Assembling genomes using short-read sequencing technology

Autor Jackman, Shaun D, Birol, İnanç
Vydáno 2010

UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation

Autor Jackman, Shaun D., Bohlmann, Joerg, Birol, İnanç
Vydáno v PLoS One (2015)

Sealer: a scalable gap-closing application for finishing draft genomes

Autor Paulino, Daniel, Warren, René L., Vandervalk, Benjamin P., Raymond, Anthony, Jackman, Shaun D., Birol, Inanç
Vydáno v BMC Bioinformatics (2015)

ABySS: A parallel assembler for short read sequence data

Autor Simpson, Jared T., Wong, Kim, Jackman, Shaun D., Schein, Jacqueline E., Jones, Steven J.M., Birol, İnanç
Vydáno 2009

DIDA: Distributed Indexing Dispatched Alignment

Autor Mohamadi, Hamid, Vandervalk, Benjamin P, Raymond, Anthony, Jackman, Shaun D, Chu, Justin, Breshears, Clay P, Birol, Inanc
Vydáno v PLoS One (2015)

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

Autor Coombe, Lauren, Zhang, Jessica, Vandervalk, Benjamin P., Chu, Justin, Jackman, Shaun D., Birol, Inanc, Warren, René L.
Vydáno v BMC Bioinformatics (2018)

ORCA: a comprehensive bioinformatics container environment for education and research

Autor Jackman, Shaun D, Mozgacheva, Tatyana, Chen, Susie, O’Huiginn, Brendan, Bailey, Lance, Birol, Inanc, Jones, Steven J M
Vydáno v Bioinformatics (2019)

Spaced Seed Data Structures for De Novo Assembly

Autor Birol, Inanç, Chu, Justin, Mohamadi, Hamid, Jackman, Shaun D., Raghavan, Karthika, Vandervalk, Benjamin P., Raymond, Anthony, Warren, René L.
Vydáno v Int J Genomics (2015)

Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain M1601

Autor Chu, Yuefeng, Gao, Pengchen, Zhao, Ping, He, Ying, Liao, Nancy, Jackman, Shaun, Zhao, Yongjun, Birol, Inanc, Duan, Xiaobo, Lu, Zhongxin
Vydáno 2011

The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera

Autor Haridas, Sajeet, Wang, Ye, Lim, Lynette, Massoumi Alamouti, Sepideh, Jackman, Shaun, Docking, Rod, Robertson, Gordon, Birol, Inanc, Bohlmann, Jörg, Breuil, Colette
Vydáno 2013

Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii

Autor Lenassi, Metka, Gostinčar, Cene, Jackman, Shaun, Turk, Martina, Sadowski, Ivan, Nislow, Corey, Jones, Steven, Birol, Inanc, Cimerman, Nina Gunde, Plemenitaš, Ana
Vydáno 2013

Konnector v2.0: pseudo-long reads from paired-end sequencing data

Autor Vandervalk, Benjamin P, Yang, Chen, Xue, Zhuyi, Raghavan, Karthika, Chu, Justin, Mohamadi, Hamid, Jackman, Shaun D, Chiu, Readman, Warren, René L, Birol, Inanç
Vydáno v BMC Med Genomics (2015)

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

Autor Chu, Justin, Sadeghi, Sara, Raymond, Anthony, Jackman, Shaun D., Nip, Ka Ming, Mar, Richard, Mohamadi, Hamid, Butterfield, Yaron S., Robertson, A. Gordon, Birol, Inanç
Vydáno v Bioinformatics (2014)

KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES()

Autor Birol, Inanç, Raymond, Anthony, Chiu, Readman, Nip, Ka Ming, Jackman, Shaun D, Kreitzman, Maayan, Docking, T Roderick, Ennis, Catherine A, Robertson, A Gordon, Karsan, Aly
Vydáno v Pac Symp Biocomput (2015)

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

Autor Jackman, Shaun D., Vandervalk, Benjamin P., Mohamadi, Hamid, Chu, Justin, Yeo, Sarah, Hammond, S. Austin, Jahesh, Golnaz, Khan, Hamza, Coombe, Lauren, Warren, Rene L., Birol, Inanc
Vydáno v Genome Res (2017)

Tigmint: correcting assembly errors using linked reads from large molecules

Autor Jackman, Shaun D., Coombe, Lauren, Chu, Justin, Warren, Rene L., Vandervalk, Benjamin P., Yeo, Sarah, Xue, Zhuyi, Mohamadi, Hamid, Bohlmann, Joerg, Jones, Steven J.M., Birol, Inanc
Vydáno v BMC Bioinformatics (2018)

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data

Autor Coombe, Lauren, Warren, René L., Jackman, Shaun D., Yang, Chen, Vandervalk, Benjamin P., Moore, Richard A., Pleasance, Stephen, Coope, Robin J., Bohlmann, Joerg, Holt, Robert A., Jones, Steven J. M., Birol, Inanc
Vydáno v PLoS One (2016)

Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure

Autor Jackman, Shaun D, Coombe, Lauren, Warren, René L, Kirk, Heather, Trinh, Eva, MacLeod, Tina, Pleasance, Stephen, Pandoh, Pawan, Zhao, Yongjun, Coope, Robin J, Bousquet, Jean, Bohlmann, Joerg, Jones, Steven J M, Birol, Inanc
Vydáno v Genome Biol Evol (2020)

Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees

Autor Chan, Queenie WT, Cornman, R Scott, Birol, Inanc, Liao, Nancy Y, Chan, Simon K, Docking, T Roderick, Jackman, Shaun D, Taylor, Greg A, Jones, Steven JM, de Graaf, Dirk C, Evans, Jay D, Foster, Leonard J
Vydáno 2011

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

Autor Jackman, Shaun D., Warren, René L., Gibb, Ewan A., Vandervalk, Benjamin P., Mohamadi, Hamid, Chu, Justin, Raymond, Anthony, Pleasance, Stephen, Coope, Robin, Wildung, Mark R., Ritland, Carol E., Bousquet, Jean, Jones, Steven J. M., Bohlmann, Joerg, Birol, Inanç
Vydáno v Genome Biol Evol (2015)