René L. Warren

27 papers C 1Journal 24Unranked 2
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
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
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 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 J jnl
Visualizing genome synteny with xmatchview.
J. Open Source Softw.
René L. Warren
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
2016 J jnl
RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences.
J. Open Source Softw.
René L. Warren
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 — 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
2011 C conf
Parallelization of the SSAKE Genomics Application.
PDP
Daniele D'Agostino, Ivan Merelli, René L. Warren, Alessandro Guffanti, Luciano Milanesi, Andrea Clematis
2009 J jnl
Profiling model T-cell metagenomes with short reads.
Bioinform.
René L. Warren, Brad H. Nelson, Robert A. Holt
2007 J jnl
Assembling millions of short DNA sequences using SSAKE.
Bioinform.
René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt
2007 J jnl
THOR: targeted high-throughput ortholog reconstructor.
Bioinform.
Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones