Investigating the fermentation dynamics structure of recombinant yeast YPB-G. - Gülnur Birol; Inanç Birol; Betül Kirdar; Z. Ilsen Önsan (Comput. Chem. Eng., 2003)

Agent-based control of autocatalytic replicators in networks of reactors. - Eric Tatara; Inanç Birol; Fouad Teymour; Ali Cinar (Comput. Chem. Eng., 2005)

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. - Iman Hajirasouliha; Fereydoun Hormozdiari; Süleyman Cenk Sahinalp; Inanç Birol (ISMB, 2008)

De novo transcriptome assembly with ABySS. - Inanç Birol; Shaun D. Jackman; Cydney B. Nielsen; Jenny Q. Qian; Richard Varhol; Greg Stazyk; Ryan D. Morin; Yongjun Zhao 002; Martin Hirst; Jacqueline E. Schein; Douglas E. Horsman; Joseph M. Connors; et al. (Bioinform., 2009)

ABySS-Explorer: Visualizing Genome Sequence Assemblies. - Cydney B. Nielsen; Shaun D. Jackman; Inanç Birol; Steven J. M. Jones (IEEE Trans. Vis. Comput. Graph., 2009)

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. - Iman Hajirasouliha; Fereydoun Hormozdiari; Can Alkan; Jeffrey M. Kidd; Inanç Birol; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2010)

Genomic analysis of a rare human tumor. - 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; et al. (BMC Bioinform., 2010)

LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. - R. T. F. Wong; Stephane Flibotte; Richard Corbett; Parvaneh Saeedi; Steven J. M. Jones; Marco A. Marra; Jacqueline E. Schein; Inanç Birol (IEEE Trans Autom. Sci. Eng., 2010)

Human variation database: an open-source database template for genomic discovery. - Anthony P. Fejes; Alireza Hadj Khodabakhshi; Inanç Birol; Steven J. M. Jones (Bioinform., 2011)

Hive plots - rational approach to visualizing networks. - Martin Krzywinski; Inanç Birol; Steven J. M. Jones; Marco A. Marra (Briefings Bioinform., 2012)

Dissect: detection and characterization of novel structural alterations in transcribed sequences. - Deniz Yörükoglu; Faraz Hach; Lucas Swanson; Colin C. Collins; Inanç Birol; Süleyman Cenk Sahinalp (Bioinform., 2012)

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. - 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; et al. (Bioinform., 2013)

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. - Alireza Hadj Khodabakhshi; Anthony P. Fejes; Inanç Birol; Steven J. M. Jones (BMC Bioinform., 2013)

Spaced seed data structures. - Inanç Birol; Hamid Mohamadi; Anthony Raymond; Karthika Raghavan; Justin Chu; Benjamin P. Vandervalk; Shaun D. Jackman; René L. Warren (BIBM, 2014)

Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph. - Benjamin P. Vandervalk; Shaun D. Jackman; Anthony Raymond; Hamid Mohamadi; Chen Yang; Dean A. Attali; Justin Chu; René L. Warren; Inanç Birol (BIBM, 2014)

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. - 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 (Bioinform., 2014)

Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering. - Djallel Bouneffouf 001; Inanç Birol (IJCAI, 2015)

KLEAT: Cleavage Site Analysis of Transcriptomes. - 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 (Pacific Symposium on Biocomputing, 2015)

Sealer: a scalable gap-closing application for finishing draft genomes. - Daniel Paulino; René L. Warren; Benjamin P. Vandervalk; Anthony Raymond; Shaun D. Jackman; Inanç Birol (BMC Bioinform., 2015)

Graph-based Semi-supervised Gene Mention Tagging. - Golnar Sheikhshab; Elizabeth Starks; Aly Karsan; Anoop Sarkar; Inanç Birol (BioNLP@ACL, 2016)

Ensemble Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. - Djallel Bouneffouf 001; Inanç Birol (IJCNN, 2016)

Theoretical analysis of the Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. - Djallel Bouneffouf 001; Inanç Birol (IJCNN, 2016)

ntHash: recursive nucleotide hashing. - Hamid Mohamadi; Justin Chu; Benjamin P. Vandervalk; Inanç Birol (Bioinform., 2016)

Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. - Justin Chu; Hamid Mohamadi; René L. Warren; Chen Yang; Inanç Birol (Bioinform., 2017)

Kollector: transcript-informed, targeted de novo assembly of gene loci. - Erdi Kucuk; Justin Chu; Benjamin P. Vandervalk; S. Austin Hammond; René L. Warren; Inanç Birol (Bioinform., 2017)

ntCard: a streaming algorithm for cardinality estimation in genomics data. - Hamid Mohamadi; Hamza Khan; Inanç Birol (Bioinform., 2017)

In-domain Context-aware Token Embeddings Improve Biomedical Named Entity Recognition. - Golnar Sheikhshab; Inanç Birol; Anoop Sarkar (Louhi@EMNLP, 2018)

ntPack: A Software Package for Big Data in Genomics. - Inanç Birol; Hamid Mohamadi; Justin Chu (BDCAT, 2018)

GraphNER: Using Corpus Level Similarities and Graph Propagation for Named Entity Recognition. - Golnar Sheikhshab; Elizabeth Starks; Aly Karsan; Readman Chiu; Anoop Sarkar; Inanç Birol (IPDPS Workshops, 2018)

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. - Hamza Khan; Hamid Mohamadi; Benjamin P. Vandervalk; René L. Warren; Justin Chu; Inanç Birol (Bioinform., 2018)

ARCS: scaffolding genome drafts with linked reads. - Sarah Yeo; Lauren Coombe; René L. Warren; Justin Chu; Inanç Birol (Bioinform., 2018)

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. - Lauren Coombe; Jessica Zhang; Benjamin P. Vandervalk; Justin Chu; Shaun D. Jackman; Inanç Birol; René L. Warren (BMC Bioinform., 2018)

Tigmint: correcting assembly errors using linked reads from large molecules. - 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 (BMC Bioinform., 2018)

ORCA: a comprehensive bioinformatics container environment for education and research. - Shaun D. Jackman; Tatyana Mozgacheva; Susie Chen; Brendan O'Huiginn; Lance Bailey; Inanç Birol; Steven J. M. Jones (Bioinform., 2019)

ntEdit: scalable genome sequence polishing. - René L. Warren; Lauren Coombe; Hamid Mohamadi; Jessica Zhang; Barry Jaquish; Nathalie Isabel; Steven J. M. Jones; Jean Bousquet; Jörg Bohlmann; Inanç Birol (Bioinform., 2019)

ENANO: Encoder for NANOpore FASTQ files. - Guillermo Dufort y Álvarez; Gadiel Seroussi; Pablo Smircich; José Sotelo; Idoia Ochoa; Álvaro Martín; Inanç Birol (Bioinform., 2020)

Fusion-Bloom: fusion detection in assembled transcriptomes. - Readman Chiu; Ka Ming Nip; Inanç Birol (Bioinform., 2020)

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. - Lauren Coombe; Vladimir Nikolic; Justin Chu; Inanç Birol; René L. Warren (Bioinform., 2020)

Portable nanopore analytics: are we there yet? - Marco Oliva; Franco Milicchio; Kaden King; Grace Benson; Christina Boucher 001; Mattia Prosperi; Inanç Birol (Bioinform., 2020)

Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters. - Justin Chu; Hamid Mohamadi; Emre Erhan; Jeffery Tse; Readman Chiu; Sarah Yeo; Inanç Birol (Proc. Natl. Acad. Sci. USA, 2020)

HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset. - René L. Warren; Inanç Birol (Bioinform., 2021)

LongStitch: high-quality genome assembly correction and scaffolding using long reads. - Lauren Coombe; Janet X. Li; Theodora Lo; Johnathan Wong; Vladimir Nikolic; René L. Warren; Inanç Birol (BMC Bioinform., 2021)

GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies. - Eric Chen; Justin Chu; Jessica Zhang; René L. Warren; Inanç Birol (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

RResolver: efficient short-read repeat resolution within ABySS. - Vladimir Nikolic; Amirhossein Afshinfard; Justin Chu; Johnathan Wong; Lauren Coombe; Ka Ming Nip; René L. Warren; Inanç Birol (BMC Bioinform., 2022)

ntHash2: recursive spaced seed hashing for nucleotide sequences. - Parham Kazemi; Johnathan Wong; Vladimir Nikolic; Hamid Mohamadi; René L. Warren; Inanç Birol (Bioinform., 2022)

btllib: A C++ library with Python interface for efficient genomic sequence processing. - Vladimir Nikolic; Parham Kazemi; Lauren Coombe; Johnathan Wong; Amirhossein Afshinfard; Justin Chu; René L. Warren; Inanç Birol (J. Open Source Softw., 2022)

GoldPolish-target: targeted long-read genome assembly polishing. - Emily Zhang; Lauren Coombe; Johnathan Wong; René L. Warren; Inanç Birol (BMC Bioinform., 2025)