Inanc Birol

Inanc Birol

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Inanc Birol

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Fusion-Bloom: fusion detection in assembled transcriptomes.

Authors:
Readman Chiu Ka Ming Nip Inanc Birol

Bioinformatics 2019 Dec 2. Epub 2019 Dec 2.

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz902DOI Listing
December 2019

ORCA: a comprehensive bioinformatics container environment for education and research.

Authors:
Shaun D Jackman Tatyana Mozgacheva Susie Chen Brendan O'Huiginn Lance Bailey Inanc Birol Steven J M Jones

Bioinformatics 2019 Nov;35(21):4448-4450

Genome Sciences Centre, BC Cancer, Vancouver BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821186PMC
November 2019

ntEdit: scalable genome sequence polishing.

Authors:
René L Warren Lauren Coombe Hamid Mohamadi Jessica Zhang Barry Jaquish Nathalie Isabel Steven J M Jones Jean Bousquet Joerg Bohlmann Inanç Birol

Bioinformatics 2019 Nov;35(21):4430-4432

Genome Sciences Centre, BC Cancer, Vancouver, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821332PMC
November 2019

Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs.

Authors:
Jared J Homola Cynthia S Loftin Kristina M Cammen Caren C Helbing Inanc Birol Thomas F Schultz Michael T Kinnison

J Hered 2019 Oct;110(6):707-719

School of Biology and Ecology, University of Maine, Orono, ME.

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http://dx.doi.org/10.1093/jhered/esz041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785938PMC
October 2019

Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada.

Authors:
Diana Lin Lauren Coombe Shaun D Jackman Kristina K Gagalova René L Warren S Austin Hammond Heather Kirk Pawan Pandoh Yongjun Zhao Richard A Moore Andrew J Mungall Carol Ritland Barry Jaquish Nathalie Isabel Jean Bousquet Steven J M Jones Joerg Bohlmann Inanc Birol

Microbiol Resour Announc 2019 Jun 6;8(23). Epub 2019 Jun 6.

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada

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http://dx.doi.org/10.1128/MRA.00381-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554609PMC
June 2019

Complete Chloroplast Genome Sequence of an Engelmann Spruce (, Genotype Se404-851) from Western Canada.

Authors:
Diana Lin Lauren Coombe Shaun D Jackman Kristina K Gagalova René L Warren S Austin Hammond Helen McDonald Heather Kirk Pawan Pandoh Yongjun Zhao Richard A Moore Andrew J Mungall Carol Ritland Trevor Doerksen Barry Jaquish Jean Bousquet Steven J M Jones Joerg Bohlmann Inanc Birol

Microbiol Resour Announc 2019 Jun 13;8(24). Epub 2019 Jun 13.

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada

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http://dx.doi.org/10.1128/MRA.00382-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588038PMC
June 2019

The Genome of the Steller Sea Lion ().

Authors:
Harwood H Kwan Luka Culibrk Gregory A Taylor Sreeja Leelakumari Ryan Tan Shaun D Jackman Kane Tse Tina MacLeod Dean Cheng Eric Chuah Heather Kirk Pawan Pandoh Rebecca Carlsen Yongjun Zhao Andrew J Mungall Richard Moore Inanc Birol Marco A Marra David A S Rosen Martin Haulena Steven J M Jones

Genes (Basel) 2019 06 26;10(7). Epub 2019 Jun 26.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada.

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http://dx.doi.org/10.3390/genes10070486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678222PMC
June 2019

Base excision repair deficiency signatures implicate germline and somatic aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis.

Authors:
My Linh Thibodeau Eric Y Zhao Caralyn Reisle Carolyn Ch'ng Hui-Li Wong Yaoqing Shen Martin R Jones Howard J Lim Sean Young Carol Cremin Erin Pleasance Wei Zhang Robert Holt Peter Eirew Joanna Karasinska Steve E Kalloger Greg Taylor Elisa Majounie Melika Bonakdar Zusheng Zong Dustin Bleile Readman Chiu Inanc Birol Karen Gelmon Caroline Lohrisch Karen L Mungall Andrew J Mungall Richard Moore Yussanne P Ma Alexandra Fok Stephen Yip Aly Karsan David Huntsman David F Schaeffer Janessa Laskin Marco A Marra Daniel J Renouf Steven J M Jones Kasmintan A Schrader

Cold Spring Harb Mol Case Stud 2019 04 1;5(2). Epub 2019 Apr 1.

Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.

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http://dx.doi.org/10.1101/mcs.a003681DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549570PMC
April 2019

Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles.

Authors:
Caren C Helbing S Austin Hammond Shireen H Jackman Simon Houston René L Warren Caroline E Cameron Inanç Birol

Sci Rep 2019 Feb 6;9(1):1529. Epub 2019 Feb 6.

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.

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http://www.nature.com/articles/s41598-018-38442-1
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http://dx.doi.org/10.1038/s41598-018-38442-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365531PMC
February 2019

The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.

Authors:
Gregory A Taylor Heather Kirk Lauren Coombe Shaun D Jackman Justin Chu Kane Tse Dean Cheng Eric Chuah Pawan Pandoh Rebecca Carlsen Yongjun Zhao Andrew J Mungall Richard Moore Inanc Birol Maria Franke Marco A Marra Christopher Dutton Steven J M Jones

Genes (Basel) 2018 Nov 30;9(12). Epub 2018 Nov 30.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z-4S6, Canada.

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http://www.mdpi.com/2073-4425/9/12/598
Publisher Site
http://dx.doi.org/10.3390/genes9120598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315469PMC
November 2018

Tigmint: correcting assembly errors using linked reads from large molecules.

Authors:
Shaun D Jackman Lauren Coombe Justin Chu Rene L Warren Benjamin P Vandervalk Sarah Yeo Zhuyi Xue Hamid Mohamadi Joerg Bohlmann Steven J M Jones Inanc Birol

BMC Bioinformatics 2018 Oct 26;19(1):393. Epub 2018 Oct 26.

BC Cancer Genome Sciences Centre, Vancouver, V5Z 4S6, BC, Canada.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
Publisher Site
http://dx.doi.org/10.1186/s12859-018-2425-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204047PMC
October 2018

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data.

Authors:
Readman Chiu Ka Ming Nip Justin Chu Inanc Birol

BMC Med Genomics 2018 Sep 10;11(1):79. Epub 2018 Sep 10.

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada.

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http://dx.doi.org/10.1186/s12920-018-0402-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6131862PMC
September 2018

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

Authors:
Zhuyi Xue René L Warren Ewan A Gibb Daniel MacMillan Johnathan Wong Readman Chiu S Austin Hammond Chen Yang Ka Ming Nip Catherine A Ennis Abigail Hahn Sheila Reynolds Inanc Birol

BMC Genomics 2018 Jul 13;19(1):536. Epub 2018 Jul 13.

BC Cancer Agency, Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada.

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http://dx.doi.org/10.1186/s12864-018-4903-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045855PMC
July 2018

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

Authors:
Lauren Coombe Jessica Zhang Benjamin P Vandervalk Justin Chu Shaun D Jackman Inanc Birol René L Warren

BMC Bioinformatics 2018 06 20;19(1):234. Epub 2018 Jun 20.

BC Cancer Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada.

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http://dx.doi.org/10.1186/s12859-018-2243-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6011487PMC
June 2018

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Authors:
Hamza Khan Hamid Mohamadi Benjamin P Vandervalk Rene L Warren Justin Chu Inanc Birol

Bioinformatics 2018 05;34(10):1697-1704

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btx839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946899PMC
May 2018

ARCS: scaffolding genome drafts with linked reads.

Authors:
Sarah Yeo Lauren Coombe René L Warren Justin Chu Inanç Birol

Bioinformatics 2018 03;34(5):725-731

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http://dx.doi.org/10.1093/bioinformatics/btx675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030987PMC
March 2018

A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations.

Authors:
Lewis J Campbell Stewart A Hammond Stephen J Price Manmohan D Sharma Trenton W J Garner Inanc Birol Caren C Helbing Lena Wilfert Amber G F Griffiths

Mol Ecol 2018 03 29;27(6):1413-1427. Epub 2018 Mar 29.

FoAM Kernow, Jubilee Wharf workshop F/G, Penryn, UK.

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http://dx.doi.org/10.1111/mec.14528DOI Listing
March 2018

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens.

Authors:
Nicolas Feau Stéphanie Beauseigle Marie-Josée Bergeron Guillaume J Bilodeau Inanc Birol Sandra Cervantes-Arango Braham Dhillon Angela L Dale Padmini Herath Steven J M Jones Josyanne Lamarche Dario I Ojeda Monique L Sakalidis Greg Taylor Clement K M Tsui Adnan Uzunovic Hesther Yueh Philippe Tanguay Richard C Hamelin

PeerJ 2018 22;6:e4392. Epub 2018 Feb 22.

Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.7717/peerj.4392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5825881PMC
February 2018

The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).

Authors:
Samantha J Jones Martin Haulena Gregory A Taylor Simon Chan Steven Bilobram René L Warren S Austin Hammond Karen L Mungall Caleb Choo Heather Kirk Pawan Pandoh Adrian Ally Noreen Dhalla Angela K Y Tam Armelle Troussard Daniel Paulino Robin J N Coope Andrew J Mungall Richard Moore Yongjun Zhao Inanc Birol Yussanne Ma Marco Marra Steven J M Jones

Genes (Basel) 2017 Dec 11;8(12). Epub 2017 Dec 11.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.

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http://dx.doi.org/10.3390/genes8120379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748697PMC
December 2017

The Genome of the Beluga Whale (Delphinapterus leucas).

Authors:
Steven J M Jones Gregory A Taylor Simon Chan René L Warren S Austin Hammond Steven Bilobram Gideon Mordecai Curtis A Suttle Kristina M Miller Angela Schulze Amy M Chan Samantha J Jones Kane Tse Irene Li Dorothy Cheung Karen L Mungall Caleb Choo Adrian Ally Noreen Dhalla Angela K Y Tam Armelle Troussard Heather Kirk Pawan Pandoh Daniel Paulino Robin J N Coope Andrew J Mungall Richard Moore Yongjun Zhao Inanc Birol Yussanne Ma Marco Marra Martin Haulena

Genes (Basel) 2017 Dec 11;8(12). Epub 2017 Dec 11.

Vancouver Aquarium, Vancouver, BC V6G 3E2, Canada.

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http://dx.doi.org/10.3390/genes8120378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748696PMC
December 2017

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.

Authors:
S Austin Hammond René L Warren Benjamin P Vandervalk Erdi Kucuk Hamza Khan Ewan A Gibb Pawan Pandoh Heather Kirk Yongjun Zhao Martin Jones Andrew J Mungall Robin Coope Stephen Pleasance Richard A Moore Robert A Holt Jessica M Round Sara Ohora Branden V Walle Nik Veldhoen Caren C Helbing Inanc Birol

Nat Commun 2017 11 10;8(1):1433. Epub 2017 Nov 10.

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 570 West 7th Ave - Suite 100, Vancouver, BC, Canada, V5Z 4S6.

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http://dx.doi.org/10.1038/s41467-017-01316-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681567PMC
November 2017

Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98.

Authors:
My Linh Thibodeau Michelle Steinraths Lindsay Brown Zheyuan Zong Naomi Shomer Stefan Taubert Karen L Mungall Yussanne P Ma Rosemary Mueller Inanc Birol Anna Lehman

Cytogenet Genome Res 2017 31;152(3):117-121. Epub 2017 Aug 31.

Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1159/000479463DOI Listing
October 2017

Complete Genome Sequence of SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease.

Authors:
Nabeeh A Hasan René L Warren L Elaine Epperson Allyson Malecha David C Alexander Christine Y Turenne Daniel MacMillan Inanc Birol Stephen Pleasance Robin Coope Steven J M Jones Marc G Romney Monica Ng Tracy Chan Mabel Rodrigues Patrick Tang Jennifer L Gardy Michael Strong

Genome Announc 2017 Sep 14;5(37). Epub 2017 Sep 14.

Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA.

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http://dx.doi.org/10.1128/genomeA.00963-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597760PMC
September 2017

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

Authors:
Lauren Coombe René L Warren Shaun D Jackman Chen Yang Benjamin P Vandervalk Richard A Moore Stephen Pleasance Robin J Coope Joerg Bohlmann Robert A Holt Steven J M Jones Inanc Birol

PLoS One 2016 15;11(9):e0163059. Epub 2016 Sep 15.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163059PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025161PMC
August 2017

Kollector: transcript-informed, targeted de novo assembly of gene loci.

Authors:
Erdi Kucuk Justin Chu Benjamin P Vandervalk S Austin Hammond René L Warren Inanc Birol

Bioinformatics 2017 Jun;33(12):1782-1788

University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btx078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572715PMC
June 2017

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

Authors:
Shaun D Jackman Benjamin P Vandervalk Hamid Mohamadi Justin Chu Sarah Yeo S Austin Hammond Golnaz Jahesh Hamza Khan Lauren Coombe Rene L Warren Inanc Birol

Genome Res 2017 05 23;27(5):768-777. Epub 2017 Feb 23.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada.

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http://dx.doi.org/10.1101/gr.214346.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411771PMC
May 2017

ntCard: a streaming algorithm for cardinality estimation in genomics data.

Authors:
Hamid Mohamadi Hamza Khan Inanc Birol

Bioinformatics 2017 05;33(9):1324-1330

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408799PMC
May 2017

Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art.

Authors:
Justin Chu Hamid Mohamadi René L Warren Chen Yang Inanç Birol

Bioinformatics 2017 Apr;33(8):1261-1270

University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408847PMC
April 2017

A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance.

Authors:
Nathalie Pavy Manuel Lamothe Betty Pelgas France Gagnon Inanç Birol Joerg Bohlmann John Mackay Nathalie Isabel Jean Bousquet

Plant J 2017 Apr 6;90(1):189-203. Epub 2017 Mar 6.

Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.

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http://dx.doi.org/10.1111/tpj.13478DOI Listing
April 2017

De novo assembly of the ringed seal (Pusa hispida) blubber transcriptome: A tool that enables identification of molecular health indicators associated with PCB exposure.

Authors:
Tanya M Brown S Austin Hammond Bahar Behsaz Nik Veldhoen Inanç Birol Caren C Helbing

Aquat Toxicol 2017 Apr 3;185:48-57. Epub 2017 Feb 3.

Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.aquatox.2017.02.004DOI Listing
April 2017

NanoSim: nanopore sequence read simulator based on statistical characterization.

Authors:
Chen Yang Justin Chu René L Warren Inanç Birol

Gigascience 2017 04;6(4):1-6

Canada's Michael Smith Genome Science Centre, British Columbia Cancer Agency, 570 W 7th Avenue, V5Z 4S6 Vancouver, Canada.

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http://dx.doi.org/10.1093/gigascience/gix010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5530317PMC
April 2017

Genome sequences of six species threatening forest ecosystems.

Authors:
Nicolas Feau Greg Taylor Angela L Dale Braham Dhillon Guillaume J Bilodeau Inanç Birol Steven J M Jones Richard C Hamelin

Genom Data 2016 Dec 3;10:85-88. Epub 2016 Oct 3.

Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Institut de Biologie Intégrative des Systèmes, Université Laval, Québec, Canada.

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http://dx.doi.org/10.1016/j.gdata.2016.09.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061060PMC
December 2016

ntHash: recursive nucleotide hashing.

Authors:
Hamid Mohamadi Justin Chu Benjamin P Vandervalk Inanc Birol

Bioinformatics 2016 11 16;32(22):3492-3494. Epub 2016 Jul 16.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181554PMC
November 2016

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

Authors:
René L Warren Chen Yang Benjamin P Vandervalk Bahar Behsaz Albert Lagman Steven J M Jones Inanç Birol

Gigascience 2015 4;4:35. Epub 2015 Aug 4.

BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6 Canada.

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http://dx.doi.org/10.1186/s13742-015-0076-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524009PMC
July 2016

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

Authors:
Benjamin P Vandervalk Chen Yang Zhuyi Xue Karthika Raghavan Justin Chu Hamid Mohamadi Shaun D Jackman Readman Chiu René L Warren Inanç Birol

BMC Med Genomics 2015 23;8 Suppl 3:S1. Epub 2015 Sep 23.

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http://dx.doi.org/10.1186/1755-8794-8-S3-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582294PMC
July 2016

Kleat: cleavage site analysis of transcriptomes.

Authors:
Inanç Birol Anthony Raymond Readman Chiu Ka Ming Nip Shaun D Jackman Maayan Kreitzman T Roderick Docking Catherine A Ennis A Gordon Robertson Aly Karsan

Pac Symp Biocomput 2015 :347-58

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350765PMC
April 2016

DIDA: Distributed Indexing Dispatched Alignment.

Authors:
Hamid Mohamadi Benjamin P Vandervalk Anthony Raymond Shaun D Jackman Justin Chu Clay P Breshears Inanc Birol

PLoS One 2015 29;10(4):e0126409. Epub 2015 Apr 29.

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126409PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414605PMC
April 2016

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

Authors:
Shaun D Jackman Joerg Bohlmann İnanç Birol

PLoS One 2015 28;10(5):e0128026. Epub 2015 May 28.

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128026PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447347PMC
April 2016

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

Authors:
Inanc Birol Bahar Behsaz S Austin Hammond Erdi Kucuk Nik Veldhoen Caren C Helbing

PLoS One 2015 29;10(6):e0130720. Epub 2015 Jun 29.

Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130720PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488148PMC
March 2016

Large-scale profiling of microRNAs for The Cancer Genome Atlas.

Authors:
Andy Chu Gordon Robertson Denise Brooks Andrew J Mungall Inanc Birol Robin Coope Yussanne Ma Steven Jones Marco A Marra

Nucleic Acids Res 2016 Jan 13;44(1):e3. Epub 2015 Aug 13.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada Department of Medical Genetics, University of British Columbia, Vancouver, V6H 3N1, Canada

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http://dx.doi.org/10.1093/nar/gkv808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705681PMC
January 2016

Divergent clonal selection dominates medulloblastoma at recurrence.

Authors:
A Sorana Morrissy Livia Garzia David J H Shih Scott Zuyderduyn Xi Huang Patryk Skowron Marc Remke Florence M G Cavalli Vijay Ramaswamy Patricia E Lindsay Salomeh Jelveh Laura K Donovan Xin Wang Betty Luu Kory Zayne Yisu Li Chelsea Mayoh Nina Thiessen Eloi Mercier Karen L Mungall Yusanne Ma Kane Tse Thomas Zeng Karey Shumansky Andrew J L Roth Sohrab Shah Hamza Farooq Noriyuki Kijima Borja L Holgado John J Y Lee Stuart Matan-Lithwick Jessica Liu Stephen C Mack Alex Manno K A Michealraj Carolina Nor John Peacock Lei Qin Juri Reimand Adi Rolider Yuan Y Thompson Xiaochong Wu Trevor Pugh Adrian Ally Mikhail Bilenky Yaron S N Butterfield Rebecca Carlsen Young Cheng Eric Chuah Richard D Corbett Noreen Dhalla An He Darlene Lee Haiyan I Li William Long Michael Mayo Patrick Plettner Jenny Q Qian Jacqueline E Schein Angela Tam Tina Wong Inanc Birol Yongjun Zhao Claudia C Faria José Pimentel Sofia Nunes Tarek Shalaby Michael Grotzer Ian F Pollack Ronald L Hamilton Xiao-Nan Li Anne E Bendel Daniel W Fults Andrew W Walter Toshihiro Kumabe Teiji Tominaga V Peter Collins Yoon-Jae Cho Caitlin Hoffman David Lyden Jeffrey H Wisoff James H Garvin Duncan S Stearns Luca Massimi Ulrich Schüller Jaroslav Sterba Karel Zitterbart Stephanie Puget Olivier Ayrault Sandra E Dunn Daniela P C Tirapelli Carlos G Carlotti Helen Wheeler Andrew R Hallahan Wendy Ingram Tobey J MacDonald Jeffrey J Olson Erwin G Van Meir Ji-Yeoun Lee Kyu-Chang Wang Seung-Ki Kim Byung-Kyu Cho Torsten Pietsch Gudrun Fleischhack Stephan Tippelt Young Shin Ra Simon Bailey Janet C Lindsey Steven C Clifford Charles G Eberhart Michael K Cooper Roger J Packer Maura Massimino Maria Luisa Garre Ute Bartels Uri Tabori Cynthia E Hawkins Peter Dirks Eric Bouffet James T Rutka Robert J Wechsler-Reya William A Weiss Lara S Collier Adam J Dupuy Andrey Korshunov David T W Jones Marcel Kool Paul A Northcott Stefan M Pfister David A Largaespada Andrew J Mungall Richard A Moore Nada Jabado Gary D Bader Steven J M Jones David Malkin Marco A Marra Michael D Taylor

Nature 2016 Jan 13;529(7586):351-7. Epub 2016 Jan 13.

Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.

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http://dx.doi.org/10.1038/nature16478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936195PMC
January 2016

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

Authors:
Shaun D Jackman René L Warren Ewan A Gibb Benjamin P Vandervalk Hamid Mohamadi Justin Chu Anthony Raymond Stephen Pleasance Robin Coope Mark R Wildung Carol E Ritland Jean Bousquet Steven J M Jones Joerg Bohlmann Inanç Birol

Genome Biol Evol 2015 Dec 8;8(1):29-41. Epub 2015 Dec 8.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada School of Computing Science, Simon Fraser University, Burnaby, BC, Canada Department of Computer Science, University of British Columbia, Vancouver, BC, Canada

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http://dx.doi.org/10.1093/gbe/evv244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758241PMC
December 2015

Spaced Seed Data Structures for De Novo Assembly.

Authors:
Inanç Birol Justin Chu Hamid Mohamadi Shaun D Jackman Karthika Raghavan Benjamin P Vandervalk Anthony Raymond René L Warren

Int J Genomics 2015 11;2015:196591. Epub 2015 Oct 11.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4S6.

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http://dx.doi.org/10.1155/2015/196591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619942PMC
November 2015

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

Authors:
René L Warren Christopher I Keeling Macaire Man Saint Yuen Anthony Raymond Greg A Taylor Benjamin P Vandervalk Hamid Mohamadi Daniel Paulino Readman Chiu Shaun D Jackman Gordon Robertson Chen Yang Brian Boyle Margarete Hoffmann Detlef Weigel David R Nelson Carol Ritland Nathalie Isabel Barry Jaquish Alvin Yanchuk Jean Bousquet Steven J M Jones John MacKay Inanc Birol Joerg Bohlmann

Plant J 2015 Jul 19;83(2):189-212. Epub 2015 Jun 19.

Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.

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http://dx.doi.org/10.1111/tpj.12886DOI Listing
July 2015

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

Authors:
Daniel Paulino René L Warren Benjamin P Vandervalk Anthony Raymond Shaun D Jackman Inanç Birol

BMC Bioinformatics 2015 Jul 25;16:230. Epub 2015 Jul 25.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.

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http://dx.doi.org/10.1186/s12859-015-0663-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515008PMC
July 2015

JAGuaR: junction alignments to genome for RNA-seq reads.

Authors:
Yaron S Butterfield Maayan Kreitzman Nina Thiessen Richard D Corbett Yisu Li Johnson Pang Yussanne P Ma Steven J M Jones İnanç Birol

PLoS One 2014 25;9(7):e102398. Epub 2014 Jul 25.

Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102398PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111418PMC
April 2015

Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis.

Authors:
Einav Shoshan Aaron K Mobley Russell R Braeuer Takafumi Kamiya Li Huang Mayra E Vasquez Ahmad Salameh Ho Jeong Lee Sun Jin Kim Cristina Ivan Guermarie Velazquez-Torres Ka Ming Nip Kelsey Zhu Denise Brooks Steven J M Jones Inanc Birol Maribel Mosqueda Yu-ye Wen Agda Karina Eterovic Anil K Sood Patrick Hwu Jeffrey E Gershenwald A Gordon Robertson George A Calin Gal Markel Isaiah J Fidler Menashe Bar-Eli

Nat Cell Biol 2015 Mar 16;17(3):311-21. Epub 2015 Feb 16.

Department of Cancer Biology, Unit 0173, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncb3110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344852PMC
March 2015

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

Authors:
Justin Chu Sara Sadeghi Anthony Raymond Shaun D Jackman Ka Ming Nip Richard Mar Hamid Mohamadi Yaron S Butterfield A Gordon Robertson Inanç Birol

Bioinformatics 2014 Dec 20;30(23):3402-4. Epub 2014 Aug 20.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816029PMC
December 2014

Insights into conifer giga-genomes.

Authors:
Amanda R De La Torre Inanc Birol Jean Bousquet Pär K Ingvarsson Stefan Jansson Steven J M Jones Christopher I Keeling John MacKay Ove Nilsson Kermit Ritland Nathaniel Street Alvin Yanchuk Philipp Zerbe Jörg Bohlmann

Plant Physiol 2014 Dec 27;166(4):1724-32. Epub 2014 Oct 27.

Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)

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http://dx.doi.org/10.1104/pp.114.248708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256843PMC
December 2014

Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii.

Authors:
Metka Lenassi Cene Gostinčar Shaun Jackman Martina Turk Ivan Sadowski Corey Nislow Steven Jones Inanc Birol Nina Gunde Cimerman Ana Plemenitaš

PLoS One 2013 15;8(8):e71328. Epub 2013 Aug 15.

Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia ; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744574PMC
April 2014

Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size.

Authors:
Juliana Stival Sena Isabelle Giguère Brian Boyle Philippe Rigault Inanc Birol Andrea Zuccolo Kermit Ritland Carol Ritland Joerg Bohlmann Steven Jones Jean Bousquet John Mackay

BMC Plant Biol 2014 Apr 16;14:95. Epub 2014 Apr 16.

Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada.

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http://dx.doi.org/10.1186/1471-2229-14-95DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108047PMC
April 2014

A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations.

Authors:
Ian E Bosdet T Roderick Docking Yaron S Butterfield Andrew J Mungall Thomas Zeng Robin J Coope Erika Yorida Katie Chow Miruna Bala Sean S Young Martin Hirst Inanc Birol Richard A Moore Steven J Jones Marco A Marra Rob Holt Aly Karsan

J Mol Diagn 2013 Nov 4;15(6):796-809. Epub 2013 Oct 4.

Cancer Genetics Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1016/j.jmoldx.2013.07.004DOI Listing
November 2013

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.

Authors:
Ryan D Morin Karen Mungall Erin Pleasance Andrew J Mungall Rodrigo Goya Ryan D Huff David W Scott Jiarui Ding Andrew Roth Readman Chiu Richard D Corbett Fong Chun Chan Maria Mendez-Lago Diane L Trinh Madison Bolger-Munro Greg Taylor Alireza Hadj Khodabakhshi Susana Ben-Neriah Julia Pon Barbara Meissner Bruce Woolcock Noushin Farnoud Sanja Rogic Emilia L Lim Nathalie A Johnson Sohrab Shah Steven Jones Christian Steidl Robert Holt Inanc Birol Richard Moore Joseph M Connors Randy D Gascoyne Marco A Marra

Blood 2013 Aug 22;122(7):1256-65. Epub 2013 May 22.

Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.

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http://dx.doi.org/10.1182/blood-2013-02-483727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744992PMC
August 2013

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.

Authors:
Lucas Swanson Gordon Robertson Karen L Mungall Yaron S Butterfield Readman Chiu Richard D Corbett T Roderick Docking Donna Hogge Shaun D Jackman Richard A Moore Andrew J Mungall Ka Ming Nip Jeremy D K Parker Jenny Qing Qian Anthony Raymond Sandy Sung Angela Tam Nina Thiessen Richard Varhol Sherry Wang Deniz Yorukoglu Yongjun Zhao Pamela A Hoodless S Cenk Sahinalp Aly Karsan Inanc Birol

BMC Genomics 2013 Aug 14;14:550. Epub 2013 Aug 14.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.

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http://dx.doi.org/10.1186/1471-2164-14-550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751903PMC
August 2013

Complete genomic landscape of a recurring sporadic parathyroid carcinoma.

Authors:
Katayoon Kasaian Sam M Wiseman Nina Thiessen Karen L Mungall Richard D Corbett Jenny Q Qian Ka Ming Nip Ann He Kane Tse Eric Chuah Richard J Varhol Pawan Pandoh Helen McDonald Thomas Zeng Angela Tam Jacquie Schein Inanc Birol Andrew J Mungall Richard A Moore Yongjun Zhao Martin Hirst Marco A Marra Blair A Walker Steven J M Jones

J Pathol 2013 Jul;230(3):249-60

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/path.4203DOI Listing
July 2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Authors:
Keith R Bradnam Joseph N Fass Anton Alexandrov Paul Baranay Michael Bechner Inanç Birol Sébastien Boisvert Jarrod A Chapman Guillaume Chapuis Rayan Chikhi Hamidreza Chitsaz Wen-Chi Chou Jacques Corbeil Cristian Del Fabbro T Roderick Docking Richard Durbin Dent Earl Scott Emrich Pavel Fedotov Nuno A Fonseca Ganeshkumar Ganapathy Richard A Gibbs Sante Gnerre Elénie Godzaridis Steve Goldstein Matthias Haimel Giles Hall David Haussler Joseph B Hiatt Isaac Y Ho Jason Howard Martin Hunt Shaun D Jackman David B Jaffe Erich D Jarvis Huaiyang Jiang Sergey Kazakov Paul J Kersey Jacob O Kitzman James R Knight Sergey Koren Tak-Wah Lam Dominique Lavenier François Laviolette Yingrui Li Zhenyu Li Binghang Liu Yue Liu Ruibang Luo Iain Maccallum Matthew D Macmanes Nicolas Maillet Sergey Melnikov Delphine Naquin Zemin Ning Thomas D Otto Benedict Paten Octávio S Paulo Adam M Phillippy Francisco Pina-Martins Michael Place Dariusz Przybylski Xiang Qin Carson Qu Filipe J Ribeiro Stephen Richards Daniel S Rokhsar J Graham Ruby Simone Scalabrin Michael C Schatz David C Schwartz Alexey Sergushichev Ted Sharpe Timothy I Shaw Jay Shendure Yujian Shi Jared T Simpson Henry Song Fedor Tsarev Francesco Vezzi Riccardo Vicedomini Bruno M Vieira Jun Wang Kim C Worley Shuangye Yin Siu-Ming Yiu Jianying Yuan Guojie Zhang Hao Zhang Shiguo Zhou Ian F Korf

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.

Authors:
Inanc Birol Anthony Raymond Shaun D Jackman Stephen Pleasance Robin Coope Greg A Taylor Macaire Man Saint Yuen Christopher I Keeling Dana Brand Benjamin P Vandervalk Heather Kirk Pawan Pandoh Richard A Moore Yongjun Zhao Andrew J Mungall Barry Jaquish Alvin Yanchuk Carol Ritland Brian Boyle Jean Bousquet Kermit Ritland John Mackay Jörg Bohlmann Steven J M Jones

Bioinformatics 2013 Jun 22;29(12):1492-7. Epub 2013 May 22.

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673215PMC
June 2013

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

Authors:
Sajeet Haridas Ye Wang Lynette Lim Sepideh Massoumi Alamouti Shaun Jackman Rod Docking Gordon Robertson Inanc Birol Jörg Bohlmann Colette Breuil

BMC Genomics 2013 Jun 2;14:373. Epub 2013 Jun 2.

Department of Wood Science, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1471-2164-14-373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3680317PMC
June 2013

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

Authors:
Timothy J Ley Christopher Miller Li Ding Benjamin J Raphael Andrew J Mungall A Gordon Robertson Katherine Hoadley Timothy J Triche Peter W Laird Jack D Baty Lucinda L Fulton Robert Fulton Sharon E Heath Joelle Kalicki-Veizer Cyriac Kandoth Jeffery M Klco Daniel C Koboldt Krishna-Latha Kanchi Shashikant Kulkarni Tamara L Lamprecht David E Larson Ling Lin Charles Lu Michael D McLellan Joshua F McMichael Jacqueline Payton Heather Schmidt David H Spencer Michael H Tomasson John W Wallis Lukas D Wartman Mark A Watson John Welch Michael C Wendl Adrian Ally Miruna Balasundaram Inanc Birol Yaron Butterfield Readman Chiu Andy Chu Eric Chuah Hye-Jung Chun Richard Corbett Noreen Dhalla Ranabir Guin An He Carrie Hirst Martin Hirst Robert A Holt Steven Jones Aly Karsan Darlene Lee Haiyan I Li Marco A Marra Michael Mayo Richard A Moore Karen Mungall Jeremy Parker Erin Pleasance Patrick Plettner Jacquie Schein Dominik Stoll Lucas Swanson Angela Tam Nina Thiessen Richard Varhol Natasja Wye Yongjun Zhao Stacey Gabriel Gad Getz Carrie Sougnez Lihua Zou Mark D M Leiserson Fabio Vandin Hsin-Ta Wu Frederick Applebaum Stephen B Baylin Rehan Akbani Bradley M Broom Ken Chen Thomas C Motter Khanh Nguyen John N Weinstein Nianziang Zhang Martin L Ferguson Christopher Adams Aaron Black Jay Bowen Julie Gastier-Foster Thomas Grossman Tara Lichtenberg Lisa Wise Tanja Davidsen John A Demchok Kenna R Mills Shaw Margi Sheth Heidi J Sofia Liming Yang James R Downing Greg Eley

N Engl J Med 2013 05 1;368(22):2059-74. Epub 2013 May 1.

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http://dx.doi.org/10.1056/NEJMoa1301689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767041PMC
May 2013

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

Authors:
Alireza Hadj Khodabakhshi Anthony P Fejes Inanc Birol Steven J M Jones

BMC Bioinformatics 2013 May 28;14:167. Epub 2013 May 28.

Genome Sciences Centre, BC Cancer Agency, Suite 100 - 570 West 7th Ave, Vancouver, British Columbia, V5Z 4S6, Canada.

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http://dx.doi.org/10.1186/1471-2105-14-167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3680031PMC
May 2013

The genetic landscape of high-risk neuroblastoma.

Authors:
Trevor J Pugh Olena Morozova Edward F Attiyeh Shahab Asgharzadeh Jun S Wei Daniel Auclair Scott L Carter Kristian Cibulskis Megan Hanna Adam Kiezun Jaegil Kim Michael S Lawrence Lee Lichenstein Aaron McKenna Chandra Sekhar Pedamallu Alex H Ramos Erica Shefler Andrey Sivachenko Carrie Sougnez Chip Stewart Adrian Ally Inanc Birol Readman Chiu Richard D Corbett Martin Hirst Shaun D Jackman Baljit Kamoh Alireza Hadj Khodabakshi Martin Krzywinski Allan Lo Richard A Moore Karen L Mungall Jenny Qian Angela Tam Nina Thiessen Yongjun Zhao Kristina A Cole Maura Diamond Sharon J Diskin Yael P Mosse Andrew C Wood Lingyun Ji Richard Sposto Thomas Badgett Wendy B London Yvonne Moyer Julie M Gastier-Foster Malcolm A Smith Jaime M Guidry Auvil Daniela S Gerhard Michael D Hogarty Steven J M Jones Eric S Lander Stacey B Gabriel Gad Getz Robert C Seeger Javed Khan Marco A Marra Matthew Meyerson John M Maris

Nat Genet 2013 Mar 20;45(3):279-84. Epub 2013 Jan 20.

The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://www.nature.com/articles/ng.2529
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http://dx.doi.org/10.1038/ng.2529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682833PMC
March 2013

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.

Authors:
Christopher I Keeling Macaire M S Yuen Nancy Y Liao T Roderick Docking Simon K Chan Greg A Taylor Diana L Palmquist Shaun D Jackman Anh Nguyen Maria Li Hannah Henderson Jasmine K Janes Yongjun Zhao Pawan Pandoh Richard Moore Felix A H Sperling Dezene P W Huber Inanc Birol Steven J M Jones Joerg Bohlmann

Genome Biol 2013 Mar 27;14(3):R27. Epub 2013 Mar 27.

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http://dx.doi.org/10.1186/gb-2013-14-3-r27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053930PMC
March 2013

Recurrent targets of aberrant somatic hypermutation in lymphoma.

Authors:
Alireza Hadj Khodabakhshi Ryan D Morin Anthony P Fejes Andrew J Mungall Karen L Mungall Madison Bolger-Munro Nathalie A Johnson Joseph M Connors Randy D Gascoyne Marco A Marra Inanc Birol Steven J M Jones

Oncotarget 2012 Nov;3(11):1308-19

Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717795PMC
http://dx.doi.org/10.18632/oncotarget.653DOI Listing
November 2012

Hive plots--rational approach to visualizing networks.

Authors:
Martin Krzywinski Inanc Birol Steven J M Jones Marco A Marra

Brief Bioinform 2012 Sep 9;13(5):627-44. Epub 2011 Dec 9.

BC Cancer Research Center, Vancouver, Canada.

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http://dx.doi.org/10.1093/bib/bbr069DOI Listing
September 2012

Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests.

Authors:
Christopher I Keeling Hannah Henderson Maria Li Mack Yuen Erin L Clark Jordie D Fraser Dezene P W Huber Nancy Y Liao T Roderick Docking Inanc Birol Simon K Chan Greg A Taylor Diana Palmquist Steven J M Jones Joerg Bohlmann

Insect Biochem Mol Biol 2012 Aug 7;42(8):525-36. Epub 2012 Apr 7.

Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1Z4.

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http://dx.doi.org/10.1016/j.ibmb.2012.03.010DOI Listing
August 2012

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Authors:
Paul A Northcott David J H Shih John Peacock Livia Garzia A Sorana Morrissy Thomas Zichner Adrian M Stütz Andrey Korshunov Jüri Reimand Steven E Schumacher Rameen Beroukhim David W Ellison Christian R Marshall Anath C Lionel Stephen Mack Adrian Dubuc Yuan Yao Vijay Ramaswamy Betty Luu Adi Rolider Florence M G Cavalli Xin Wang Marc Remke Xiaochong Wu Readman Y B Chiu Andy Chu Eric Chuah Richard D Corbett Gemma R Hoad Shaun D Jackman Yisu Li Allan Lo Karen L Mungall Ka Ming Nip Jenny Q Qian Anthony G J Raymond Nina T Thiessen Richard J Varhol Inanc Birol Richard A Moore Andrew J Mungall Robert Holt Daisuke Kawauchi Martine F Roussel Marcel Kool David T W Jones Hendrick Witt Africa Fernandez-L Anna M Kenney Robert J Wechsler-Reya Peter Dirks Tzvi Aviv Wieslawa A Grajkowska Marta Perek-Polnik Christine C Haberler Olivier Delattre Stéphanie S Reynaud François F Doz Sarah S Pernet-Fattet Byung-Kyu Cho Seung-Ki Kim Kyu-Chang Wang Wolfram Scheurlen Charles G Eberhart Michelle Fèvre-Montange Anne Jouvet Ian F Pollack Xing Fan Karin M Muraszko G Yancey Gillespie Concezio Di Rocco Luca Massimi Erna M C Michiels Nanne K Kloosterhof Pim J French Johan M Kros James M Olson Richard G Ellenbogen Karel Zitterbart Leos Kren Reid C Thompson Michael K Cooper Boleslaw Lach Roger E McLendon Darell D Bigner Adam Fontebasso Steffen Albrecht Nada Jabado Janet C Lindsey Simon Bailey Nalin Gupta William A Weiss László Bognár Almos Klekner Timothy E Van Meter Toshihiro Kumabe Teiji Tominaga Samer K Elbabaa Jeffrey R Leonard Joshua B Rubin Linda M Liau Erwin G Van Meir Maryam Fouladi Hideo Nakamura Giuseppe Cinalli Miklós Garami Peter Hauser Ali G Saad Achille Iolascon Shin Jung Carlos G Carlotti Rajeev Vibhakar Young Shin Ra Shenandoah Robinson Massimo Zollo Claudia C Faria Jennifer A Chan Michael L Levy Poul H B Sorensen Matthew Meyerson Scott L Pomeroy Yoon-Jae Cho Gary D Bader Uri Tabori Cynthia E Hawkins Eric Bouffet Stephen W Scherer James T Rutka David Malkin Steven C Clifford Steven J M Jones Jan O Korbel Stefan M Pfister Marco A Marra Michael D Taylor

Nature 2012 Aug;488(7409):49-56

Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.

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http://is.muni.cz/repo/990835/nature11327.pdf
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683624PMC
August 2012

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia.

Authors:
Kathryn G Roberts Ryan D Morin Jinghui Zhang Martin Hirst Yongjun Zhao Xiaoping Su Shann-Ching Chen Debbie Payne-Turner Michelle L Churchman Richard C Harvey Xiang Chen Corynn Kasap Chunhua Yan Jared Becksfort Richard P Finney David T Teachey Shannon L Maude Kane Tse Richard Moore Steven Jones Karen Mungall Inanc Birol Michael N Edmonson Ying Hu Kenneth E Buetow I-Ming Chen William L Carroll Lei Wei Jing Ma Maria Kleppe Ross L Levine Guillermo Garcia-Manero Eric Larsen Neil P Shah Meenakshi Devidas Gregory Reaman Malcolm Smith Steven W Paugh William E Evans Stephan A Grupp Sima Jeha Ching-Hon Pui Daniela S Gerhard James R Downing Cheryl L Willman Mignon Loh Stephen P Hunger Marco A Marra Charles G Mullighan

Cancer Cell 2012 Aug;22(2):153-66

Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.

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http://www.cell.com/cms/attachment/2003030372/2011721297/mmc
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http://dx.doi.org/10.1016/j.ccr.2012.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422513PMC
August 2012

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

Authors:
Deniz Yorukoglu Faraz Hach Lucas Swanson Colin C Collins Inanc Birol S Cenk Sahinalp

Bioinformatics 2012 Jun;28(12):i179-87

School of Computing Science, Simon Fraser University, Burnaby, V5A 1S6 BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/bts214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371846PMC
June 2012

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Authors:
Sohrab P Shah Andrew Roth Rodrigo Goya Arusha Oloumi Gavin Ha Yongjun Zhao Gulisa Turashvili Jiarui Ding Kane Tse Gholamreza Haffari Ali Bashashati Leah M Prentice Jaswinder Khattra Angela Burleigh Damian Yap Virginie Bernard Andrew McPherson Karey Shumansky Anamaria Crisan Ryan Giuliany Alireza Heravi-Moussavi Jamie Rosner Daniel Lai Inanc Birol Richard Varhol Angela Tam Noreen Dhalla Thomas Zeng Kevin Ma Simon K Chan Malachi Griffith Annie Moradian S-W Grace Cheng Gregg B Morin Peter Watson Karen Gelmon Stephen Chia Suet-Feung Chin Christina Curtis Oscar M Rueda Paul D Pharoah Sambasivarao Damaraju John Mackey Kelly Hoon Timothy Harkins Vasisht Tadigotla Mahvash Sigaroudinia Philippe Gascard Thea Tlsty Joseph F Costello Irmtraud M Meyer Connie J Eaves Wyeth W Wasserman Steven Jones David Huntsman Martin Hirst Carlos Caldas Marco A Marra Samuel Aparicio

Nature 2012 Apr 4;486(7403):395-9. Epub 2012 Apr 4.

Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.

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http://dx.doi.org/10.1038/nature10933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863681PMC
April 2012

Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers.

Authors:
Stephen Yip Yaron S Butterfield Olena Morozova Suganthi Chittaranjan Michael D Blough Jianghong An Inanc Birol Charles Chesnelong Readman Chiu Eric Chuah Richard Corbett Rod Docking Marlo Firme Martin Hirst Shaun Jackman Aly Karsan Haiyan Li David N Louis Alexandra Maslova Richard Moore Annie Moradian Karen L Mungall Marco Perizzolo Jenny Qian Gloria Roldan Eric E Smith Jessica Tamura-Wells Nina Thiessen Richard Varhol Samuel Weiss Wei Wu Sean Young Yongjun Zhao Andrew J Mungall Steven J M Jones Gregg B Morin Jennifer A Chan J Gregory Cairncross Marco A Marra

J Pathol 2012 Jan 10;226(1):7-16. Epub 2011 Nov 10.

Department of Pathology and Laboratory Medicine, BC Cancer Agency, BC, Canada.

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http://dx.doi.org/10.1002/path.2995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246739PMC
January 2012

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Authors:
Dent Earl Keith Bradnam John St John Aaron Darling Dawei Lin Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T Simpson Nuno A Fonseca İnanç Birol T Roderick Docking Isaac Y Ho Daniel S Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C Schatz David R Kelley Adam M Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I Shaw J Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J Kersey Richard Durbin Shaun D Jackman Jarrod A Chapman Xiaoqiu Huang Joseph L DeRisi Mario Caccamo Yingrui Li David B Jaffe Richard E Green David Haussler Ian Korf Benedict Paten

Genome Res 2011 Dec 16;21(12):2224-41. Epub 2011 Sep 16.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.126599.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227110PMC
December 2011

Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601.

Authors:
Yuefeng Chu Pengchen Gao Ping Zhao Ying He Nancy Liao Shaun Jackman Yongjun Zhao Inanc Birol Xiaobo Duan Zhongxin Lu

J Bacteriol 2011 Nov;193(21):6098-9

State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Epizootic Diseases of Grazing Animals of Ministry ofAgriculture, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China.

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http://dx.doi.org/10.1128/JB.05980-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194924PMC
November 2011

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

Authors:
Queenie W T Chan R Scott Cornman Inanc Birol Nancy Y Liao Simon K Chan T Roderick Docking Shaun D Jackman Greg A Taylor Steven J M Jones Dirk C de Graaf Jay D Evans Leonard J Foster

BMC Genomics 2011 Sep 16;12:450. Epub 2011 Sep 16.

Department of Biochemistry Ž Molecular Biology, Centre for High-throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, V6T 1Z4 Canada.

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http://dx.doi.org/10.1186/1471-2164-12-450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188533PMC
September 2011

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.

Authors:
Ryan D Morin Maria Mendez-Lago Andrew J Mungall Rodrigo Goya Karen L Mungall Richard D Corbett Nathalie A Johnson Tesa M Severson Readman Chiu Matthew Field Shaun Jackman Martin Krzywinski David W Scott Diane L Trinh Jessica Tamura-Wells Sa Li Marlo R Firme Sanja Rogic Malachi Griffith Susanna Chan Oleksandr Yakovenko Irmtraud M Meyer Eric Y Zhao Duane Smailus Michelle Moksa Suganthi Chittaranjan Lisa Rimsza Angela Brooks-Wilson John J Spinelli Susana Ben-Neriah Barbara Meissner Bruce Woolcock Merrill Boyle Helen McDonald Angela Tam Yongjun Zhao Allen Delaney Thomas Zeng Kane Tse Yaron Butterfield Inanç Birol Rob Holt Jacqueline Schein Douglas E Horsman Richard Moore Steven J M Jones Joseph M Connors Martin Hirst Randy D Gascoyne Marco A Marra

Nature 2011 Jul 27;476(7360):298-303. Epub 2011 Jul 27.

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.

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http://dx.doi.org/10.1038/nature10351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210554PMC
July 2011

Human variation database: an open-source database template for genomic discovery.

Authors:
Anthony P Fejes Alireza Hadj Khodabakhshi Inanc Birol Steven J M Jones

Bioinformatics 2011 Apr 2;27(8):1155-6. Epub 2011 Mar 2.

Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6.

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http://dx.doi.org/10.1093/bioinformatics/btr100DOI Listing
April 2011

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.

Authors:
Armando Geraldes Johnson Pang Nina Thiessen Timothee Cezard Richard Moore Yongjun Zhao Angela Tam Shucai Wang Michael Friedmann Inanc Birol Steven J M Jones Quentin C B Cronk Carl J Douglas

Mol Ecol Resour 2011 Mar;11 Suppl 1:81-92

Department of Botany, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1111/j.1755-0998.2010.02960.xDOI Listing
March 2011

Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen.

Authors:
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 Feb 24;108(6):2504-9. Epub 2011 Jan 24.

Department of Wood Science, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.

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http://dx.doi.org/10.1073/pnas.1011289108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038703PMC
February 2011

Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.

Authors:
Jennifer L Gardy James C Johnston Shannan J Ho Sui Victoria J Cook Lena Shah Elizabeth Brodkin Shirley Rempel Richard Moore Yongjun Zhao Robert Holt Richard Varhol Inanc Birol Marcus Lem Meenu K Sharma Kevin Elwood Steven J M Jones Fiona S L Brinkman Robert C Brunham Patrick Tang

N Engl J Med 2011 Feb;364(8):730-9

British Columbia Centre for Disease Control, Vancouver, BC, Canada.

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http://dx.doi.org/10.1056/NEJMoa1003176DOI Listing
February 2011

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.

Authors:
Steven Jm Jones Janessa Laskin Yvonne Y Li Obi L Griffith Jianghong An Mikhail Bilenky Yaron S Butterfield Timothee Cezard Eric Chuah Richard Corbett Anthony P Fejes Malachi Griffith John Yee Montgomery Martin Michael Mayo Nataliya Melnyk Ryan D Morin Trevor J Pugh Tesa Severson Sohrab P Shah Margaret Sutcliffe Angela Tam Jefferson Terry Nina Thiessen Thomas Thomson Richard Varhol Thomas Zeng Yongjun Zhao Richard A Moore David G Huntsman Inanc Birol Martin Hirst Robert A Holt Marco A Marra

Genome Biol 2010 9;11(8):R82. Epub 2010 Aug 9.

Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2010-11-8-r82DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945784PMC
January 2011

De novo assembly and analysis of RNA-seq data.

Authors:
Gordon Robertson Jacqueline Schein Readman Chiu Richard Corbett Matthew Field Shaun D Jackman Karen Mungall Sam Lee Hisanaga Mark Okada Jenny Q Qian Malachi Griffith Anthony Raymond Nina Thiessen Timothee Cezard Yaron S Butterfield Richard Newsome Simon K Chan Rong She Richard Varhol Baljit Kamoh Anna-Liisa Prabhu Angela Tam YongJun Zhao Richard A Moore Martin Hirst Marco A Marra Steven J M Jones Pamela A Hoodless Inanc Birol

Nat Methods 2010 Nov 10;7(11):909-12. Epub 2010 Oct 10.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.

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http://dx.doi.org/10.1038/nmeth.1517DOI Listing
November 2010

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver.

Authors:
Brad G Hoffman Gordon Robertson Bogard Zavaglia Mike Beach Rebecca Cullum Sam Lee Galina Soukhatcheva Leping Li Elizabeth D Wederell Nina Thiessen Mikhail Bilenky Timothee Cezard Angela Tam Baljit Kamoh Inanc Birol Derek Dai Yongjun Zhao Martin Hirst C Bruce Verchere Cheryl D Helgason Marco A Marra Steven J M Jones Pamela A Hoodless

Genome Res 2010 Aug 15;20(8):1037-51. Epub 2010 Jun 15.

Department of Cancer Endocrinology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.

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http://dx.doi.org/10.1101/gr.104356.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909568PMC
August 2010

mrsFAST: a cache-oblivious algorithm for short-read mapping.

Authors:
Faraz Hach Fereydoun Hormozdiari Can Alkan Farhad Hormozdiari Inanc Birol Evan E Eichler S Cenk Sahinalp

Nat Methods 2010 Aug;7(8):576-7

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http://www.nature.com/articles/nmeth0810-576
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http://dx.doi.org/10.1038/nmeth0810-576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115707PMC
August 2010

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.

Authors:
Santosh S Atanur Inanç Birol Victor Guryev Martin Hirst Oliver Hummel Catherine Morrissey Jacques Behmoaras Xose M Fernandez-Suarez Michelle D Johnson William M McLaren Giannino Patone Enrico Petretto Charles Plessy Kathleen S Rockland Charles Rockland Kathrin Saar Yongjun Zhao Piero Carninci Paul Flicek Ted Kurtz Edwin Cuppen Michal Pravenec Norbert Hubner Steven J M Jones Ewan Birney Timothy J Aitman

Genome Res 2010 Jun 29;20(6):791-803. Epub 2010 Apr 29.

Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom.

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http://dx.doi.org/10.1101/gr.103499.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877576PMC
June 2010

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

Authors:
Iman Hajirasouliha Fereydoun Hormozdiari Can Alkan Jeffrey M Kidd Inanc Birol Evan E Eichler S Cenk Sahinalp

Bioinformatics 2010 May 12;26(10):1277-83. Epub 2010 Apr 12.

Lab for Computational Biology, Simon Fraser University, Burnaby, BC, Canada.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865866PMC
May 2010

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.

Authors:
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 11;10(9):R94. Epub 2009 Sep 11.

Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.

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http://dx.doi.org/10.1186/gb-2009-10-9-r94DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768983PMC
February 2010

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin.

Authors:
Ryan D Morin Nathalie A Johnson Tesa M Severson Andrew J Mungall Jianghong An Rodrigo Goya Jessica E Paul Merrill Boyle Bruce W Woolcock Florian Kuchenbauer Damian Yap R Keith Humphries Obi L Griffith Sohrab Shah Henry Zhu Michelle Kimbara Pavel Shashkin Jean F Charlot Marianna Tcherpakov Richard Corbett Angela Tam Richard Varhol Duane Smailus Michelle Moksa Yongjun Zhao Allen Delaney Hong Qian Inanc Birol Jacqueline Schein Richard Moore Robert Holt Doug E Horsman Joseph M Connors Steven Jones Samuel Aparicio Martin Hirst Randy D Gascoyne Marco A Marra

Nat Genet 2010 Feb 17;42(2):181-5. Epub 2010 Jan 17.

Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/ng.518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850970PMC
February 2010

ABySS-Explorer: visualizing genome sequence assemblies.

Authors:
Cydney B Nielsen Shaun D Jackman Inanç Birol Steven J M Jones

IEEE Trans Vis Comput Graph 2009 Nov-Dec;15(6):881-8

BC Cancer Agency, Genome Sciences Centre.

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http://dx.doi.org/10.1109/TVCG.2009.116DOI Listing
January 2010

Assembling genomes using short-read sequencing technology.

Authors:
Shaun D Jackman Inanç Birol

Genome Biol 2010 Jan 28;11(1):202. Epub 2010 Jan 28.

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British, Columbia V5Z 4E6, Canada.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2010-11-1-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847710PMC
January 2010

De novo transcriptome assembly with ABySS.

Authors:
Inanç Birol Shaun D Jackman Cydney B Nielsen Jenny Q Qian Richard Varhol Greg Stazyk Ryan D Morin Yongjun Zhao Martin Hirst Jacqueline E Schein Doug E Horsman Joseph M Connors Randy D Gascoyne Marco A Marra Steven J M Jones

Bioinformatics 2009 Nov 15;25(21):2872-7. Epub 2009 Jun 15.

Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btp367DOI Listing
November 2009

Circos: an information aesthetic for comparative genomics.

Authors:
Martin Krzywinski Jacqueline Schein Inanç Birol Joseph Connors Randy Gascoyne Doug Horsman Steven J Jones Marco A Marra

Genome Res 2009 Sep 18;19(9):1639-45. Epub 2009 Jun 18.

Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia V5Z 4S6, Canada.

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http://dx.doi.org/10.1101/gr.092759.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752132PMC
September 2009

ABySS: a parallel assembler for short read sequence data.

Authors:
Jared T Simpson Kim Wong Shaun D Jackman Jacqueline E Schein Steven J M Jones Inanç Birol

Genome Res 2009 Jun 27;19(6):1117-23. Epub 2009 Feb 27.

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada.

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http://dx.doi.org/10.1101/gr.089532.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694472PMC
June 2009

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Authors:
A Gordon Robertson Mikhail Bilenky Angela Tam Yongjun Zhao Thomas Zeng Nina Thiessen Timothee Cezard Anthony P Fejes Elizabeth D Wederell Rebecca Cullum Ghia Euskirchen Martin Krzywinski Inanc Birol Michael Snyder Pamela A Hoodless Martin Hirst Marco A Marra Steven J M Jones

Genome Res 2008 Dec 11;18(12):1906-17. Epub 2008 Sep 11.

BC Cancer Agency Genome Sciences Centre, Vancouver, Canada.

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http://dx.doi.org/10.1101/gr.078519.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593584PMC
December 2008

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

Authors:
Iman Hajirasouliha Fereydoun Hormozdiari S Cenk Sahinalp Inanc Birol

Bioinformatics 2008 Jul;24(13):i32-40

Lab for Computational Biology, Simon Fraser University, Burnaby, BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btn173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718651PMC
July 2008

Metabolic control analysis under uncertainty: framework development and case studies.

Authors:
Liqing Wang Inanç Birol Vassily Hatzimanikatis

Biophys J 2004 Dec 1;87(6):3750-63. Epub 2004 Oct 1.

Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60616, USA.

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http://dx.doi.org/10.1529/biophysj.104.048090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304888PMC
December 2004

Effect of environment partitioning on the survival and coexistence of autocatalytic replicators.

Authors:
Inanç Birol Satish J Parulekar Fouad Teymour

Phys Rev E Stat Nonlin Soft Matter Phys 2002 Nov 26;66(5 Pt 1):051916. Epub 2002 Nov 26.

Department of Chemical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA.

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http://dx.doi.org/10.1103/PhysRevE.66.051916DOI Listing
November 2002