J
Jorja G. Henikoff
Researcher at Fred Hutchinson Cancer Research Center
Publications - 66
Citations - 21496
Jorja G. Henikoff is an academic researcher from Fred Hutchinson Cancer Research Center. The author has contributed to research in topics: Chromatin & Nucleosome. The author has an hindex of 46, co-authored 64 publications receiving 19163 citations. Previous affiliations of Jorja G. Henikoff include Memorial Sloan Kettering Cancer Center & University of Washington.
Papers
More filters
Journal ArticleDOI
Amino acid substitution matrices from protein blocks
TL;DR: This work has derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins, leading to marked improvements in alignments and in searches using queries from each of the groups.
Journal ArticleDOI
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Sushmita Roy,Jason Ernst,Peter V. Kharchenko,Pouya Kheradpour,Nicolas Nègre,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 G. Artieri,Benjamin W. Booth,Angela N. Brooks,Qi Dai,Carrie A. Davis,Michael O. Duff,X. Feng,Andrey A. Gorchakov,Tingting Gu,Jorja G. Henikoff,Philipp Kapranov,Renhua Li,Heather K. MacAlpine,John H. Malone,Aki Minoda,Jared T. Nordman,Katsutomo Okamura,Marc D. Perry,Sara K. Powell,Nicole C. Riddle,Akiko Sakai,Anastasia Samsonova,Jeremy E. Sandler,Yuri B. Schwartz,Noa Sher,Rebecca Spokony,David Sturgill,Marijke J. van Baren,Kenneth H. Wan,Li Yang,Charles Yu,Elise A. Feingold,Peter J. Good,Mark S. Guyer,Rebecca F. Lowdon,Kami Ahmad,Justen Andrews,Bonnie Berger,Steven E. Brenner,Michael R. Brent,Lucy Cherbas,Sarah C. R. Elgin,Thomas R. Gingeras,Robert L. Grossman,Roger A. Hoskins,Thomas C. Kaufman,W. J. Kent,Mitzi I. Kuroda,Terry L. Orr-Weaver,Norbert Perrimon,Vincenzo Pirrotta,James W. Posakony,Bing Ren,Steven Russell,Peter Cherbas,Brenton R. Graveley,Suzanna E. Lewis,Gos Micklem,Brian Oliver,Peter J. Park,Susan E. Celniker,Steven Henikoff,Gary H. Karpen,Eric C. Lai,David M. MacAlpine,Lincoln Stein,Kevin P. White,Manolis Kellis +95 more
TL;DR: The Drosophila Encyclopedia of DNA Elements (modENCODE) project as mentioned in this paper has been used to map transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines.
Journal ArticleDOI
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
Mark Gerstein,Zhi John Lu,Eric L. Van Nostrand,Chao Cheng,Bradley I. Arshinoff,Tao Liu,Kevin Y. Yip,R. Robilotto,Andreas Rechtsteiner,Kohta Ikegami,P. Alves,A. Chateigner,Marc D. Perry,Mitzi Morris,Raymond K. Auerbach,X. Feng,Jing Leng,A. Vielle,Wei Niu,Kahn Rhrissorrakrai,Ashish Agarwal,Roger P. Alexander,Galt P. Barber,Cathleen M. Brdlik,J. Brennan,Jeremy Brouillet,Adrian Carr,Ming Sin Cheung,Hiram Clawson,Sergio Contrino,Luke Dannenberg,Abby F. Dernburg,Arshad Desai,L. Dick,Andréa C. Dosé,Jiang Du,Thea A. Egelhofer,Sevinc Ercan,Ghia Euskirchen,Brent Ewing,Elise A. Feingold,Reto Gassmann,Peter J. Good,Philip Green,Francois Gullier,M. Gutwein,Mark S. Guyer,Lukas Habegger,Ting Han,Jorja G. Henikoff,Stefan R. Henz,Angie S. Hinrichs,H. Holster,Tony Hyman,A. Leo Iniguez,J. Janette,M. Jensen,Masaomi Kato,W. James Kent,E. Kephart,Vishal Khivansara,Ekta Khurana,John Kim,P. Kolasinska-Zwierz,Eric C. Lai,Isabel J. Latorre,Amber Leahey,Suzanna E. Lewis,Paul Lloyd,Lucas Lochovsky,Rebecca F. Lowdon,Yaniv Lubling,Rachel Lyne,Michael J. MacCoss,Sebastian D. Mackowiak,Marco Mangone,Sheldon J. McKay,D. Mecenas,Gennifer E. Merrihew,David M. Miller,A. Muroyama,John I. Murray,Siew Loon Ooi,Hoang Pham,T. Phippen,Elicia Preston,Nikolaus Rajewsky,Gunnar Rätsch,Heidi Rosenbaum,Joel Rozowsky,Kim Rutherford,P. Ruzanov,Mihail Sarov,Rajkumar Sasidharan,Andrea Sboner,P. Scheid,Eran Segal,Hyunjin Shin,C. Shou,Frank J. Slack,C. Slightam,Richard J.H. Smith,William C. Spencer,Eo Stinson,S. Taing,Teruaki Takasaki,D. Vafeados,Ksenia Voronina,Guilin Wang,Nicole L. Washington,Christina M. Whittle,Beijing Wu,Koon-Kiu Yan,Georg Zeller,Z. 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 +130 more
TL;DR: These studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized, providing insights into the organization, structure, and function of the two genomes.
Journal ArticleDOI
CUT&Tag for efficient epigenomic profiling of small samples and single cells
Hatice S. Kaya-Okur,Steven J. Wu,Steven J. Wu,Christine A. Codomo,Erica S. Pledger,Terri D. Bryson,Jorja G. Henikoff,Kami Ahmad,Steven Henikoff +8 more
TL;DR: Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components, is described.
Journal ArticleDOI
Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences.
Timothy M. Rose,Emily R. Schultz,Jorja G. Henikoff,Shmuel Pietrokovski,Claire M. McCallum,Steven Henikoff,Steven Henikoff +6 more
TL;DR: A new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences that consists of a short 3' degenerate core region and a longer 5' consensus clamp region, which demonstrates the practical utility of this hybrid primer method.