My NCBISign In
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman
Genome Biol. 2008; 9(1): R7. Published online 2008 January 11. doi: 10.1186/gb-2008-9-1-r7
PMCID:
PMC2395244
Abstract Full Text PDF–722K Supplementary Material

Is Cited by the Following 21 Articles in this Archive:

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy
Adam James Reid, Sarah J. Vermont, James A. Cotton, David Harris, Grant A. Hill-Cawthorne, Stephanie Könen-Waisman, Sophia M. Latham, Tobias Mourier, Rebecca Norton, Michael A. Quail, Mandy Sanders, Dhanasekaran Shanmugam, Amandeep Sohal, James D. Wasmuth, Brian Brunk, Michael E. Grigg, Jonathan C. Howard, John Parkinson, David S. Roos, Alexander J. Trees, Matthew Berriman, Arnab Pain, Jonathan M. Wastling
PLoS Pathog. 2012 March; 8(3): e1002567. Published online 2012 March 22. doi: 10.1371/journal.ppat.1002567
PMCID:
PMC3310773
Abstract Full Text PDF–1.0M Supplementary Material
The Diversification of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization
Bernard J. Koch, Joseph F. Ryan, Andreas D. Baxevanis
PLoS One. 2012; 7(3): e33261. Published online 2012 March 15. doi: 10.1371/journal.pone.0033261
PMCID:
PMC3305314
Abstract Full Text PDF–691K Supplementary Material
Genome Characterization of the Oleaginous Fungus Mortierella alpina
Lei Wang, Wei Chen, Yun Feng, Yan Ren, Zhennan Gu, Haiqin Chen, Hongchao Wang, Michael J. Thomas, Baixi Zhang, Isabelle M. Berquin, Yang Li, Jiansheng Wu, Huanxin Zhang, Yuanda Song, Xiang Liu, James S. Norris, Suriguga Wang, Peng Du, Junguo Shen, Na Wang, Yanlin Yang, Wei Wang, Lu Feng, Colin Ratledge, Hao Zhang, Yong Q. Chen
PLoS One. 2011; 6(12): e28319. Published online 2011 December 8. doi: 10.1371/journal.pone.0028319
PMCID:
PMC3234268
Abstract Full Text PDF–1.3M Supplementary Material
RNA-Seq improves annotation of protein-coding genes in the cucumber genome
Zhen Li, Zhonghua Zhang, Pengcheng Yan, Sanwen Huang, Zhangjun Fei, Kui Lin
BMC Genomics. 2011; 12: 540. Published online 2011 November 2. doi: 10.1186/1471-2164-12-540
PMCID:
PMC3219749
Abstract Full Text PDF–1.4M Supplementary Material
The draft genome of the carcinogenic human liver fluke Clonorchis sinensis
Xiaoyun Wang, Wenjun Chen, Yan Huang, Jiufeng Sun, Jingtao Men, Hailiang Liu, Fang Luo, Lei Guo, Xiaoli Lv, Chuanhuan Deng, Chenhui Zhou, Yongxiu Fan, Xuerong Li, Lisi Huang, Yue Hu, Chi Liang, Xuchu Hu, Jin Xu, Xinbing Yu
Genome Biol. 2011; 12(10): R107. Published online 2011 October 24. doi: 10.1186/gb-2011-12-10-r107
PMCID:
PMC3333777
Abstract Full Text PDF–699K Supplementary Material
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark
Genome Biol. 2011; 12(10): R100. Published online 2011 October 17. doi: 10.1186/gb-2011-12-10-r100
PMCID:
PMC3341644
Abstract Full Text PDF–907K Supplementary Material
De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes
Matthew G Links, Eric Holub, Rays HY Jiang, Andrew G Sharpe, Dwayne Hegedus, Elena Beynon, Dean Sillito, Wayne E Clarke, Shihomi Uzuhashi, Mohammad H Borhan
BMC Genomics. 2011; 12: 503. Published online 2011 October 13. doi: 10.1186/1471-2164-12-503
PMCID:
PMC3206522
Abstract Full Text PDF–1.0M Supplementary Material
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 and Proteomic Analyses of the Fungus Arthrobotrys oligospora Provide Insights into Nematode-Trap Formation
Jinkui Yang, Lei Wang, Xinglai Ji, Yun Feng, Xiaomin Li, Chenggang Zou, Jianping Xu, Yan Ren, Qili Mi, Junli Wu, Shuqun Liu, Yu Liu, Xiaowei Huang, Haiyan Wang, Xuemei Niu, Juan Li, Lianming Liang, Yanlu Luo, Kaifang Ji, Wei Zhou, Zefen Yu, Guohong Li, Yajun Liu, Lei Li, Min Qiao, Lu Feng, Ke-Qin Zhang
PLoS Pathog. 2011 September; 7(9): e1002179. Published online 2011 September 1. doi: 10.1371/journal.ppat.1002179
PMCID:
PMC3164635
Abstract Full Text PDF–698K Supplementary Material
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
The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants
Rafał Wóycicki, Justyna Witkowicz, Piotr Gawroński, Joanna Dąbrowska, Alexandre Lomsadze, Magdalena Pawełkowicz, Ewa Siedlecka, Kohei Yagi, Wojciech Pląder, Anna Seroczyńska, Mieczysław Śmiech, Wojciech Gutman, Katarzyna Niemirowicz-Szczytt, Grzegorz Bartoszewski, Norikazu Tagashira, Yoshikazu Hoshi, Mark Borodovsky, Stanisław Karpiński, Stefan Malepszy, Zbigniew Przybecki
PLoS One. 2011; 6(7): e22728. Published online 2011 July 28. doi: 10.1371/journal.pone.0022728
PMCID:
PMC3145757
Abstract Full Text PDF–394K Supplementary Material
Sequence and structure of Brassica rapa chromosome A3
Jeong-Hwan Mun, Soo-Jin Kwon, Young-Joo Seol, Jin A Kim, Mina Jin, Jung Sun Kim, Myung-Ho Lim, Soo-In Lee, Joon Ki Hong, Tae-Ho Park, Sang-Choon Lee, Beom-Jin Kim, Mi-Suk Seo, Seunghoon Baek, Min-Jee Lee, Ja Young Shin, Jang-Ho Hahn, Yoon-Jung Hwang, Ki-Byung Lim, Jee Young Park, Jonghoon Lee, Tae-Jin Yang, Hee-Ju Yu, Ik-Young Choi, Beom-Soon Choi, Su Ryun Choi, Nirala Ramchiary, Yong Pyo Lim, Fiona Fraser, Nizar Drou, Eleni Soumpourou, Martin Trick, Ian Bancroft, Andrew G Sharpe, Isobel AP Parkin, Jacqueline Batley, Dave Edwards, Beom-Seok Park
Genome Biol. 2010; 11(9): R94. Published online 2010 September 27. doi: 10.1186/gb-2010-11-9-r94
PMCID:
PMC2965386
Abstract Full Text PDF–930K Supplementary Material
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
New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information
Hernan A. Lorenzi, Daniela Puiu, Jason R. Miller, Lauren M. Brinkac, Paolo Amedeo, Neil Hall, Elisabet V. Caler
PLoS Negl Trop Dis. 2010 June; 4(6): e716. Published online 2010 June 15. doi: 10.1371/journal.pntd.0000716
PMCID:
PMC2886108
Abstract Full Text PDF–619K Supplementary Material
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq
Thomas D Otto, Daniel Wilinski, Sammy Assefa, Thomas M Keane, Louis R Sarry, Ulrike Böhme, Jacob Lemieux, Bart Barrell, Arnab Pain, Matthew Berriman, Chris Newbold, Manuel Llinás
Mol Microbiol. 2010 April; 76(1): 12–24. Published online 2010 February 5. doi: 10.1111/j.1365-2958.2009.07026.x
PMCID:
PMC2859250
Abstract Full Text PDF–512K Supplementary Material
MaizeGDB becomes ‘sequence-centric’
Taner Z. Sen, Carson M. Andorf, Mary L. Schaeffer, Lisa C. Harper, Michael E. Sparks, Jon Duvick, Volker P. Brendel, Ethalinda Cannon, Darwin A. Campbell, Carolyn J. Lawrence
Database (Oxford) 2009; 2009: bap020. Published online 2009 December 7. doi: 10.1093/database/bap020
PMCID:
PMC2964019
Abstract Full Text PDF–781K
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication
Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Young-Joo Seol, Mina Jin, Jin-A Kim, Myung-Ho Lim, Jung Sun Kim, Seunghoon Baek, Beom-Soon Choi, Hee-Ju Yu, Dae-Soo Kim, Namshin Kim, Ki-Byung Lim, Soo-In Lee, Jang-Ho Hahn, Yong Pyo Lim, Ian Bancroft, Beom-Seok Park
Genome Biol. 2009; 10(10): R111. Published online 2009 October 12. doi: 10.1186/gb-2009-10-10-r111
PMCID:
PMC2784326
Abstract Full Text PDF–1.3M Supplementary Material
Identification and characterization of pseudogenes in the rice gene complement
Françoise Thibaud-Nissen, Shu Ouyang, C Robin Buell
BMC Genomics. 2009; 10: 317. Published online 2009 July 16. doi: 10.1186/1471-2164-10-317
PMCID:
PMC2724416
Abstract Full Text PDF–423K Supplementary Material
Novel thigmomorphogenetic responses in Carica papaya: touch decreases anthocyanin levels and stimulates petiole cork outgrowths
Brad W. Porter, Yun J. Zhu, David T. Webb, David A. Christopher
Ann Bot. 2009 April; 103(6): 847–858. Published online 2009 January 31. doi: 10.1093/aob/mcp009
PMCID:
PMC2707888
Abstract Full Text PDF–467K
Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
Robert S Coyne, Mathangi Thiagarajan, Kristie M Jones, Jennifer R Wortman, Luke J Tallon, Brian J Haas, Donna M Cassidy-Hanley, Emily A Wiley, Joshua J Smith, Kathleen Collins, Suzanne R Lee, Mary T Couvillion, Yifan Liu, Jyoti Garg, Ronald E Pearlman, Eileen P Hamilton, Eduardo Orias, Jonathan A Eisen, Barbara A Methé
BMC Genomics. 2008; 9: 562. Published online 2008 November 26. doi: 10.1186/1471-2164-9-562
PMCID:
PMC2612030
Abstract Full Text PDF–672K Supplementary Material
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
Natalie D. Fedorova, Nora Khaldi, Vinita S. Joardar, Rama Maiti, Paolo Amedeo, Michael J. Anderson, Jonathan Crabtree, Joana C. Silva, Jonathan H. Badger, Ahmed Albarraq, Sam Angiuoli, Howard Bussey, Paul Bowyer, Peter J. Cotty, Paul S. Dyer, Amy Egan, Kevin Galens, Claire M. Fraser-Liggett, Brian J. Haas, Jason M. Inman, Richard Kent, Sebastien Lemieux, Iran Malavazi, Joshua Orvis, Terry Roemer, Catherine M. Ronning, Jaideep P. Sundaram, Granger Sutton, Geoff Turner, J. Craig Venter, Owen R. White, Brett R. Whitty, Phil Youngman, Kenneth H. Wolfe, Gustavo H. Goldman, Jennifer R. Wortman, Bo Jiang, David W. Denning, William C. Nierman
PLoS Genet. 2008 April; 4(4): e1000046. Published online 2008 April 11. doi: 10.1371/journal.pgen.1000046
PMCID:
PMC2289846
Abstract Full Text PDF–572K Supplementary Material
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