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ORCIDInanç Birol
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- affiliation: University of British Columbia, Department of Medical Genetics, Vancouver, Canada
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2020 – today
- 2022
[j36]Parham Kazemi
, Johnathan Wong, Vladimir Nikolic, Hamid Mohamadi, René L. Warren, Inanç Birol:
ntHash2: recursive spaced seed hashing for nucleotide sequences. Bioinform. 38(20): 4812-4813 (2022)- [j35]Vladimir Nikolic, Amirhossein Afshinfard, Justin Chu, Johnathan Wong, Lauren Coombe, Ka Ming Nip, René L. Warren, Inanç Birol:
RResolver: efficient short-read repeat resolution within ABySS. BMC Bioinform. 23(1): 246 (2022) - [j34]Vladimir Nikolic, Parham Kazemi, Lauren Coombe, Johnathan Wong, Amirhossein Afshinfard, Justin Chu, René L. Warren, Inanç Birol:
btllib: A C++ library with Python interface for efficient genomic sequence processing. J. Open Source Softw. 7(79): 4720 (2022) - 2021
- [j33]René L. Warren, Inanç Birol:
HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset. Bioinform. 36(21): 5271-5273 (2021) - [j32]Lauren Coombe, Janet X. Li, Theodora Lo, Johnathan Wong, Vladimir Nikolic, René L. Warren, Inanç Birol:
LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinform. 22(3): 534 (2021) - [j31]Eric Chen, Justin Chu, Jessica Zhang, René L. Warren, Inanç Birol:
GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2802-2808 (2021) - [i1]Eric Chen, Justin Chu, Jessica Zhang, René L. Warren, Inanç Birol:
GapPredict: A Language Model for Resolving Gaps in Draft Genome Assemblies. CoRR abs/2105.10552 (2021) - 2020
- [j30]Readman Chiu, Ka Ming Nip, Inanç Birol:
Fusion-Bloom: fusion detection in assembled transcriptomes. Bioinform. 36(7): 2256-2257 (2020) - [j29]Lauren Coombe, Vladimir Nikolic, Justin Chu, Inanç Birol, René L. Warren:
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. Bioinform. 36(12): 3885-3887 (2020) - [j28]Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia Prosperi, Inanç Birol:
Portable nanopore analytics: are we there yet? Bioinform. 36(16): 4399-4405 (2020) - [j27]Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín, Inanç Birol:
ENANO: Encoder for NANOpore FASTQ files. Bioinform. 36(16): 4506-4507 (2020) - [j26]Justin Chu, Hamid Mohamadi, Emre Erhan, Jeffery Tse, Readman Chiu, Sarah Yeo, Inanç Birol:
Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters. Proc. Natl. Acad. Sci. USA 117(29): 16961-16968 (2020)
2010 – 2019
- 2019
- [j25]René L. Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish, Nathalie Isabel, Steven J. M. Jones, Jean Bousquet, Jörg Bohlmann, Inanç Birol:
ntEdit: scalable genome sequence polishing. Bioinform. 35(21): 4430-4432 (2019) - [j24]Shaun D. Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O'Huiginn, Lance Bailey, Inanç Birol, Steven J. M. Jones:
ORCA: a comprehensive bioinformatics container environment for education and research. Bioinform. 35(21): 4448-4450 (2019) - 2018
- [j23]Sarah Yeo, Lauren Coombe, René L. Warren, Justin Chu, Inanç Birol:
ARCS: scaffolding genome drafts with linked reads. Bioinform. 34(5): 725-731 (2018) - [j22]Hamza Khan, Hamid Mohamadi, Benjamin P. Vandervalk, René L. Warren, Justin Chu, Inanç Birol:
ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. Bioinform. 34(10): 1697-1704 (2018) - [j21]Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, Inanç Birol, René L. Warren:
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. BMC Bioinform. 19(1): 234:1-234:10 (2018) - [j20]Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Benjamin P. Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Jörg Bohlmann, Steven J. M. Jones, Inanç Birol:
Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinform. 19(1): 393:1-393:10 (2018) - [c11]Golnar Sheikhshab, Inanç Birol, Anoop Sarkar:
In-domain Context-aware Token Embeddings Improve Biomedical Named Entity Recognition. Louhi@EMNLP 2018: 160-164 - [c10]Inanç Birol, Hamid Mohamadi, Justin Chu:
ntPack: A Software Package for Big Data in Genomics. BDCAT 2018: 41-50 - [c9]Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Readman Chiu, Anoop Sarkar, Inanç Birol:
GraphNER: Using Corpus Level Similarities and Graph Propagation for Named Entity Recognition. IPDPS Workshops 2018: 229-238 - 2017
- [j19]Justin Chu, Hamid Mohamadi, René L. Warren, Chen Yang, Inanç Birol:
Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. Bioinform. 33(8): 1261-1270 (2017) - [j18]Hamid Mohamadi, Hamza Khan, Inanç Birol:
ntCard: a streaming algorithm for cardinality estimation in genomics data. Bioinform. 33(9): 1324-1330 (2017) - [j17]Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol:
Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinform. 33(12): 1782-1788 (2017) - [j16]Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol:
Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinform. 33(17): 2789 (2017) - 2016
- [j15]Hamid Mohamadi, Justin Chu, Benjamin P. Vandervalk, Inanç Birol:
ntHash: recursive nucleotide hashing. Bioinform. 32(22): 3492-3494 (2016) - [c8]Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Anoop Sarkar, Inanç Birol:
Graph-based Semi-supervised Gene Mention Tagging. BioNLP@ACL 2016: 27-35 - [c7]Djallel Bouneffouf, Inanç Birol:
Ensemble Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. IJCNN 2016: 3851-3855 - [c6]Djallel Bouneffouf, Inanç Birol:
Theoretical analysis of the Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. IJCNN 2016: 3856-3862 - 2015
- [j14]Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman, Inanç Birol:
Sealer: a scalable gap-closing application for finishing draft genomes. BMC Bioinform. 16: 230:1-230:8 (2015) - [c5]Djallel Bouneffouf, Inanç Birol:
Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering. IJCAI 2015: 2313-2319 - [c4]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:
KLEAT: Cleavage Site Analysis of Transcriptomes. Pacific Symposium on Biocomputing 2015: 347-358 - 2014
- [j13]Justin Chu, Sara Sadeghi, Anthony Raymond, Shaun D. Jackman, Ka Ming Nip, Richard Mar, Hamid Mohamadi, Yaron S. N. Butterfield, A. Gordon Robertson, Inanç Birol:
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. Bioinform. 30(23): 3402-3404 (2014) - [c3]Inanç Birol, Hamid Mohamadi, Anthony Raymond, Karthika Raghavan, Justin Chu, Benjamin P. Vandervalk, Shaun D. Jackman, René L. Warren:
Spaced seed data structures. BIBM 2014: 15-22 - [c2]Benjamin P. Vandervalk, Shaun D. Jackman, Anthony Raymond, Hamid Mohamadi, Chen Yang, Dean A. Attali, Justin Chu, René L. Warren, Inanç Birol:
Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph. BIBM 2014: 51-58 - 2013
- [j12]Inanç 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:
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinform. 29(12): 1492-1497 (2013) - [j11]Alireza Hadj Khodabakhshi, Anthony P. Fejes, Inanç Birol, Steven J. M. Jones:
Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. BMC Bioinform. 14: 167 (2013) - 2012
- [j10]Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra:
Hive plots - rational approach to visualizing networks. Briefings Bioinform. 13(5): 627-644 (2012) - [j9]Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp:
Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinform. 28(12): 179-187 (2012) - 2011
- [j8]Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanç Birol, Steven J. M. Jones:
Human variation database: an open-source database template for genomic discovery. Bioinform. 27(8): 1155-1156 (2011) - 2010
- [j7]Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp:
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinform. 26(10): 1277-1283 (2010) - [j6]Steven J. M. Jones, Janessa Laskin, Yvonne Y. Li, Obi L. Griffith, Jianghong An, Mikhail Bilenky, Yaron S. N. 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, Inanç Birol, Martin Hirst, Robert A. Holt, Marco A. Marra:
Genomic analysis of a rare human tumor. BMC Bioinform. 11(S-4): O3 (2010) - [j5]R. T. F. Wong, Stephane Flibotte, Richard Corbett, Parvaneh Saeedi, Steven J. M. Jones, Marco A. Marra, Jacqueline E. Schein, Inanç Birol:
LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. IEEE Trans Autom. Sci. Eng. 7(3): 706-708 (2010)
2000 – 2009
- 2009
- [j4]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, Douglas E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Steven J. M. Jones:
De novo transcriptome assembly with ABySS. Bioinform. 25(21): 2872-2877 (2009) - [j3]Cydney B. Nielsen, Shaun D. Jackman, Inanç Birol, Steven J. M. Jones:
ABySS-Explorer: Visualizing Genome Sequence Assemblies. IEEE Trans. Vis. Comput. Graph. 15(6): 881-888 (2009) - 2008
- [c1]Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol:
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB 2008: 32-40 - 2005
- [j2]Eric Tatara, Inanç Birol, Fouad Teymour, Ali Cinar:
Agent-based control of autocatalytic replicators in networks of reactors. Comput. Chem. Eng. 29(4): 807-815 (2005) - 2003
- [j1]Gülnur Birol, Inanç Birol, Betül Kirdar, Z. Ilsen Önsan:
Investigating the fermentation dynamics structure of recombinant yeast YPB-G. Comput. Chem. Eng. 27(1): 45-54 (2003)
Coauthor Index
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