Searching journal content for articles similar to Elnitski et al. 17 (6): 954.

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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
...; Drexler et al. 2004; Butler and Hirano 2014). Along with the H1 human embryonic stem cell line and the GM12878 lymphoblastoid cell line, K562 is one of the three tier-one cell lines of the ENCyclopedia Of DNA Elements Project (ENCODE) (The ENCODE Project Consortium 2012), forming the basis of more than...
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Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
- Wenli Xu,
- Chang Liu,
- Bing Deng,
- Penghui Lin,
- Zhenghua Sun,
- Anrui Liu,
- Jiajia Xuan,
- Yuying Li,
- Keren Zhou,
- Xiaoqin Zhang,
- Qiaojuan Huang,
- Hui Zhou,
- Qingyu He,
- Bin Li,
- Lianghu Qu,
- and Jianhua Yang
Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
...equally to this work. Corresponding authors: yangjh7@mail.sysu.edu.cn, lssqlh@mail.sysu.edu.cn, libin73@mail.sysu.edu.cn, tqyhe@email.jnu.edu.cnAbstractPolypeptides encoded by long noncoding RNAs (lncRNAs) are a novel class of functional molecules. However, whether these hidden polypeptides participate...
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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...What does our genome encode? John A. Stamatoyannopoulos 1 Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington 98195, USA Abstract In its first production phase, The ENCODE Project Consortium (ENCODE...
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Research: High-throughput functional testing of ENCODE segmentation predictions
- Jamie C. Kwasnieski,
- Christopher Fiore,
- Hemangi G. Chaudhari,
- and Barak A. Cohen
Genome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014, doi:10.1101/gr.173518.114
...the regulatory activity of the underlying genomic DNA. Based on this hypothesis, the ENCODE Project Consortium measured the status of multiple histone modifications across the genome in several cell types and used these data to segment the genome into regions with different predicted regulatory activities. We...
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Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Stephen G. Landt,
- Georgi K. Marinov,
- Anshul Kundaje,
- Pouya Kheradpour,
- Florencia Pauli,
- Serafim Batzoglou,
- Bradley E. Bernstein,
- Peter Bickel,
- James B. Brown,
- Philip Cayting,
- Yiwen Chen,
- Gilberto DeSalvo,
- Charles Epstein,
- Katherine I. Fisher-Aylor,
- Ghia Euskirchen,
- Mark Gerstein,
- Jason Gertz,
- Alexander J. Hartemink,
- Michael M. Hoffman,
- Vishwanath R. Iyer,
- Youngsook L. Jung,
- Subhradip Karmakar,
- Manolis Kellis,
- Peter V. Kharchenko,
- Qunhua Li,
- Tao Liu,
- X. Shirley Liu,
- Lijia Ma,
- Aleksandar Milosavljevic,
- Richard M. Myers,
- Peter J. Park,
- Michael J. Pazin,
- Marc D. Perry,
- Debasish Raha,
- Timothy E. Reddy,
- Joel Rozowsky,
- Noam Shoresh,
- Arend Sidow,
- Matthew Slattery,
- John A. Stamatoyannopoulos,
- Michael Y. Tolstorukov,
- Kevin P. White,
- Simon Xi,
- Peggy J. Farnham,
- Jason D. Lieb,
- Barbara J. Wold,
- and Michael Snyder
Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
...individual ChIP-seq experiments for more than 140 different factors and histone modifications in more than 100 cell types in four different organisms (D. melanogaster, C. elegans, mouse, and human), using multiple independent data production and processing pipelines (The ENCODE Project Consortium 2004, 2011...
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Perspective: Functional transcriptomics in the post-ENCODE era
- Jonathan M. Mudge,
- Adam Frankish,
- and Jennifer Harrow
Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
...(Fig. 1B; Frenkel-Morgenstern et al. 2012), while the discovery of long noncoding RNAs (lncRNAs) suggests that most human transcripts may not encode proteins (Rinn and Chang 2012). In fact, the bulk of the appears to be ‘‘pervasively’’ transcribed (The ENCODE Project Consortium 2012), although...
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RESOURCE: GeneLynx: A Gene-Centric Portal to the Human Genome
- Boris Lenhard,
- William S. Hayes,
- and Wyeth W. Wasserman
Genome Res. December 1, 2001 11: 2151-2157; doi:10.1101/gr.199801
...of the human ( International Human Genome Sequencing Consortium 2001 ) marks a climax of the international project. Despite this great success, data describing individual human genes and their encoded protein products continue to accumulate haphazardly, filling widely distributed databases accessible via...
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Resource: GENCODE: The reference human genome annotation for The ENCODE Project
- Jennifer Harrow,
- Adam Frankish,
- Jose M. Gonzalez,
- Electra Tapanari,
- Mark Diekhans,
- Felix Kokocinski,
- Bronwen L. Aken,
- Daniel Barrell,
- Amonida Zadissa,
- Stephen Searle,
- If Barnes,
- Alexandra Bignell,
- Veronika Boychenko,
- Toby Hunt,
- Mike Kay,
- Gaurab Mukherjee,
- Jeena Rajan,
- Gloria Despacio-Reyes,
- Gary Saunders,
- Charles Steward,
- Rachel Harte,
- Michael Lin,
- Cédric Howald,
- Andrea Tanzer,
- Thomas Derrien,
- Jacqueline Chrast,
- Nathalie Walters,
- Suganthi Balasubramanian,
- Baikang Pei,
- Michael Tress,
- Jose Manuel Rodriguez,
- Iakes Ezkurdia,
- Jeltje van Baren,
- Michael Brent,
- David Haussler,
- Manolis Kellis,
- Alfonso Valencia,
- Alexandre Reymond,
- Mark Gerstein,
- Roderic Guigó,
- and Tim J. Hubbard
Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111
...available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. [Supplemental material is available for this article.] Launched in September 2003, the Encyclopedia of DNA Elements (The ENCODE Project Consortium 2011) project brought together an international group of scientists tasked...
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Research: RNA editing in the human ENCODE RNA-seq data
- Eddie Park,
- Brian Williams,
- Barbara J. Wold,
- and Ali Mortazavi
Genome Res. September 2012 22: 1626-1633; doi:10.1101/gr.134957.111
...single nucleotide variants (SNVs) for 12 of the 14 cell types using either 1000 Genomes resequencing data (The 1000 Genomes Project Consortium 2010) or ENCODE ChIP-seq data sets. We identified between 500 and 3000 reproducible A-to-I RNA editing events per cell type in biological duplicate RNA...
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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...activating or repressive transcription factors (The ENCODE Project Consortium et al. 41 2020). Epigenetic regulation to compact chromatin restricts transcription and we 42 recently reported that only about 20% of the in human cells is actively 43 producing measurable amounts of RNA (McShane et al. 2024...
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