Zobrazeno 1 - 10
of 18
pro vyhledávání: '"Gavin D. Bascom"'
Autor:
Chigusa Kobayashi, Wataru Nishima, Anna Lappala, Will Fischer, Marcus Daniels, Jaewoon Jung, Tamar Schlick, Karissa Y. Sanbonmatsu, Dominic Phillips, Gavin D. Bascom, Yuji Sugita, Chang-Shung Tung, Adetokunbo Adedoyin, Michael E. Wall
Publikováno v:
J Comput Chem
The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a lar
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5cf049658b724aa4bff403e0981c8ace
https://doi.org/10.1002/jcc.25840
https://doi.org/10.1002/jcc.25840
Publikováno v:
Proceedings of the National Academy of Sciences. 116:4955-4962
Gene expression is orchestrated at the structural level by nucleosome positioning, histone tail acetylation, and linker histone (LH) binding. Here, we integrate available data on nucleosome positioning, nucleosome-free regions (NFRs), acetylation isl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::76b240e7fb0f14e09775c63f1dc62188
https://doi.org/10.1073/pnas.1816424116
https://doi.org/10.1073/pnas.1816424116
Publikováno v:
The Journal of Physical Chemistry B. 121:3882-3894
Nucleosome placement, or DNA linker length patterns, are believed to yield specific spatial features in chromatin fibers, but details are unknown. Here we examine by mesoscale modeling how kilobase (kb) range contacts and fiber looping depend on link
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0c10928777bcf69f06d17f1e0a0fcf2c
https://doi.org/10.1021/acs.jpcb.7b00998
https://doi.org/10.1021/acs.jpcb.7b00998
Autor:
Tamar Schlick, Gavin D. Bascom
Publikováno v:
Biophysical journal. 114(10)
In eukaryotic chromatin, islands of histone tail acetylation are found near transcription start sites and enhancers, whereas linker histones (LHs) are localized in intergenic regions with wild-type (WT) histone tails. However, the structural mechanis
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::275588eac0a19657b2c22622859ba40b
https://pubmed.ncbi.nlm.nih.gov/29655483
https://pubmed.ncbi.nlm.nih.gov/29655483
Autor:
Gavin D. Bascom, Tamar Schlick
Although many computational approaches for treating general nucleic acids exist, there are few available for treating the nucleic-acid/protein complex which packages eukaryotic DNA, namely the chromatin fiber. Understanding chromatin structure and it
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7e28731e98c65265b35b7d35173625c9
https://doi.org/10.1016/b978-0-12-803480-4.00005-3
https://doi.org/10.1016/b978-0-12-803480-4.00005-3
Autor:
Etienne Almayrac, Françoise Argoul, Alain Arneodo, Benjamin Audit, Laura Baranello, Daniel A. Bartlett, Gavin D. Bascom, Sébastien Bloyer, Maya Capelson, Olivier Cuvier, Ann Dean, Guénola Drillon, Miroslav Dundr, Sarah Elderkin, Ralf Everaers, Emmanuelle Fabre, Marie-Cécile Gaillard, David M. Gilbert, Adriana Gonzalez-Sandoval, Molly R. Gordon, Damien F. Hudson, Sébastien Huet, Daniel Jost, Fedor Kouzine, Ivan Krivega, Théo Lebeaupin, David Levens, Kazuhiro Maeshima, John F. Marko, Louise Matheson, Peter Meister, Yoichi Miyamoto, Anne M. Molitor, Raphaël Mourad, Daan Noordermeer, Josette M. Northcott, Tadasu Nozaki, Masahiro Oka, Argyris Papantonis, Piergiorgio Percipalle, Karen L. Reddy, Angelo Rosa, Iain A. Sawyer, Tamar Schlick, Tom Sexton, Jane A. Skok, Rebecca Smith, Valentina Snetkova, Konstantinos Sofiadis, Charbel Souaid, Sachiko Tamura, Christophe Thiriet, Laura Trinkle-Mulcahy, Cédric Vaillant, Tomas Venit, Valerie M. Weaver, Xin Xie, Yoshihiro Yoneda, Yousra B. Zouari
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c2a874f56c9527e9bb5a0f273b6a8f7e
https://doi.org/10.1016/b978-0-12-803480-4.00041-7
https://doi.org/10.1016/b978-0-12-803480-4.00041-7
Autor:
Gavin D. Bascom, Jesse M. Engreitz, Douglass Turner, Elizabeth M. Perez, James T. Robinson, Tamar Schlick, Muhammad S. Shamim, Jaeweon Shin, Arina D. Omer, Rafael Casellas, Kyong-Rim Kieffer-Kwon, Erez Lieberman Aiden, Sarah E. Johnstone, Bradley E. Bernstein, Eric S. Lander, Xingfan Huang, Ziyi Ye, Adrian L. Sanborn, Ivan D. Bochkov, Brian Glenn St Hilaire, Su Chen Huang, Suhas S.P. Rao
Publikováno v:
PMC
The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci—almost always bound by CTCF and cohesin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18d47bd839bf5e77bc950748cd4e6e6f
http://hdl.handle.net/1721.1/118942
http://hdl.handle.net/1721.1/118942
Autor:
Gavin D. Bascom
Publikováno v:
Astronomers' Universe ISBN: 9783319606897
On the Inside of a Marble
On the Inside of a Marble
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d3403aac796ed744d70ea3db936180f5
https://doi.org/10.1007/978-3-319-60690-3
https://doi.org/10.1007/978-3-319-60690-3
Autor:
Gavin D. Bascom
Publikováno v:
Astronomers' Universe ISBN: 9783319606897
Talking precisely about the universe in terms that come from rules solely deriving from inside said universe is difficult, to say the least. This funny conundrum, namely one of not being able to separate the observer from the observed, is a central t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0c7f248d363bd9ecf52eecdcade66e21
https://doi.org/10.1007/978-3-319-60690-3_5
https://doi.org/10.1007/978-3-319-60690-3_5
Autor:
Ioan Andricioaei, Gavin D. Bascom
Publikováno v:
The Journal of Physical Chemistry. C, Nanomaterials and Interfaces
We study the conformational equilibrium between B-to-A forms of ds-DNA adsorbed onto a single-walled carbon nanotube (SWNT) using free energy profile calculations based on all-atom molecular dynamics simulations. The potential of mean force (PMF) of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3845e5469c3edea74501006bfbc666f7
https://doi.org/10.1021/jp5081274
https://doi.org/10.1021/jp5081274