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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“Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
, “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
, “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
, “Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.”, ISME J, vol. 9, no. 1, pp. 68-80, 2015.
, “Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.”, Mol Cell Biol, vol. 32, no. 23, pp. 4861-76, 2012.
, “It's all about the talent.”, Mol Biol Cell, vol. 21, no. 22, p. 3823, 2010.
, “Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth.”, Med (N Y), vol. 3, no. 2, pp. 119-136, 2022.
, “Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”, J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
, “Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis.”, ACS Chem Biol, 2016.
, “Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.”, Mol Biol Evol, vol. 31, no. 7, pp. 1750-66, 2014.
, “An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate.”, Anal Bioanal Chem, 2017.
, “Lessons learned, promises kept: a biologist's eye view of the Genome Project.”, Genome Res, vol. 6, no. 9, pp. 773-80, 1996.
, “Linkage between vitamin D-binding protein and alpha-fetoprotein in the mouse.”, Mamm Genome, vol. 7, no. 2, pp. 103-6, 1996.
, “Location of enhancers is essential for the imprinting of H19 and Igf2 genes.”, Nature, vol. 391, no. 6668, pp. 711-5, 1998.
, “The long walk to African genomics.”, Genome Biol, vol. 20, no. 1, p. 130, 2019.
, “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.
, “Looping back to leap forward: transcription enters a new era.”, Cell, vol. 157, no. 1, pp. 13-25, 2014.
, “Loss of NAD Homeostasis Leads to Progressive and Reversible Degeneration of Skeletal Muscle.”, Cell Metab, vol. 24, no. 2, pp. 269-82, 2016.
, “Loss of Uch-L1 and Uch-L3 leads to neurodegeneration, posterior paralysis and dysphagia.”, Hum Mol Genet, vol. 10, no. 18, pp. 1963-70, 2001.
, “Low-variance RNAs identify Parkinson's disease molecular signature in blood.”, Mov Disord, vol. 30, no. 6, pp. 813-21, 2015.
, “Lymphocyte invasion in IC10/Basal-like breast tumors is associated with wild-type TP53.”, Mol Cancer Res, 2014.
, “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.
, “Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons.”, Mol Psychiatry, 2019.
, “Measurement and perturbation of morphogen lifetime: effects on gradient shape.”, Biophys J, vol. 101, no. 8, pp. 1807-15, 2011.
, “Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.”, Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
, “Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.”, Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
, “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 network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.”, Elife, vol. 5, 2016.
, “Metabolic profiling reveals a dependency of human metastatic breast cancer on mitochondrial serine and one-carbon unit metabolism.”, Mol. Cancer Res., vol. 18, no. 4, pp. 599-611, 2020.
, “A method for detecting and correcting feature misidentification on expression microarrays.”, BMC Genomics, vol. 5, p. 64, 2004.
, “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.
, “Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.”, mSystems, vol. 4, no. 1, 2019.
, “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.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
, “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.
, “Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene.”, Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
, “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 mouse genomic library of yeast artificial chromosome clones.”, Mamm Genome, vol. 1, no. 1, p. 65, 1991.
, “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.
, “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
, “Near-equilibrium glycolysis supports metabolic homeostasis and energy yield.”, Nat Chem Biol, vol. 15, no. 10, pp. 1001-1008, 2019.
, “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
, “Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response.”, Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
, “Nested effects models for high-dimensional phenotyping screens.”, Bioinformatics, vol. 23, no. 13, pp. i305-12, 2007.
, “Neural tube patterning by Ephrin, FGF and Notch signaling relays.”, Development, vol. 138, no. 24, pp. 5429-39, 2011.
, “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
, “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
, “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
, “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
, “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
, “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
, “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
, “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
, “Nonparametric methods for identifying differentially expressed genes in microarray data.”, Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
, “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.
, “Nucleosome-coupled expression differences in closely-related species.”, BMC Genomics, vol. 12, p. 466, 2011.
, “Nucleosome-coupled expression differences in closely-related species.”, BMC Genomics, vol. 12, p. 466, 2011.
, “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
, “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
, “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.
, “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.
, “Optimizing information flow in small genetic networks.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 3 Pt 1, p. 031920, 2009.
, “Optimizing information flow in small genetic networks. II. Feed-forward interactions.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 81, no. 4 Pt 1, p. 041905, 2010.
, “Optimizing information flow in small genetic networks. III. A self-interacting gene.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 85, no. 4 Pt 1, p. 041903, 2012.
, “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
, “Organoid single cell profiling identifies a transcriptional signature of glomerular disease.”, JCI Insight, vol. 4, no. 1, 2019.
, “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
, “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
, “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
, “Parental imprinting in the mouse.”, Harvey Lect, vol. 87, pp. 69-84, 1991.
, “Parental imprinting of the H19 and Igf2 genes in the mouse.”, Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
, “Parental imprinting of the mouse H19 gene.”, Nature, vol. 351, no. 6322, pp. 153-5, 1991.
, “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
, “Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity.”, Nat Immunol, vol. 20, no. 8, pp. 1023-1034, 2019.
, “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.
, “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.
, “Physical linkage of two mammalian imprinted genes, H19 and insulin-like growth factor 2.”, Nat Genet, vol. 2, no. 1, pp. 61-5, 1992.
, “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.”, Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
, “Piebald lethal (sl) acts early to disrupt the development of neural crest-derived melanocytes.”, Proc Natl Acad Sci U S A, vol. 91, no. 15, pp. 7159-63, 1994.
, “PILGRM: an interactive data-driven discovery platform for expert biologists.”, Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
, “Planning the genome institute's future.”, Science, vol. 299, no. 5612, p. 1515; author reply 1515, 2003.
, “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.
, “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
, “Positional information, positional error, and readout precision in morphogenesis: a mathematical framework.”, Genetics, vol. 199, no. 1, pp. 39-59, 2015.
, “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
, “PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity.”, Cell, vol. 154, no. 3, pp. 676-90, 2013.
, “PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism.”, Cell Stem Cell, 2019.
, “A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate.”, Cell Metab, vol. 30, no. 1, pp. 174-189.e5, 2019.
, “Precise developmental gene expression arises from globally stochastic transcriptional activity.”, Cell, vol. 154, no. 4, pp. 789-800, 2013.
, “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
, “Predicting effects of noncoding variants with deep learning-based sequence model.”, Nat Methods, 2015.
, “Predicting gene function in a hierarchical context with an ensemble of classifiers.”, Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 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.
, “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
, “Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states.”, Nat Commun, vol. 7, p. 10528, 2016.
, “Probing the limits to positional information.”, Cell, vol. 130, no. 1, pp. 153-64, 2007.
, “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
, “Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”, Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
, “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.
, “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.
, “pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos.”, Genes Dev, vol. 18, no. 6, pp. 687-99, 2004.
, “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
, “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
, “Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning.”, Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
, “Quantitative trait loci that modify the severity of spotting in piebald mice.”, Genome Res, vol. 5, no. 1, pp. 29-41, 1995.
, “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.
, “Recurated protein interaction datasets.”, Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
, “Recurated protein interaction datasets.”, Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
, “Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli.”, Mol Syst Biol, vol. 6, p. 378, 2010.
, “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.
, “Rethinking WNT signaling.”, Trends Genet, vol. 20, no. 4, pp. 177-81, 2004.
, “Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway.”, Cell Metab, 2016.
, “Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group.”, G3 (Bethesda), vol. 4, no. 12, pp. 2345-51, 2014.
, “A roadmap for interpreting (13)C metabolite labeling patterns from cells.”, Curr Opin Biotechnol, vol. 34, pp. 189-201, 2015.
, “Role of alpha-fetoprotein regulatory elements in transcriptional activation in transient heterokaryons.”, Mol Cell Biol, vol. 10, no. 10, pp. 5047-54, 1990.
, “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.
, “Saccharomyces Genome Database.”, Methods Enzymol, vol. 350, pp. 329-46, 2002.
, “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
, “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.
, “A scalable method for integration and functional analysis of multiple microarray datasets.”, Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
, “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
, “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
, “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
, “Selected proceedings of the First Summit on Translational Bioinformatics 2008.”, BMC Bioinformatics, vol. 10 Suppl 2, p. I1, 2009.
, “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
, “Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”, Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
, “Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia.”, Cancer Discov, vol. 4, no. 12, pp. 1406-17, 2014.
, “Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.”, Oncoimmunology, vol. 7, no. 11, p. e1457598, 2018.
, “Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.”, Oncoimmunology, vol. 7, no. 11, p. e1457598, 2018.
, “A simplified miRNA-based gene silencing method for Drosophila melanogaster.”, Dev Biol, vol. 321, no. 2, pp. 482-90, 2008.
, “Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.”, PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
, “Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker.”, JCI Insight, vol. 5, no. 6, 2020.
, “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
, “The sins of the fathers and mothers: genomic imprinting in mammalian development.”, Cell, vol. 96, no. 2, pp. 185-93, 1999.
, “The Sleipnir library for computational functional genomics.”, Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
, “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
, “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
, “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
, “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
, “Stability and nuclear dynamics of the bicoid morphogen gradient.”, Cell, vol. 130, no. 1, pp. 141-52, 2007.
, “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.
, “Statistical thermodynamics of natural images.”, Phys Rev Lett, vol. 110, no. 1, p. 018701, 2013.
, “The structural H19 gene is required for transgene imprinting.”, Proc Natl Acad Sci U S A, vol. 93, no. 24, pp. 13876-83, 1996.
, “The structure and expression of a novel gene activated in early mouse embryogenesis.”, EMBO J, vol. 7, no. 3, pp. 673-81, 1988.
, “Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.”, Bioinformatics, vol. 36, no. 4, pp. 994-999, 2020.
, “Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.”, Bioinformatics, vol. 36, no. 4, pp. 994-999, 2020.
, “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
, “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.
, “T Cell Activation Depends on Extracellular Alanine.”, Cell Rep, vol. 28, no. 12, pp. 3011-3021.e4, 2019.
, “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
, “Targeted exploration and analysis of large cross-platform human transcriptomic compendia.”, Nat Methods, vol. 12, no. 3, pp. 211-4, 3 p following 214, 2015.
, “Targeted exploration and analysis of large cross-platform human transcriptomic compendia.”, Nat Methods, vol. 12, no. 3, pp. 211-4, 3 p following 214, 2015.
, “The temporal requirement for endothelin receptor-B signalling during neural crest development.”, Nature, vol. 402, no. 6761, pp. 496-501, 1999.
, “Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.”, Bioinformatics, 2014.
, “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
, “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.
, “Tools and applications for large-scale display walls.”, IEEE Comput Graph Appl, vol. 25, no. 4, pp. 24-33, 2005.
, “Transcription regulation and animal diversity.”, Nature, vol. 424, no. 6945, pp. 147-51, 2003.
, “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
, “Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”, BMC Immunol, vol. 3, p. 5, 2002.
, “Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”, BMC Immunol, vol. 3, p. 5, 2002.
, “Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.”, PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
, “Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.”, PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
, “Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”, Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
, “Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin.”, Clin Cancer Res, vol. 23, no. 18, pp. 5639-5647, 2017.
, “Twists and turns: a scientific journey.”, Annu Rev Cell Dev Biol, vol. 30, pp. 1-21, 2014.
, “Two dominant mutations in the mouse fused gene are the result of transposon insertions.”, Genetics, vol. 147, no. 2, pp. 777-86, 1997.
, “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
, “Understanding multicellular function and disease with human tissue-specific networks.”, Nat Genet, vol. 47, no. 6, pp. 569-76, 2015.
, “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.
, “Voices in methods development.”, Nat Methods, vol. 16, no. 10, pp. 945-951, 2019.
, “Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis.”, Proc Natl Acad Sci U S A, vol. 109, no. 47, pp. 19298-303, 2012.
, “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.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
, “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.
, “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
, “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
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