Assembling genomes using short-read sequencing technology

Por Jackman, Shaun D, Birol, İnanç
Publicado em 2010

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

Por Jackman, Shaun D., Bohlmann, Joerg, Birol, İnanç
Publicado no PLoS One (2015)

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

Por Paulino, Daniel, Warren, René L., Vandervalk, Benjamin P., Raymond, Anthony, Jackman, Shaun D., Birol, Inanç
Publicado no BMC Bioinformatics (2015)

ABySS: A parallel assembler for short read sequence data

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

DIDA: Distributed Indexing Dispatched Alignment

Por Mohamadi, Hamid, Vandervalk, Benjamin P, Raymond, Anthony, Jackman, Shaun D, Chu, Justin, Breshears, Clay P, Birol, Inanc
Publicado no PLoS One (2015)

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

Por Coombe, Lauren, Zhang, Jessica, Vandervalk, Benjamin P., Chu, Justin, Jackman, Shaun D., Birol, Inanc, Warren, René L.
Publicado no BMC Bioinformatics (2018)

ORCA: a comprehensive bioinformatics container environment for education and research

Por Jackman, Shaun D, Mozgacheva, Tatyana, Chen, Susie, O’Huiginn, Brendan, Bailey, Lance, Birol, Inanc, Jones, Steven J M
Publicado no Bioinformatics (2019)

Spaced Seed Data Structures for De Novo Assembly

Por Birol, Inanç, Chu, Justin, Mohamadi, Hamid, Jackman, Shaun D., Raghavan, Karthika, Vandervalk, Benjamin P., Raymond, Anthony, Warren, René L.
Publicado no Int J Genomics (2015)

Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain M1601

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

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

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

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

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

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

Por Vandervalk, Benjamin P, Yang, Chen, Xue, Zhuyi, Raghavan, Karthika, Chu, Justin, Mohamadi, Hamid, Jackman, Shaun D, Chiu, Readman, Warren, René L, Birol, Inanç
Publicado no BMC Med Genomics (2015)

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

Por Chu, Justin, Sadeghi, Sara, Raymond, Anthony, Jackman, Shaun D., Nip, Ka Ming, Mar, Richard, Mohamadi, Hamid, Butterfield, Yaron S., Robertson, A. Gordon, Birol, Inanç
Publicado no Bioinformatics (2014)

KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES()

Por 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
Publicado no Pac Symp Biocomput (2015)

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

Por 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
Publicado no Genome Res (2017)

Tigmint: correcting assembly errors using linked reads from large molecules

Por 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
Publicado no BMC Bioinformatics (2018)

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

Por 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
Publicado no PLoS One (2016)

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

Por 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
Publicado no Genome Biol Evol (2020)

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

Por 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
Publicado em 2011

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

Por 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
Publicado no Genome Biol Evol (2015)