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
“Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
, “Discovery of biological networks from diverse functional genomic data.”, Genome Biol, vol. 6, no. 13, p. R114, 2005.
, “A DNA microarray survey of gene expression in normal human tissues.”, Genome Biol, vol. 6, no. 3, p. R22, 2005.
, “folded gastrulation, cell shape change and the control of myosin localization.”, Development, vol. 132, no. 18, pp. 4165-78, 2005.
, “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.
, “Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).”, Nucleic Acids Res, vol. 33, no. Database issue, pp. D374-7, 2005.
, “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.
, “Gene regulatory networks for development.”, Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4936-42, 2005.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 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.
, “Insect behaviour: arboreal ants build traps to capture prey.”, Nature, vol. 434, no. 7036, p. 973, 2005.
, “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
, “Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo.”, Dev Biol, vol. 280, no. 2, pp. 482-93, 2005.
, “Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.”, Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
, “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
, “Physical limits to biochemical signaling.”, Proc Natl Acad Sci U S A, vol. 102, no. 29, pp. 10040-5, 2005.
, “Picocalorimetry of transcription by RNA polymerase.”, Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
, “Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila.”, Genes Dev, vol. 19, no. 24, pp. 2941-6, 2005.
, “Precise domain specification in the developing Drosophila embryo.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 72, no. 6 Pt 1, p. 061920, 2005.
, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
, “Putting the 'bio' into bioinformatics.”, Genome Biol, vol. 6, no. 10, p. 351, 2005.
, “Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4966-71, 2005.
, “A sensory source for motor variation.”, Nature, vol. 437, no. 7057, pp. 412-6, 2005.
, “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
, “Spatial regulation of microRNA gene expression in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 102, no. 44, pp. 15907-11, 2005.
, “Spiroplasma swim by a processive change in body helicity.”, Cell, vol. 122, no. 6, pp. 941-5, 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.
, “Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis.”, Development, vol. 132, no. 21, pp. 4811-8, 2005.
, “Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis.”, Genome Res, vol. 15, no. 12, pp. 1668-74, 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.
, “Wolbachia utilizes host microtubules and Dynein for anterior localization in the Drosophila oocyte.”, PLoS Pathog, vol. 1, no. 2, p. e14, 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.
, “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
, “Boundary homogenization for trapping by patchy surfaces.”, J Chem Phys, vol. 121, no. 22, pp. 11390-4, 2004.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
, “Coordinate enhancers share common organizational features in the Drosophila genome.”, Proc Natl Acad Sci U S A, vol. 101, no. 11, pp. 3851-6, 2004.
, “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
, “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
, “Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.”, Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
, “Diverse and specific gene expression responses to stresses in cultured human cells.”, Mol Biol Cell, vol. 15, no. 5, pp. 2361-74, 2004.
, “Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.”, Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
, “Entropy and information in neural spike trains: progress on the sampling problem.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 69, no. 5 Pt 2, p. 056111, 2004.
, “Fast accurate evaluation of protein solvent exposure.”, Proteins, vol. 57, no. 3, pp. 565-76, 2004.
, “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
, “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 signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.”, PLoS Biol, vol. 2, no. 2, p. E7, 2004.
, “GeneXplorer: an interactive web application for microarray data visualization and analysis.”, BMC Bioinformatics, vol. 5, p. 141, 2004.
, “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.
, “How many clusters? An information-theoretic perspective.”, Neural Comput, vol. 16, no. 12, pp. 2483-506, 2004.
, “Immunity regulatory DNAs share common organizational features in Drosophila.”, Mol Cell, vol. 13, no. 1, pp. 19-32, 2004.
, “Introductory science and mathematics education for 21st-Century biologists.”, Science, vol. 303, no. 5659, pp. 788-90, 2004.
, “Ira Herskowitz: 1946-2003.”, Genetics, vol. 166, no. 2, pp. 653-60, 2004.
, “Ligand trapping in epithelial layers and cell cultures.”, Biophys Chem, vol. 107, no. 3, pp. 221-7, 2004.
, “A method for detecting and correcting feature misidentification on expression microarrays.”, BMC Genomics, vol. 5, p. 64, 2004.
, “Min-protein oscillations in round bacteria.”, Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
, “A nuclear escort for beta-catenin.”, Nat Cell Biol, vol. 6, no. 7, pp. 579-80, 2004.
, “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
, “Nutritional homeostasis in batch and steady-state culture of yeast.”, Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
, “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
, “Patterned gene expression directs bipolar planar polarity in Drosophila.”, Dev Cell, vol. 6, no. 3, pp. 343-55, 2004.
, “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
, “Physics. Quantum many-body effects in a single-electron transistor.”, Science, vol. 304, no. 5675, pp. 1258-9, 2004.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “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.
, “pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos.”, Genes Dev, vol. 18, no. 6, pp. 687-99, 2004.
, “A regulatory code for neurogenic gene expression in the Drosophila embryo.”, Development, vol. 131, no. 10, pp. 2387-94, 2004.
, “Rethinking WNT signaling.”, Trends Genet, vol. 20, no. 4, pp. 177-81, 2004.
, “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.
, “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.
, “Saccharomyces genome database: underlying principles and organisation.”, Brief Bioinform, vol. 5, no. 1, pp. 9-22, 2004.
, “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
, “The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.”, Cell, vol. 118, no. 1, pp. 69-82, 2004.
, “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
, “Time course of information about motion direction in visual area MT of macaque monkeys.”, J Neurosci, vol. 24, no. 13, pp. 3210-22, 2004.
, “Toward an atomistic model for predicting transcription-factor binding sites.”, Proteins, vol. 57, no. 2, pp. 262-8, 2004.
, “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
, “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
, “Whole-genome analysis of Drosophila gastrulation.”, Curr Opin Genet Dev, vol. 14, no. 5, pp. 477-84, 2004.
, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
, “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.
, “Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1.”, Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
, “Bringing classical embryology to C elegans gastrulation.”, Dev Cell, vol. 4, no. 1, pp. 6-8, 2003.
, “Computation in a single neuron: Hodgkin and Huxley revisited.”, Neural Comput, vol. 15, no. 8, pp. 1715-49, 2003.
, “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
, “Control of cleavage cycles in Drosophila embryos by frühstart.”, Dev Cell, vol. 5, no. 2, pp. 285-94, 2003.
, “Coordinate regulation of an extended chromosome domain.”, Cell, vol. 113, no. 3, pp. 278-80, 2003.
, “CtBP-independent repression in the Drosophila embryo.”, Mol Cell Biol, vol. 23, no. 11, pp. 3990-9, 2003.
, “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.
, “Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease.”, Nat Genet, vol. 33 Suppl, pp. 228-37, 2003.
, “Discrete models of autocrine cell communication in epithelial layers.”, Biophys J, vol. 84, no. 6, pp. 3624-35, 2003.
, “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
, “Endothelial cell diversity revealed by global expression profiling.”, Proc Natl Acad Sci U S A, vol. 100, no. 19, pp. 10623-8, 2003.
, “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.
, “Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis.”, Proc Natl Acad Sci U S A, vol. 100, no. 20, pp. 11469-73, 2003.
, “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
, “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.
, “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.
, “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
, “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
, “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.
, “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
, “A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins.”, Am J Hypertens, vol. 16, no. 2, pp. 158-62, 2003.
, “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
, “Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.”, Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
, “Local moment formation in quantum point contacts.”, Phys Rev Lett, vol. 90, no. 2, p. 026804, 2003.
, “Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex.”, Proc Natl Acad Sci U S A, vol. 100, no. 17, pp. 9878-83, 2003.
, “Long-range signal transmission in autocrine relays.”, Biophys J, vol. 84, no. 2 Pt 1, pp. 883-96, 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.
, “Network information and connected correlations.”, Phys Rev Lett, vol. 91, no. 23, p. 238701, 2003.
, “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
, “Planning the genome institute's future.”, Science, vol. 299, no. 5612, p. 1515; author reply 1515, 2003.
, “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
, “Regulation of aging and age-related disease by DAF-16 and heat-shock factor.”, Science, vol. 300, no. 5622, pp. 1142-5, 2003.
, “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.
, “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
, “Scaling of mutational effects in models for pleiotropy.”, Genetics, vol. 164, no. 3, pp. 1221-8, 2003.
, “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.
, “Statistical mechanics of RNA folding: importance of alphabet size.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 68, no. 4 Pt 1, p. 041904, 2003.
, “Stochastic model of autocrine and paracrine signals in cell culture assays.”, Biophys J, vol. 85, no. 6, pp. 3659-65, 2003.
, “Synergy, redundancy, and independence in population codes.”, J Neurosci, vol. 23, no. 37, pp. 11539-53, 2003.
, “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.
, “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
, “Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.”, Am J Pathol, vol. 163, no. 4, pp. 1449-56, 2003.
, “Transcription regulation and animal diversity.”, Nature, vol. 424, no. 6945, pp. 147-51, 2003.
, “Transitions in the model of epithelial patterning.”, Dev Dyn, vol. 226, no. 1, pp. 155-9, 2003.
, “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.
, “Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo.”, Dev Biol, vol. 262, no. 2, pp. 335-49, 2003.
, “Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.”, EMBO J, vol. 22, no. 4, pp. 870-81, 2003.
, “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.
, “Analyzing gene regulation in ascidian embryos: new tools for new perspectives.”, Differentiation, vol. 70, no. 4-5, pp. 132-9, 2002.
, “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
, “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.
, “Challenges in developing a molecular characterization of cancer.”, Semin Oncol, vol. 29, no. 3, pp. 280-5, 2002.
, “Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16144-9, 2002.
, “Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16847-52, 2002.
, “Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis.”, Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
, “Conserved domains of the Nullo protein required for cell-surface localization and formation of adherens junctions.”, Mol Biol Cell, vol. 13, no. 1, pp. 146-57, 2002.
, “Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis.”, Dev Biol, vol. 246, no. 2, pp. 329-40, 2002.
, “Coordination of opposite-polarity microtubule motors.”, J Cell Biol, vol. 156, no. 4, pp. 715-24, 2002.
, “Decoding cis-regulatory DNAs in the Drosophila genome.”, Curr Opin Genet Dev, vol. 12, no. 5, pp. 601-6, 2002.
, “Designability of alpha-helical proteins.”, Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
, “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
, “Diversity, topographic differentiation, and positional memory in human fibroblasts.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
, “Dorsal gradient networks in the Drosophila embryo.”, Dev Biol, vol. 246, no. 1, pp. 57-67, 2002.
, “Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development.”, Development, vol. 129, no. 7, pp. 1751-62, 2002.
, “Emergence of highly designable protein-backbone conformations in an off-lattice model.”, Proteins, vol. 47, no. 4, pp. 506-12, 2002.
, “Establishment of developmental precision and proportions in the early Drosophila embryo.”, Nature, vol. 415, no. 6873, pp. 798-802, 2002.
, “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.”, Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
, “Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
, “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
, “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
, “Gene expression patterns in human liver cancers.”, Mol Biol Cell, vol. 13, no. 6, pp. 1929-39, 2002.
, “Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 763-8, 2002.
, “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.
, “Genome-wide identification of tissue-specific enhancers in the Ciona tadpole.”, Proc Natl Acad Sci U S A, vol. 99, no. 10, pp. 6802-5, 2002.
, “Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”, Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
, “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.
, “Identification of genes periodically expressed in the human cell cycle and their expression in tumors.”, Mol Biol Cell, vol. 13, no. 6, pp. 1977-2000, 2002.
, “Identifying proteins of high designability via surface-exposure patterns.”, Proteins, vol. 47, no. 3, pp. 295-304, 2002.
, “Immunoelectron microscopy of aldehyde-fixed yeast cells.”, Methods Enzymol, vol. 351, pp. 50-81, 2002.
, “Junctions as organizing centers in epithelial cells? A fly perspective.”, Traffic, vol. 3, no. 2, pp. 92-7, 2002.
, “Kondo model for the "0.7 anomaly" in transport through a quantum point contact.”, Phys Rev Lett, vol. 89, no. 19, p. 196802, 2002.
, “Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset.”, Development, vol. 129, no. 14, pp. 3411-9, 2002.
, “Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12963-8, 2002.
, “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
, “Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.”, Development, vol. 129, no. 11, pp. 2577-89, 2002.
, “Molecular characterisation of soft tissue tumours: a gene expression study.”, Lancet, vol. 359, no. 9314, pp. 1301-7, 2002.
, “Nonparametric methods for identifying differentially expressed genes in microarray data.”, Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
, “Occam factors and model independent Bayesian learning of continuous distributions.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 65, no. 2 Pt 2, p. 026137, 2002.
, “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 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.
, “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
, “Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex.”, Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9243-7, 2002.
, “Saccharomyces Genome Database.”, Methods Enzymol, vol. 350, pp. 329-46, 2002.
, “Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).”, Nucleic Acids Res, vol. 30, no. 1, pp. 69-72, 2002.
, “SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila.”, J Cell Biol, vol. 156, no. 4, pp. 689-701, 2002.
, “Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”, Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
, “Shooting from the hip: spatial control of signal release by intracellular waves.”, Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9087-9, 2002.
, “slam encodes a developmental regulator of polarized membrane growth during cleavage of the Drosophila embryo.”, Dev Cell, vol. 2, no. 4, pp. 425-36, 2002.
, “The Snail repressor positions Notch signaling in the Drosophila embryo.”, Development, vol. 129, no. 7, pp. 1785-93, 2002.
, “Statistical properties of spike trains: universal and stimulus-dependent aspects.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 66, no. 3 Pt 1, p. 031907, 2002.
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