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
Filters: Keyword is Mice [Clear All Filters]
“The absence of enhancer competition between Igf2 and H19 following transfer into differentiated cells.”, Mol Cell Biol, vol. 18, no. 4, pp. 1903-10, 1998.
, “Allele-specific gene expression in mammals: the curious case of the imprinted RNAs.”, Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
, “Autophagy maintains tumour growth through circulating arginine.”, Nature, vol. 563, no. 7732, pp. 569-573, 2018.
, “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.
, “Chromatin conformation of the H19 epigenetic mark.”, Hum Mol Genet, vol. 7, no. 12, pp. 1979-85, 1998.
, “Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis.”, Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
, “Complementation mapping of skeletal and central nervous system abnormalities in mice of the piebald deletion complex.”, Genetics, vol. 143, no. 1, pp. 447-61, 1996.
, “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
, “Configuration of the alpha-fetoprotein regulatory domain during development.”, Genes Dev, vol. 2, no. 8, pp. 949-56, 1988.
, “Coordinate regulation of an extended chromosome domain.”, Cell, vol. 113, no. 3, pp. 278-80, 2003.
, “A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.”, Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
, “CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus.”, Nature, vol. 405, no. 6785, pp. 486-9, 2000.
, “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.
, “Defining cell-type specificity at the transcriptional level in human disease.”, Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
, “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.
, “Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes.”, Cell, vol. 174, no. 4, pp. 831-842.e12, 2018.
, “A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer.”, Hum Mol Genet, vol. 12, no. 3, pp. 283-94, 2003.
, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
, “Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice.”, Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
, “Disruption of imprinting caused by deletion of the H19 gene region in mice.”, Nature, vol. 375, no. 6526, pp. 34-9, 1995.
, “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
, “Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.”, Nature, vol. 571, no. 7765, pp. 403-407, 2019.
, “DNA methylation: a phoenix rises.”, Proc Natl Acad Sci U S A, vol. 90, no. 19, pp. 8761-2, 1993.
, “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
, “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
, “Ectopic expression of the H19 gene in mice causes prenatal lethality.”, Genes Dev, vol. 5, no. 6, pp. 1092-101, 1991.
, “Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes.”, Genes Dev, vol. 20, no. 10, pp. 1268-82, 2006.
, “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
, “Enhancer competition between H19 and Igf2 does not mediate their imprinting.”, Proc Natl Acad Sci U S A, vol. 96, no. 17, pp. 9733-8, 1999.
, “An enhancer deletion affects both H19 and Igf2 expression.”, Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
, “Epigenetic mechanisms underlying the imprinting of the mouse H19 gene.”, Genes Dev, vol. 7, no. 9, pp. 1663-73, 1993.
, “Expression and functional analysis of Uch-L3 during mouse development.”, Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
, “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.
, “Fine structure mapping and deletion analysis of the murine piebald locus.”, Genetics, vol. 136, no. 1, pp. 217-23, 1994.
, “Fine-structure mapping of the three mouse alpha-fetoprotein gene enhancers.”, Mol Cell Biol, vol. 8, no. 3, pp. 1169-78, 1988.
, “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.
, “Functional characterization of a testis-specific DNA binding activity at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 23, no. 22, pp. 8345-51, 2003.
, “Functional genomics complements quantitative genetics in identifying disease-gene associations.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
, “Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.”, PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
, “Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.”, Mol Cell, vol. 55, no. 6, pp. 916-30, 2014.
, “Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta.”, Proc Natl Acad Sci U S A, vol. 100, no. 8, pp. 4622-7, 2003.
, “Genetic map of the fused locus on mouse chromosome 17.”, Genomics, vol. 23, no. 1, pp. 178-84, 1994.
, “A genomewide functional network for the laboratory mouse.”, PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
, “Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts.”, Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
, “Genomic imprinting in mice: its function and mechanism.”, Biol Reprod, vol. 54, no. 2, pp. 273-8, 1996.
, “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
, “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.
, “Host-parasite interactions revealed by Plasmodium falciparum metabolomics.”, Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
, “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.
, “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.
, “Identification of alterations in DNA copy number in host stromal cells during tumor progression.”, Proc Natl Acad Sci U S A, vol. 103, no. 52, pp. 19848-53, 2006.
, “IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.”, Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
, “Igf2 imprinting does not require its own DNA methylation or H19 RNA.”, Genes Dev, vol. 12, no. 14, pp. 2200-7, 1998.
, “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.
, “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
, “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.
, “Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”, J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
, “Lessons learned, promises kept: a biologist's eye view of the Genome Project.”, Genome Res, vol. 6, no. 9, pp. 773-80, 1996.
, “Linkage between vitamin D-binding protein and alpha-fetoprotein in the mouse.”, Mamm Genome, vol. 7, no. 2, pp. 103-6, 1996.
, “Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism.”, Anal Chem, vol. 83, no. 23, pp. 9114-22, 2011.
, “Location of enhancers is essential for the imprinting of H19 and Igf2 genes.”, Nature, vol. 391, no. 6668, pp. 711-5, 1998.
, “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.
, “Macrophage de novo NAD synthesis specifies immune function in aging and inflammation.”, Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
, “Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.”, PLoS Comput Biol, vol. 6, no. 12, p. e1001034, 2010.
, “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
, “A method for detecting and correcting feature misidentification on expression microarrays.”, BMC Genomics, vol. 5, p. 64, 2004.
, “Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene.”, Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
, “Molecular characterization of four induced alleles at the Ednrb locus.”, Proc Natl Acad Sci U S A, vol. 94, no. 24, pp. 13105-10, 1997.
, “A mouse genomic library of yeast artificial chromosome clones.”, Mamm Genome, vol. 1, no. 1, p. 65, 1991.
, “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.
, “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
, “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.
, “Nicotinamide adenine dinucleotide is transported into mammalian mitochondria.”, Elife, vol. 7, 2018.
, “A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”, Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
, “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
, “Oppositely imprinted genes p57(Kip2) and igf2 interact in a mouse model for Beckwith-Wiedemann syndrome.”, Genes Dev, vol. 13, no. 23, pp. 3115-24, 1999.
, “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
, “Parental imprinting in the mouse.”, Harvey Lect, vol. 87, pp. 69-84, 1991.
, “Parental imprinting of the H19 and Igf2 genes in the mouse.”, Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
, “Parental imprinting of the mouse H19 gene.”, Nature, vol. 351, no. 6322, pp. 153-5, 1991.
, “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.
, “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
, “Physical linkage of two mammalian imprinted genes, H19 and insulin-like growth factor 2.”, Nat Genet, vol. 2, no. 1, pp. 61-5, 1992.
, “Piebald lethal (sl) acts early to disrupt the development of neural crest-derived melanocytes.”, Proc Natl Acad Sci U S A, vol. 91, no. 15, pp. 7159-63, 1994.
, “PILGRM: an interactive data-driven discovery platform for expert biologists.”, Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
, “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
, “Predicting gene function in a hierarchical context with an ensemble of classifiers.”, Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
, “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
, “Quantitative trait loci that modify the severity of spotting in piebald mice.”, Genome Res, vol. 5, no. 1, pp. 29-41, 1995.
, “raf regulates the postnatal repression of the mouse alpha-fetoprotein gene at the posttranscriptional level.”, Mol Cell Biol, vol. 12, no. 2, pp. 856-64, 1992.
, “Role of alpha-fetoprotein regulatory elements in transcriptional activation in transient heterokaryons.”, Mol Cell Biol, vol. 10, no. 10, pp. 5047-54, 1990.
, “The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.”, Mol Biol Cell, vol. 15, no. 3, pp. 1254-61, 2004.
, “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
, “SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”, Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
, “The structural H19 gene is required for transgene imprinting.”, Proc Natl Acad Sci U S A, vol. 93, no. 24, pp. 13876-83, 1996.
, “The structure and expression of a novel gene activated in early mouse embryogenesis.”, EMBO J, vol. 7, no. 3, pp. 673-81, 1988.
, “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
, “Systems-level dynamic analyses of fate change in murine embryonic stem cells.”, Nature, vol. 462, no. 7271, pp. 358-62, 2009.
, “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
, “The temporal requirement for endothelin receptor-B signalling during neural crest development.”, Nature, vol. 402, no. 6761, pp. 496-501, 1999.
, “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
, “Tissue-specific transcription of the mouse alpha-fetoprotein gene promoter is dependent on HNF-1.”, Mol Cell Biol, vol. 9, no. 10, pp. 4204-12, 1989.
, “Two dominant mutations in the mouse fused gene are the result of transposon insertions.”, Genetics, vol. 147, no. 2, pp. 777-86, 1997.
, “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
, “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
, “The vertebrate adhesive junction proteins beta-catenin and plakoglobin and the Drosophila segment polarity gene armadillo form a multigene family with similar properties.”, J Cell Biol, vol. 118, no. 3, pp. 681-91, 1992.
, “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
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