THOR: targeted high-throughput ortholog reconstructor. - Matthew N. Bainbridge; René L. Warren; An He; Mikhail Bilenky; Gordon Robertson; Steven J. M. Jones (Bioinform., 2007)

Assembling millions of short DNA sequences using SSAKE. - René L. Warren; Granger G. Sutton; Steven J. M. Jones; Robert A. Holt (Bioinform., 2007)

Profiling model T-cell metagenomes with short reads. - René L. Warren; Brad H. Nelson; Robert A. Holt (Bioinform., 2009)

Parallelization of the SSAKE Genomics Application. - Daniele D'Agostino; Ivan Merelli; René L. Warren; Alessandro Guffanti; Luciano Milanesi; Andrea Clematis (PDP, 2011)

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)

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)

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences. - René L. Warren (J. Open Source Softw., 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)

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)

Visualizing genome synteny with xmatchview. - René L. Warren (J. Open Source Softw., 2018)

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)

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