My NCBISign In
Apollo: a sequence annotation editor
SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall, ME Clamp
Genome Biol. 2002; 3(12): research0082.1–82.14. Published online 2002 December 23. doi: 10.1186/gb-2002-3-12-research0082
PMCID:
PMC151184
Abstract Full Text PDF–2.3M

Is Cited by the Following 67 Articles in this Archive:

Chado Controller: advanced annotation management with a community annotation system
Valentin Guignon, Gaëtan Droc, Michael Alaux, Franc-Christophe Baurens, Olivier Garsmeur, Claire Poiron, Tim Carver, Mathieu Rouard, Stéphanie Bocs
Bioinformatics. 2012 April 1; 28(7): 1054–1056. Published online 2012 January 28. doi: 10.1093/bioinformatics/bts046
PMCID:
PMC3315714
Abstract Full Text PDF–374K Supplementary Material
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
Philippe Lamesch, Tanya Z. Berardini, Donghui Li, David Swarbreck, Christopher Wilks, Rajkumar Sasidharan, Robert Muller, Kate Dreher, Debbie L. Alexander, Margarita Garcia-Hernandez, Athikkattuvalasu S. Karthikeyan, Cynthia H. Lee, William D. Nelson, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala
Nucleic Acids Res. 2012 January; 40(D1): D1202–D1210. Published online 2011 December 2. doi: 10.1093/nar/gkr1090
PMCID:
PMC3245047
Abstract Full Text PDF–243K
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA
Marie-Josée Cros, Antoine de Monte, Jérôme Mariette, Philippe Bardou, Benjamin Grenier-Boley, Daniel Gautheret, Hélène Touzet, Christine Gaspin
RNA. 2011 November; 17(11): 1947–1956. doi: 10.1261/rna.2844911
PMCID:
PMC3198588
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
The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming
Sanne Nygaard, Guojie Zhang, Morten Schiøtt, Cai Li, Yannick Wurm, Haofu Hu, Jiajian Zhou, Lu Ji, Feng Qiu, Morten Rasmussen, Hailin Pan, Frank Hauser, Anders Krogh, Cornelis J.P. Grimmelikhuijzen, Jun Wang, Jacobus J. Boomsma
Genome Res. 2011 August; 21(8): 1339–1348. doi: 10.1101/gr.121392.111
PMCID:
PMC3149500
Abstract Full Text PDF–588K
Gain, Loss and Divergence in Primate Zinc-Finger Genes: A Rich Resource for Evolution of Gene Regulatory Differences between Species
Katja Nowick, Christopher Fields, Tim Gernat, Derek Caetano-Anolles, Nadezda Kholina, Lisa Stubbs
PLoS One. 2011; 6(6): e21553. Published online 2011 June 29. doi: 10.1371/journal.pone.0021553
PMCID:
PMC3126818
Abstract Full Text PDF–444K Supplementary Material
Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi
Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin, Béatrice Clouet-d'Orval
BMC Genomics. 2011; 12: 312. Published online 2011 June 13. doi: 10.1186/1471-2164-12-312
PMCID:
PMC3124441
Abstract Full Text PDF–1.4M Supplementary Material
Methods and strategies for gene structure curation in WormBase
G.W. Williams, P.A. Davis, A.S. Rogers, T. Bieri, P. Ozersky, J. Spieth
Database (Oxford) 2011; 2011: baq039. Published online 2011 May 3. doi: 10.1093/database/baq039
PMCID:
PMC3092607
Abstract Full Text PDF–459K
Gene Space Dynamics During the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes
A. N. Massa, H. Wanjugi, K. R. Deal, K. O'Brien, F. M. You, R. Maiti, A. P. Chan, Y. Q. Gu, M. C. Luo, O. D. Anderson, P. D. Rabinowicz, J. Dvorak, K. M. Devos
Mol Biol Evol. 2011 September; 28(9): 2537–2547. Published online 2011 April 6. doi: 10.1093/molbev/msr080
PMCID:
PMC3163431
Abstract Full Text PDF–503K
Comparative visualization of genetic and physical maps with Strudel
Micha Bayer, Iain Milne, Gordon Stephen, Paul Shaw, Linda Cardle, Frank Wright, David Marshall
Bioinformatics. 2011 May 1; 27(9): 1307–1308. Published online 2011 March 3. doi: 10.1093/bioinformatics/btr111
PMCID:
PMC3077070
Abstract Full Text PDF–186K
The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle
Garret Suen, Clotilde Teiling, Lewyn Li, Carson Holt, Ehab Abouheif, Erich Bornberg-Bauer, Pascal Bouffard, Eric J. Caldera, Elizabeth Cash, Amy Cavanaugh, Olgert Denas, Eran Elhaik, Marie-Julie Favé, Jürgen Gadau, Joshua D. Gibson, Dan Graur, Kirk J. Grubbs, Darren E. Hagen, Timothy T. Harkins, Martin Helmkampf, Hao Hu, Brian R. Johnson, Jay Kim, Sarah E. Marsh, Joseph A. Moeller, Mónica C. Muñoz-Torres, Marguerite C. Murphy, Meredith C. Naughton, Surabhi Nigam, Rick Overson, Rajendhran Rajakumar, Justin T. Reese, Jarrod J. Scott, Chris R. Smith, Shu Tao, Neil D. Tsutsui, Lumi Viljakainen, Lothar Wissler, Mark D. Yandell, Fabian Zimmer, James Taylor, Steven C. Slater, Sandra W. Clifton, Wesley C. Warren, Christine G. Elsik, Christopher D. Smith, George M. Weinstock, Nicole M. Gerardo, Cameron R. Currie
PLoS Genet. 2011 February; 7(2): e1002007. Published online 2011 February 10. doi: 10.1371/journal.pgen.1002007
PMCID:
PMC3037820
Abstract Full Text PDF–685K Supplementary Material
Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts
C. A. D’Souza, J. W. Kronstad, G. Taylor, R. Warren, M. Yuen, G. Hu, W. H. Jung, A. Sham, S. E. Kidd, K. Tangen, N. Lee, T. Zeilmaker, J. Sawkins, G. McVicker, S. Shah, S. Gnerre, A. Griggs, Q. Zeng, K. Bartlett, W. Li, X. Wang, J. Heitman, J. E. Stajich, J. A. Fraser, W. Meyer, D. Carter, J. Schein, M. Krzywinski, K. J. Kwon-Chung, A. Varma, J. Wang, R. Brunham, M. Fyfe, B. F. F. Ouellette, A. Siddiqui, M. Marra, S. Jones, R. Holt, B. W. Birren, J. E. Galagan, C. A. Cuomo
mBio. 2011 Jan-Feb; 2(1): e00342-10. Published online 2011 February 8. doi: 10.1128/mBio.00342-10
PMCID:
PMC3037005
Abstract Full Text PDF–2.2M Supplementary Material
Natural diversity of potato (Solanum tuberosum) invertases
Astrid M Draffehn, Sebastian Meller, Li Li, Christiane Gebhardt
BMC Plant Biol. 2010; 10: 271. Published online 2010 December 9. doi: 10.1186/1471-2229-10-271
PMCID:
PMC3012049
Abstract Full Text PDF–413K Supplementary Material
Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome
Justin T Reese, Christopher P Childers, Jaideep P Sundaram, C Michael Dickens, Kevin L Childs, Donald C Vile, Christine G Elsik
BMC Genomics. 2010; 11: 645. Published online 2010 November 19. doi: 10.1186/1471-2164-11-645
PMCID:
PMC3012608
Abstract Full Text PDF–1.4M
Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy
Víctor M González, Andrej Benjak, Elizabeth Marie Hénaff, Gisela Mir, Josep M Casacuberta, Jordi Garcia-Mas, Pere Puigdomènech
BMC Plant Biol. 2010; 10: 246. Published online 2010 November 12. doi: 10.1186/1471-2229-10-246
PMCID:
PMC3095328
Abstract Full Text PDF–656K 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
Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region from Phaseolus vulgaris
Jer-Young Lin, Robert M. Stupar, Christian Hans, David L. Hyten, Scott A. Jackson
Plant Cell. 2010 August; 22(8): 2545–2561. Published online 2010 August 20. doi: 10.1105/tpc.110.074229
PMCID:
PMC2947175
Abstract Full Text PDF–1.1M Supplementary Material
Sequence and annotation of the Wizard007 mycobacterium phage genome
Ejike Anyanwu, Kaitlyn Cole, Karlee Driver, Anthony Falcone, Elizabeth Farnsworth, Benjamin Howard, Brittney Howard, Courtney Howard, Rodney King, Jordan Olberding, Mackenzie Perkins, Claire Rinehart, Heidi Sayre, Tyler Scaff, Sarah Schrader, Prasanna Tamarapu Parthasarathy, Cynthia Tope
BMC Bioinformatics. 2010; 11(Suppl 4): P15. Published online 2010 July 23. doi: 10.1186/1471-2105-11-S4-P15
PMCID:
PMC3290069
Full Text PDF–116K
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris, Vipaporn Phuntmart, Daniela Puiu, Jyoti Shetty, Jason E Stajich, Sucheta Tripathy, Stephan Wawra, Pieter van West, Brett R Whitty, Pedro M Coutinho, Bernard Henrissat, Frank Martin, Paul D Thomas, Brett M Tyler, Ronald P De Vries, Sophien Kamoun, Mark Yandell, Ned Tisserat, C Robin Buell
Genome Biol. 2010; 11(7): R73. Published online 2010 July 13. doi: 10.1186/gb-2010-11-7-r73
PMCID:
PMC2926784
Abstract Full Text PDF–1.7M Supplementary Material
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
Allen Kovach, Jill L Wegrzyn, Genis Parra, Carson Holt, George E Bruening, Carol A Loopstra, James Hartigan, Mark Yandell, Charles H Langley, Ian Korf, David B Neale
BMC Genomics. 2010; 11: 420. Published online 2010 July 7. doi: 10.1186/1471-2164-11-420
PMCID:
PMC2996948
Abstract Full Text PDF–2.2M Supplementary Material
Evolution of the CD163 family and its relationship to the bovine gamma delta T cell co-receptor WC1
Carolyn TA Herzig, Ray W Waters, Cynthia L Baldwin, Janice C Telfer
BMC Evol Biol. 2010; 10: 181. Published online 2010 June 15. doi: 10.1186/1471-2148-10-181
PMCID:
PMC2906472
Abstract Full Text PDF–2.2M Supplementary Material
Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature
Wasila M. Dahdul, James P. Balhoff, Jeffrey Engeman, Terry Grande, Eric J. Hilton, Cartik Kothari, Hilmar Lapp, John G. Lundberg, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee
PLoS One. 2010; 5(5): e10708. Published online 2010 May 20. doi: 10.1371/journal.pone.0010708
PMCID:
PMC2873956
Abstract Full Text PDF–370K Supplementary Material
Polymorphisms in the gene encoding bovine interleukin-10 receptor alpha are associated with Mycobacterium avium ssp. paratuberculosis infection status
Chris P Verschoor, Sameer D Pant, Qiumei You, Flavio S Schenkel, David F Kelton, Niel A Karrow
BMC Genet. 2010; 11: 23. Published online 2010 April 15. doi: 10.1186/1471-2156-11-23
PMCID:
PMC2873551
Abstract Full Text PDF–680K
Neural expression and post-transcriptional dosage compensation of the steroid metabolic enzyme 17β-HSD type 4
Sarah E London, Yuichiro Itoh, Valentin A Lance, Petra M Wise, Preethika S Ekanayake, Randi K Oyama, Arthur P Arnold, Barney A Schlinger
BMC Neurosci. 2010; 11: 47. Published online 2010 April 1. doi: 10.1186/1471-2202-11-47
PMCID:
PMC2858028
Abstract Full Text PDF–2.2M
Genomic and neural analysis of the estradiol-synthetic pathway in the zebra finch
Sarah E London, David F Clayton
BMC Neurosci. 2010; 11: 46. Published online 2010 April 1. doi: 10.1186/1471-2202-11-46
PMCID:
PMC2865489
Abstract Full Text PDF–2.0M Supplementary Material
Annotation and classification of the bovine T cell receptor delta genes
Carolyn TA Herzig, Marie-Paule Lefranc, Cynthia L Baldwin
BMC Genomics. 2010; 11: 100. Published online 2010 February 9. doi: 10.1186/1471-2164-11-100
PMCID:
PMC2846910
Abstract Full Text PDF–2.9M Supplementary Material
Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome
Fusheng Wei, Joshua C. Stein, Chengzhi Liang, Jianwei Zhang, Robert S. Fulton, Regina S. Baucom, Emanuele De Paoli, Shiguo Zhou, Lixing Yang, Yujun Han, Shiran Pasternak, Apurva Narechania, Lifang Zhang, Cheng-Ting Yeh, Kai Ying, Dawn H. Nagel, Kristi Collura, David Kudrna, Jennifer Currie, Jinke Lin, HyeRan Kim, Angelina Angelova, Gabriel Scara, Marina Wissotski, Wolfgang Golser, Laura Courtney, Scott Kruchowski, Tina A. Graves, Susan M. Rock, Stephanie Adams, Lucinda A. Fulton, Catrina Fronick, William Courtney, Melissa Kramer, Lori Spiegel, Lydia Nascimento, Ananth Kalyanaraman, Cristian Chaparro, Jean-Marc Deragon, Phillip San Miguel, Ning Jiang, Susan R. Wessler, Pamela J. Green, Yeisoo Yu, David C. Schwartz, Blake C. Meyers, Jeffrey L. Bennetzen, Robert A. Martienssen, W. Richard McCombie, Srinivas Aluru, Sandra W. Clifton, Patrick S. Schnable, Doreen Ware, Richard K. Wilson, Rod A. Wing
PLoS Genet. 2009 November; 5(11): e1000728. Published online 2009 November 20. doi: 10.1371/journal.pgen.1000728
PMCID:
PMC2773423
Abstract Full Text PDF–1.0M Supplementary Material
Identification and characterisation of a novel immune-type receptor (NITR) gene cluster in the European sea bass, Dicentrarchus labrax, reveals recurrent gene expansion and diversification by positive selection
Serena Ferraresso, Heiner Kuhl, Massimo Milan, David W. Ritchie, Christopher J. Secombes, Richard Reinhardt, Luca Bargelloni
Immunogenetics. 2009 December; 61(11-12): 773–788. Published online 2009 November 19. doi: 10.1007/s00251-009-0398-3
PMCID:
PMC2921055
Abstract Full Text PDF–838K Supplementary Material
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes
James C Estill, Jeffrey L Bennetzen
Plant Methods. 2009; 5: 8. Published online 2009 June 19. doi: 10.1186/1746-4811-5-8
PMCID:
PMC2705364
Abstract Full Text PDF–1.4M
Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle
Anna Ekman, Mikael Niku, Jenni Liljavirta, Antti Iivanainen
BMC Immunol. 2009; 10: 22. Published online 2009 April 30. doi: 10.1186/1471-2172-10-22
PMCID:
PMC2686674
Abstract Full Text PDF–1.6M Supplementary Material
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