My NCBISign In
EGASP: the human ENCODE Genome Annotation Assessment Project
Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E Lewis, Martin G Reese
Genome Biol. 2006; 7(Suppl 1): S2. Published online 2006 August 7. doi: 10.1186/gb-2006-7-s1-s2
PMCID:
PMC1810551
Abstract Full Text PDF–2.1M

Is Cited by the Following 49 Articles in this Archive:

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
The Proteome Folding Project: Proteome-scale prediction of structure and function
Kevin Drew, Patrick Winters, Glenn L. Butterfoss, Viktors Berstis, Keith Uplinger, Jonathan Armstrong, Michael Riffle, Erik Schweighofer, Bill Bovermann, David R. Goodlett, Trisha N. Davis, Dennis Shasha, Lars Malmström, Richard Bonneau
Genome Res. 2011 November; 21(11): 1981–1994. doi: 10.1101/gr.121475.111
PMCID:
PMC3205581
Abstract Full Text PDF–1.1M
Approaches to Fungal Genome Annotation
Brian J. Haas, Qiandong Zeng, Matthew D. Pearson, Christina A. Cuomo, Jennifer R. Wortman
Mycology. Author manuscript; available in PMC 2012 October 3.
Published in final edited form as: Mycology. 2011 October 3; 2(3): 118–141. doi: 10.1080/21501203.2011.606851
PMCID:
PMC3207268
Free in PMC on 2012/10/03
Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus
Taisei Kikuchi, James A. Cotton, Jonathan J. Dalzell, Koichi Hasegawa, Natsumi Kanzaki, Paul McVeigh, Takuma Takanashi, Isheng J. Tsai, Samuel A. Assefa, Peter J. A. Cock, Thomas Dan Otto, Martin Hunt, Adam J. Reid, Alejandro Sanchez-Flores, Kazuko Tsuchihara, Toshiro Yokoi, Mattias C. Larsson, Johji Miwa, Aaron G. Maule, Norio Sahashi, John T. Jones, Matthew Berriman
PLoS Pathog. 2011 September; 7(9): e1002219. Published online 2011 September 1. doi: 10.1371/journal.ppat.1002219
PMCID:
PMC3164644
Abstract Full Text PDF–891K Supplementary Material
Small Open Reading Frames: Current Prediction Techniques and Future Prospect
Haoyu Cheng, Wai Soon Chan, Zhixiu Li, Dan Wang, Song Liu, Yaoqi Zhou
Curr Protein Pept Sci. Author manuscript; available in PMC 2012 September 1.
Published in final edited form as: Curr Protein Pept Sci. 2011 September 1; 12(6): 503–507.
PMCID:
PMC3203329
Free in PMC on 2012/09/01
Synergistic use of plant-prokaryote comparative genomics for functional annotations
Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson, Valérie de Crécy-Lagard
BMC Genomics. 2011; 12(Suppl 1): S2. Published online 2011 June 15. doi: 10.1186/1471-2164-12-S1-S2
PMCID:
PMC3223725
Abstract Full Text PDF–718K Supplementary Material
A novel and well-defined benchmarking method for second generation read mapping
Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert
BMC Bioinformatics. 2011; 12: 210. Published online 2011 May 26. doi: 10.1186/1471-2105-12-210
PMCID:
PMC3128034
Abstract Full Text PDF–286K Supplementary Material
The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates
Jonathan M. Mudge, Adam Frankish, Julio Fernandez-Banet, Tyler Alioto, Thomas Derrien, Cédric Howald, Alexandre Reymond, Roderic Guigó, Tim Hubbard, Jennifer Harrow
Mol Biol Evol. 2011 October; 28(10): 2949–2959. Published online 2011 May 6. doi: 10.1093/molbev/msr127
PMCID:
PMC3176834
Abstract Full Text PDF–645K Supplementary Material
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
Markus Brosch, Gary I. Saunders, Adam Frankish, Mark O. Collins, Lu Yu, James Wright, Ruth Verstraten, David J. Adams, Jennifer Harrow, Jyoti S. Choudhary, Tim Hubbard
Genome Res. 2011 May; 21(5): 756–767. doi: 10.1101/gr.114272.110
PMCID:
PMC3083093
Abstract Full Text PDF–1.5M
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
The ENCODE Project Consortium
PLoS Biol. 2011 April; 9(4): e1001046. Published online 2011 April 19. doi: 10.1371/journal.pbio.1001046
PMCID:
PMC3079585
Abstract Full Text PDF–2.2M Supplementary Material
RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data
Stefan Washietl, Sven Findeiß, Stephan A. Müller, Stefan Kalkhof, Martin von Bergen, Ivo L. Hofacker, Peter F. Stadler, Nick Goldman
RNA. 2011 April; 17(4): 578–594. doi: 10.1261/rna.2536111
PMCID:
PMC3062170
Abstract Full Text PDF–1.5M
Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome
Michael Specht, Mario Stanke, Mia Terashima, Bianca Naumann-Busch, Ingrid Janßen, Ricarda Höhner, Erik F. Y. Hom, Chun Liang, Michael Hippler
Proteomics. Author manuscript; available in PMC 2012 May 1.
Published in final edited form as: Proteomics. 2011 May; 11(9): 1814–1823. Published online 2011 March 22. doi: 10.1002/pmic.201000621
PMCID:
PMC3145493
Abstract Full Text PDF–1.2M Supplementary Material
Comprehensive Proteomic Analysis of Membrane Proteins in Toxoplasma gondii
Fa-Yun Che, Carlos Madrid-Aliste, Berta Burd, Hongshan Zhang, Edward Nieves, Kami Kim, Andras Fiser, Ruth Hogue Angeletti, Louis M. Weiss
Mol Cell Proteomics. 2011 January; 10(1): M110.000745. Published online 2010 October 10. doi: 10.1074/mcp.M110.000745
PMCID:
PMC3013445
Abstract Full Text
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
M. Mariotti, R. Guigó
Bioinformatics. 2010 November 1; 26(21): 2656–2663. Published online 2010 September 21. doi: 10.1093/bioinformatics/btq516
PMCID:
PMC2958745
Abstract Full Text PDF–1022K Supplementary Material
A standard variation file format for human genome sequences
Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck
Genome Biol. 2010; 11(8): R88. Published online 2010 August 26. doi: 10.1186/gb-2010-11-8-r88
PMCID:
PMC2945790
Abstract Full Text PDF–1.0M
Using Deep RNA Sequencing for the Structural Annotation of the Laccaria Bicolor Mycorrhizal Transcriptome
Peter E. Larsen, Geetika Trivedi, Avinash Sreedasyam, Vincent Lu, Gopi K. Podila, Frank R. Collart
PLoS One. 2010; 5(7): e9780. Published online 2010 July 6. doi: 10.1371/journal.pone.0009780
PMCID:
PMC2897884
Abstract Full Text PDF–472K Supplementary Material
An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
Danny A. Bitton, Duncan L. Smith, Yvonne Connolly, Paul J. Scutt, Crispin J. Miller
PLoS One. 2010; 5(1): e8949. Published online 2010 January 28. doi: 10.1371/journal.pone.0008949
PMCID:
PMC2812506
Abstract Full Text PDF–378K Supplementary Material
Evidence-based gene predictions in plant genomes
Chengzhi Liang, Long Mao, Doreen Ware, Lincoln Stein
Genome Res. 2009 October; 19(10): 1912–1923. doi: 10.1101/gr.088997.108
PMCID:
PMC2765265
Abstract Full Text PDF–556K
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes
Chun Liang, Lin Liu, Guoli Ji
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W77–W83. Published online 2009 July 1. doi: 10.1093/nar/gkp389
PMCID:
PMC2703992
Abstract Full Text PDF–7.6M
Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships
Eric J. Vallender
Methods. Author manuscript; available in PMC 2010 September 1.
Published in final edited form as: Methods. 2009 September; 49(1): 50–55. Published online 2009 May 23. doi: 10.1016/j.ymeth.2009.05.010
PMCID:
PMC2732758
Abstract Full Text PDF–741K
Quantitative measures for the management and comparison of annotated genomes
Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell
BMC Bioinformatics. 2009; 10: 67. Published online 2009 February 23. doi: 10.1186/1471-2105-10-67
PMCID:
PMC2653490
Abstract Full Text PDF–1.5M Supplementary Material
Identifying protein-coding genes in genomic sequences
Jennifer Harrow, Alinda Nagy, Alexandre Reymond, Tyler Alioto, Laszlo Patthy, Stylianos E Antonarakis, Roderic Guigó
Genome Biol. 2009; 10(1): 201. Published online 2009 January 30. doi: 10.1186/gb-2009-10-1-201
PMCID:
PMC2687780
Abstract Full Text PDF–709K Supplementary Material
Ensembl 2009
T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, G. Coates, S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon, S. Graf, S. Haider, M. Hammond, R. Holland, K. Howe, A. Jenkinson, N. Johnson, A. Kahari, D. Keefe, S. Keenan, R. Kinsella, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios, M. Schuster, G. Slater, D. Smedley, W. Spooner, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, S. Wilder, A. Zadissa, E. Birney, F. Cunningham, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, A. Kasprzyk, G. Proctor, J. Smith, S. Searle, P. Flicek
Nucleic Acids Res. 2009 January; 37(Database issue): D690–D697. Published online 2009 January. doi: 10.1093/nar/gkn828
PMCID:
PMC2686571
Abstract Full Text PDF–4.1M
Annotating genomes with massive-scale RNA sequencing
France Denoeud, Jean-Marc Aury, Corinne Da Silva, Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, François Artiguenave
Genome Biol. 2008; 9(12): R175. Published online 2008 December 16. doi: 10.1186/gb-2008-9-12-r175
PMCID:
PMC2646279
Abstract Full Text PDF–511K Supplementary Material
Computational Analysis and Experimental Validation of Gene Predictions in Toxoplasma gondii
Joseph M. Dybas, Carlos J. Madrid-Aliste, Fa-Yun Che, Edward Nieves, Dmitry Rykunov, Ruth Hogue Angeletti, Louis M. Weiss, Kami Kim, Andras Fiser
PLoS ONE. 2008; 3(12): e3899. Published online 2008 December 9. doi: 10.1371/journal.pone.0003899
PMCID:
PMC2587701
Abstract Full Text PDF–585K Supplementary Material
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases
Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai, László Patthy
BMC Bioinformatics. 2008; 9: 353. Published online 2008 August 27. doi: 10.1186/1471-2105-9-353
PMCID:
PMC2542381
Abstract Full Text PDF–443K Supplementary Material
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer
Bioinformatics. 2008 July 1; 24(13): i24–i31. doi: 10.1093/bioinformatics/btn172
PMCID:
PMC2718650
Abstract Full Text PDF–259K
Gene prediction: compare and CONTRAST
Paul Flicek
Genome Biol. 2007; 8(12): 233. Published online 2007 December 20. doi: 10.1186/gb-2007-8-12-233
PMCID:
PMC2246255
Abstract Full Text PDF–68K
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou
Genome Biol. 2007; 8(12): R269. Published online 2007 December 20. doi: 10.1186/gb-2007-8-12-r269
PMCID:
PMC2246271
Abstract Full Text PDF–1.9M
Initial sequence and comparative analysis of the cat genome
Joan U. Pontius, James C. Mullikin, Douglas R. Smith, Agencourt Sequencing Team, Kerstin Lindblad-Toh, Sante Gnerre, Michele Clamp, Jean Chang, Robert Stephens, Beena Neelam, Natalia Volfovsky, Alejandro A. Schäffer, Richa Agarwala, Kristina Narfström, William J. Murphy, Urs Giger, Alfred L. Roca, Agostinho Antunes, Marilyn Menotti-Raymond, Naoya Yuhki, Jill Pecon-Slattery, Warren E. Johnson, Guillaume Bourque, Glenn Tesler, NISC Comparative Sequencing Program, Stephen J. O’Brien
Genome Res. 2007 November; 17(11): 1675–1689. doi: 10.1101/gr.6380007
PMCID:
PMC2045150
Abstract Full Text PDF–1.1M
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