Inanç Birol

49 papers A* 1A 1B 2C 1Misc 1Journal 38Unranked 5
YearRankTypeTitle / Venue / Authors
2026 J jnl
ntStat: k-mer characterization using occurrence statistics in raw sequencing data.
PLoS Comput. Biol.
Parham Kazemi, Lauren Coombe, René L. Warren, Inanç Birol
2025 J jnl
GoldPolish-target: targeted long-read genome assembly polishing.
BMC Bioinform.
Emily Zhang, Lauren Coombe, Johnathan Wong, René L. Warren, Inanç Birol
2022 J jnl
RResolver: efficient short-read repeat resolution within ABySS.
BMC Bioinform.
Vladimir Nikolic, Amirhossein Afshinfard, Justin Chu, Johnathan Wong, Lauren Coombe, Ka Ming Nip, René L. Warren, Inanç Birol
2022 J jnl
btllib: A C++ library with Python interface for efficient genomic sequence processing.
J. Open Source Softw.
Vladimir Nikolic, Parham Kazemi, Lauren Coombe, Johnathan Wong, Amirhossein Afshinfard, Justin Chu, René L. Warren, Inanç Birol
2022 J jnl
ntHash2: recursive spaced seed hashing for nucleotide sequences.
Bioinform.
Parham Kazemi, Johnathan Wong, Vladimir Nikolic, Hamid Mohamadi, René L. Warren, Inanç Birol
2021 J jnl
GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies.
IEEE ACM Trans. Comput. Biol. Bioinform.
Eric Chen, Justin Chu, Jessica Zhang, René L. Warren, Inanç Birol
2021 J jnl
GapPredict: A Language Model for Resolving Gaps in Draft Genome Assemblies.
CoRR
Eric Chen, Justin Chu, Jessica Zhang, René L. Warren, Inanç Birol
2021 J jnl
HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset.
Bioinform.
René L. Warren, Inanç Birol
2021 J jnl
LongStitch: high-quality genome assembly correction and scaffolding using long reads.
BMC Bioinform.
Lauren Coombe, Janet X. Li, Theodora Lo, Johnathan Wong, Vladimir Nikolic, René L. Warren, Inanç Birol
2020 J jnl
ENANO: Encoder for NANOpore FASTQ files.
Bioinform.
Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín, Inanç Birol
2020 J jnl
Fusion-Bloom: fusion detection in assembled transcriptomes.
Bioinform.
Readman Chiu, Ka Ming Nip, Inanç Birol
2020 J jnl
Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters.
Proc. Natl. Acad. Sci. USA
Justin Chu, Hamid Mohamadi, Emre Erhan, Jeffery Tse, Readman Chiu, Sarah Yeo, Inanç Birol
2020 J jnl
Portable nanopore analytics: are we there yet?
Bioinform.
Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia Prosperi, Inanç Birol
2020 J jnl
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs.
Bioinform.
Lauren Coombe, Vladimir Nikolic, Justin Chu, Inanç Birol, René L. Warren
2019 J jnl
ORCA: a comprehensive bioinformatics container environment for education and research.
Bioinform.
Shaun D. Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O'Huiginn, Lance Bailey, Inanç Birol, Steven J. M. Jones
2019 J jnl
ntEdit: scalable genome sequence polishing.
Bioinform.
René L. Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish, Nathalie Isabel, Steven J. M. Jones, Jean Bousquet, Jörg Bohlmann, Inanç Birol
2018 J jnl
ARCS: scaffolding genome drafts with linked reads.
Bioinform.
Sarah Yeo, Lauren Coombe, René L. Warren, Justin Chu, Inanç Birol
2018 J jnl
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.
BMC Bioinform.
Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, Inanç Birol, René L. Warren
2018 J jnl
ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.
Bioinform.
Hamza Khan, Hamid Mohamadi, Benjamin P. Vandervalk, René L. Warren, Justin Chu, Inanç Birol
2018 — conf
GraphNER: Using Corpus Level Similarities and Graph Propagation for Named Entity Recognition.
IPDPS Workshops
Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Readman Chiu, Anoop Sarkar, Inanç Birol
2018 — conf
In-domain Context-aware Token Embeddings Improve Biomedical Named Entity Recognition.
Louhi@EMNLP
Golnar Sheikhshab, Inanç Birol, Anoop Sarkar
2018 J jnl
Tigmint: correcting assembly errors using linked reads from large molecules.
BMC Bioinform.
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
2018 C conf
ntPack: A Software Package for Big Data in Genomics.
BDCAT
Inanç Birol, Hamid Mohamadi, Justin Chu
2017 J jnl
Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art.
Bioinform.
Justin Chu, Hamid Mohamadi, René L. Warren, Chen Yang, Inanç Birol
2017 J jnl
Kollector: transcript-informed, targeted de novo assembly of gene loci.
Bioinform.
Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol
2017 J jnl
Kollector: transcript-informed, targeted de novo assembly of gene loci.
Bioinform.
Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol
2017 J jnl
ntCard: a streaming algorithm for cardinality estimation in genomics data.
Bioinform.
Hamid Mohamadi, Hamza Khan, Inanç Birol
2016 B conf
Ensemble Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering.
IJCNN
Djallel Bouneffouf, Inanç Birol
2016 — conf
Graph-based Semi-supervised Gene Mention Tagging.
BioNLP@ACL
Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Anoop Sarkar, Inanç Birol
2016 B conf
Theoretical analysis of the Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering.
IJCNN
Djallel Bouneffouf, Inanç Birol
2016 J jnl
ntHash: recursive nucleotide hashing.
Bioinform.
Hamid Mohamadi, Justin Chu, Benjamin P. Vandervalk, Inanç Birol
2015 Misc conf
KLEAT: Cleavage Site Analysis of Transcriptomes.
Pacific Symposium on Biocomputing
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
2015 A* conf
Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering.
IJCAI
Djallel Bouneffouf, Inanç Birol
2015 J jnl
Sealer: a scalable gap-closing application for finishing draft genomes.
BMC Bioinform.
Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman, Inanç Birol
2014 J jnl
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.
Bioinform.
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
2014 — conf
Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph.
BIBM
Benjamin P. Vandervalk, Shaun D. Jackman, Anthony Raymond, Hamid Mohamadi, Chen Yang, Dean A. Attali, Justin Chu, René L. Warren, Inanç Birol
2014 — conf
Spaced seed data structures.
BIBM
Inanç Birol, Hamid Mohamadi, Anthony Raymond, Karthika Raghavan, Justin Chu, Benjamin P. Vandervalk, Shaun D. Jackman, René L. Warren
2013 J jnl
Assembling the 20 Gb white spruce (
Bioinform.
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
2013 J jnl
Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline.
BMC Bioinform.
Alireza Hadj Khodabakhshi, Anthony P. Fejes, Inanç Birol, Steven J. M. Jones
2012 J jnl
Dissect: detection and characterization of novel structural alterations in transcribed sequences.
Bioinform.
Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp
2012 J jnl
Hive plots - rational approach to visualizing networks.
Briefings Bioinform.
Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra
2011 J jnl
Human variation database: an open-source database template for genomic discovery.
Bioinform.
Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanç Birol, Steven J. M. Jones
2010 J jnl
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
Bioinform.
Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp
2010 J jnl
Genomic analysis of a rare human tumor.
BMC Bioinform.
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
2010 J jnl
LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images.
IEEE Trans Autom. Sci. Eng.
R. T. F. Wong, Stephane Flibotte, Richard Corbett, Parvaneh Saeedi, Steven J. M. Jones, Marco A. Marra, Jacqueline E. Schein, Inanç Birol
2009 J jnl
ABySS-Explorer: Visualizing Genome Sequence Assemblies.
IEEE Trans. Vis. Comput. Graph.
Cydney B. Nielsen, Shaun D. Jackman, Inanç Birol, Steven J. M. Jones
2008 A conf
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.
ISMB
Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol
2005 J jnl
Agent-based control of autocatalytic replicators in networks of reactors.
Comput. Chem. Eng.
Eric Tatara, Inanç Birol, Fouad Teymour, Ali Cinar
2003 J jnl
Investigating the fermentation dynamics structure of recombinant yeast YPB-G.
Comput. Chem. Eng.
Gülnur Birol, Inanç Birol, Betül Kirdar, Z. Ilsen Önsan