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
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“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.
, “DNA methylation: a phoenix rises.”, Proc Natl Acad Sci U S A, vol. 90, no. 19, pp. 8761-2, 1993.
, “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
, “Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis.”, Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
, “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
, “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.
, “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.
, “Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli.”, Mol Syst Biol, vol. 6, p. 378, 2010.
, “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
, “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
, “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
, “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
, “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
, “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
, “A nuclear escort for beta-catenin.”, Nat Cell Biol, vol. 6, no. 7, pp. 579-80, 2004.
, “Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli.”, Mol Syst Biol, vol. 6, p. 378, 2010.
, “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
, “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
, “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 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.
, “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
, “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Diversity of gene expression in adenocarcinoma of the lung.”, Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “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.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Diverse and specific gene expression responses to stresses in cultured human cells.”, Mol Biol Cell, vol. 15, no. 5, pp. 2361-74, 2004.
, “Variation in gene expression patterns in human gastric cancers.”, Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Diversity of gene expression in adenocarcinoma of the lung.”, Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
, “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.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
, “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.
, “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
, “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
, “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
, “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.
, “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
, “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
, “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
, “The long walk to African genomics.”, Genome Biol, vol. 20, no. 1, p. 130, 2019.
, “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
, “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.
, “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
, “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
, “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
, “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
, “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
, “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
, “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
, “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.
, “Finding function: evaluation methods for functional genomic data.”, BMC Genomics, vol. 7, p. 187, 2006.
, “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “An effective statistical evaluation of ChIPseq dataset similarity.”, Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 2003.
, “A scalable method for integration and functional analysis of multiple microarray datasets.”, Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
, “Tools and applications for large-scale display walls.”, IEEE Comput Graph Appl, vol. 25, no. 4, pp. 24-33, 2005.
, “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.”, PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
, “Context-sensitive data integration and prediction of biological networks.”, Bioinformatics, vol. 23, no. 17, pp. 2322-30, 2007.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “Functional genomics complements quantitative genetics in identifying disease-gene associations.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
, “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.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
, “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
, “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
, “Nested effects models for high-dimensional phenotyping screens.”, Bioinformatics, vol. 23, no. 13, pp. i305-12, 2007.
, “Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.”, PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “Accurate evaluation and analysis of functional genomics data and methods.”, Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
, “Detailing regulatory networks through large scale data integration.”, Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
, “Visualization-based discovery and analysis of genomic aberrations in microarray data.”, BMC Bioinformatics, vol. 6, p. 146, 2005.
, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
, “The Sleipnir library for computational functional genomics.”, Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
, “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
, “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.
, “Accurate detection of aneuploidies in array CGH and gene expression microarray data.”, Bioinformatics, vol. 20, no. 18, pp. 3533-43, 2004.
, “Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.”, Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
, “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.”, Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
, “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
, “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.
, “A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.”, Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
, “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
, “Information-based clustering.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
, “Predicting gene function in a hierarchical context with an ensemble of classifiers.”, Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
, “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”, Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
, “A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.”, Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
, “Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
, “Exploring the functional landscape of gene expression: directed search of large microarray compendia.”, Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
, “Global quantitative modeling of chromatin factor interactions.”, PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
, “Assessing the functional structure of genomic data.”, Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
, “Hierarchical multi-label prediction of gene function.”, Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
, “The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.”, Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
, “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
, “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.
, “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
, “Visualization methods for statistical analysis of microarray clusters.”, BMC Bioinformatics, vol. 6, p. 115, 2005.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
, “Epigenetic mechanisms underlying the imprinting of the mouse H19 gene.”, Genes Dev, vol. 7, no. 9, pp. 1663-73, 1993.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “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.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
, “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 of the H19 and Igf2 genes in the mouse.”, Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
, “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
, “Allele-specific gene expression in mammals: the curious case of the imprinted RNAs.”, Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
, “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
, “Location of enhancers is essential for the imprinting of H19 and Igf2 genes.”, Nature, vol. 391, no. 6668, pp. 711-5, 1998.
, “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 Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
, “Allelic expression of IGF2 in marsupials and birds.”, Dev Genes Evol, vol. 210, no. 1, pp. 18-20, 2000.
, “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.
, “Fine-structure mapping of the three mouse alpha-fetoprotein gene enhancers.”, Mol Cell Biol, vol. 8, no. 3, pp. 1169-78, 1988.
, “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
, “Role of alpha-fetoprotein regulatory elements in transcriptional activation in transient heterokaryons.”, Mol Cell Biol, vol. 10, no. 10, pp. 5047-54, 1990.
, “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
, “Configuration of the alpha-fetoprotein regulatory domain during development.”, Genes Dev, vol. 2, no. 8, pp. 949-56, 1988.
, “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
, “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.
, “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
, “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 regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
, “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
, “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
, “Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene.”, Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
, “Linkage between vitamin D-binding protein and alpha-fetoprotein in the mouse.”, Mamm Genome, vol. 7, no. 2, pp. 103-6, 1996.
, “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.
, “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
, “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.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “Emergence of highly designable protein-backbone conformations in an off-lattice model.”, Proteins, vol. 47, no. 4, pp. 506-12, 2002.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
, “Expression and functional analysis of Uch-L3 during mouse development.”, Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
, “Designability of alpha-helical proteins.”, Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
, “Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.”, Nucleic Acids Res, vol. 32, no. Database issue, pp. D311-4, 2004.
, “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
, “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
, “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
, “Emergence of highly designable protein-backbone conformations in an off-lattice model.”, Proteins, vol. 47, no. 4, pp. 506-12, 2002.
, “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
, “As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid.”, Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
, “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
, “Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
, “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.
, “Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.”, Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
, “Accurate detection of aneuploidies in array CGH and gene expression microarray data.”, Bioinformatics, vol. 20, no. 18, pp. 3533-43, 2004.
, “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
, “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
, “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
, “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.
, “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
, “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
, “Two dominant mutations in the mouse fused gene are the result of transposon insertions.”, Genetics, vol. 147, no. 2, pp. 777-86, 1997.
, “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.
, “Optimizing information flow in small genetic networks.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 3 Pt 1, p. 031920, 2009.
, “PILGRM: an interactive data-driven discovery platform for expert biologists.”, Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
, “Functional genomics complements quantitative genetics in identifying disease-gene associations.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
, “Exploring genome space.”, Nature, vol. 405, no. 6788, pp. 820-2, 2000.
, “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
, “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
, “Probing the limits to positional information.”, Cell, vol. 130, no. 1, pp. 153-64, 2007.
, “Systems-level dynamic analyses of fate change in murine embryonic stem cells.”, Nature, vol. 462, no. 7271, pp. 358-62, 2009.
, “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
, “Precise developmental gene expression arises from globally stochastic transcriptional activity.”, Cell, vol. 154, no. 4, pp. 789-800, 2013.
, “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.
, “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
, “Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.”, PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
, “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
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