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Literature DB >> 21878916

Making sense of chromatin states.

Monya Baker¹.
1. m.baker@us.nature.com

Abstract

Researchers find new pieces in the puzzle of genome regulation.

Mesh：

Substances：

Year: 2011 PMID： 21878916 DOI： 10.1038/nmeth.1673

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

16 in total

1. Broad chromosomal domains of histone modification patterns in C. elegans.

Authors: Tao Liu; Andreas Rechtsteiner; Thea A Egelhofer; Anne Vielle; Isabel Latorre; Ming-Sin Cheung; Sevinc Ercan; Kohta Ikegami; Morten Jensen; Paulina Kolasinska-Zwierz; Heidi Rosenbaum; Hyunjin Shin; Scott Taing; Teruaki Takasaki; A Leonardo Iniguez; Arshad Desai; Abby F Dernburg; Hiroshi Kimura; Jason D Lieb; Julie Ahringer; Susan Strome; X Shirley Liu
Journal: Genome Res Date: 2010-12-22 Impact factor: 9.043

2. Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Authors: Sushmita Roy; Jason Ernst; Peter V Kharchenko; Pouya Kheradpour; Nicolas Negre; Matthew L Eaton; Jane M Landolin; Christopher A Bristow; Lijia Ma; Michael F Lin; Stefan Washietl; Bradley I Arshinoff; Ferhat Ay; Patrick E Meyer; Nicolas Robine; Nicole L Washington; Luisa Di Stefano; Eugene Berezikov; Christopher D Brown; Rogerio Candeias; Joseph W Carlson; Adrian Carr; Irwin Jungreis; Daniel Marbach; Rachel Sealfon; Michael Y Tolstorukov; Sebastian Will; Artyom A Alekseyenko; Carlo Artieri; Benjamin W Booth; Angela N Brooks; Qi Dai; Carrie A Davis; Michael O Duff; Xin Feng; Andrey A Gorchakov; Tingting Gu; Jorja G Henikoff; Philipp Kapranov; Renhua Li; Heather K MacAlpine; John Malone; Aki Minoda; Jared Nordman; Katsutomo Okamura; Marc Perry; Sara K Powell; Nicole C Riddle; Akiko Sakai; Anastasia Samsonova; Jeremy E Sandler; Yuri B Schwartz; Noa Sher; Rebecca Spokony; David Sturgill; Marijke van Baren; Kenneth H Wan; Li Yang; Charles Yu; Elise Feingold; Peter Good; Mark Guyer; Rebecca Lowdon; Kami Ahmad; Justen Andrews; Bonnie Berger; Steven E Brenner; Michael R Brent; Lucy Cherbas; Sarah C R Elgin; Thomas R Gingeras; Robert Grossman; Roger A Hoskins; Thomas C Kaufman; William Kent; Mitzi I Kuroda; Terry Orr-Weaver; Norbert Perrimon; Vincenzo Pirrotta; James W Posakony; Bing Ren; Steven Russell; Peter Cherbas; Brenton R Graveley; Suzanna Lewis; Gos Micklem; Brian Oliver; Peter J Park; Susan E Celniker; Steven Henikoff; Gary H Karpen; Eric C Lai; David M MacAlpine; Lincoln D Stein; Kevin P White; Manolis Kellis
Journal: Science Date: 2010-12-22 Impact factor: 47.728

3. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors: Mark B Gerstein; Zhi John Lu; Eric L Van Nostrand; Chao Cheng; Bradley I Arshinoff; Tao Liu; Kevin Y Yip; Rebecca Robilotto; Andreas Rechtsteiner; Kohta Ikegami; Pedro Alves; Aurelien Chateigner; Marc Perry; Mitzi Morris; Raymond K Auerbach; Xin Feng; Jing Leng; Anne Vielle; Wei Niu; Kahn Rhrissorrakrai; Ashish Agarwal; Roger P Alexander; Galt Barber; Cathleen M Brdlik; Jennifer Brennan; Jeremy Jean Brouillet; Adrian Carr; Ming-Sin Cheung; Hiram Clawson; Sergio Contrino; Luke O Dannenberg; Abby F Dernburg; Arshad Desai; Lindsay Dick; Andréa C Dosé; Jiang Du; Thea Egelhofer; Sevinc Ercan; Ghia Euskirchen; Brent Ewing; Elise A Feingold; Reto Gassmann; Peter J Good; Phil Green; Francois Gullier; Michelle Gutwein; Mark S Guyer; Lukas Habegger; Ting Han; Jorja G Henikoff; Stefan R Henz; Angie Hinrichs; Heather Holster; Tony Hyman; A Leo Iniguez; Judith Janette; Morten Jensen; Masaomi Kato; W James Kent; Ellen Kephart; Vishal Khivansara; Ekta Khurana; John K Kim; Paulina Kolasinska-Zwierz; Eric C Lai; Isabel Latorre; Amber Leahey; Suzanna Lewis; Paul Lloyd; Lucas Lochovsky; Rebecca F Lowdon; Yaniv Lubling; Rachel Lyne; Michael MacCoss; Sebastian D Mackowiak; Marco Mangone; Sheldon McKay; Desirea Mecenas; Gennifer Merrihew; David M Miller; Andrew Muroyama; John I Murray; Siew-Loon Ooi; Hoang Pham; Taryn Phippen; Elicia A Preston; Nikolaus Rajewsky; Gunnar Rätsch; Heidi Rosenbaum; Joel Rozowsky; Kim Rutherford; Peter Ruzanov; Mihail Sarov; Rajkumar Sasidharan; Andrea Sboner; Paul Scheid; Eran Segal; Hyunjin Shin; Chong Shou; Frank J Slack; Cindie Slightam; Richard Smith; William C Spencer; E O Stinson; Scott Taing; Teruaki Takasaki; Dionne Vafeados; Ksenia Voronina; Guilin Wang; Nicole L Washington; Christina M Whittle; Beijing Wu; Koon-Kiu Yan; Georg Zeller; Zheng Zha; Mei Zhong; Xingliang Zhou; Julie Ahringer; Susan Strome; Kristin C Gunsalus; Gos Micklem; X Shirley Liu; Valerie Reinke; Stuart K Kim; LaDeana W Hillier; Steven Henikoff; Fabio Piano; Michael Snyder; Lincoln Stein; Jason D Lieb; Robert H Waterston
Journal: Science Date: 2010-12-22 Impact factor: 47.728

4. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.

Authors: Guillaume J Filion; Joke G van Bemmel; Ulrich Braunschweig; Wendy Talhout; Jop Kind; Lucas D Ward; Wim Brugman; Inês J de Castro; Ron M Kerkhoven; Harmen J Bussemaker; Bas van Steensel
Journal: Cell Date: 2010-09-30 Impact factor: 41.582

5. A map of open chromatin in human pancreatic islets.

Authors: Kyle J Gaulton; Takao Nammo; Lorenzo Pasquali; Jeremy M Simon; Paul G Giresi; Marie P Fogarty; Tami M Panhuis; Piotr Mieczkowski; Antonio Secchi; Domenico Bosco; Thierry Berney; Eduard Montanya; Karen L Mohlke; Jason D Lieb; Jorge Ferrer
Journal: Nat Genet Date: 2010-01-31 Impact factor: 38.330

6. Discovery and characterization of chromatin states for systematic annotation of the human genome.

Authors: Jason Ernst; Manolis Kellis
Journal: Nat Biotechnol Date: 2010-07-25 Impact factor: 54.908

7. Distinct factors control histone variant H3.3 localization at specific genomic regions.

Authors: Aaron D Goldberg; Laura A Banaszynski; Kyung-Min Noh; Peter W Lewis; Simon J Elsaesser; Sonja Stadler; Scott Dewell; Martin Law; Xingyi Guo; Xuan Li; Duancheng Wen; Ariane Chapgier; Russell C DeKelver; Jeffrey C Miller; Ya-Li Lee; Elizabeth A Boydston; Michael C Holmes; Philip D Gregory; John M Greally; Shahin Rafii; Chingwen Yang; Peter J Scambler; David Garrick; Richard J Gibbons; Douglas R Higgs; Ileana M Cristea; Fyodor D Urnov; Deyou Zheng; C David Allis
Journal: Cell Date: 2010-03-05 Impact factor: 41.582

8. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis.

Authors: François Roudier; Ikhlak Ahmed; Caroline Bérard; Alexis Sarazin; Tristan Mary-Huard; Sandra Cortijo; Daniel Bouyer; Erwann Caillieux; Evelyne Duvernois-Berthet; Liza Al-Shikhley; Laurène Giraut; Barbara Després; Stéphanie Drevensek; Frédy Barneche; Sandra Dèrozier; Véronique Brunaud; Sébastien Aubourg; Arp Schnittger; Chris Bowler; Marie-Laure Martin-Magniette; Stéphane Robin; Michel Caboche; Vincent Colot
Journal: EMBO J Date: 2011-04-12 Impact factor: 11.598

9. An assessment of histone-modification antibody quality.

Authors: Thea A Egelhofer; Aki Minoda; Sarit Klugman; Kyungjoon Lee; Paulina Kolasinska-Zwierz; Artyom A Alekseyenko; Ming-Sin Cheung; Daniel S Day; Sarah Gadel; Andrey A Gorchakov; Tingting Gu; Peter V Kharchenko; Samantha Kuan; Isabel Latorre; Daniela Linder-Basso; Ying Luu; Queminh Ngo; Marc Perry; Andreas Rechtsteiner; Nicole C Riddle; Yuri B Schwartz; Gregory A Shanower; Anne Vielle; Julie Ahringer; Sarah C R Elgin; Mitzi I Kuroda; Vincenzo Pirrotta; Bing Ren; Susan Strome; Peter J Park; Gary H Karpen; R David Hawkins; Jason D Lieb
Journal: Nat Struct Mol Biol Date: 2010-12-05 Impact factor: 15.369

10. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Authors: Peter V Kharchenko; Artyom A Alekseyenko; Yuri B Schwartz; Aki Minoda; Nicole C Riddle; Jason Ernst; Peter J Sabo; Erica Larschan; Andrey A Gorchakov; Tingting Gu; Daniela Linder-Basso; Annette Plachetka; Gregory Shanower; Michael Y Tolstorukov; Lovelace J Luquette; Ruibin Xi; Youngsook L Jung; Richard W Park; Eric P Bishop; Theresa K Canfield; Richard Sandstrom; Robert E Thurman; David M MacAlpine; John A Stamatoyannopoulos; Manolis Kellis; Sarah C R Elgin; Mitzi I Kuroda; Vincenzo Pirrotta; Gary H Karpen; Peter J Park
Journal: Nature Date: 2010-12-22 Impact factor: 49.962

14 in total

1. Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence.

Authors: Shaunna L Clark; Joseph L McClay; Daniel E Adkins; Gaurav Kumar; Karolina A Aberg; Srilaxmi Nerella; Linying Xie; Ann L Collins; James J Crowley; Corey R Quackenbush; Christopher E Hilliard; Andrey A Shabalin; Scott I Vrieze; Roseann E Peterson; William E Copeland; Judy L Silberg; Matt McGue; Hermine Maes; William G Iacono; Patrick F Sullivan; Elizabeth J Costello; Edwin J van den Oord
Journal: Alcohol Clin Exp Res Date: 2017-03-24 Impact factor: 3.455

Review 2. Histones: at the crossroads of peptide and protein chemistry.

Authors: Manuel M Müller; Tom W Muir
Journal: Chem Rev Date: 2014-10-20 Impact factor: 60.622

Review 3. From profiles to function in epigenomics.

Authors: Stefan H Stricker; Anna Köferle; Stephan Beck
Journal: Nat Rev Genet Date: 2016-11-21 Impact factor: 53.242

4. RNA m⁶A regulates transcription via DNA demethylation and chromatin accessibility.

Authors: Shuang Deng; Jialiang Zhang; Jiachun Su; Zhixiang Zuo; Lingxing Zeng; Kaijing Liu; Yanfen Zheng; Xudong Huang; Ruihong Bai; Lisha Zhuang; Ying Ye; Mei Li; Ling Pan; Junge Deng; Guandi Wu; Rui Li; Shaoping Zhang; Chen Wu; Dongxin Lin; Jianjun Chen; Jian Zheng
Journal: Nat Genet Date: 2022-09-07 Impact factor: 41.307

5. Structural considerations for chromatin state models with transcription as a functional readout.

Authors: Haodong Chen; Emma Monte; Michelle S Parvatiyar; Manuel Rosa-Garrido; Sarah Franklin; Thomas M Vondriska
Journal: FEBS Lett Date: 2012-08-31 Impact factor: 4.124

6. Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis.

Authors: Clara Bourbousse; Ikhlak Ahmed; François Roudier; Gérald Zabulon; Eddy Blondet; Sandrine Balzergue; Vincent Colot; Chris Bowler; Fredy Barneche
Journal: PLoS Genet Date: 2012-07-19 Impact factor: 5.917

7. Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain.

Authors: Ry Y Tweedie-Cullen; Andrea M Brunner; Jonas Grossmann; Safa Mohanna; David Sichau; Paolo Nanni; Christian Panse; Isabelle M Mansuy
Journal: PLoS One Date: 2012-05-31 Impact factor: 3.240