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“The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
, “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
, “Picocalorimetry of transcription by RNA polymerase.”, Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
, “Identification of a rudimentary neural crest in a non-vertebrate chordate.”, Nature, vol. 492, no. 7427, pp. 104-7, 2012.
, “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
, “Fly wing vein patterns have spatial reproducibility of a single cell.”, J R Soc Interface, vol. 11, no. 97, p. 20140443, 2014.
, “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
, “Computation in a single neuron: Hodgkin and Huxley revisited.”, Neural Comput, vol. 15, no. 8, pp. 1715-49, 2003.
, “Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development.”, Development, vol. 129, no. 7, pp. 1751-62, 2002.
, “Regulation of armadillo by a Drosophila APC inhibits neuronal apoptosis during retinal development.”, Cell, vol. 93, no. 7, pp. 1171-82, 1998.
, “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
, “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.
, “Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum.”, J Bacteriol, vol. 192, no. 17, pp. 4452-61, 2010.
, “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
, “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
, “Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.”, Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
, “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
, “Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.”, Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
, “Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.”, Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
, “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
, “Voices in methods development.”, Nat Methods, vol. 16, no. 10, pp. 945-951, 2019.
, “Conserved regulators of cognitive aging: From worms to humans.”, Behav Brain Res, vol. 322, no. Pt B, pp. 299-310, 2017.
, “Hierarchy in Pentose Sugar Metabolism in Clostridium Acetobutylicum.”, Appl Environ Microbiol, 2014.
, “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.
, “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
, “Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.”, Genome Biol, vol. 14, no. 11, p. R126, 2013.
, “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
, “Behavioral idiosyncrasy reveals genetic control of phenotypic variability.”, Proc Natl Acad Sci U S A, vol. 112, no. 21, pp. 6706-11, 2015.
, “A genomewide assessment of inbreeding depression: gene number, function, and mode of action.”, Conserv Biol, vol. 23, no. 4, pp. 920-30, 2009.
, “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
, “Analysis of variance of microarray data.”, Methods Enzymol, vol. 411, pp. 214-33, 2006.
, “Selection, recombination and demographic history in Drosophila miranda.”, Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
, “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
, “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.
, “Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.”, Nature, vol. 571, no. 7765, pp. 403-407, 2019.
, “Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry.”, J Chromatogr A, vol. 1125, no. 1, pp. 76-88, 2006.
, “Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility.”, PLoS Comput Biol, vol. 10, no. 5, p. e1003619, 2014.
, “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.
, “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “NetGrep: fast network schema searches in interactomes.”, Genome Biol, vol. 9, no. 9, p. R138, 2008.
, “Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1.”, Mol Cell, vol. 25, no. 2, pp. 181-92, 2007.
, “Large-scale filament formation inhibits the activity of CTP synthetase.”, Elife, vol. 3, p. e03638, 2014.
, “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
, “Parental imprinting of the mouse H19 gene.”, Nature, vol. 351, no. 6322, pp. 153-5, 1991.
, “Epigenetic mechanisms underlying the imprinting of the mouse H19 gene.”, Genes Dev, vol. 7, no. 9, pp. 1663-73, 1993.
, “Hierarchical multi-label prediction of gene function.”, Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
, “Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.”, Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
, “Working together at the interface of physics and biology.”, Phys Biol, vol. 11, no. 5, p. 053010, 2014.
, “Stochastic model of autocrine and paracrine signals in cell culture assays.”, Biophys J, vol. 85, no. 6, pp. 3659-65, 2003.
, “Signaling activities of the Drosophila wingless gene are separately mutable and appear to be transduced at the cell surface.”, Genetics, vol. 139, no. 1, pp. 309-20, 1995.
, “Segment polarity gene interactions modulate epidermal patterning in Drosophila embryos.”, Development, vol. 119, no. 2, pp. 501-17, 1993.
, “Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach.”, Nat Protoc, vol. 3, no. 8, pp. 1299-311, 2008.
, “Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.”, Nat Chem Biol, vol. 5, no. 8, pp. 593-9, 2009.
, “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.
, “On the GFP-based analysis of dynamic concentration profiles.”, Biophys J, vol. 106, no. 3, pp. L13-5, 2014.
, “Kinetics of receptor occupancy during morphogen gradient formation.”, J Chem Phys, vol. 138, no. 24, p. 244105, 2013.
, “Formation of morphogen gradients: local accumulation time.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 5 Pt 1, p. 051906, 2011.
, “Signaling gradients in cascades of two-state reaction-diffusion systems.”, Proc Natl Acad Sci U S A, vol. 106, no. 4, pp. 1087-92, 2009.
, “How long does it take to establish a morphogen gradient?”, Biophys J, vol. 99, no. 8, pp. L59-61, 2010.
, “Homogenization of boundary conditions for surfaces with regular arrays of traps.”, J Chem Phys, vol. 124, no. 3, p. 036103, 2006.
, “Physical interpretation of mean local accumulation time of morphogen gradient formation.”, J Chem Phys, vol. 135, no. 15, p. 154115, 2011.
, “Ligand trapping in epithelial layers and cell cultures.”, Biophys Chem, vol. 107, no. 3, pp. 221-7, 2004.
, “Boundary homogenization for trapping by patchy surfaces.”, J Chem Phys, vol. 121, no. 22, pp. 11390-4, 2004.
, “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.
, “Predictability and hierarchy in Drosophila behavior.”, Proc Natl Acad Sci U S A, vol. 113, no. 42, pp. 11943-11948, 2016.
, “Mapping the stereotyped behaviour of freely moving fruit flies.”, J R Soc Interface, vol. 11, no. 99, 2014.
, “Statistical mechanics for natural flocks of birds.”, Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 2012.
, “Introductory science and mathematics education for 21st-Century biologists.”, Science, vol. 303, no. 5659, pp. 788-90, 2004.
, “Physical limits to biochemical signaling.”, Proc Natl Acad Sci U S A, vol. 102, no. 29, pp. 10040-5, 2005.
, “Cooperativity, sensitivity, and noise in biochemical signaling.”, Phys Rev Lett, vol. 100, no. 25, p. 258101, 2008.
, “Social interactions dominate speed control in poising natural flocks near criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
, “QnAs with William Bialek.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, p. 16288, 2013.
, “Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.”, Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
, “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.
, “Two new roles for the Drosophila AP patterning system in early morphogenesis.”, Development, vol. 128, no. 24, pp. 5129-38, 2001.
, “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.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “Influence of genotype and nutrition on survival and metabolism of starving yeast.”, Proc Natl Acad Sci U S A, vol. 105, no. 19, pp. 6930-5, 2008.
, “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
, “Synchronous and stochastic patterns of gene activation in the Drosophila embryo.”, Science, vol. 325, no. 5939, pp. 471-3, 2009.
, “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.
, “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.
, “Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”, PLoS One, vol. 8, no. 5, p. e63304, 2013.
, “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
, “Development: lights, camera, action--the Drosophila embryo goes live!”, Curr Biol, vol. 23, no. 21, pp. R965-7, 2013.
, “The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo.”, Curr Biol, vol. 21, no. 18, pp. 1571-7, 2011.
, “Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos.”, Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
, “Morphogen gradients: limits to signaling or limits to measurement?”, Curr Biol, vol. 20, no. 5, pp. R232-4, 2010.
, “It's the data!”, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
, “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
, “Ira Herskowitz: 1946-2003.”, Genetics, vol. 166, no. 2, pp. 653-60, 2004.
, “Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier.”, PLoS Genet, vol. 2, no. 5, p. e79, 2006.
, “Why we need more basic biology research, not less.”, Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.
, “Genome-sequencing anniversary. Fruits of genome sequences for biology.”, Science, vol. 331, no. 6020, p. 1025, 2011.
, “Technological innovation leads to fundamental understanding in cell biology.”, Mol Biol Cell, vol. 21, no. 22, pp. 3791-2, 2010.
, “Lasker∼Koshland to genetics pioneer.”, Cell, vol. 158, no. 6, pp. 1230-2, 2014.
, “Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease.”, Nat Genet, vol. 33 Suppl, pp. 228-37, 2003.
, “Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation.”, Cell Metab, vol. 22, no. 6, pp. 1068-77, 2015.
, “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.
, “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.
, “Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
, “Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.”, mSystems, vol. 4, no. 1, 2019.
, “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
, “Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System.”, PLoS One, vol. 10, no. 8, p. e0134616, 2015.
, “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
, “Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.”, Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
, “Conservation of the metabolomic response to starvation across two divergent microbes.”, Proc Natl Acad Sci U S A, vol. 103, no. 51, pp. 19302-7, 2006.
, “Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP.”, Sci Rep, vol. 6, p. 24834, 2016.
, “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.
, “Genetic basis of metabolome variation in yeast.”, PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
, “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.
, “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.
, “Global analysis of gene function in yeast by quantitative phenotypic profiling.”, Mol Syst Biol, vol. 2, p. 2006.0001, 2006.
, “Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.”, Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
, “Ectopic expression of the H19 gene in mice causes prenatal lethality.”, Genes Dev, vol. 5, no. 6, pp. 1092-101, 1991.
, “A roadmap for interpreting (13)C metabolite labeling patterns from cells.”, Curr Opin Biotechnol, vol. 34, pp. 189-201, 2015.
, “A mouse genomic library of yeast artificial chromosome clones.”, Mamm Genome, vol. 1, no. 1, p. 65, 1991.
, “Selected proceedings of the First Summit on Translational Bioinformatics 2008.”, BMC Bioinformatics, vol. 10 Suppl 2, p. I1, 2009.
, “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.
, “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.
, “Coordinate regulation of an extended chromosome domain.”, Cell, vol. 113, no. 3, pp. 278-80, 2003.
, “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
, “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
, “Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum.”, Development, vol. 136, no. 18, pp. 3153-60, 2009.
, “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
, “Conservation of enhancer location in divergent insects.”, Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
, “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
, “Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma.”, PLoS One, vol. 4, no. 1, p. e4216, 2009.
, “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.
, “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
, “Inverse spin glass and related maximum entropy problems.”, Phys Rev Lett, vol. 113, no. 11, p. 117204, 2014.
, “Enzyme clustering accelerates processing of intermediates through metabolic channeling.”, Nat Biotechnol, vol. 32, no. 10, pp. 1011-8, 2014.
, “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
, “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.
, “Diversity, topographic differentiation, and positional memory in human fibroblasts.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
, “Variation in gene expression patterns in human gastric cancers.”, Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
, “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
, “An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate.”, Anal Bioanal Chem, 2017.
, “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
, “Gene expression patterns in human liver cancers.”, Mol Biol Cell, vol. 13, no. 6, pp. 1929-39, 2002.
, “Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.”, Cell, vol. 180, no. 4, pp. 677-687.e16, 2020.
, “NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism.”, Nat Metab, vol. 1, pp. 404-415, 2019.
, “Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis.”, Curr Opin Genet Dev, vol. 21, no. 6, pp. 719-25, 2011.
, “Dynamic model for the coordination of two enhancers of broad by EGFR signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 44, pp. 17939-44, 2013.
, “Endothelial cell diversity revealed by global expression profiling.”, Proc Natl Acad Sci U S A, vol. 100, no. 19, pp. 10623-8, 2003.
, “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”, Proc Natl Acad Sci U S A, vol. 104, no. 7, pp. 2193-8, 2007.
, “Low-variance RNAs identify Parkinson's disease molecular signature in blood.”, Mov Disord, vol. 30, no. 6, pp. 813-21, 2015.
, “An effective statistical evaluation of ChIPseq dataset similarity.”, Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
, “Accurate quantification of functional analogy among close homologs.”, PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
, “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.
, “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
, “Regulation of Hox gene activity by transcriptional elongation in Drosophila.”, Curr Biol, vol. 19, no. 8, pp. 688-93, 2009.
, “Stalled Hox promoters as chromosomal boundaries.”, Genes Dev, vol. 23, no. 13, pp. 1505-9, 2009.
, “The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.”, Mol Cell, vol. 42, no. 6, pp. 837-44, 2011.
, “Transcriptional repression via antilooping in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
, “Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5347, 2009.
, “Electroporation of transgenic DNAs in the sea squirt Ciona.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5345, 2009.
, “Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp.”, Dev Biol, vol. 328, no. 2, pp. 552-60, 2009.
, “Isolation of sea squirt (Ciona) gametes, fertilization, dechorionation, and development.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5344, 2009.
, “X-gal staining of electroporated sea squirt (Ciona) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5346, 2009.
, “Isolation of individual cells and tissues from electroporated sea squirt (Ciona) embryos by fluorescence-activated cell sorting (FACS).”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5349, 2009.
, “Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5348, 2009.
, “BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.”, Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
, “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
, “The sea squirt Ciona intestinalis.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.emo138, 2009.
, “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.
, “A microfluidic array for large-scale ordering and orientation of embryos.”, Nat Methods, vol. 8, no. 2, pp. 171-6, 2011.
, “Statistical significance of variables driving systematic variation in high-dimensional data.”, Bioinformatics, 2014.
, “Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.”, Curr Pharm Des, 2017.
, “Riboneogenesis in yeast.”, Cell, vol. 145, no. 6, pp. 969-80, 2011.
, “LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine.”, Curr Protoc Bioinformatics, vol. Chapter 14, p. Unit14.11, 2012.
, “Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice.”, Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
, “Systematic structure-function analysis of the small GTPase Arf1 in yeast.”, Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
, “Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis.”, Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
, “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”, PLoS One, vol. 7, no. 3, p. e33528, 2012.
, “Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein.”, Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
, “Time and length scales of autocrine signals in three dimensions.”, Biophys J, vol. 93, no. 6, pp. 1917-22, 2007.
, “Nuclear trapping shapes the terminal gradient in the Drosophila embryo.”, Curr Biol, vol. 18, no. 12, pp. 915-9, 2008.
, “Genetic incompatibilities are widespread within species.”, Nature, vol. 504, no. 7478, pp. 135-7, 2013.
, “A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation.”, Cell, vol. 76, no. 6, pp. 1075-89, 1994.
, “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
, “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 2010.
, “Molecular analysis of odd-skipped, a zinc finger encoding segmentation gene with a novel pair-rule expression pattern.”, EMBO J, vol. 9, no. 11, pp. 3795-804, 1990.
, “Gene activities and segmental patterning in Drosophila: analysis of odd-skipped and pair-rule double mutants.”, Genes Dev, vol. 2, no. 12B, pp. 1812-23, 1988.
, “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.
, “The Snail repressor positions Notch signaling in the Drosophila embryo.”, Development, vol. 129, no. 7, pp. 1785-93, 2002.
, “Mass spectrometry-based metabolomics of yeast.”, Methods Enzymol, vol. 470, pp. 393-426, 2010.
, “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
, “Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 4 Pt 1, p. 041922, 2011.
, “Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.”, Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
, “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.
, “Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis.”, Development, vol. 132, no. 21, pp. 4811-8, 2005.
,