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Items: 21

1.

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

Cokus SJ, De La Torre M, Medina EF, Rasmussen JP, Ramirez-Gutierrez J, Sagasti A, Wang F.

G3 (Bethesda). 2019 Oct 7;9(10):3439-3452. doi: 10.1534/g3.119.400402.

2.

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

Roth MS, Cokus SJ, Gallaher SD, Walter A, Lopez D, Erickson E, Endelman B, Westcott D, Larabell CA, Merchant SS, Pellegrini M, Niyogi KK.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4296-E4305. doi: 10.1073/pnas.1619928114. Epub 2017 May 8.

3.

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

Feng W, Hale CJ, Over RS, Cokus SJ, Jacobsen SE, Michaels SD.

Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):406-411. doi: 10.1073/pnas.1619774114. Epub 2016 Dec 27.

4.

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

Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M.

Biotechnol Biofuels. 2016 Nov 25;9:258. eCollection 2016.

5.

MTHFD1 controls DNA methylation in Arabidopsis.

Groth M, Moissiard G, Wirtz M, Wang H, Garcia-Salinas C, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Díaz de la Garza RI, Jacobsen SE.

Nat Commun. 2016 Jun 13;7:11640. doi: 10.1038/ncomms11640.

6.

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

Cokus SJ, Gugger PF, Sork VL.

BMC Genomics. 2015 Jul 28;16:552. doi: 10.1186/s12864-015-1761-4.

7.

Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis.

Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE.

Mol Cell. 2014 Sep 4;55(5):694-707. doi: 10.1016/j.molcel.2014.07.008. Epub 2014 Aug 14.

8.

MORC family ATPases required for heterochromatin condensation and gene silencing.

Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, Jacobsen SE.

Science. 2012 Jun 15;336(6087):1448-51. doi: 10.1126/science.1221472. Epub 2012 May 3.

9.

Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas.

Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS.

J Biol Chem. 2012 May 4;287(19):15811-25. doi: 10.1074/jbc.M111.334052. Epub 2012 Mar 8.

10.

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.

Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M.

BMC Bioinformatics. 2011 Jul 12;12:282. doi: 10.1186/1471-2105-12-282.

11.

Identification of genes required for de novo DNA methylation in Arabidopsis.

Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE.

Epigenetics. 2011 Mar;6(3):344-54. Epub 2011 Mar 1.

12.

Relationship between nucleosome positioning and DNA methylation.

Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M.

Nature. 2010 Jul 15;466(7304):388-92. doi: 10.1038/nature09147. Epub 2010 May 30.

13.

BS Seeker: precise mapping for bisulfite sequencing.

Chen PY, Cokus SJ, Pellegrini M.

BMC Bioinformatics. 2010 Apr 23;11:203. doi: 10.1186/1471-2105-11-203.

14.

Conservation and divergence of methylation patterning in plants and animals.

Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE.

Proc Natl Acad Sci U S A. 2010 May 11;107(19):8689-94. doi: 10.1073/pnas.1002720107. Epub 2010 Apr 15.

15.

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

Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W.

Nature. 2010 Feb 25;463(7284):1101-5. doi: 10.1038/nature08829.

16.

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

Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M.

BMC Syst Biol. 2009 Dec 14;3:115. doi: 10.1186/1752-0509-3-115.

17.

Copy number variation influences gene expression and metabolic traits in mice.

Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ.

Hum Mol Genet. 2009 Nov 1;18(21):4118-29. doi: 10.1093/hmg/ddp360. Epub 2009 Jul 31.

18.

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE.

Nature. 2008 Mar 13;452(7184):215-9. doi: 10.1038/nature06745. Epub 2008 Feb 17.

19.

Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae.

Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M.

Mol Syst Biol. 2007;3:153. Epub 2007 Dec 18.

20.

Utilizing logical relationships in genomic data to decipher cellular processes.

Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D.

FEBS J. 2005 Oct;272(20):5110-8. Review.

21.

Use of logic relationships to decipher protein network organization.

Bowers PM, Cokus SJ, Eisenberg D, Yeates TO.

Science. 2004 Dec 24;306(5705):2246-9.

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