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
“Local moment formation in quantum point contacts.”, Phys Rev Lett, vol. 90, no. 2, p. 026804, 2003.
, “Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.”, Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
, “A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.”, Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
, “How the Dorsal gradient works: insights from postgenome technologies.”, Proc Natl Acad Sci U S A, vol. 105, no. 51, pp. 20072-6, 2008.
, “Gene Ontology annotations at SGD: new data sources and annotation methods.”, Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.
, “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
, “Shadow enhancers as a source of evolutionary novelty.”, Science, vol. 321, no. 5894, p. 1314, 2008.
, “Precise domain specification in the developing Drosophila embryo.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 72, no. 6 Pt 1, p. 061920, 2005.
, “Establishment of developmental precision and proportions in the early Drosophila embryo.”, Nature, vol. 415, no. 6873, pp. 798-802, 2002.
, “Network-Based Coverage of Mutational Profiles Reveals Cancer Genes.”, Cell Syst, vol. 5, no. 3, pp. 221-229.e4, 2017.
, “Regulation of aging and age-related disease by DAF-16 and heat-shock factor.”, Science, vol. 300, no. 5622, pp. 1142-5, 2003.
, “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.
, “Min-protein oscillations in round bacteria.”, Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
, “A curvature-mediated mechanism for localization of lipids to bacterial poles.”, PLoS Comput Biol, vol. 2, no. 11, p. e151, 2006.
, “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
, “Cell shape and cell-wall organization in Gram-negative bacteria.”, Proc Natl Acad Sci U S A, vol. 105, no. 49, pp. 19282-7, 2008.
, “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
, “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
, “Structurama: bayesian inference of population structure.”, Evol Bioinform Online, vol. 7, pp. 55-9, 2011.
, “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
, “Segregating variation in the transcriptome: cis regulation and additivity of effects.”, Genetics, vol. 173, no. 3, pp. 1347-55, 2006.
, “An unexpected trigger for calorie burning in brown fat.”, Nature, vol. 560, no. 7716, pp. 38-39, 2018.
, “Glucose feeds the TCA cycle via circulating lactate.”, Nature, vol. 551, no. 7678, pp. 115-118, 2017.
, “Conserved domains of the Nullo protein required for cell-surface localization and formation of adherens junctions.”, Mol Biol Cell, vol. 13, no. 1, pp. 146-57, 2002.
, “Regulated expression of nullo is required for the formation of distinct apical and basal adherens junctions in the Drosophila blastoderm.”, J Cell Biol, vol. 150, no. 2, pp. 391-401, 2000.
, “Assessing the functional structure of genomic data.”, Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
, “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
, “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
, “The Sleipnir library for computational functional genomics.”, Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
, “A scalable method for integration and functional analysis of multiple microarray datasets.”, Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
, “Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.”, Methods Mol Biol, vol. 548, pp. 273-93, 2009.
, “The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.”, Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
, “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
, “Detailing regulatory networks through large scale data integration.”, Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
, “Graphle: Interactive exploration of large, dense graphs.”, BMC Bioinformatics, vol. 10, p. 417, 2009.
, “Estrogen-related receptor α is required for efficient human cytomegalovirus replication.”, Proc Natl Acad Sci U S A, vol. 111, no. 52, pp. E5706-15, 2014.
, “fringe, a Boundary-specific signaling molecule, mediates interactions between dorsal and ventral cells during Drosophila wing development.”, Cell, vol. 79, no. 4, pp. 595-606, 1994.
, “Cell intercalation during Drosophila germband extension and its regulation by pair-rule segmentation genes.”, Development, vol. 120, no. 4, pp. 827-41, 1994.
, “Saccharomyces Genome Database.”, Methods Enzymol, vol. 350, pp. 329-46, 2002.
, “Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.”, Oncoimmunology, vol. 7, no. 11, p. e1457598, 2018.
, “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
, “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.
, “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
, “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 Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation.”, Cell, vol. 96, no. 4, pp. 563-73, 1999.
, “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
, “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
, “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
, “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “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.
, “Evolution of DNAase I hypersensitive sites in MHC regulatory regions of primates.”, Genetics, vol. 209, no. 2, pp. 579-589, 2018.
, “A human H19 transgene exhibits impaired paternal-specific imprint acquisition and maintenance in mice.”, Hum Mol Genet, vol. 11, no. 4, pp. 411-8, 2002.
, “Igf2 imprinting does not require its own DNA methylation or H19 RNA.”, Genes Dev, vol. 12, no. 14, pp. 2200-7, 1998.
, “Deletion of a nuclease-sensitive region between the Igf2 and H19 genes leads to Igf2 misregulation and increased adiposity.”, Hum Mol Genet, vol. 10, no. 8, pp. 807-14, 2001.
, “Defining cell-type specificity at the transcriptional level in human disease.”, Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
, “Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster.”, BMC Genomics, vol. 11, p. 297, 2010.
, “The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators.”, Nature, vol. 529, no. 7584, pp. 92-6, 2016.
, “Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.”, PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
, “The role of insulin/IGF-like signaling in C. elegans longevity and aging.”, Dis Model Mech, vol. 3, no. 7-8, pp. 415-9, 2010.
, “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.
, “Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein.”, Cancer Res, vol. 75, no. 3, pp. 544-53, 2015.
, “Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate.”, Cancer Metab, vol. 2, p. 23, 2014.
, “Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism.”, Anal Chem, vol. 83, no. 23, pp. 9114-22, 2011.
, “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
, “Pattern formation by graded and uniform signals in the early Drosophila embryo.”, Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
, “Dynamics of the Dorsal morphogen gradient.”, Proc Natl Acad Sci U S A, vol. 106, no. 51, pp. 21707-12, 2009.
, “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
, “Autophagy is required for glucose homeostasis and lung tumor maintenance.”, Cancer Discov, vol. 4, no. 8, pp. 914-27, 2014.
, “Diels-Alder reactivity of binuclear complexes with calixarene-like structures.”, Angew Chem Int Ed Engl, vol. 45, no. 1, pp. 101-4, 2005.
, “Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 25, no. 10, pp. 3855-63, 2005.
, “Insulin signaling and dietary restriction differentially influence the decline of learning and memory with age.”, PLoS Biol, vol. 8, no. 5, p. e1000372, 2010.
, “A compartmental model for the bicoid gradient.”, Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
, “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
, “Enrichment of regulatory motifs upstream of predicted DAF-16 targets.”, Nat Genet, vol. 38, no. 4, pp. 397-8; author reply 398, 2006.
, “Chemosensing in Escherichia coli: two regimes of two-state receptors.”, Proc Natl Acad Sci U S A, vol. 103, no. 6, pp. 1786-91, 2006.
, “Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis.”, Dev Biol, vol. 246, no. 2, pp. 329-40, 2002.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.”, Development, vol. 141, no. 14, pp. 2895-900, 2014.
, “A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.”, Bioinformatics, vol. 25, no. 13, pp. 1609-16, 2009.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism.”, Phys Biol, vol. 7, no. 1, p. 016006, 2010.
, “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.
, “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 2013.
, “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
, “MAPK substrate competition integrates patterning signals in the Drosophila embryo.”, Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
, “Gene regulation by MAPK substrate competition.”, Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
, “Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death.”, Genome Med, vol. 6, no. 5, p. 40, 2014.
, “Identifying decomposition products in extracts of cellular metabolites.”, Anal Biochem, vol. 358, no. 2, pp. 273-80, 2006.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
, “An unsupervised method for quantifying the behavior of paired animals.”, Phys Biol, vol. 14, no. 1, p. 015006, 2017.
, “Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.”, Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
, “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
, “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.
, “Introduction to Optical Tweezers.”, Methods Mol Biol, vol. 1486, pp. 3-24, 2017.
, “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.
, “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
, “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.
, “Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny.”, PLoS Pathog, vol. 9, no. 5, p. e1003333, 2013.
, “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
, “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.
, “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
, “Expression and functional analysis of Uch-L3 during mouse development.”, Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
, “Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22.”, Genomics, vol. 79, no. 2, pp. 154-61, 2002.
, “Loss of Uch-L1 and Uch-L3 leads to neurodegeneration, posterior paralysis and dysphagia.”, Hum Mol Genet, vol. 10, no. 18, pp. 1963-70, 2001.
, “Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli.”, ACS Chem Biol, vol. 5, no. 8, pp. 787-95, 2010.
, “A domino effect in antifolate drug action in Escherichia coli.”, Nat Chem Biol, vol. 4, no. 10, pp. 602-8, 2008.
, “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
, “Mechanisms of transcriptional precision in animal development.”, Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
, “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.
, “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.
, “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.
, “Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”, J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
, “Integration of diverse inputs in the regulation of Caenorhabditis elegans DAF-16/FOXO.”, Dev Dyn, vol. 239, no. 5, pp. 1405-12, 2010.
, “Genetic variation and the fate of beneficial mutations in asexual populations.”, Genetics, vol. 188, no. 3, pp. 647-61, 2011.
, “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
, “A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.”, PLoS One, vol. 6, no. 9, p. e25290, 2011.
, “Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.”, Nature, vol. 500, no. 7464, pp. 571-4, 2013.
, “The cost of gene expression underlies a fitness trade-off in yeast.”, Proc Natl Acad Sci U S A, vol. 106, no. 14, pp. 5755-60, 2009.
, “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
, “slam encodes a developmental regulator of polarized membrane growth during cleavage of the Drosophila embryo.”, Dev Cell, vol. 2, no. 4, pp. 425-36, 2002.
, “Junctions as organizing centers in epithelial cells? A fly perspective.”, Traffic, vol. 3, no. 2, pp. 92-7, 2002.
, “Polarized insertion of new membrane from a cytoplasmic reservoir during cleavage of the Drosophila embryo.”, J Cell Biol, vol. 150, no. 4, pp. 849-60, 2000.
, “Glucose shortens the life span of C. elegans by downregulating DAF-16/FOXO activity and aquaporin gene expression.”, Cell Metab, vol. 10, no. 5, pp. 379-91, 2009.
, “Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies.”, Bioinformatics, vol. 29, no. 23, pp. 3036-44, 2013.
, “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
, “A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.”, Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
, “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
, “An enhancer deletion affects both H19 and Igf2 expression.”, Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
, “Genomic imprinting in mice: its function and mechanism.”, Biol Reprod, vol. 54, no. 2, pp. 273-8, 1996.
, “Disruption of imprinting caused by deletion of the H19 gene region in mice.”, Nature, vol. 375, no. 6526, pp. 34-9, 1995.
, “Pattern formation by dynamically interacting network motifs.”, Proc Natl Acad Sci U S A, vol. 106, no. 9, pp. 3213-8, 2009.
, “Spatial regulation of BMP signaling by patterned receptor expression.”, Tissue Eng Part A, vol. 14, no. 9, pp. 1469-77, 2008.
, “Quiescent fibroblasts exhibit high metabolic activity.”, PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
, “The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.”, Cell, vol. 118, no. 1, pp. 69-82, 2004.
, “Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16203-8, 2002.
, “Microfluidic trap array for massively parallel imaging of Drosophila embryos.”, Nat Protoc, vol. 8, no. 4, pp. 721-36, 2013.
, “The contraction of time and space in remote chromosomal interactions.”, Cell, vol. 158, no. 2, pp. 243-4, 2014.
, “Retrospective. Walter Gehring (1939-2014).”, Science, vol. 345, no. 6194, p. 277, 2014.
, “Paused RNA polymerase II as a developmental checkpoint.”, Cell, vol. 145, no. 4, pp. 502-11, 2011.
, “Gene regulatory networks for development.”, Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4936-42, 2005.
, “Computing away the magic?”, Elife, vol. 2, p. e01135, 2013.
, “Looping back to leap forward: transcription enters a new era.”, Cell, vol. 157, no. 1, pp. 13-25, 2014.
, “Transcription regulation and animal diversity.”, Nature, vol. 424, no. 6945, pp. 147-51, 2003.
, “Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water.”, Proc Natl Acad Sci U S A, vol. 104, no. 8, pp. 2626-30, 2007.
, “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.
, “A microfluidic device and automatic counting system for the study of C. elegans reproductive aging.”, Lab Chip, 2014.
, “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.
, “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
, “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.
, “Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.”, Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.
, “Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”, Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
, “Kinetics of gene derepression by ERK signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
, “Transcriptional Pre-patterning of Drosophila Gastrulation.”, Curr Biol, vol. 27, no. 2, pp. 286-290, 2017.
, “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
, “Sorting sloppy Sonic.”, Cell, vol. 153, no. 3, pp. 509-10, 2013.
, “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA.”, PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
, “Precise developmental gene expression arises from globally stochastic transcriptional activity.”, Cell, vol. 154, no. 4, pp. 789-800, 2013.
, “Shifting patterns: merging molecules, morphogens, motility, and methodology.”, Dev Cell, vol. 21, no. 1, pp. 2-4, 2011.
, “Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress.”, Proc Natl Acad Sci U S A, vol. 108, no. 31, pp. 12869-74, 2011.
, “PDK4 Inhibits Cardiac Pyruvate Oxidation in Late Pregnancy.”, Circ Res, 2017.
, “Substrate-dependent control of ERK phosphorylation can lead to oscillations.”, Biophys J, vol. 101, no. 11, pp. 2572-81, 2011.
, “The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane.”, PLoS One, vol. 12, no. 10, p. e0185810, 2017.
, “Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity.”, Nat Immunol, vol. 20, no. 8, pp. 1023-1034, 2019.
, “EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan.”, EMBO J, vol. 30, no. 15, pp. 2990-3003, 2011.
, “Quantitative Analysis of NAD Synthesis-Breakdown Fluxes.”, Cell Metab, vol. 27, no. 5, pp. 1067-1080.e5, 2018.
, “Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage.”, Nat Chem Biol, vol. 12, no. 5, pp. 345-52, 2016.
, “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.
, “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
, “Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.”, N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
, “Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”, Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
, “Slow growth induces heat-shock resistance in normal and respiratory-deficient yeast.”, Mol Biol Cell, vol. 20, no. 3, pp. 891-903, 2009.
, “Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition.”, Development, vol. 136, no. 12, pp. 2101-10, 2009.
, “Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer.”, Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
, “Analytical strategies for LC-MS-based targeted metabolomics.”, J Chromatogr B Analyt Technol Biomed Life Sci, vol. 871, no. 2, pp. 236-42, 2008.
, “Isotope ratio-based profiling of microbial folates.”, J Am Soc Mass Spectrom, vol. 18, no. 5, pp. 898-909, 2007.
, “Systems-level dynamic analyses of fate change in murine embryonic stem cells.”, Nature, vol. 462, no. 7271, pp. 358-62, 2009.
, “Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors.”, Antioxid Redox Signal, 2017.
, “A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites.”, J Am Soc Mass Spectrom, vol. 17, no. 1, pp. 37-50, 2006.
, “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
, “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.
, “TGF-β and insulin signaling regulate reproductive aging via oocyte and germline quality maintenance.”, Cell, vol. 143, no. 2, pp. 299-312, 2010.
, “TGF-beta Sma/Mab signaling mutations uncouple reproductive aging from somatic aging.”, PLoS Genet, vol. 5, no. 12, p. e1000789, 2009.
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