Shawn J. Cokus: search on Z-Library

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1

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

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, Matt

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 2.16 MB

english, 2017

2

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, Scott I. Hsieh, Weihong Yan, Shawn Cokus, Joseph A. Loo, Christoph Benning, Matteo Pellegrini and Sabeeha S. Merchan

Journal:

Year:

2011

Language:

english

File:

PDF, 3.58 MB

english, 2011

3

Decomposition Theorems for Conditional Sign-Solvability and Sign-Solvability of General Systems

Cokus, Shawn, Klee, Victor

Journal:

SIAM Journal on Matrix Analysis and Applications

Year:

2000

Language:

english

File:

PDF, 182 KB

english, 2000

4

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

Bernatavichute, Yana V., Zhang, Xiaoyu, Cokus, Shawn, Pellegrini, Matteo, Jacobsen, Steven E., Dilkes, Brian P.

Journal:

Year:

2008

Language:

english

File:

PDF, 764 KB

english, 2008

5

Genome and methylome of the oleaginous diatomCyclotella crypticareveal genetic flexibility toward a high lipid phenotype

Jesse C. Traller,Shawn J. Cokus,David A. Lopez…

Journal:

Biotechnology for Biofuels

Year:

2016

Language:

english

File:

PDF, 4.12 MB

english, 2016

6

Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis

Zhang, Xiaoyu, Clarenz, Oliver, Cokus, Shawn, Bernatavichute, Yana V, Pellegrini, Matteo, Goodrich, Justin, Jacobsen, Steven E, Carrington, James C

Journal:

Year:

2007

Language:

english

File:

PDF, 1.68 MB

english, 2007

7

Identification of genes required for de novo DNA methylation in Arabidopsis

Greenberg, Maxim V.C., Ausin, Israel, Chan, Simon W.L., Cokus, Shawn J., Cuperus, Josh T., Feng, Suhua, Law, Julie A., Chu, Carolyn, Pellegrini, Matteo, Carrington, James C., Jacobsen, Steven E.

Journal:

Year:

2011

Language:

english

File:

PDF, 4.75 MB

english, 2011

8

On the hardness of efficiently approximating maximal non-L submatrices

Andreas Brieden, Shawn Cokus

Journal:

Linear Algebra and its Applications

Year:

2004

Language:

english

File:

PDF, 206 KB

english, 2004

9

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

Cokus, Shawn J., De La Torre, Maricruz, Medina, Eric F., Rasmussen, Jeffrey P., Ramirez-Gutierrez, Joselyn, Sagasti, Alvaro, Wang, Fang

Journal:

G3 Genes|Genome|Genetics

Year:

2019

File:

PDF, 2.67 MB

2019

10

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

Guo, Weilong, Fiziev, Petko, Yan, Weihong, Cokus, Shawn, Sun, Xueguang, Zhang, Michael Q, Chen, Pao-Yang, Pellegrini, Matteo

Journal:

Year:

2013

Language:

english

File:

PDF, 349 KB

english, 2013

11

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

Feng, Suhua, Cokus, Shawn J., Schubert, Veit, Zhai, Jixian, Pellegrini, Matteo, Jacobsen, Steven E.

Journal:

Year:

2014

Language:

english

File:

PDF, 8.13 MB

english, 2014

12

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

Cokus, Shawn J., Gugger, Paul F., Sork, Victoria L.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.98 MB

english, 2015

13

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

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 482 KB

english, 2009

14

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W.-L. Chan, Huaming Chen, Ian R. Henderson, Paul Shinn, Matteo Pellegrini, Steve E. Jacobsen, Joseph R. Ecker

Journal:

Year:

2006

Language:

english

File:

PDF, 1021 KB

english, 2006

15

Relationship between nucleosome positioning and DNA methylation

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,

Journal:

Year:

2010

Language:

english

File:

PDF, 1.16 MB

english, 2010

16

MTHFD1 controls DNA methylation in Arabidopsis

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., Zha

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.66 MB

english, 2016

17

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 inArabidopsis thaliana

Xiaoyu Zhang, Yana V Bernatavichute, Shawn Cokus, Matteo Pellegrini…

Journal:

Year:

2009

Language:

english

File:

PDF, 854 KB

english, 2009

18

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

Popp, Christian, Dean, Wendy, Feng, Suhua, Cokus, Shawn J., Andrews, Simon, Pellegrini, Matteo, Jacobsen, Steven E., Reik, Wolf

Journal:

Year:

2010

Language:

english

File:

PDF, 721 KB

english, 2010

19

BS Seeker: precise mapping for bisulfite sequencing

Pao-Yang Chen, Shawn J Cokus, Matteo Pellegrini

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

20

Correction: 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 and Arthur R. Grossman

Journal:

Year:

2011

Language:

english

File:

PDF, 219 KB

english, 2011

21

Conservation and divergence of methylation patterning in plants and animals

Suhua Feng, Shawn J. Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G. Goll, Jonathan Hetzel, Jayati Jain, Steven H. Strauss, Marnie E. Halpern, Chinweike Ukomadu, Kirsten C. Sadler, Sriha

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.47 MB

english, 2010

22

RNA-Seq Analysis of Sulfur-DeprivedChlamydomonasCells Reveals Aspects of Acclimation Critical for Cell Survival

David González-Ballester, David Casero, Shawn Cokus, Matteo Pellegrini, Sabeeha S. Merchant and Arthur R. Grossman

Journal:

Year:

2010

Language:

english

File:

PDF, 4.68 MB

english, 2010

23

Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae

Pham, Hung, Ferrari, Roberto, Cokus, Shawn J, Kurdistani, Siavash K, Pellegrini, Matteo

Journal:

Molecular Systems Biology

Year:

2007

Language:

english

File:

PDF, 247 KB

english, 2007

24

Modelling the network of cell cycle transcription factors in the yeastSaccharomyces cerevisiae

Shawn Cokus, Sherri Rose, David Haynor, Niels Grønbech-Jensen, Matteo Pellegrini

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1004 KB

english, 2006

25

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

Cokus, Shawn J., Feng, Suhua, Zhang, Xiaoyu, Chen, Zugen, Merriman, Barry, Haudenschild, Christian D., Pradhan, Sriharsa, Nelson, Stanley F., Pellegrini, Matteo, Jacobsen, Steven E.

Journal:

Year:

2008

Language:

english

File:

PDF, 1.26 MB

english, 2008

26

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

Feng, Wei, Hale, Christopher J., Over, Ryan S., Cokus, Shawn J., Jacobsen, Steven E., Michaels, Scott D.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.35 MB

english, 2017

27

An improved method for identifying functionally linked proteins using phylogenetic profiles

Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 418 KB

english, 2007

28

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

Gugger, Paul F., Cokus, Shawn J., Sork, Victoria L.

Journal:

Tree Genetics & Genomes

Year:

2016

Language:

english

File:

PDF, 1.80 MB

english, 2016

29

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

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.52 MB

english, 2011

30

Utilizing logical relationships in genomic data to decipher cellular processes

Peter M. Bowers, Brian D. O'Connor, Shawn J. Cokus, Einat Sprinzak, Todd O. Yeates, David Eisenberg

Journal:

Year:

2005

Language:

english

File:

PDF, 529 KB

english, 2005

31

ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing

Jacob, Yannick, Feng, Suhua, LeBlanc, Chantal A, Bernatavichute, Yana V, Stroud, Hume, Cokus, Shawn, Johnson, Lianna M, Pellegrini, Matteo, Jacobsen, Steven E, Michaels, Scott D

Journal:

Nature Structural and Molecular Biology

Year:

2009

Language:

english

File:

PDF, 508 KB

english, 2009

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