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Dr. Inanc Birol, PhD

Distinguished Scientist, Michael Smith Genome Sciences Centre, BC Cancer Agency
Professor, Department of Medical Genetics, University of British Columbia
Adjunct Professor, School of Computing Science, Simon Fraser University

Phone 604-707-5800
Fax 604-876-3561
Email ibirol@bcgsc.ca

Research

Dr. Inanc Birol is a Scientist at the British Columbia Cancer Agency in the Genome Sciences Centre, a Professor of Medical Genetics and an Adjunct Faculty of Computer Science at the University of British Columbia.

Dr. Birol’s research interests include the analysis of data from modern sequencing instruments to study genomes and transcriptomes of model species and humans. He directs the Bioinformatics Technology Lab, which develops bioinformatics tools for de novo sequence assembly, sequence mapping, downstream data analysis, and visualization. His lab website can be reached at birollab.ca.

 

Recent Publications

    Campbell LJ, Hammond SA, Price SJ, Sharma MD, Garner TWJ, Birol I, Helbing CC, Wilfert L, Griffiths AGF. A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations. Mol Ecol. 2018 Feb 8. doi: 10.1111/mec.14528. [Epub ahead of print] PMID: 29420865. 

    Khan H, Mohamadi H, Vandervalk BP, Warren RL, Chu J, Birol I. ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. Bioinformatics. 2017 Dec 29. doi: 10.1093/bioinformatics/btx839. [Epub ahead of print]. PMID: 29300846.

    Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Tse K, Li I, Cheung D, Mungall KL, Choo C, Ally A, Dhalla N, Tam AKY, Troussard A, Kirk H, Pandoh P, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Haulena M. The Genome of the Beluga Whale (Delphinapterus leucas). Genes (Basel). 2017 Dec 11;8(12). pii: E378. doi: 10.3390/genes8120378. PMID: 29232881.
     
    Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni). Genes (Basel).  2017 Dec 11;8(12). pii: E379. doi: 10.3390/genes8120379. PMID: 29232880.

    Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao Y, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I. The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7. PMID: 29127278.

    TCGA Research Network (including Inanc Birol & 170 collaborators). Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell. 2017 Oct 19;171(3):540-556.e25. doi: 10.1016/j.cell.2017.09.007. Epub 2017 Oct 5. PMID: 28988769.

    Hasan NA, Warren RL, Epperson LE, Malecha A, Alexander DC, Turenne CY, MacMillan D, Birol I, Pleasance S, Coope R, Jones SJM, Romney MG, Ng M, Chan T, Rodrigues M, Tang P, Gardy JL, Strong M. Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease. Genome Announc. 2017 Sep 14;5(37). pii: e00963-17. doi: 10.1128/genomeA.00963-17. PMID: 28912319.

    Kucuk E, Chu J, Vandervalk BP, Austin Hammond S, Warren RL, Birol I. Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics. 2017 Sep 1;33(17):2789. doi: 10.1093/bioinformatics/btx405. PMID: 28903539.

    Thibodeau ML, Steinraths M, Brown L, Zong Z, Shomer N, Taubert S, Mungall KL, Ma YP, Mueller R, Birol I, Lehman A. Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98. Cytogenet Genome Res. 2017 Aug 31. doi: 10.1159/000479463. PMID: 28854430.

    Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017 Aug 14;32(2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007. PMID: 28810144.
     
    Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell. 2017 Aug 14;32(2):204-220.e15. doi: 10.1016/j.ccell.2017.07.003. PMID: 28810145.

    Mohamadi H, Khan H, Birol I. ntCard: A streaming algorithm for cardinality estimation in genomics data. Bioinformatics. 2017 May 1 ;33(9):1324-1330. doi: 10.1093/bioinformatics/btw832. PMID: 28453674.

    Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. Plant J.  2017 Apr;90(1):189-203. doi: 10.1111/tpj.13478. PMID: 28090692.

    Chu J, Mohamadi H, Warren RL, Yang C, Birol I. Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. Bioinformatics. 2017 Apr 15;33(8):1261-1270. doi: 10.1093/bioinformatics/btw811. PMID: 28003261.

    Inanc Birol's Complete Publication List

    Education

    B.Sc., Electrical and Electronics Engineering, Bogazici University, Istanbul
    M.Sc., Systems and Control Engineering, Bogazici University, Istanbul
    Ph.D., Physics, Bogazici University, Istanbul