List of works - Colin N Dewey

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

scientific article published in March 2006

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

scientific article published on April 2004

Aligning multiple whole genomes with Mercator and MAVID.

scientific article

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

scientific article published in June 2007

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

scientific article

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

scientific article published on 17 August 2021

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

scientific article

Bicaudal-C spatially controls translation of vertebrate maternal mRNAs

scientific article published on 23 September 2013

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

scientific article published on 24 September 2020

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

journal article from 'iScience' published in 2021

Cis-regulatory mechanisms governing stem and progenitor cell transitions

scientific article

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.

scientific article

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

scientific article published on 8 December 2006

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

scientific article (publication date: August 2013)

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data

scientific article

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

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

scientific article published on 5 April 2015

Evaluation of de novo transcriptome assemblies from RNA-Seq data

scientific article

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

scientific article

Fast statistical alignment

scientific article

Fine-scale phylogenetic discordance across the house mouse genome

scientific article

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

scientific article published on August 2017

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

scientific article

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

scientific article

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

scientific article published on 10 April 2019

Genomic variation in natural populations of Drosophila melanogaster

scientific article published on 5 June 2012

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

scientific article published on 12 June 2020

Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome

scientific article

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

scientific article published in June 2007

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

scientific article

Initial sequencing and comparative analysis of the mouse genome

scientific article

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

scientific article published on 12 July 2016

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

scientific article published on 23 December 2015

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

scientific article published on 11 November 2020

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

scientific article published on 21 September 2020

Parametric alignment of Drosophila genomes

scientific article

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

scientific article published on 20 October 2015

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

scientific article

Positional orthology: putting genomic evolutionary relationships into context ⬇️

scientific article published on June 24, 2011

RNA-Seq gene expression estimation with read mapping uncertainty

scientific article published on 18 December 2009

RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis

scientific article published on 01 September 2021

Rbm20 regulates titin alternative splicing as a splicing repressor

scientific article published on 9 January 2013

Sequence Surveyor: leveraging overview for scalable genomic alignment visualization

scientific article published in December 2011

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

scientific article

Whole-Genome Alignment

scientific article published on 01 January 2019

Whole-genome alignment

scientific article published on January 2012

List of works by Colin N Dewey

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

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

Aligning multiple whole genomes with Mercator and MAVID.

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

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

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

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

Bicaudal-C spatially controls translation of vertebrate maternal mRNAs

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

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

Cis-regulatory mechanisms governing stem and progenitor cell transitions

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.

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

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

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

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

Evaluation of de novo transcriptome assemblies from RNA-Seq data

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

Fast statistical alignment

Fine-scale phylogenetic discordance across the house mouse genome

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

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

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

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

Genomic variation in natural populations of Drosophila melanogaster

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

Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome

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

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

Initial sequencing and comparative analysis of the mouse genome

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

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

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

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

Parametric alignment of Drosophila genomes

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

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

Positional orthology: putting genomic evolutionary relationships into context ⬇️

RNA-Seq gene expression estimation with read mapping uncertainty

RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis

Rbm20 regulates titin alternative splicing as a splicing repressor

Sequence Surveyor: leveraging overview for scalable genomic alignment visualization

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

Whole-Genome Alignment

Whole-genome alignment