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ArticlesPeer ReviewedFull Text
BS Seeker: precise mapping for bisulfite sequencing
Author / Creator:Chen, Pao-Yang ; Cokus, Shawn J ; Pellegrini, Matteo
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2010-04, Vol.11 (1), p.203-203, Article 203
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Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency
Author / Creator:Popp, Christian ; Dean, Wendy ; Feng, Suhua ; Cokus, Shawn J. ; Andrews, Simon ; Pellegrini, Matteo ; Jacobsen, Steven E. ; Reik, Wolf
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2010-02, Vol.463 (7284), p.1101-1105
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ArticlesPeer ReviewedFull Text
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Author / Creator:Cokus, Shawn J ; Feng, Suhua ; Zhang, Xiaoyu ; Chen, Zugen ; Merriman, Barry ; Haudenschild,Christian D ; Pradhan, Sriharsa ; Nelson, Stanley F ; Pellegrini, Matteo ; Jacobsen, Steven E
Publisher:London: Nature Publishing Group UK
Journal title:Nature, 2008-03, Vol.452 (7184), p.215-219
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ArticlesPeer ReviewedFull Text
Conservation and divergence of methylation patterning in plants and animals
Author / Creator:Feng, Suhua ; Cokus, Shawn J ; Zhang, Xiaoyu ; Chen, Pao-Yang ; Bostick, Magnolia ; Goll, Mary G ; Hetzel, Jonathan ; Jain, Jayati ; Strauss, Steven H ; Halpern, Marnie E ; Ukomadu, Chinweike ; Sadler, Kirsten C ; Pradhan, Sriharsa ; Pellegrini, Matteo ; Jacobsen, Steven E
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2010-05, Vol.107 (19), p.8689-8694
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High-quality genome and methylomes illustrate features underlying evolutionary success of oaks
Author / Creator:Sork, Victoria L. ; Cokus, Shawn J. ; Fitz-Gibbon, Sorel T. ; Zimin, Aleksey V. ; Puiu, Daniela ; Garcia, Jesse A. ; Gugger, Paul F. ; Henriquez, Claudia L. ; Zhen, Ying ; Lohmueller, Kirk E. ; Pellegrini, Matteo ; Salzberg, Steven L.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-04, Vol.13 (1), p.2047-15, Article 2047
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Relationship between nucleosome positioning and DNA methylation
Author / Creator:Chodavarapu, Ramakrishna K. ; Feng, Suhua ; Bernatavichute, Yana V. ; Chen, Pao-Yang ; Stroud, Hume ; Yu, Yanchun ; Hetzel, Jonathan A. ; Kuo, Frank ; Kim, Jin ; Cokus, Shawn J. ; Casero, David ; Bernal, Maria ; Huijser, Peter ; Clark, Amander T. ; Krämer, Ute ; Merchant, Sabeeha S. ; Zhang, Xiaoyu ; Jacobsen, Steven E. ; Pellegrini, Matteo
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2010-07, Vol.466 (7304), p.388-392
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ArticlesPeer ReviewedFull Text
MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing
Author / Creator:Moissiard, Guillaume ; Cokus, Shawn J. ; Cary, Joshua ; Feng, Suhua ; Billi, Allison C. ; Stroud, Hume ; Husmann, Dylan ; Zhan, Ye ; Lajoie, Bryan R. ; McCord, Rachel Patton ; Hale, Christopher J. ; Feng, Wei ; Michaels, Scott D. ; Frand, Alison R. ; Pellegrini, Matteo ; Dekker, Job ; Kim, John K. ; Jacobsen, Steven E.
Publisher:Washington, DC: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2012-06, Vol.336 (6087), p.1448-1451
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ArticlesPeer ReviewedFull Text
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data
Author / Creator:Lopez, David ; Casero, David ; Cokus, Shawn J ; Merchant, Sabeeha S ; Pellegrini, Matteo
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2011-07, Vol.12 (1), p.282-282, Article 282
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Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage
Author / Creator:Feng, Wei ; Hale, Christopher J. ; Over, Ryan S. ; Cokus, Shawn J. ; Jacobsen, Steven E. ; Michaels, Scott D.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2017-01, Vol.114 (2), p.406-411
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ArticlesPeer ReviewedFull Text
MTHFD1 controls DNA methylation in Arabidopsis
Author / Creator:Groth, Martin ; Moissiard, Guillaume ; Wirtz, Markus ; Wang, Haifeng ; Garcia-Salinas, Carolina ; Ramos-Parra, Perla A. ; Bischof, Sylvain ; Feng, Suhua ; Cokus, Shawn J. ; John, Amala ; Smith, Danielle C. ; Zhai, Jixian ; Hale, Christopher J. ; Long, Jeff A. ; Hell, Ruediger ; Díaz de la Garza, Rocío I. ; Jacobsen, Steven E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2016-06, Vol.7 (1), p.11640-13, Article 11640
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ArticlesPeer ReviewedFull Text
Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos
Author / Creator:Cokus, Shawn J ; Maricruz De La Torre ; Medina, Eric F ; Rasmussen, Jeffrey P ; Ramirez-Gutierrez, Joselyn ; Sagasti, Alvaro ; Wang, Fang
Publisher:Oxford: Oxford University Press
Journal title:G3 : genes - genomes - genetics, 2019-10, Vol.9 (10), p.3439-3452
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ArticlesPeer ReviewedFull Text
Use of Logic Relationships to Decipher Protein Network Organization
Author / Creator:Bowers, Peter M ; Cokus, Shawn J ; Eisenberg, David ; Yeates, Todd O
Publisher:Washington, DC: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2004-12, Vol.306 (5705), p.2246-2249
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ArticlesPeer ReviewedFull Text
Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production
Author / Creator:Roth, Melissa S. ; Cokus, Shawn J. ; Gallaher, Sean D. ; Walter, Andreas ; Lopez, David ; Erickson, Erika ; Endelman, Benjamin ; Westcott, Daniel ; Larabell, Carolyn A. ; Merchant, Sabeeha S. ; Pellegrini, Matteo ; Niyogi, Krishna K.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2017-05, Vol.114 (21), p.E4296-E4305
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Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype
Author / Creator:Traller, Jesse C ; Cokus, Shawn J ; Lopez, David A ; Gaidarenko, Olga ; Smith, Sarah R ; McCrow, John P ; Gallaher, Sean D ; Podell, Sheila ; Thompson, Michael ; Cook, Orna ; Morselli, Marco ; Jaroszewicz, Artur ; Allen, Eric E ; Allen, Andrew E ; Merchant, Sabeeha S ; Pellegrini, Matteo ; Hildebrand, Mark
Publisher:England: BioMed Central Ltd
Journal title:Biotechnology for biofuels, 2016-11, Vol.9 (1), p.258-258, Article 258
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Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression
Author / Creator:Sprinzak, Einat ; Cokus, Shawn J ; Yeates, Todd O ; Eisenberg, David ; Pellegrini, Matteo
Publisher:England: BioMed Central Ltd
Journal title:BMC systems biology, 2009-12, Vol.3 (1), p.115-115, Article 115
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Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae
Author / Creator:Pham, Hung ; Ferrari, Roberto ; Cokus, Shawn J ; Kurdistani, Siavash K ; Pellegrini, Matteo
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2007, Vol.3 (1), p.153-n/a
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Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks
Author / Creator:Cokus, Shawn J ; Gugger, Paul F ; Sork, Victoria L
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2015-07, Vol.16 (1), p.552-552, Article 552
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Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)
Author / Creator:Gugger, Paul F. ; Cokus, Shawn J. ; Sork, Victoria L.
Publisher:Berlin/Heidelberg: Springer Berlin Heidelberg
Journal title:Tree genetics & genomes, 2016-04, Vol.12 (2), p.1-14, Article 15
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Growth of the Fucus embryo: insights into wall-mediated cell expansion through mechanics and transcriptomics
Author / Creator:Linardić, Marina ; Cokus, Shawn J ; Pellegrini, Matteo ; Braybrook, Siobhan Ariel
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-01
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ArticlesPeer ReviewedFull Text
Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production
Author / Creator:Roth, Melissa S. ; Cokus, Shawn J. ; Gallaher, Sean D. ; Walter, Andreas ; Lopez, David ; Erickson, Erika ; Endelman, Benjamin ; Westcott, Daniel ; Larabell, Carolyn A. ; Merchant, Sabeeha S. ; Pellegrini, Matteo ; Niyogi, Krishna K.
Publisher:United States: National Academy of Sciences, Washington, DC (United States)
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2017-05, Vol.114 (21)
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Showing 1 to 20 of 24 results

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BS Seeker: precise mapping for bisulfite sequencing

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Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

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Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

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Conservation and divergence of methylation patterning in plants and animals

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High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

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Relationship between nucleosome positioning and DNA methylation

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MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

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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

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Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage

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MTHFD1 controls DNA methylation in Arabidopsis

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Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos

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Use of Logic Relationships to Decipher Protein Network Organization

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Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

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Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

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Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression

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Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae

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Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks

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Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)

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Growth of the Fucus embryo: insights into wall-mediated cell expansion through mechanics and transcriptomics

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Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

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