Publications by authors named "Colin Dewey"

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IsoBayes: a Bayesian approach for single-isoform proteomics inference.
Jordy Bollon, Michael R Shortreed, Erin Jeffery, Ben T Jordan, Rachel Miller, Colin N Dewey

Bioinformatics· August 2025

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: a Bayesian approach for single-isoform proteomics inference.
Jordy Bollon, Michael R Shortreed, Ben T Jordan, Rachel Miller, Erin Jeffery, Colin Dewey

bioRxiv· May 2025

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Deletion detection in SARS-CoV-2 genomes using multiplex-PCR sequencing from COVID-19 patients: elimination of false positives.
Nan Jiang, Colin N Dewey, John Yin

medRxiv· April 2025

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Infection induced inflammation impairs wound healing through IL-1β signaling.
Simone Shen, Veronika Miskolci, Colin N Dewey, John-Demian Sauer, Anna Huttenlocher

iScience· April 2024

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RNA-regulatory exosome complex suppresses an apoptotic program to confer erythroid progenitor cell survival in vivo.
Isabela Fraga de Andrade, Kirby D Johnson, Charu Mehta, Colin N Dewey, Uttiya Basu

Blood Adv· February 2023

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A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP).
Huishi Toh, Atefeh Bagheri, Colin Dewey, Ron Stewart, Lili Yan

Comput Biol Chem· February 2023

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Distinctive populations of CD4T cells associated with vaccine efficacy.
Therese Woodring, Colin N Dewey, Lucas Dos Santos Dias, Xin He, Hannah E Dobson

iScience· September 2022

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Cell Type-Specific Transcriptome Profiling Reveals a Role for Thioredoxin During Tumor Initiation.
Benjamin G Korte, Morgan A Giese, Gayathri Ramakrishnan, Stella Ma, David Bennin, Colin N Dewey

Front Immunol· May 2022

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RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis.
Charu Mehta, Isabela Fraga de Andrade, Daniel R Matson, Colin N Dewey, Emery H Bresnick

Nucleic Acids Res· September 2021

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Annotating cell types in human single-cell RNA-seq data with CellO.
Matthew N Bernstein, Colin N Dewey

STAR Protoc· September 2021

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PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways.
Shengqin Su, Gagan Chhabra, Mary A Ndiaye, Chandra K Singh, Ting Ye, Colin N Dewey

Mol Cancer Ther· January 2021

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CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology.
Matthew N Bernstein, Zhongjie Ma, Michael Gleicher, Colin N Dewey

iScience· January 2021

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PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.
Peng Liu, Alexandra A Soukup, Emery H Bresnick, Colin N Dewey, Sündüz Keleş

Genome Res· November 2020

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Cell type specific gene expression profiling reveals a role for complement component C3 in neutrophil responses to tissue damage.
Ruth A Houseright, Emily E Rosowski, Pui-Ying Lam, Sebastien J M Tauzin, Oscar Mulvaney, Colin N Dewey

Sci Rep· September 2020

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Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs.
Mark J Nolte, Peicheng Jing, Colin N Dewey, Bret A Payseur

Genome Biol Evol· August 2020

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Whole-Genome Alignment.
Colin N Dewey

Methods Mol Biol· January 2020

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Genome-wide effects on transcription from ppGpp binding to its two sites on RNA polymerase.
Patricia Sanchez-Vazquez, Colin N Dewey, Nicole Kitten, Wilma Ross, Richard L Gourse

Proc Natl Acad Sci U S A· April 2019

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MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.
Matthew N Bernstein, AnHai Doan, Colin N Dewey

Bioinformatics· September 2017

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Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.
Irina Sedykh, Baul Yoon, Laura Roberson, Oleg Moskvin, Colin N Dewey

Dev Biol· September 2017

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GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia.
Kyle J Hewitt, Koichi R Katsumura, Daniel R Matson, Prithvia Devadas, Nobuyuki Tanimura, Colin N Dewey

Dev Cell· August 2017

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Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.
Peng Jiang, Jeffrey D Nelson, Ning Leng, Michael Collins, Scott Swanson, Colin N Dewey

Dev Biol· June 2017

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Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq.
Peng Liu, Rajendran Sanalkumar, Emery H Bresnick, Sündüz Keleş, Colin N Dewey

Genome Res· August 2016

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Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation.
Nobuyuki Tanimura, Eli Miller, Kazuhiko Igarashi, David Yang, Judith N Burstyn, Colin N Dewey

EMBO Rep· February 2016

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Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.
Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N Dewey

PLoS Comput Biol· October 2015

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Cis-regulatory mechanisms governing stem and progenitor cell transitions.
Kirby D Johnson, Guangyao Kong, Xin Gao, Yuan-I Chang, Kyle J Hewitt, Colin N Dewey

Sci Adv· September 2015

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