Zobrazeno 1 - 10
of 27
pro vyhledávání: '"Diane Trout"'
Autor:
Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Liang, Barbara J. Wold, Ali Mortazavi
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-28 (2021)
Abstract The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develo
Externí odkaz:
https://doaj.org/article/a9cc96a7c7b943598bdcc02de250db7e
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:
Chongyuan Luo, Diane E. Dickel, David U. Gorkin, Diane Trout, Huaming Chen, Rosa Castanon, Bin Li, Brian A. Williams, Joseph R. Ecker, Joseph R. Nery, Axel Visel, Ah Young Lee, Henry Amrhein, Bing Ren, Yupeng He, Rongxin Fang, Manoj Hariharan, Len A. Pennacchio, Hui Huang, Yuan Zhao
Publikováno v:
Nature
Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 16
Autor:
Katherine Williams, Heidi Liang, Diane Trout, Gabriela Balderrama-Gutierrez, Fairlie Reese, Elisabeth Rebboah, Isaryhia Rodriguez, Ali Mortazavi, Cassandra Joan McGill, Barbara J. Wold
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-28 (2021)
Genome biology, vol 22, iss 1
Genome Biology
Genome biology, vol 22, iss 1
Genome Biology
Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e67a51038dd05f86aef1eff04f0852de
https://resolver.caltech.edu/CaltechAUTHORS:20210429-100236539
https://resolver.caltech.edu/CaltechAUTHORS:20210429-100236539
Autor:
Axel Visel, Libera Berghella, Peng He, Ross C. Hardison, Yu Zhang, Georgi K. Marinov, Barbara J. Wold, Bing Ren, Say Tar Goh, Diane E. Dickel, Brian A. Williams, Len A. Pennacchio, Diane Trout, Veena Afzal, Henry Amrhein, Ingrid Plajzer-Frick
Publikováno v:
Nature, vol 583, iss 7818
Nature
Nature
During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system1. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9399e40e733f4e63dfe21127e2096df8
https://resolver.caltech.edu/CaltechAUTHORS:20200618-081148283
https://resolver.caltech.edu/CaltechAUTHORS:20200618-081148283
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:
Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Shan Jiang, Sorena Rahmanian, Stefania Forner, Dina Matheos, Weihua Zeng, Brian Williams, Diane Trout, Whitney England, Shu-Hui Chu, Robert C. Spitale, Andrea J. Tenner, Barbara J. Wold, Ali Mortazavi
Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lack
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7f42cb50b56b4b72d59b4b0a73cccc51
https://doi.org/10.1101/672931
https://doi.org/10.1101/672931
Autor:
Ali Mortazavi, Brian Williams, Mark Mackiewicz, Weihua Zeng, Alexander Dobin, Brian S. Roberts, Carrie A. Davis, Dianna E. Moore, Rabi Murad, Alessandra Breschi, Chris Zaleski, Alex Scavelli, Thomas R. Gingeras, Sorena Rahmanian, Lei-Hoon Sei, Sarah Meadows, Diane Trout, Roderic Guigó, Richard M. Myers, Jorg Drenkow, Barbara J. Wold
Publikováno v:
Recercat. Dipósit de la Recerca de Catalunya
instname
instname
MicroRNAs (miRNAs) play a critical role as post-transcriptional regulators of gene expression. The ENCODE project profiled the expression of miRNAs in a comprehensive set of tissues during a time-course of mouse embryonic development and captured the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::43b1374845e10f4e08ad8dc0bf428db2
http://hdl.handle.net/10230/43159
http://hdl.handle.net/10230/43159
Autor:
Catherine S. Novak, Quan T. Pham, Bo Ding, Diane Trout, Ingrid Plajzer-Frick, Yuan Zhao, J. Seth Strattan, Elizabeth Lee, Jee Yun Han, Bin Li, Jennifer A. Akiyama, Veena Afzal, Hongbo Yang, Ah Young Lee, Joseph R. Ecker, Sebastian Preissl, Kyle J. Gaulton, Anne N. Harrington, Momoe Kato, Andre Wildberg, Yupeng He, Diane E. Dickel, Tyler H. Garvin, Jean M. Davidson, Joshua Chiou, Bo Zhang, Len A. Pennacchio, Hui Huang, Yoko Fukuda-Yuzawa, Iros Barozzi, Brian A. Williams, Yanxiao Zhang, Yunjiang Qiu, Sora Chee, Axel Visel, Henry Amrhein, Bing Ren, J. Michael Cherry, Wei Wang, Mengchi Wang, David U. Gorkin, Yin Shen, Brandon J. Mannion
Publikováno v:
Nature
Nature, vol 589, iss 7842
Nature, vol 586, iss 7831
Nature, vol 589, iss 7842
Nature, vol 586, iss 7831
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