My NCBISign In
GENCODE: producing a reference annotation for ENCODE
Jennifer Harrow, France Denoeud, Adam Frankish, Alexandre Reymond, Chao-Kung Chen, Jacqueline Chrast, Julien Lagarde, James GR Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos E Antonarakis, Roderic Guigo
Genome Biol. 2006; 7(Suppl 1): S4. Published online 2006 August 7. doi: 10.1186/gb-2006-7-s1-s4
PMCID:
PMC1810553
Abstract Full Text PDF–579K

Is Cited by the Following 78 Articles in this Archive:

RNA-SeQC: RNA-seq metrics for quality control and process optimization
David S. DeLuca, Joshua Z. Levin, Andrey Sivachenko, Timothy Fennell, Marc-Danie Nazaire, Chris Williams, Michael Reich, Wendy Winckler, Gad Getz
Bioinformatics. 2012 June 1; 28(11): 1530–1532. Published online 2012 April 25. doi: 10.1093/bioinformatics/bts196
PMCID:
PMC3356847
Abstract Full Text PDF–111K Supplementary Material
Dark Matter RNA: Existence, Function, and Controversy
Philipp Kapranov, Georges St. Laurent
Front Genet. 2012; 3: 60. Published online 2012 April 23. doi: 10.3389/fgene.2012.00060
PMCID:
PMC3332219
Abstract Full Text PDF–1.3M
Evaluation of the Metabochip Genotyping Array in African Americans and Implications for Fine Mapping of GWAS-Identified Loci: The PAGE Study
Steven Buyske, Ying Wu, Cara L. Carty, Iona Cheng, Themistocles L. Assimes, Logan Dumitrescu, Lucia A. Hindorff, Sabrina Mitchell, Jose Luis Ambite, Eric Boerwinkle, Petra Buzkova, Chris S. Carlson, Barbara Cochran, David Duggan, Charles B. Eaton, Megan D. Fesinmeyer, Nora Franceschini, Jeffrey Haessler, Nancy Jenny, Hyun Min Kang, Charles Kooperberg, Yi Lin, Loic Le Marchand, Tara C. Matise, Jennifer G. Robinson, Carlos Rodriguez, Fredrick R. Schumacher, Benjamin F. Voight, Alicia Young, Teri A. Manolio, Karen L. Mohlke, Christopher A. Haiman, Ulrike Peters, Dana C. Crawford, Kari E. North
PLoS One. 2012; 7(4): e35651. Published online 2012 April 23. doi: 10.1371/journal.pone.0035651
PMCID:
PMC3335090
Abstract Full Text PDF–324K Supplementary Material
The importance of identifying alternative splicing in vertebrate genome annotation
Adam Frankish, Jonathan M. Mudge, Mark Thomas, Jennifer Harrow
Database (Oxford) 2012; 2012: bas014. Published online 2012 March 20. doi: 10.1093/database/bas014
PMCID:
PMC3308168
Abstract Full Text PDF–1.1M
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
Nat Methods. Author manuscript; available in PMC 2012 September 18.
Published in final edited form as: Nat Methods. 2012 March 18; 9(5): 473–476. doi: 10.1038/nmeth.1937
PMCID:
PMC3340533
Free in PMC on 2012/09/18
Estimation of alternative splicing variability in human populations
Mar Gonzàlez-Porta, Miquel Calvo, Michael Sammeth, Roderic Guigó
Genome Res. 2012 March; 22(3): 528–538. doi: 10.1101/gr.121947.111
PMCID:
PMC3290788
Abstract Full Text PDF–1.2M
A systematic survey of loss-of-function variants in human protein-coding genes
Daniel G. MacArthur, Suganthi Balasubramanian, Adam Frankish, Ni Huang, James Morris, Klaudia Walter, Luke Jostins, Lukas Habegger, Joseph K. Pickrell, Stephen B. Montgomery, Cornelis A. Albers, Zhengdong Zhang, Donald F. Conrad, Gerton Lunter, Hancheng Zheng, Qasim Ayub, Mark A. DePristo, Eric Banks, Min Hu, Robert E. Handsaker, Jeffrey Rosenfeld, Menachem Fromer, Mike Jin, Xinmeng Jasmine Mu, Ekta Khurana, Kai Ye, Mike Kay, Gary Ian Saunders, Marie-Marthe Suner, Toby Hunt, If H.A. Barnes, Clara Amid, Denise R. Carvalho-Silva, Alexandra H Bignell, Catherine Snow, Bryndis Yngvadottir, Suzannah Bumpstead, David N. Cooper, Yali Xue, Irene Gallego Romero, 1000 Genomes Project Consortium, Jun Wang, Yingrui Li, Richard A. Gibbs, Steven A. McCarroll, Emmanouil T. Dermitzakis, Jonathan K. Pritchard, Jeffrey C. Barrett, Jennifer Harrow, Matthew E. Hurles, Mark B. Gerstein, Chris Tyler-Smith
Science. Author manuscript; available in PMC 2012 August 17.
Published in final edited form as: Science. 2012 February 17; 335(6070): 823–828. doi: 10.1126/science.1215040
PMCID:
PMC3299548
Free in PMC on 2012/08/17
Tracking and coordinating an international curation effort for the CCDS Project
Rachel A. Harte, Catherine M. Farrell, Jane E. Loveland, Marie-Marthe Suner, Laurens Wilming, Bronwen Aken, Daniel Barrell, Adam Frankish, Craig Wallin, Steve Searle, Mark Diekhans, Jennifer Harrow, Kim D. Pruitt
Database (Oxford) 2012; 2012: bas008. Published online 2012 February 13. doi: 10.1093/database/bas008
PMCID:
PMC3308164
Abstract Full Text PDF–757K
Community gene annotation in practice
Jane E. Loveland, James G.R. Gilbert, Ed Griffiths, Jennifer L. Harrow
Database (Oxford) 2012; 2012: bas009. Published online 2012 February 13. doi: 10.1093/database/bas009
PMCID:
PMC3308165
Abstract Full Text PDF–638K
Fast Computation and Applications of Genome Mappability
Thomas Derrien, Jordi Estellé, Santiago Marco Sola, David G. Knowles, Emanuele Raineri, Roderic Guigó, Paolo Ribeca
PLoS One. 2012; 7(1): e30377. Published online 2012 January 19. doi: 10.1371/journal.pone.0030377
PMCID:
PMC3261895
Abstract Full Text PDF–1.4M
The Long Non-Coding RNAs: A New (P)layer in the “Dark Matter”
Thomas Derrien, Roderic Guigó, Rory Johnson
Front Genet. 2011; 2: 107. Published online 2012 January 9. doi: 10.3389/fgene.2011.00107
PMCID:
PMC3266617
Abstract Full Text PDF–495K
IQSeq: Integrated Isoform Quantification Analysis Based on Next-Generation Sequencing
Jiang Du, Jing Leng, Lukas Habegger, Andrea Sboner, Drew McDermott, Mark Gerstein
PLoS One. 2012; 7(1): e29175. Published online 2012 January 6. doi: 10.1371/journal.pone.0029175
PMCID:
PMC3253133
Abstract Full Text PDF–2.8M Supplementary Material
Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation
Wenqian Hu, Bingbing Yuan, Johan Flygare, Harvey F. Lodish
Genes Dev. 2011 December 15; 25(24): 2573–2578. doi: 10.1101/gad.178780.111
PMCID:
PMC3248679
Free in PMC on 2012/06/15
The UCSC Genome Browser database: extensions and updates 2011
Timothy R. Dreszer, Donna Karolchik, Ann S. Zweig, Angie S. Hinrichs, Brian J. Raney, Robert M. Kuhn, Laurence R. Meyer, Mathew Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke Rhead, Andy Pohl, Venkat S. Malladi, Chin H. Li, Katrina Learned, Vanessa Kirkup, Fan Hsu, Rachel A. Harte, Luvina Guruvadoo, Mary Goldman, Belinda M. Giardine, Pauline A. Fujita, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent
Nucleic Acids Res. 2012 January; 40(D1): D918–D923. Published online 2011 November 15. doi: 10.1093/nar/gkr1055
PMCID:
PMC3245018
Abstract Full Text PDF–3.0M
Ensembl 2012
Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas K. Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha, Pontus Larsson, Ian Longden, William McLaren, Matthieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y. Amy Tang, Kieron Taylor, Stephen Trevanion, Jana Vandrovcova, Simon White, Mark Wilson, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suarez, Jennifer Harrow, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa, Stephen M. J. Searle
Nucleic Acids Res. 2012 January; 40(D1): D84–D90. Published online 2011 November 15. doi: 10.1093/nar/gkr991
PMCID:
PMC3245178
Abstract Full Text PDF–4.6M
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
Lucas D. Ward, Manolis Kellis
Nucleic Acids Res. 2012 January; 40(D1): D930–D934. Published online 2011 November 7. doi: 10.1093/nar/gkr917
PMCID:
PMC3245002
Abstract Full Text PDF–5.7M
Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome
Masako Suzuki, Mayumi Oda, María-Paz Ramos, Marién Pascual, Kevin Lau, Edyta Stasiek, Frederick Agyiri, Reid F. Thompson, Jacob L. Glass, Qiang Jing, Richard Sandstrom, Melissa J. Fazzari, R. Scott Hansen, John A. Stamatoyannopoulos, Andrew S. McLellan, John M. Greally
Genome Res. 2011 November; 21(11): 1833–1840. doi: 10.1101/gr.116509.110
PMCID:
PMC3205568
Abstract Full Text PDF–1.0M
Exploratory analysis of genomic segmentations with Segtools
Orion J Buske, Michael M Hoffman, Nadia Ponts, Karine G Le Roch, William Stafford Noble
BMC Bioinformatics. 2011; 12: 415. Published online 2011 October 26. doi: 10.1186/1471-2105-12-415
PMCID:
PMC3224787
Abstract Full Text PDF–861K
A high-resolution map of human evolutionary constraint using 29 mammals
Kerstin Lindblad-Toh, Manuel Garber, Or Zuk, Michael F. Lin, Brian J. Parker, Stefan Washietl, Pouya Kheradpour, Jason Ernst, Gregory Jordan, Evan Mauceli, Lucas D. Ward, Craig B. Lowe, Alisha K. Holloway, Michele Clamp, Sante Gnerre, Jessica Alfoldi, Kathryn Beal, Jean Chang, Hiram Clawson, James Cuff, Federica Di Palma, Stephen Fitzgerald, Paul Flicek, Mitchell Guttman, Melissa J Hubisz, David B. Jaffe, Irwin Jungreis, W James Kent, Dennis Kostka, Marcia Lara, Andre L Martins, Tim Massingham, Ida Moltke, Brian J. Raney, Matthew D. Rasmussen, Jim Robinson, Alexander Stark, Albert J. Vilella, Jiayu Wen, Xiaohui Xie, Michael C. Zody, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Kim C. Worley, Christie L. Kovar, Donna M. Muzny, Richard A. Gibbs, Baylor College of Medicine Human Genome Sequencing Center, Wesley C. Warren, Elaine R Mardis, George M. Weinstock, Richard K. Wilson, Genome Institute at Washington University, Ewan Birney, Elliott H. Margulies, Javier Herrero, Eric D. Green, David Haussler, Adam Siepel, Nick Goldman, Katherine S. Pollard, Jakob S. Pedersen, Eric S. Lander, Manolis Kellis
Nature. Author manuscript; available in PMC 2012 April 27.
Published in final edited form as: Nature. 2011 October 12; 478(7370): 476–482. doi: 10.1038/nature10530
PMCID:
PMC3207357
Abstract Full Text PDF–1.0M Supplementary Material
The UCSC Genome Browser
Donna Karolchik, Angie S. Hinrichs, W. James Kent
Curr Protoc Hum Genet. Author manuscript; available in PMC 2012 October 1.
Published in final edited form as: Curr Protoc Hum Genet. 2011 October; CHAPTER: Unit18.6. doi: 10.1002/0471142905.hg1806s71
PMCID:
PMC3222792
Free in PMC on 2012/10/01
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
Moran N. Cabili, Cole Trapnell, Loyal Goff, Magdalena Koziol, Barbara Tazon-Vega, Aviv Regev, John L. Rinn
Genes Dev. 2011 September 15; 25(18): 1915–1927. doi: 10.1101/gad.17446611
PMCID:
PMC3185964
Abstract Full Text PDF–1.3M
AlleleSeq: analysis of allele-specific expression and binding in a network framework
Joel Rozowsky, Alexej Abyzov, Jing Wang, Pedro Alves, Debasish Raha, Arif Harmanci, Jing Leng, Robert Bjornson, Yong Kong, Naoki Kitabayashi, Nitin Bhardwaj, Mark Rubin, Michael Snyder, Mark Gerstein
Mol Syst Biol. 2011; 7: 522. Published online 2011 August 2. doi: 10.1038/msb.2011.54
PMCID:
PMC3208341
Abstract Full Text PDF–787K Supplementary Material
Shaping the Genome with Non-Coding RNAs
Xue Q.D Wang, Jennifer L Crutchley, Josée Dostie
Curr Genomics. 2011 August; 12(5): 307–321. doi: 10.2174/138920211796429772
PMCID:
PMC3145261
Abstract Full Text PDF–409K
Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes
Stephen B. Montgomery, Tuuli Lappalainen, Maria Gutierrez-Arcelus, Emmanouil T. Dermitzakis
PLoS Genet. 2011 July; 7(7): e1002144. Published online 2011 July 21. doi: 10.1371/journal.pgen.1002144
PMCID:
PMC3141000
Abstract Full Text PDF–361K Supplementary Material
Poly (A)+ Transcriptome Assessment of ERBB2-Induced Alterations in Breast Cell Lines
Dirce Maria Carraro, Elisa Napolitano Ferreira, Gustavo de Campos Molina, Renato David Puga, Eduardo Fernandes Abrantes, Adriana Priscila Trapé, Bedrich L. Ekhardt, Diana Noronha Nunes, Maria Mitzi Brentani, Wadih Arap, Renata Pasqualini, Helena Brentani, Emmanuel Dias-Neto, Ricardo Renzo Brentani
PLoS One. 2011; 6(6): e21022. Published online 2011 June 22. doi: 10.1371/journal.pone.0021022
Correction in:
PLoS One. 2011; 6(7): 10.1371/annotation/b8888ae6-e402-43af-a425-6fd5e58deef6.
PMCID:
PMC3120832
Abstract Full Text PDF–884K Supplementary Material Correction
Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains
Wenjie Shu, Hebing Chen, Xiaochen Bo, Shengqi Wang
Nucleic Acids Res. 2011 September; 39(17): 7428–7443. Published online 2011 June 17. doi: 10.1093/nar/gkr443
PMCID:
PMC3177195
Abstract Full Text PDF–3.1M Supplementary Material
firestar—advances in the prediction of functionally important residues
Gonzalo Lopez, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, Michael L. Tress
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W235–W241. Published online 2011 June 14. doi: 10.1093/nar/gkr437
PMCID:
PMC3125799
Abstract Full Text PDF–4.7M
RNA-sequence analysis of human B-cells
Jonathan M. Toung, Michael Morley, Mingyao Li, Vivian G. Cheung
Genome Res. 2011 June; 21(6): 991–998. doi: 10.1101/gr.116335.110
PMCID:
PMC3106332
Abstract Full Text PDF–1.2M
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
Xinmeng Jasmine Mu, Zhi John Lu, Yong Kong, Hugo Y. K. Lam, Mark B. Gerstein
Nucleic Acids Res. 2011 September; 39(16): 7058–7076. Published online 2011 May 19. doi: 10.1093/nar/gkr342
PMCID:
PMC3167619
Abstract Full Text PDF–1.9M Supplementary Material
Widespread RNA and DNA Sequence Differences in the Human Transcriptome
Mingyao Li, Isabel X. Wang, Yun Li, Alan Bruzel, Allison L. Richards, Jonathan M. Toung, Vivian G. Cheung
Science. Author manuscript; available in PMC 2012 January 1.
Published in final edited form as: Science. 2011 July 1; 333(6038): 53–58. Published online 2011 May 19. doi: 10.1126/science.1207018
PMCID:
PMC3204392
Abstract Full Text PDF–428K Supplementary Material
You are here: NCBI > Literature > PubMed Central (PMC)
Write to the Help Desk