Publications by authors named "Shawn Cokus"

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Mitochondrial reactive oxygen species regulate acetyl-CoA flux between cytokine production and fatty acid synthesis in effector T cells.
Beibei Wu, Jin Seok Woo, Spyridon Hasiakos, Calvin Pan, Shawn Cokus

Cell Rep· March 2025

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High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.
Victoria L Sork, Shawn J Cokus, Sorel T Fitz-Gibbon, Aleksey V Zimin, Daniela Puiu

Nat Commun· April 2022

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Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies.
Min Chen, Jer-Young Lin, Xiaomeng Wu, Nestor R Apuya, Kelli F Henry, Shawn Cokus

Proc Natl Acad Sci U S A· February 2021

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Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos.
Shawn J Cokus, Maricruz De La Torre, Eric F Medina, Jeffrey P Rasmussen, Joselyn Ramirez-Gutierrez

G3 (Bethesda)· October 2019

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Chromosome-level genome assembly and transcriptome of the green alga illuminates astaxanthin production.
Melissa S Roth, Shawn J Cokus, Sean D Gallaher, Andreas Walter, David Lopez

Proc Natl Acad Sci U S A· May 2017

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Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage.
Wei Feng, Christopher J Hale, Ryan S Over, Shawn J Cokus, Steven E Jacobsen

Proc Natl Acad Sci U S A· January 2017

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Genome and methylome of the oleaginous diatom reveal genetic flexibility toward a high lipid phenotype.
Jesse C Traller, Shawn J Cokus, David A Lopez, Olga Gaidarenko, Sarah R Smith

Biotechnol Biofuels· November 2016

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A naïve Bayesian classifier for identifying plant microRNAs.
Stephen Douglass, Ssu-Wei Hsu, Shawn Cokus, Robert B Goldberg, John J Harada

Plant J· June 2016

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MTHFD1 controls DNA methylation in Arabidopsis.
Martin Groth, Guillaume Moissiard, Markus Wirtz, Haifeng Wang, Carolina Garcia-Salinas, Shawn J Cokus

Nat Commun· June 2016

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Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks.
Shawn J Cokus, Paul F Gugger, Victoria L Sork

BMC Genomics· July 2015

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Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis.
Suhua Feng, Shawn J Cokus, Veit Schubert, Jixian Zhai, Matteo Pellegrini

Mol Cell· September 2014

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BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun

BMC Genomics· November 2013

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Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates.
Laura J Marinelli, Sorel Fitz-Gibbon, Clarmyra Hayes, Charles Bowman, Megan Inkeles, Shawn Cokus

mBio· January 2013

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MORC family ATPases required for heterochromatin condensation and gene silencing.
Guillaume Moissiard, Shawn J Cokus, Joshua Cary, Suhua Feng, Allison C Billi

Science· June 2012

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Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas.
Nanette R Boyle, Mark Dudley Page, Bensheng Liu, Ian K Blaby, David Casero, Shawn J Cokus

J Biol Chem· May 2012

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Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.
David Lopez, David Casero, Shawn J Cokus, Sabeeha S Merchant, Matteo Pellegrini

BMC Bioinformatics· July 2011

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Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.
Madeli Castruita, David Casero, Steven J Karpowicz, Janette Kropat, Astrid Vieler, Shawn Cokus

Plant Cell· April 2011

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Identification of genes required for de novo DNA methylation in Arabidopsis.
Maxim V C Greenberg, Israel Ausin, Simon W L Chan, Shawn J Cokus, Josh T Cuperus

Epigenetics· March 2011

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Relationship between nucleosome positioning and DNA methylation.
Ramakrishna K Chodavarapu, Suhua Feng, Yana V Bernatavichute, Pao-Yang Chen, Hume Stroud, Shawn J Cokus

Nature· July 2010

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RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival.
David González-Ballester, David Casero, Shawn Cokus, Matteo Pellegrini, Sabeeha S Merchant

Plant Cell· June 2010

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Conservation and divergence of methylation patterning in plants and animals.
Suhua Feng, Shawn J Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick

Proc Natl Acad Sci U S A· May 2010

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BS Seeker: precise mapping for bisulfite sequencing.
Pao-Yang Chen, Shawn J Cokus, Matteo Pellegrini

BMC Bioinformatics· April 2010

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Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.
Christian Popp, Wendy Dean, Suhua Feng, Shawn J Cokus, Simon Andrews

Nature· February 2010

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Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.
Einat Sprinzak, Shawn J Cokus, Todd O Yeates, David Eisenberg, Matteo Pellegrini

BMC Syst Biol· December 2009

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Copy number variation influences gene expression and metabolic traits in mice.
Luz D Orozco, Shawn J Cokus, Anatole Ghazalpour, Leslie Ingram-Drake, Susanna Wang

Hum Mol Genet· November 2009

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