Assembling genomes using short-read sequencing technology

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

Metabolic Control Analysis under Uncertainty: Framework Development and Case Studies

Por Wang, Liqing, Birol, İnanç, Hatzimanikatis, Vassily
Publicado em 2004

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

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

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

Por Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, S. Cenk, Birol, Inanc
Publicado em 2008

ntHash: recursive nucleotide hashing

Por Mohamadi, Hamid, Chu, Justin, Vandervalk, Benjamin P., Birol, Inanc
Publicado no Bioinformatics (2016)

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline

Por Hadj Khodabakhshi, Alireza, Fejes, Anthony P, Birol, Inanc, Jones, Steven JM
Publicado em 2013

Dissect: detection and characterization of novel structural alterations in transcribed sequences

Por Yorukoglu, Deniz, Hach, Faraz, Swanson, Lucas, Collins, Colin C., Birol, Inanc, Sahinalp, S. Cenk
Publicado em 2012

De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

Por Birol, Inanc, Behsaz, Bahar, Hammond, S. Austin, Kucuk, Erdi, Veldhoen, Nik, Helbing, Caren C.
Publicado no PLoS One (2015)

mrsFast: a cache-oblivious algorithm for short-read mapping

Por Hach, Faraz, Hormozdiari, Fereydoun, Alkan, Can, Hormozdiari, Farhad, Birol, Inanc, Eichler, Evan E, Sahinalp, S Cenk
Publicado em 2010

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

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

Por Hajirasouliha, Iman, Hormozdiari, Fereydoun, Alkan, Can, Kidd, Jeffrey M., Birol, Inanc, Eichler, Evan E., Sahinalp, S. Cenk
Publicado em 2010

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)

Circos: An information aesthetic for comparative genomics

Por Krzywinski, Martin, Schein, Jacqueline, Birol, İnanç, Connors, Joseph, Gascoyne, Randy, Horsman, Doug, Jones, Steven J., Marra, Marco A.
Publicado em 2009

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

Por Warren, René L., Yang, Chen, Vandervalk, Benjamin P., Behsaz, Bahar, Lagman, Albert, Jones, Steven J. M., Birol, Inanç
Publicado no Gigascience (2015)

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

Large-scale profiling of microRNAs for The Cancer Genome Atlas

Por Chu, Andy, Robertson, Gordon, Brooks, Denise, Mungall, Andrew J., Birol, Inanc, Coope, Robin, Ma, Yussanne, Jones, Steven, Marra, Marco A.
Publicado no Nucleic Acids Res (2016)

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