Author details

Full Name

Colin N Dewey

Affiliation

ORCID

Career Start Year

2002

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36436489	A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP).		2023
36161469	RNA-regulatory exosome complex suppresses an apoptotic program to confer erythroid progenitor cell survival inÂ vivo.	Blood Adv	2023
35250998	Cell Type-Specific Transcriptome Profiling Reveals a Role for Thioredoxin During Tumor Initiation.	Frontiers in Immunology	2022
36060075	Distinctive populations of CD4T cells associated with vaccine efficacy.	iScience	2022
34458864	Annotating cell types in human single-cell RNA-seq data with CellO.	STAR Protocols	2021
34059908	RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis.	Nucleic Acids Research	2021
33364592	CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology.	iScience	2021
33177155	PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways.	Molecular Cancer Therapeutics	2021
32958497	PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.	Genome Research	2020
32531054	Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs.	Genome Biology and Evolution	2020
32973200	Cell type specific gene expression profiling reveals a role for complement component C3 in neutrophil responses to tissue damage.	Scientific Reports	2020
30971496	Genome-wide effects on transcription from ppGpp binding to its two sites on RNA polymerase.	Proceedings of the National Academy of Sciences of the United States of America	2019
31278663	Whole-Genome Alignment.	Methods in Molecular Biology	2019
27475628	Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.	Developmental Biology	2017
28689736	Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.	Developmental Biology	2017
28535296	MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.		2017
28787589	GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia.	Dev Cell	2017
26698166	Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation.	EMBO Reports	2016
27405803	Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq.	Genome Research	2016
26484757	Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.	PLoS Computational Biology	2015
25847007	EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.	Bioinformatics	2015
26601269	Cis-regulatory mechanisms governing stem and progenitor cell transitions.	Science advances	2015
26073540	Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.	Mol Cell	2015
25608678	Evaluation of de novo transcriptome assemblies from RNA-Seq data.		2014
23505351	Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.	PLoS Comput Biol	2013
24297994	Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo.	Journal of Experimental Medicine	2013
23846746	Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.		2013
23845962	De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.	Nat Protoc	2013
24062572	Bicaudal-C spatially controls translation of vertebrate maternal mRNAs.	RNA	2013
23307558	Rbm20 regulates titin alternative splicing as a splicing repressor.	Nucleic Acids Research	2013
22407711	Whole-genome alignment.	Methods in Molecular Biology	2012
22673804	Genomic variation in natural populations of Drosophila melanogaster.	Genetics	2012
21816040	RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.	BMC Bioinformatics	2011
22034360	Sequence Surveyor: leveraging overview for scalable genomic alignment visualization.		2011
21705766	Positional orthology: putting genomic evolutionary relationships into context.	Briefings in Bioinformatics	2011
21779159	Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.	PLoS Computational Biology	2011
20022975	RNA-Seq gene expression estimation with read mapping uncertainty.		2010
20861028	BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.		2010
19936022	Fine-scale phylogenetic discordance across the house mouse genome.	PLoS Genetics	2009
19478997	Fast statistical alignment.	PLoS Comput Biol	2009
17571346	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.	Nature	2007
17567995	Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.	Genome Res	2007
17994088	Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.	Nature	2007
17993677	Aligning multiple whole genomes with Mercator and MAVID.	Methods in Molecular Biology	2007
17988176	Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.	PLoS Biol	2007
16651369	Evolution at the nucleotide level: the problem of multiple whole-genome alignment.	Human Molecular Genetics	2006
17156453	Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns.	BMC Genomics	2006
16458514	A genome-wide map of conserved microRNA targets in C. elegans.	Curr Biol	2006
16789815	Parametric alignment of Drosophila genomes.	PLoS Comput Biol	2006
15057822	Genome sequence of the Brown Norway rat yields insights into mammalian evolution.	Nature	2004