J
Jonathan H. Dennis
Researcher at Florida State University
Publications - 41
Citations - 3863
Jonathan H. Dennis is an academic researcher from Florida State University. The author has contributed to research in topics: Nucleosome & Chromatin. The author has an hindex of 15, co-authored 40 publications receiving 3441 citations. Previous affiliations of Jonathan H. Dennis include Powerlink Queensland & Harvard University.
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Journal ArticleDOI
The ENCODE (ENCyclopedia of DNA elements) Project
Elise A. Feingold,Peter J. Good,Mark S. Guyer,S. Kamholz,L. Liefer,Kris A. Wetterstrand,Francis S. Collins,Thomas R. Gingeras,Dione Kampa,E. A. Sekinger,Jill Cheng,H. Hirsch,Srinka Ghosh,Zhou Zhu,Sandeep Patel,Antonio Piccolboni,A. Yang,Hari Tammana,Stefan Bekiranov,Philipp Kapranov,Rhonda Harrison,George M. Church,Kevin Struhl,Bing Ren,Tae Hoon Kim,Leah O. Barrera,Chunxu Qu,S. van Calcar,R. Luna,C. K. Glass,M. G. Rosenfeld,Roderic Guigó,Stylianos E. Antonarakis,Ewan Birney,Michael R. Brent,Lior Pachter,Alexandre Reymond,Emmanouil T. Dermitzakis,Colin N. Dewey,Damian Keefe,F. Denoeud,Julien Lagarde,Jennifer L. Ashurst,Tim Hubbard,Jan-Jaap Wesselink,Robert Castelo,Eduardo Eyras,Richard M. Myers,Arend Sidow,Serafim Batzoglou,Nathan D. Trinklein,Sara J. Hartman,Shelley Force Aldred,Elizabeth Anton,Diane I. Schroeder,S. S. Marticke,Long H. Nguyen,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Gregory M. Cooper,Eric A. Stone,George Asimenos,Michael Brudno,Anindya Dutta,Neerja Karnani,Christopher M. Taylor,H. K. Kim,Gabriel Robins,George Stamatoyannopoulos,John A. Stamatoyannopoulos,Michael O. Dorschner,Peter J. Sabo,Michael Hawrylycz,Richard Humbert,James C. Wallace,Min-Feng Yu,Patrick A. Navas,M. McArthur,William Stafford Noble,Ian Dunham,Christof Koch,Robert M. Andrews,Gayle K. Clelland,Sarah Wilcox,Joanna C. Fowler,Keith D. James,P. Groth,Oliver M. Dovey,Peter D. Ellis,Vicki L. Wraight,Andrew J. Mungall,Pawandeep Dhami,Heike Fiegler,Cordelia Langford,Nigel P. Carter,David Vetrie,Michael Snyder,Ghia Euskirchen,Alexander E. Urban,Ugrappa Nagalakshmi,John L. Rinn,George V. Popescu,Paul Bertone,Stephen Hartman,Joel Rozowsky,Olof Emanuelsson,Thomas Royce,Sambath Chung,Mark Gerstein,Zheng Lian,Jane B. Lian,Y. Nakayama,Sherman M. Weissman,Viktor Stolc,W. Tongprasit,H. Sethi,Steven J.M. Jones,Marco A. Marra,H. Shin,Jacquie Schein,Michele Clamp,Kerstin Lindblad-Toh,Jean L. Chang,David B. Jaffe,Michael Kamal,Eric S. Lander,Tarjei S. Mikkelsen,Jade P. Vinson,Michael C. Zody,P. J. De Jong,Kazutoyo Osoegawa,Mikhail Nefedov,Baoli Zhu,Andreas D. Baxevanis,Tyra G. Wolfsberg,Gregory E. Crawford,James R R Whittle,Ingeborg Holt,T. J. Vasicek,D. Zhou,Shu-Jin Luo,Eric D. Green,Gerry Bouffard,Elliott H. Margulies,Matthew E. Portnoy,Nancy F. Hansen,Pamela J. Thomas,Jenny McDowell,Baishali Maskeri,Alice C. Young,Jacquelyn R. Idol,Robert W. Blakesley,Greg Schuler,Webb Miller,Ross C. Hardison,Laura Elnitski,Prachi Shah,Steven L. Salzberg,Mihaela Pertea,William H. Majoros,David Haussler,Daryl J. Thomas,Kate R. Rosenbloom,Hiram Clawson,Adam Siepel,W. J. Kent,Zhiping Weng,S. Jin,Anason S. Halees,H. Burden,Ulas Karaoz,Yutao Fu,Yong Yu,C. Ding,Charles R. Cantor,Robert E. Kingston,Jonathan H. Dennis,Roland Green,Michael A. Singer,Todd Richmond,J. E. Norton,Peggy J. Farnham,Matthew J. Oberley,D. R. Inman,M. R. McCormick,H. Kim,C. L. Middle,Michael C. Pirrung,Xiang-Dong Fu,Y. S. Kwon,Z. Ye,Job Dekker,Tomoko M. Tabuchi,Nele Gheldof,Josée Dostie,S. C. Harvey +196 more
TL;DR: The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function.
Journal ArticleDOI
Topologically associating domains are stable units of replication-timing regulation
Benjamin D. Pope,Tyrone Ryba,Vishnu Dileep,Feng Yue,Weisheng Wu,Olgert Denas,Daniel L. Vera,Yanli Wang,R. Scott Hansen,Theresa K. Canfield,Robert E. Thurman,Yong Cheng,Günhan Gülsoy,Jonathan H. Dennis,Michael Snyder,John A. Stamatoyannopoulos,James Taylor,Ross C. Hardison,Tamer Kahveci,Bing Ren,David M. Gilbert +20 more
TL;DR: It is demonstrated that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replicationdomain boundaries, largely accounting for the previously reported lack of alignment.
Journal ArticleDOI
Predicting Human Nucleosome Occupancy from Primary Sequence
Shobhit Gupta,Jonathan H. Dennis,Robert E. Thurman,Robert E. Kingston,John A. Stamatoyannopoulos,William Stafford Noble +5 more
TL;DR: The results suggest that the major mechanism of nucleosome positioning in vivo is boundary-event-driven and affirm the classical statistical positioning theory of nucleOSome organization.
Journal ArticleDOI
Differential Nuclease Sensitivity Profiling of Chromatin Reveals Biochemical Footprints Coupled to Gene Expression and Functional DNA Elements in Maize
Daniel L. Vera,Thelma F. Madzima,Jonathan D J Labonne,Mohammad Parwez Alam,Gregg G. Hoffman,S.B. Girimurugan,Jinfeng Zhang,Karen M. McGinnis,Jonathan H. Dennis,Hank W. Bass +9 more
TL;DR: This work presents a technique to identify specific regions of maize chromatin that are hypersensitive to digestion by micrococcal nuclease, which preferentially cleaves DNA not bound into nucleosomes, which helps elucidate how global changes in gene expression relate to changes in nucleosome position.
Journal ArticleDOI
Bidirectional Binding of the TATA Box Binding Protein to the TATA Box
Julia M. Cox,Matthew Merrill Hayward,Jennifer F. Sanchez,Laura D. Gegnas,Sarina van der Zee,Jonathan H. Dennis,Paul B. Sigler,Alanna Schepartz +7 more
TL;DR: It is concluded that TBP alone cannot define the productive orientation of general factor assembly on a promoter, and the general factors TFIIA and TFIIB each increase the rotational and translational selectivity of yTBP but are not sufficient, at least individually, to confer a unique polarity to the preinitiation complex.