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 genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “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.
, “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.
, “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 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.
, “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
, “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “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.
, “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
, “Global quantitative modeling of chromatin factor interactions.”, PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
, “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
, “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
, “Local accumulation times for source, diffusion, and degradation models in two and three dimensions.”, J Chem Phys, vol. 138, no. 10, p. 104121, 2013.
, “Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.”, J Vis Exp, no. 76, p. e50382, 2013.
, “Accurate evaluation and analysis of functional genomics data and methods.”, Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
, “An effective statistical evaluation of ChIPseq dataset similarity.”, Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
, “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”, PLoS One, vol. 7, no. 3, p. e33528, 2012.
, “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.
, “LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine.”, Curr Protoc Bioinformatics, vol. Chapter 14, p. Unit14.11, 2012.
, “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
, “Pattern formation by a moving morphogen source.”, Phys Biol, vol. 8, no. 4, p. 045003, 2011.
, “Physical interpretation of mean local accumulation time of morphogen gradient formation.”, J Chem Phys, vol. 135, no. 15, p. 154115, 2011.
, “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
, “A compartmental model for the bicoid gradient.”, Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
, “A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli.”, Proc Natl Acad Sci U S A, vol. 107, no. 40, pp. 17170-5, 2010.
, “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
, “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
, “Functional genomics complements quantitative genetics in identifying disease-gene associations.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
, “Limits of sensing temporal concentration changes by single cells.”, Phys Rev Lett, vol. 104, no. 24, p. 248101, 2010.
, “Metabolomic analysis and visualization engine for LC-MS data.”, Anal Chem, vol. 82, no. 23, pp. 9818-26, 2010.
, “Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.”, Proc Natl Acad Sci U S A, vol. 107, no. 4, pp. 1482-7, 2010.
, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
, “Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.”, PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
, “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
, “Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.”, Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
, “Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
, “Detailing regulatory networks through large scale data integration.”, Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
, “Effect of aberration on height calibration in three-dimensional localization-based microscopy and particle tracking.”, Appl Opt, vol. 48, no. 10, pp. 1886-90, 2009.
, “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
, “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.
, “How and when should interactome-derived clusters be used to predict functional modules and protein function?”, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
, “The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.”, Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
, “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “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.
, “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
, “Steps in the bacterial flagellar motor.”, PLoS Comput Biol, vol. 5, no. 10, p. e1000540, 2009.
, “Assessing the functional structure of genomic data.”, Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
, “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
, “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
, “A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.”, Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
, “Descriptor-free molecular discovery in large libraries by adaptive substituent reordering.”, Bioorg Med Chem Lett, vol. 18, no. 22, pp. 5967-70, 2008.
, “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
, “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
, “NetGrep: fast network schema searches in interactomes.”, Genome Biol, vol. 9, no. 9, p. R138, 2008.
, “The neural basis for combinatorial coding in a cortical population response.”, J Neurosci, vol. 28, no. 50, pp. 13522-31, 2008.
, “Neural coding of natural stimuli: information at sub-millisecond resolution.”, PLoS Comput Biol, vol. 4, no. 3, p. e1000025, 2008.
, “Predicting gene function in a hierarchical context with an ensemble of classifiers.”, Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
, “PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution.”, PLoS Comput Biol, vol. 4, no. 11, p. e1000233, 2008.
, “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
, “Self-organized periodicity of protein clusters in growing bacteria.”, Phys Rev Lett, vol. 101, no. 21, p. 218101, 2008.
, “The Sleipnir library for computational functional genomics.”, Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
, “Bistability and oscillations in the Huang-Ferrell model of MAPK signaling.”, PLoS Comput Biol, vol. 3, no. 9, pp. 1819-26, 2007.
, “Context-sensitive data integration and prediction of biological networks.”, Bioinformatics, vol. 23, no. 17, pp. 2322-30, 2007.
, “Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function.”, J Opt Soc Am A Opt Image Sci Vis, vol. 24, no. 9, pp. 2622-7, 2007.
, “Exploring the functional landscape of gene expression: directed search of large microarray compendia.”, Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
, “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
, “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
, “Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein.”, Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
, “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.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.”, PLoS One, vol. 2, no. 8, p. e766, 2007.
, “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
, “Finding function: evaluation methods for functional genomic data.”, BMC Genomics, vol. 7, p. 187, 2006.
, “Hierarchical multi-label prediction of gene function.”, Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
, “A scalable method for integration and functional analysis of multiple microarray datasets.”, Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
, “Weight matrices for protein-DNA binding sites from a single co-crystal structure.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 73, no. 6 Pt 1, p. 061921, 2006.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “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.
, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
, “Tools and applications for large-scale display walls.”, IEEE Comput Graph Appl, vol. 25, no. 4, pp. 24-33, 2005.
, “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-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
, “Accurate detection of aneuploidies in array CGH and gene expression microarray data.”, Bioinformatics, vol. 20, no. 18, pp. 3533-43, 2004.
, “Analyzing neural responses to natural signals: maximally informative dimensions.”, Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “Toward an atomistic model for predicting transcription-factor binding sites.”, Proteins, vol. 57, no. 2, pp. 262-8, 2004.
, “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.
, “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.”, Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
, “Stochastic model of autocrine and paracrine signals in cell culture assays.”, Biophys J, vol. 85, no. 6, pp. 3659-65, 2003.
, “Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”, Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
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