Colin N. Dewey

发表

PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments

Peng Liu, Alexandra A. Soukup, Emery H. Bresnick, 2019, bioRxiv.

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments

Yuan Li, Colin N. Dewey, Ning Leng, 2015, Bioinform..

CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

Michael Gleicher, Colin N. Dewey, Matthew N. Bernstein, 2019, bioRxiv.

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive

AnHai Doan, Colin N. Dewey, Matthew Bernstein, 2017, Bioinform..

Positional orthology: putting genomic evolutionary relationships into context

Colin N. Dewey, 2011, Briefings Bioinform..

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Colin N. Dewey, Bo Li, Bo Li, 2011, BMC Bioinformatics.

Parametric Alignment of Drosophila Genomes

Lior Pachter, Bernd Sturmfels, Peter Huggins, 2005, PLoS Comput. Biol..

Fast Statistical Alignment

Lior Pachter, Jaeyoung Do, Ian Holmes, 2009, PLoS Comput. Biol..

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs

Colin N. Dewey, Laura H. LeGault, L. Legault, 2013, Bioinform..

CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

Michael Gleicher, Colin N. Dewey, Matthew N. Bernstein, 2021, iScience.

RNA-Seq gene expression estimation with read mapping uncertainty

Colin N. Dewey, Bo Li, James A. Thomson, 2009, Bioinform..

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema

Colin N. Dewey, Chris Barry, Bianca Habermann, 2013, PLoS Comput. Biol..

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping

Ye Zheng, Colin N. Dewey, Xin Zeng, 2015, PLoS Comput. Biol..

Sequence Surveyor: Leveraging Overview for Scalable Genomic Alignment Visualization

Michael Gleicher, Colin N. Dewey, Danielle Albers, 2011, IEEE Transactions on Visualization and Computer Graphics.

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

Colin N. Dewey, Cécile Ané, Bret R. Larget, 2010, Bioinform..

Hierarchical cell type classification using mass, heterogeneous RNA-seq data from human primary cells

Colin N. Dewey, Matthew N. Bernstein, M. Bernstein, 2019 .

Reconstructing latent periods in genome sequences with insertions and deletions

William A. Sethares, Raman Arora, Colin N. Dewey, 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics.

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

AnHai Doan, Colin N. Dewey, Matthew N. Bernstein, 2016 .

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans

Colin N. Dewey, L. Pachter, S. Lall, 2006, Current Biology.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Colin N. Dewey, Richard A. Moore, James B. Brown, 2007, Genome research.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Colin N. Dewey, Paul E. Boardman, David D. Shteynberg, 2004, Nature.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Lisa M. D'Souza, Colin N. Dewey, Martin S. Taylor, 2004, Nature.

Initial sequencing and comparative analysis of the mouse genome.

Colin N. Dewey, Simon C. Potter, James A. Cuff, 2002 .

The ENCODE (ENCyclopedia Of DNA Elements) Project

Paul T. Groth, William Stafford Noble, Colin N. Dewey, 2004, Science.

Genomic Variation in Natural Populations of Drosophila melanogaster

Colin N. Dewey, Matthew W. Hahn, Daniel R. Schrider, 2012, Genetics.

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Colin N. Dewey, Philip D. Blood, David A. Eccles, 2013, Nature Protocols.

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Colin N. Dewey, P. Kuan, S. Keleş, 2011, PLoS Comput. Biol..

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Colin N. Dewey, Mira V. Han, Matthew D. Rasmussen, 2007, Nature.

Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.

Colin N. Dewey, R. Stewart, Ning Leng, 2017, Developmental biology.

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

Colin N. Dewey, Matthew W. Hahn, E. Myers, 2007, PLoS biology.

Evolution at the nucleotide level: the problem of multiple whole-genome alignment.

Colin N. Dewey, L. Pachter, 2006, Human molecular genetics.

Parametric inference of recombination in HIV genomes

Colin N. Dewey, N. Beerenwinkel, Kevin M. Woods, 2005, q-bio/0512019.

Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns

Colin N. Dewey, E. Koonin, I. Rogozin, 2006, BMC Genomics.

Evaluation of de novo transcriptome assemblies from RNA-Seq data

Yongsheng Bai, Colin N. Dewey, Bo Li, 2014, Genome Biology.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Whole-genome alignments and polytopes for comparative genomics

Lior Pachter, Colin N. Dewey, L. Pachter, 2006 .

Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy

Colin N. Dewey, Satish K. Kotha, B. Larget, 2010 .

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

Michael Ott, Nir Friedman, Aviv Regev, 2013 .

Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project The ENCODE Project Consortium *

Colin N. Dewey, James B. Brown, Anason S. Halees, 2007 .

Rbm20 regulates titin alternative splicing as a splicing repressor

Colin N. Dewey, W. Guo, M. Greaser, 2013, Nucleic acids research.

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq

Colin N. Dewey, S. Keleş, P. Liu, 2016, Genome research.

A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP)

Colin N. Dewey, R. Stewart, D. Clegg, 2022, Comput. Biol. Chem..

Bicaudal-C spatially controls translation of vertebrate maternal mRNAs

Colin N. Dewey, M. Wickens, M. Sheets, 2013, RNA.

Cell type specific gene expression profiling reveals a role for the complement component C3A in neutrophil migration to tissue damage

Colin N. Dewey, S. Tauzin, A. Huttenlocher, 2019, bioRxiv.

Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo

Colin N. Dewey, Kirby D. Johnson, E. Bresnick, 2013, The Journal of experimental medicine.

Novel populations of CD4+ T cells associated with vaccine efficacy

Colin N. Dewey, M. Wüthrich, B. Klein, 2022, bioRxiv.

Distinctive populations of CD4+T cells associated with vaccine efficacy

Colin N. Dewey, B. Klein, Xin He, 2022, iScience.

Algebraic Statistics for Computational Biology: Parametric Sequence Alignment

Colin N. Dewey, Kevin M. Woods, 2005 .

Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation

Colin N. Dewey, E. Bresnick, K. Igarashi, 2016, EMBO reports.

Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.

Colin N. Dewey, O. Moskvin, Y. Grinblat, 2017, Developmental biology.

Whole-Genome Alignment.

Colin N. Dewey, 2019, Methods in molecular biology.

Fast Statistical Alignment : Text S 1

Lior Pachter, Jaeyoung Do, Ian Holmes, 2009 .

Cis-regulatory mechanisms governing stem and progenitor cell transitions

Colin N. Dewey, Kirby D. Johnson, E. Ranheim, 2015, Science Advances.

Aligning multiple whole genomes with Mercator and MAVID.

Colin N. Dewey, Colin N Dewey, 2007, Methods in molecular biology.

Fine-Scale Phylogenetic Discordance across the House Mouse Genome

Colin N. Dewey, B. Payseur, B. Larget, 2009, PLoS genetics.

Whole-genome alignment.

Colin N. Dewey, Colin N Dewey, 2012, Methods in molecular biology.

PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways

Colin N. Dewey, N. Ahmad, C. Singh, 2020, Molecular Cancer Therapeutics.

Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs

Colin N. Dewey, B. Payseur, Mark J Nolte, 2020, Genome biology and evolution.

Cell type specific gene expression profiling reveals a role for complement component C3 in neutrophil responses to tissue damage

Colin N. Dewey, S. Tauzin, A. Huttenlocher, 2020, Scientific Reports.

Learning Probabilistic Splice Graphs from RNA-Seq data

Colin N. Dewey, Laura H. LeGault, Colin N. Dewey, 2010 .

Detectability of Varied Hybridization Scenarios using Genome-Scale Hybrid Detection Methods

Colin N. Dewey, Erin K. Molloy, Claudia R. Solís-Lemus, 2022, 2211.00712.

RNA-regulatory exosome complex suppresses an apoptotic program to confer erythroid progenitor cell survival in vivo

Colin N. Dewey, Kirby D. Johnson, Uttiya Basu, 2022, Blood advances.

Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

Colin N. Dewey, R. Gourse, W. Ross, 2019, Proceedings of the National Academy of Sciences.

RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis

Colin N. Dewey, E. Bresnick, D. Matson, 2021, Nucleic acids research.

GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia.

Colin N. Dewey, S. Keleş, J. Coon, 2017, Developmental cell.

Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.

Colin N. Dewey, Kirby D. Johnson, S. Keleş, 2015, Molecular cell.

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.

Simon Cawley, Lior Pachter, Marina Alexandersson, 2004, Genome research.

Cell Type-Specific Transcriptome Profiling Reveals a Role for Thioredoxin During Tumor Initiation

Colin N. Dewey, A. Huttenlocher, David A Bennin, 2022, Frontiers in Immunology.

Annotating cell types in human single-cell RNA-seq data with CellO

Colin N. Dewey, M. Bernstein, 2021, STAR protocols.

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Colin N. Dewey, Philip D. Blood, Richard D. LeDuc, 2013, Nature Protocols.

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

Colin N. Dewey, E. Myers, L. Pachter, 2007, PLoS biology.

Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation

Colin N. Dewey, E. Bresnick, K. Igarashi, 2016, EMBO reports.

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

Colin N. Dewey, Philip D. Blood, Richard D. LeDuc, 2013 .