Inanç Birol

Publication Activity (10 Years)

Years Active: 2003-2022
Publications (10 Years): 29

Top Topics

Top Venues

Publications

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) (2022)
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) (2022)
Parham Kazemi, Johnathan Wong, Vladimir Nikolic, Hamid Mohamadi, René L. Warren, Inanç Birol
ntHash2: recursive spaced seed hashing for nucleotide sequences. Bioinform. 38 (20) (2022)
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) (2021)
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) (2021)
Eric Chen, Justin Chu, Jessica Zhang, René L. Warren, Inanç Birol
GapPredict: A Language Model for Resolving Gaps in Draft Genome Assemblies. CoRR (2021)
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) (2021)
Readman Chiu, Ka Ming Nip, Inanç Birol
Fusion-Bloom: fusion detection in assembled transcriptomes. Bioinform. 36 (7) (2020)
Lauren Coombe, Vladimir Nikolic, Justin Chu, Inanç Birol, René L. Warren
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. Bioinform. 36 (12) (2020)
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) (2020)
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) (2020)
Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia C. F. Prosperi, Inanç Birol
Portable nanopore analytics: are we there yet? Bioinform. 36 (16) (2020)
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) (2019)
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) (2019)
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) (2018)
Inanç Birol, Hamid Mohamadi, Justin Chu
ntPack: A Software Package for Big Data in Genomics. BDCAT (2018)
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) (2018)
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) (2018)
Golnar Sheikhshab, Inanç Birol, Anoop Sarkar
In-domain Context-aware Token Embeddings Improve Biomedical Named Entity Recognition. Louhi@EMNLP (2018)
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)
Sarah Yeo, Lauren Coombe, René L. Warren, Justin Chu, Inanç Birol
ARCS: scaffolding genome drafts with linked reads. Bioinform. 34 (5) (2018)
Hamid Mohamadi, Hamza Khan, Inanç Birol
ntCard: a streaming algorithm for cardinality estimation in genomics data. Bioinform. 33 (9) (2017)
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) (2017)
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) (2017)
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) (2017)
Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Anoop Sarkar, Inanç Birol
Graph-based Semi-supervised Gene Mention Tagging. BioNLP@ACL (2016)
Djallel Bouneffouf, Inanç Birol
Theoretical analysis of the Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. IJCNN (2016)
Djallel Bouneffouf, Inanç Birol
Ensemble Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. IJCNN (2016)
Hamid Mohamadi, Justin Chu, Benjamin P. Vandervalk, Inanç Birol
ntHash: recursive nucleotide hashing. Bioinform. 32 (22) (2016)
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)
Djallel Bouneffouf, Inanç Birol
Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering. IJCAI (2015)
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 (2015)
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) (2014)
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)
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)
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
) genome from whole-genome shotgun sequencing data. Bioinform. 29 (12) (2013)
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 (2013)
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) (2012)
Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra
Hive plots - rational approach to visualizing networks. Briefings Bioinform. 13 (5) (2012)
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) (2011)
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) (2010)
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) (2010)
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) (2010)
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
transcriptome assembly with ABySS. Bioinform. 25 (21) (2009)
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) (2009)
Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB (2008)
Eric Tatara, Inanç Birol, Fouad Teymour, Ali Cinar
Agent-based control of autocatalytic replicators in networks of reactors. Comput. Chem. Eng. 29 (4) (2005)
Gülnur Birol, Inanç Birol, Betül Kirdar, Z. Ilsen Önsan
Investigating the fermentation dynamics structure of recombinant yeast YPB-G. Comput. Chem. Eng. 27 (1) (2003)