. 221-229.e4, 2017.
, “PDK4 Inhibits Cardiac Pyruvate Oxidation in Late Pregnancy.”, Circ Res, 2017.
, “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
, “Rapid Rates of Pol II Elongation in the Drosophila Embryo.”, Curr Biol, vol. 27, no. 9, pp. 1387-1391, 2017.
, “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.
, “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
, “Transcriptional Pre-patterning of Drosophila Gastrulation.”, Curr Biol, vol. 27, no. 2, pp. 286-290, 2017.
, “Transvection.”, Curr Biol, vol. 27, no. 19, pp. R1047-R1049, 2017.
, “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.
, “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 2-oxoglutarate analog 3-oxoglutarate decreases normoxic hypoxia-inducible factor-1α in cancer cells, induces cell death, and reduces tumor xenograft growth.”, Hypoxia (Auckl), vol. 4, pp. 15-27, 2016.
, “Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells.”, Genes Dev, vol. 30, no. 15, pp. 1704-17, 2016.
, “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.
, “Biophysical Measurements of Bacterial Cell Shape.”, Methods Mol Biol, vol. 1440, pp. 227-45, 2016.
, “A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance.”, Nat Med, vol. 22, no. 4, pp. 421-6, 2016.
, “The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators.”, Nature, vol. 529, no. 7584, pp. 92-6, 2016.
, “Direct Hepatocyte Insulin Signaling Is Required for Lipogenesis but Is Dispensable for the Suppression of Glucose Production.”, Cell Metab, 2016.
, “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
, “Enhancer Control of Transcriptional Bursting.”, Cell, vol. 166, no. 2, pp. 358-68, 2016.
, “Feeding the germline.”, Genes Dev, vol. 30, no. 3, pp. 249-50, 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.
, “Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.”, J Vis Exp, no. 110, p. e54239 |, 2016.
, “GIANT API: an application programming interface for functional genomics.”, Nucleic Acids Res, 2016.
, “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
, “Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP.”, Sci Rep, vol. 6, p. 24834, 2016.
, “Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis.”, ACS Chem Biol, 2016.
, “Loss of NAD Homeostasis Leads to Progressive and Reversible Degeneration of Skeletal Muscle.”, Cell Metab, vol. 24, no. 2, pp. 269-82, 2016.
, “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.
, “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.
, “One-Carbon Metabolism in Health and Disease.”, Cell Metab, 2016.
, “Partners in the Warburg effect.”, Elife, vol. 5, 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.
, “Predictability and hierarchy in Drosophila behavior.”, Proc Natl Acad Sci U S A, vol. 113, no. 42, pp. 11943-11948, 2016.
, “Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states.”, Nat Commun, vol. 7, p. 10528, 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.
, “Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway.”, Cell Metab, 2016.
, “Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo.”, Curr Biol, vol. 26, no. 9, pp. 1164-9, 2016.
, “Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.”, Proc Natl Acad Sci U S A, vol. 113, no. 23, pp. 6508-13, 2016.
, “Systems-level analysis of mechanisms regulating yeast metabolic flux.”, Science, vol. 354, no. 6311, 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.
, “Transcriptional Memory in the Drosophila Embryo.”, Curr Biol, vol. 26, no. 2, pp. 212-8, 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.
, “Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics.”, Anal Chem, vol. 87, no. 4, pp. 2273-81, 2015.
, “Behavioral idiosyncrasy reveals genetic control of phenotypic variability.”, Proc Natl Acad Sci U S A, vol. 112, no. 21, pp. 6706-11, 2015.
, “Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.”, PLoS Comput Biol, vol. 11, no. 11, p. e1004509, 2015.
, “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.
, “Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter.”, Proc Natl Acad Sci U S A, 2015.
, “Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity.”, Nature, vol. 519, no. 7541, pp. 97-101, 2015.
, “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.
, “Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate.”, Dev Biol, 2015.
, “ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System.”, Mol Cell, vol. 57, no. 2, pp. 341-8, 2015.
, “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
, “Fatty acid elongase 7 catalyzes lipidome remodeling essential for human cytomegalovirus replication.”, Cell Rep, vol. 10, no. 8, pp. 1375-85, 2015.
, “FNTM: a server for predicting functional networks of tissues in mouse.”, Nucleic Acids Res, 2015.
, “For longevity, perception is everything.”, Cell, vol. 160, no. 5, pp. 807-9, 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 Detection and Analysis of Multifunctional Genes.”, PLoS Comput Biol, vol. 11, no. 10, p. e1004467, 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.
, “Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein.”, Cancer Res, vol. 75, no. 3, pp. 544-53, 2015.
, “IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.”, Nucleic Acids Res, 2015.
, “Implications of Big Data for cell biology.”, Mol Biol Cell, vol. 26, no. 14, pp. 2575-8, 2015.
, “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.”, ISME J, vol. 9, no. 1, pp. 68-80, 2015.
, “Low-variance RNAs identify Parkinson's disease molecular signature in blood.”, Mov Disord, vol. 30, no. 6, pp. 813-21, 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.
, “Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation.”, Cell Metab, vol. 22, no. 6, pp. 1068-77, 2015.
, “Pervasive variation of transcription factor orthologs contributes to regulatory network evolution.”, PLoS Genet, vol. 11, no. 3, p. e1005011, 2015.
, “Positional information, positional error, and readout precision in morphogenesis: a mathematical framework.”, Genetics, vol. 199, no. 1, pp. 39-59, 2015.
, “Predicting effects of noncoding variants with deep learning-based sequence model.”, Nat Methods, 2015.
, “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
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