My NCBISign In
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones
Genome Biol. 2009; 10(9): R94. Published online 2009 September 11. doi: 10.1186/gb-2009-10-9-r94
PMCID:
PMC2768983
Abstract Full Text PDF–1.3M Supplementary Material

Is Cited by the Following 25 Articles in this Archive:

Short-Read Sequencing for Genomic Analysis of the Brown Rot Fungus Fibroporia radiculosa
Juliet D. Tang, Andy D. Perkins, Tad S. Sonstegard, Steven G. Schroeder, Shane C. Burgess, Susan V. Diehl
Appl Environ Microbiol. 2012 April; 78(7): 2272–2281. doi: 10.1128/AEM.06745-11
PMCID:
PMC3302605
Free in PMC on 2012/10/01
Identifying Single Copy Orthologs in Metazoa
Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork
PLoS Comput Biol. 2011 December; 7(12): e1002269. Published online 2011 December 1. doi: 10.1371/journal.pcbi.1002269
PMCID:
PMC3228760
Abstract Full Text PDF–1.3M Supplementary Material
Graph accordance of next-generation sequence assemblies
Guohui Yao, Liang Ye, Hongyu Gao, Patrick Minx, Wesley C. Warren, George M. Weinstock
Bioinformatics. 2012 January 1; 28(1): 13–16. Published online 2011 October 23. doi: 10.1093/bioinformatics/btr588
PMCID:
PMC3244760
Free in PMC on 2013/01/01
diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data
Björn Hammesfahr, Florian Odronitz, Marcel Hellkamp, Martin Kollmar
BMC Res Notes. 2011; 4: 338. Published online 2011 September 9. doi: 10.1186/1756-0500-4-338
PMCID:
PMC3180467
Abstract Full Text PDF–2.3M Supplementary Material
Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results
Niina Haiminen, David N. Kuhn, Laxmi Parida, Isidore Rigoutsos
PLoS One. 2011; 6(9): e24182. Published online 2011 September 7. doi: 10.1371/journal.pone.0024182
Correction in:
PLoS One. 2011; 6(10): 10.1371/annotation/bb125f93-80d3-4dd1-adfe-03d9fb740f3b.
Correction in:
PLoS One. 2011; 6(10): 10.1371/annotation/176d83be-ed67-4205-9265-7208792d3dcf.
PMCID:
PMC3168497
Abstract Full Text PDF–528K Supplementary Material Correction Correction
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-specific error profile of Illumina sequencers
Kensuke Nakamura, Taku Oshima, Takuya Morimoto, Shun Ikeda, Hirofumi Yoshikawa, Yuh Shiwa, Shu Ishikawa, Margaret C. Linak, Aki Hirai, Hiroki Takahashi, Md. Altaf-Ul-Amin, Naotake Ogasawara, Shigehiko Kanaya
Nucleic Acids Res. 2011 July; 39(13): e90. Published online 2011 May 14. doi: 10.1093/nar/gkr344
PMCID:
PMC3141275
Abstract Full Text PDF–1.1M Supplementary Material
A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies
Wenyu Zhang, Jiajia Chen, Yang Yang, Yifei Tang, Jing Shang, Bairong Shen
PLoS One. 2011; 6(3): e17915. Published online 2011 March 14. doi: 10.1371/journal.pone.0017915
PMCID:
PMC3056720
Abstract Full Text PDF–2.2M Supplementary Material
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti
Mariangela Bonizzoni, W Augustine Dunn, Corey L Campbell, Ken E Olson, Michelle T Dimon, Osvaldo Marinotti, Anthony A James
BMC Genomics. 2011; 12: 82. Published online 2011 January 28. doi: 10.1186/1471-2164-12-82
PMCID:
PMC3042412
Abstract Full Text PDF–602K Supplementary Material
Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen
Scott DiGuistini, Ye Wang, Nancy Y. Liao, Greg Taylor, Philippe Tanguay, Nicolas Feau, Bernard Henrissat, Simon K. Chan, Uljana Hesse-Orce, Sepideh Massoumi Alamouti, Clement K. M. Tsui, Roderick T. Docking, Anthony Levasseur, Sajeet Haridas, Gordon Robertson, Inanc Birol, Robert A. Holt, Marco A. Marra, Richard C. Hamelin, Martin Hirst, Steven J. M. Jones, Jörg Bohlmann, Colette Breuil
Proc Natl Acad Sci U S A. 2011 February 8; 108(6): 2504–2509. Published online 2011 January 24. doi: 10.1073/pnas.1011289108
PMCID:
PMC3038703
Abstract Full Text PDF–633K Supplementary Material
Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map
Jean-Marc Celton, Alan Christoffels, Daniel J Sargent, Xiangming Xu, D Jasper G Rees
BMC Biol. 2010; 8: 155. Published online 2010 December 30. doi: 10.1186/1741-7007-8-155
PMCID:
PMC3024234
Abstract Full Text PDF–666K Supplementary Material
Design, Validation and Annotation of Transcriptome-Wide Oligonucleotide Probes for the Oligochaete Annelid Eisenia fetida
Ping Gong, Mehdi Pirooznia, Xin Guan, Edward J. Perkins
PLoS One. 2010; 5(12): e14266. Published online 2010 December 8. doi: 10.1371/journal.pone.0014266
PMCID:
PMC2999564
Abstract Full Text PDF–286K Supplementary Material
Applications of next generation sequencing in molecular ecology of non-model organisms
R Ekblom, J Galindo
Heredity. 2011 July; 107(1): 1–15. Published online 2010 December 8. doi: 10.1038/hdy.2010.152
PMCID:
PMC3186121
Free in PMC on 2012/07/01
De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq
Eshchar Mizrachi, Charles A Hefer, Martin Ranik, Fourie Joubert, Alexander A Myburg
BMC Genomics. 2010; 11: 681. Published online 2010 December 1. doi: 10.1186/1471-2164-11-681
PMCID:
PMC3053591
Abstract Full Text PDF–963K Supplementary Material
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
Sébastien Boisvert, François Laviolette, Jacques Corbeil
J Comput Biol. 2010 November; 17(11): 1519–1533. doi: 10.1089/cmb.2009.0238
PMCID:
PMC3119603
Abstract Full Text PDF–771K Supplementary Material
Proteomics of industrial fungi: trends and insights for biotechnology
José Miguel P. Ferreira de Oliveira, Leo H. de Graaff
Appl Microbiol Biotechnol. 2011 January; 89(2): 225–237. Published online 2010 October 5. doi: 10.1007/s00253-010-2900-0
PMCID:
PMC3016146
Abstract Full Text PDF–475K
Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera
Uljana Hesse-Orce, Scott DiGuistini, Christopher I Keeling, Ye Wang, Maria Li, Hannah Henderson, T Roderick Docking, Nancy Y Liao, Gordon Robertson, Robert A Holt, Steven JM Jones, Jörg Bohlmann, Colette Breuil
BMC Genomics. 2010; 11: 536. Published online 2010 October 4. doi: 10.1186/1471-2164-11-536
PMCID:
PMC3091685
Abstract Full Text PDF–433K Supplementary Material
Integrating genome assemblies with MAIA
Jurgen Nijkamp, Wynand Winterbach, Marcel van den Broek, Jean-Marc Daran, Marcel Reinders, Dick de Ridder
Bioinformatics. 2010 September 15; 26(18): i433–i439. Published online 2010 September 4. doi: 10.1093/bioinformatics/btq366
PMCID:
PMC2935414
Abstract Full Text PDF–562K
Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems
Minou Nowrousian
Eukaryot Cell. 2010 September; 9(9): 1300–1310. doi: 10.1128/EC.00123-10
PMCID:
PMC2937339
Abstract Full Text PDF–343K
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
Robert Schmieder, Yan Wei Lim, Forest Rohwer, Robert Edwards
BMC Bioinformatics. 2010; 11: 341. Published online 2010 June 23. doi: 10.1186/1471-2105-11-341
PMCID:
PMC2910026
Abstract Full Text PDF–1.8M Supplementary Material
Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing
Stefan Taudien, Marco Groth, Klaus Huse, Andreas Petzold, Karol Szafranski, Jochen Hampe, Philip Rosenstiel, Stefan Schreiber, Matthias Platzer
BMC Genomics. 2010; 11: 252. Published online 2010 April 19. doi: 10.1186/1471-2164-11-252
PMCID:
PMC2873476
Abstract Full Text PDF–1.5M Supplementary Material
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
Isheng J Tsai, Thomas D Otto, Matthew Berriman
Genome Biol. 2010; 11(4): R41. Published online 2010 April 13. doi: 10.1186/gb-2010-11-4-r41
PMCID:
PMC2884544
Abstract Full Text PDF–1.2M Supplementary Material
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis
Minou Nowrousian, Jason E. Stajich, Meiling Chu, Ines Engh, Eric Espagne, Karen Halliday, Jens Kamerewerd, Frank Kempken, Birgit Knab, Hsiao-Che Kuo, Heinz D. Osiewacz, Stefanie Pöggeler, Nick D. Read, Stephan Seiler, Kristina M. Smith, Denise Zickler, Ulrich Kück, Michael Freitag
PLoS Genet. 2010 April; 6(4): e1000891. Published online 2010 April 8. doi: 10.1371/journal.pgen.1000891
PMCID:
PMC2851567
Abstract Full Text PDF–1.0M Supplementary Material
Assembly Algorithms for Next-Generation Sequencing Data
Jason R. Miller, Sergey Koren, Granger Sutton
Genomics. Author manuscript; available in PMC 2011 June 1.
Published in final edited form as: Genomics. 2010 June; 95(6): 315–327. Published online 2010 March 6. doi: 10.1016/j.ygeno.2010.03.001
PMCID:
PMC2874646
Abstract Full Text PDF–367K
Assembling genomes using short-read sequencing technology
Shaun D Jackman, İnanç Birol
Genome Biol. 2010; 11(1): 202. Published online 2010 January 28. doi: 10.1186/gb-2010-11-1-202
PMCID:
PMC2847710
Abstract Full Text PDF–140K
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