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
“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.
, “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.
, “Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons.”, Mol Psychiatry, 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.
, “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.
, “Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity.”, Nat Immunol, vol. 20, no. 8, pp. 1023-1034, 2019.
, “Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity.”, Nat Immunol, vol. 20, no. 8, pp. 1023-1034, 2019.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 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.
, “Autophagy maintains tumour growth through circulating arginine.”, Nature, vol. 563, no. 7732, pp. 569-573, 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.
, “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.
, “An integrative tissue-network approach to identify and test human disease genes.”, Nat Biotechnol, 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.
, “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
, “Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.”, PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
, “IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.”, Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
, “PDK4 Inhibits Cardiac Pyruvate Oxidation in Late Pregnancy.”, Circ Res, 2017.
, “Transcriptional Pre-patterning of Drosophila Gastrulation.”, Curr Biol, vol. 27, no. 2, pp. 286-290, 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.
, “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.
, “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
, , “FNTM: a server for predicting functional networks of tissues in mouse.”, Nucleic Acids Res, 2015.
, “IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.”, Nucleic Acids Res, 2015.
, “Low-variance RNAs identify Parkinson's disease molecular signature in blood.”, Mov Disord, vol. 30, no. 6, pp. 813-21, 2015.
, “A roadmap for interpreting (13)C metabolite labeling patterns from cells.”, Curr Opin Biotechnol, vol. 34, pp. 189-201, 2015.
, “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
, “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
, “Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function.”, Cancer Res, vol. 75, no. 16, pp. 3355-64, 2015.
, “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.
, “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
, “Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia.”, Cancer Discov, vol. 4, no. 12, pp. 1406-17, 2014.
, “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
, “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
, “Nucleotide degradation and ribose salvage in yeast.”, Mol Syst Biol, vol. 9, p. 665, 2013.
, “Pyrimidine homeostasis is accomplished by directed overflow metabolism.”, Nature, vol. 500, no. 7461, pp. 237-41, 2013.
, “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
, “Nucleosome-coupled expression differences in closely-related species.”, BMC Genomics, vol. 12, p. 466, 2011.
, “Pattern formation by a moving morphogen source.”, Phys Biol, vol. 8, no. 4, p. 045003, 2011.
, “Riboneogenesis in yeast.”, Cell, vol. 145, no. 6, pp. 969-80, 2011.
, “Achieving optimal growth through product feedback inhibition in metabolism.”, PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
, “Early chordate origins of the vertebrate second heart field.”, Science, vol. 329, no. 5991, pp. 565-8, 2010.
, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
, “Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation.”, Mol Syst Biol, vol. 5, p. 278, 2009.
, “Detailing regulatory networks through large scale data integration.”, Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
, “Expression patterns of cadherin genes in Drosophila oogenesis.”, Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
, “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
, “Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.”, Phys Rev Lett, vol. 103, no. 24, p. 248102, 2009.
, “A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.”, Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
, “Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma.”, PLoS One, vol. 4, no. 1, p. e4216, 2009.
, “Pattern formation by dynamically interacting network motifs.”, Proc Natl Acad Sci U S A, vol. 106, no. 9, pp. 3213-8, 2009.
, “Steps in the bacterial flagellar motor.”, PLoS Comput Biol, vol. 5, no. 10, p. e1000540, 2009.
, “Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach.”, Nat Protoc, vol. 3, no. 8, pp. 1299-311, 2008.
, “Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis.”, Dev Biol, vol. 322, no. 2, pp. 289-301, 2008.
, “A combinatorial code for pattern formation in Drosophila oogenesis.”, Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
, “Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.”, Development, vol. 135, no. 2, pp. 343-51, 2008.
, “Kinetic flux profiling for quantitation of cellular metabolic fluxes.”, Nat Protoc, vol. 3, no. 8, pp. 1328-40, 2008.
, “Spatial regulation of BMP signaling by patterned receptor expression.”, Tissue Eng Part A, vol. 14, no. 9, pp. 1469-77, 2008.
, “Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition.”, J Am Chem Soc, vol. 129, no. 30, pp. 9294-5, 2007.
, “Conservation of the metabolomic response to starvation across two divergent microbes.”, Proc Natl Acad Sci U S A, vol. 103, no. 51, pp. 19302-7, 2006.
, “Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway.”, Dev Cell, vol. 10, no. 2, pp. 257-64, 2006.
, “Kinetic flux profiling of nitrogen assimilation in Escherichia coli.”, Nat Chem Biol, vol. 2, no. 10, pp. 529-30, 2006.
, “Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis.”, Genesis, vol. 44, no. 2, pp. 66-74, 2006.
, “Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry.”, J Chromatogr A, vol. 1125, no. 1, pp. 76-88, 2006.
, “A regulatory code for neurogenic gene expression in the Drosophila embryo.”, Development, vol. 131, no. 10, pp. 2387-94, 2004.
, “Variation in gene expression patterns in human gastric cancers.”, Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
, “Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 34, pp. 31079-88, 2002.
, “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.
, “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
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