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
“Accurate detection of aneuploidies in array CGH and gene expression microarray data.”, Bioinformatics, vol. 20, no. 18, pp. 3533-43, 2004.
, “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
, “Accurate quantification of functional analogy among close homologs.”, PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
, “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.
, “Challenges in developing a molecular characterization of cancer.”, Semin Oncol, vol. 29, no. 3, pp. 280-5, 2002.
, “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
, “Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles.”, PLoS Biol, vol. 9, no. 1, p. e1000584, 2011.
, “Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 3008-24, 2012.
, “Comparative gene expression between two yeast species.”, BMC Genomics, vol. 14, p. 33, 2013.
, “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
, “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
, “Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
, “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
, “Defining cell-type specificity at the transcriptional level in human disease.”, Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
, “Detailing regulatory networks through large scale data integration.”, Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
, “Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo.”, Dev Biol, vol. 330, no. 2, pp. 462-70, 2009.
, “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
, “Diffusion and scaling during early embryonic pattern formation.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
, “Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.”, Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
, “Diversity of gene expression in adenocarcinoma of the lung.”, Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
, “A DNA microarray survey of gene expression in normal human tissues.”, Genome Biol, vol. 6, no. 3, p. R22, 2005.
, “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
, “Electroporation of transgenic DNAs in the sea squirt Ciona.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5345, 2009.
, “Endothelial cell diversity revealed by global expression profiling.”, Proc Natl Acad Sci U S A, vol. 100, no. 19, pp. 10623-8, 2003.
, “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
, “Exploring the functional landscape of gene expression: directed search of large microarray compendia.”, Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
, “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
, “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
, “Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 22, no. 22, pp. 4447-59, 2011.
, “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
, “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
, “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.
, “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.
, “Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.”, Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
, “GeneXplorer: an interactive web application for microarray data visualization and analysis.”, BMC Bioinformatics, vol. 5, p. 141, 2004.
, “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.
, “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.
, “GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.”, Bioinformatics, vol. 20, no. 18, pp. 3710-5, 2004.
, “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
, “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
, “Identification of a rudimentary neural crest in a non-vertebrate chordate.”, Nature, vol. 492, no. 7427, pp. 104-7, 2012.
, “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
, “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.
, “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
, “Information-based clustering.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
, “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.
, “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.
, “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.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.”, Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
, “Metabolic cycling without cell division cycling in respiring yeast.”, Proc Natl Acad Sci U S A, vol. 108, no. 47, pp. 19090-5, 2011.
, “A method for detecting and correcting feature misidentification on expression microarrays.”, BMC Genomics, vol. 5, p. 64, 2004.
, “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
, “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.”, Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
, “Molecular characterisation of soft tissue tumours: a gene expression study.”, Lancet, vol. 359, no. 9314, pp. 1301-7, 2002.
, “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
, “Nested effects models for high-dimensional phenotyping screens.”, Bioinformatics, vol. 23, no. 13, pp. i305-12, 2007.
, “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
, “Nonparametric methods for identifying differentially expressed genes in microarray data.”, Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
, “Nutritional homeostasis in batch and steady-state culture of yeast.”, Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
, “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.
, “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.
, “PILGRM: an interactive data-driven discovery platform for expert biologists.”, Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
, “Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila.”, Genes Dev, vol. 19, no. 24, pp. 2941-6, 2005.
, “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 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.
, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
, “Quantifying the Bicoid morphogen gradient in living fly embryos.”, Cold Spring Harb Protoc, vol. 2012, no. 4, pp. 398-406, 2012.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Repeated observation of breast tumor subtypes in independent gene expression data sets.”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8418-23, 2003.
, “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
, “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.
, “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
, “A scalable method for integration and functional analysis of multiple microarray datasets.”, Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
, “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 Stanford Microarray Database: data access and quality assessment tools.”, Nucleic Acids Res, vol. 31, no. 1, pp. 94-6, 2003.
, “Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
, “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
, “Systematic planning of genome-scale experiments in poorly studied species.”, PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
, “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.
, “Systems-level dynamic analyses of fate change in murine embryonic stem cells.”, Nature, vol. 462, no. 7271, pp. 358-62, 2009.
, “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
, “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
, “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
, “Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.”, PLoS Biol, vol. 5, no. 5, p. e117, 2007.
, “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.
, “Variation in gene expression patterns in human gastric cancers.”, Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
, “Visualization methods for statistical analysis of microarray clusters.”, BMC Bioinformatics, vol. 6, p. 115, 2005.
, “Visualization-based discovery and analysis of genomic aberrations in microarray data.”, BMC Bioinformatics, vol. 6, p. 146, 2005.
, “Whole-genome expression profiles identify gene batteries in Drosophila.”, Dev Cell, vol. 3, no. 4, pp. 464-5, 2002.
, “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
, “Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes.”, Proc Natl Acad Sci U S A, vol. 110, no. 46, pp. E4393-402, 2013.
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