Zobrazeno 1 - 10
of 22
pro vyhledávání: '"J Seth Strattan"'
Autor:
Benjamin C Hitz, Laurence D Rowe, Nikhil R Podduturi, David I Glick, Ulugbek K Baymuradov, Venkat S Malladi, Esther T Chan, Jean M Davidson, Idan Gabdank, Aditi K Narayana, Kathrina C Onate, Jason Hilton, Marcus C Ho, Brian T Lee, Stuart R Miyasato, Timothy R Dreszer, Cricket A Sloan, J Seth Strattan, Forrest Y Tanaka, Eurie L Hong, J Michael Cherry
Publikováno v:
PLoS ONE, Vol 12, Iss 4, p e0175310 (2017)
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experi
Externí odkaz:
https://doaj.org/article/cf8bf0b218bf4681a26f6c1f90ae58cd
Autor:
Jacob Schreiber, Carles Boix, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y. Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje, ENCODE Imputation Challenge Participants
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-22 (2023)
Abstract A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measu
Externí odkaz:
https://doaj.org/article/af322f5b401248609628ec2ad86cadd9
Autor:
Fairlie Reese, Brian Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Elisabeth Rebboah, Narges Rezaie, Diane Trout, Milad Razavi-Mohseni, Yunzhe Jiang, Beatrice Borsari, Samuel Morabito, Heidi Yahan Liang, Cassandra J. McGill, Sorena Rahmanian, Jasmine Sakr, Shan Jiang, Weihua Zeng, Klebea Carvalho, Annika K. Weimer, Louise A. Dionne, Ariel McShane, Karan Bedi, Shaimae I. Elhajjajy, Sean Upchurch, Jennifer Jou, Ingrid Youngworth, Idan Gabdank, Paul Sud, Otto Jolanki, J. Seth Strattan, Meenakshi S. Kagda, Michael P. Snyder, Ben C. Hitz, Jill E. Moore, Zhiping Weng, David Bennett, Laura Reinholdt, Mats Ljungman, Michael A. Beer, Mark B. Gerstein, Lior Pachter, Roderic Guigó, Barbara J. Wold, Ali Mortazavi
Publikováno v:
bioRxiv
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3’ end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b322239296bd726f9e03969616ed0b86
https://europepmc.org/articles/PMC10245583/
https://europepmc.org/articles/PMC10245583/
Autor:
Benjamin C. Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham, Paul Sud, Idan Gabdank, J. Seth Strattan, Cricket A. Sloan, Timothy Dreszer, Laurence D. Rowe, Nikhil R. Podduturi, Venkat S. Malladi, Esther T. Chan, Jean M. Davidson, Marcus Ho, Stuart Miyasato, Matt Simison, Forrest Tanaka, Yunhai Luo, Ian Whaling, Eurie L. Hong, Brian T. Lee, Richard Sandstrom, Eric Rynes, Jemma Nelson, Andrew Nishida, Alyssa Ingersoll, Michael Buckley, Mark Frerker, Daniel S Kim, Nathan Boley, Diane Trout, Alex Dobin, Sorena Rahmanian, Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Neva C. Durand, Olga Dudchenko, David Weisz, Suhas S. P. Rao, Alyssa Blackburn, Dimos Gkountaroulis, Mahdi Sadr, Moshe Olshansky, Yossi Eliaz, Dat Nguyen, Ivan Bochkov, Muhammad Saad Shamim, Ragini Mahajan, Erez Aiden, Tom Gingeras, Simon Heath, Martin Hirst, W. James Kent, Anshul Kundaje, Ali Mortazavi, Barbara Wold, J. Michael Cherry
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f3ede3b75e1612917e82c16d5ca40cfb
https://doi.org/10.1101/2023.04.04.535623
https://doi.org/10.1101/2023.04.04.535623
Autor:
Joel Rozowsky, Jiahao Gao, Beatrice Borsari, Yucheng T. Yang, Timur Galeev, Gamze Gürsoy, Charles B. Epstein, Kun Xiong, Jinrui Xu, Tianxiao Li, Jason Liu, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Maxwell S. Sun, James Wright, Justin Chang, Christopher J.F. Cameron, Noam Shoresh, Elizabeth Gaskell, Jorg Drenkow, Jessika Adrian, Sergey Aganezov, François Aguet, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya B. Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie A. Davis, Daniel Farid, Nina P. Farrell, Idan Gabdank, Yoel Gofin, David U. Gorkin, Mengting Gu, Vivian Hecht, Benjamin C. Hitz, Robbyn Issner, Yunzhe Jiang, Melanie Kirsche, Xiangmeng Kong, Bonita R. Lam, Shantao Li, Bian Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Ran Meng, Jill E. Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry E. Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob M. Schreiber, Fritz J. Sedlazeck, Lei Hoon See, Rachel M. Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, J Seth Strattan, Zhen Tan, Forrest Y. Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, Kristin Ardlie, J Michael Cherry, Eric M. Mendenhall, William S. Noble, Zhiping Weng, Morgan E. Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard M. Myers, Michael P. Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael C. Schatz, Bradley E. Bernstein, Roderic Guigó, Thomas R. Gingeras, Mark Gerstein
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four don
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::464939170ba93b49ee4e474d325702f1
http://hdl.handle.net/10230/56942
http://hdl.handle.net/10230/56942
Autor:
Casey Litton, Zachary Myers, Ulugbek K. Baymuradov, Benjamin C. Hitz, Meenakshi S. Kagda, Otto Jolanki, Jin-Wook Lee, Stuart R. Miyasato, Keenan Graham, Idan Gabdank, Forrest Y. Tanaka, Bonita R. Lam, J. Seth Strattan, Jason A. Hilton, J. Michael Cherry, Yunhai Luo, Philip Adenekan, Paul Sud, Emma O'Neill, Jennifer Jou, Khine Lin
Publikováno v:
Nucleic Acids Research
The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal
Autor:
Joel Rozowsky, Jorg Drenkow, Yucheng T Yang, Gamze Gursoy, Timur Galeev, Beatrice Borsari, Charles B Epstein, Kun Xiong, Jinrui Xu, Jiahao Gao, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Jason Liu, Maxwell S Sun, James Wright, Justin Chang, Christopher JF Cameron, Noam Shoresh, Elizabeth Gaskell, Jessika Adrian, Sergey Aganezov, François Aguet, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya B Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie A Davis, Daniel Farid, Nina P Farrell, Idan Gabdank, Yoel Gofin, David U Gorkin, Mengting Gu, Vivian Hecht, Benjamin C Hitz, Robbyn Issner, Melanie Kirsche, Xiangmeng Kong, Bonita R Lam, Shantao Li, Bian Li, Tianxiao Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Jill E Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry E Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob M Schreiber, Fritz J Sedlazeck, Lei Hoon See, Rachel M Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, J Seth Strattan, Zhen Tan, Forrest Y Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, Kristin Ardlie, J Michael Cherry, Eric M Mendenhall, William S Noble, Zhiping Weng, Morgan E Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard M Myers, Michael P Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael C Schatz, Roderic Guigó, Bradley E Bernstein, Thomas R Gingeras, Mark Gerstein
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of personal epigenomes, for ∼25 tissues a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f293c3be99001dfcca0596fbe318c048
https://doi.org/10.1101/2021.04.26.441442
https://doi.org/10.1101/2021.04.26.441442
Autor:
Axel Visel, Catherine S. Novak, Tyler H. Garvin, Hongbo Yang, Anne N. Harrington, Diane E. Dickel, Yin Shen, Kyle J. Gaulton, J. Michael Cherry, Bin Li, Quan T. Pham, Yunjiang Qiu, Mengchi Wang, Jean M. Davidson, Bo Ding, Elizabeth Lee, Ingrid Plajzer-Frick, Sora Chee, Sebastian Preissl, Jee Yun Han, Diane Trout, Henry Amrhein, Yupeng He, Jennifer A. Akiyama, Momoe Kato, Joseph R. Ecker, Veena Afzal, J. Seth Strattan, Yuan Zhao, Bo Zhang, Wei Wang, Len A. Pennacchio, David U. Gorkin, Brian A. Williams, Iros Barozzi, Ah Young Lee, Hui Huang, Yoko Fukuda-Yuzawa, Yanxiao Zhang, Brandon J. Mannion, Bing Ren, Andre Wildberg, Joshua Chiou
Publikováno v:
Nature, vol 583, iss 7818
Nature
Nature
The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6f247784ec64efc5f84e457834a66464
https://escholarship.org/uc/item/5ch369qm
https://escholarship.org/uc/item/5ch369qm
Autor:
Prashant Emani, Gamze Gürsoy, Charlotte M. Brannon, Andrew D. Miranker, Mark Gerstein, Arif Harmanci, J. Michael Cherry, J. Seth Strattan, Otto Jolanki
Publikováno v:
Cell
The generation of functional genomics datasets is surging, because they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in cancer). The intent behind functional genomics experiments is not necessarily to study
Autor:
J. Seth Strattan, Khine Lin, Keenan Graham, Casey Litton, Emma O'Neill, Philip Adenekan, Jason A. Hilton, Paul Sud, Benjamin C. Hitz, Idan Gabdank, J. Michael Cherry, Yunhai Luo, Forrest Y. Tanaka, Zachary Myers, Jennifer Jou, Stuart R. Miyasato, Ulugbek K. Baymuradov, Otto Jolanki, Meenakshi S. Kagda, Jin-Wook Lee, Bonita R. Lam
Publikováno v:
Curr Protoc Bioinformatics
The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is