René L. Warren

Publication Activity (10 Years)

Years Active: 2007-2022
Publications (10 Years): 19

Top Topics

Cognitive Apprenticeship

Top Venues

J. Open Source Softw.

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)
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)
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)
René L. Warren
Visualizing genome synteny with xmatchview. J. Open Source Softw. 3 (21) (2018)
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)
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)
Sarah Yeo, Lauren Coombe, René L. Warren, Justin Chu, Inanç Birol
ARCS: scaffolding genome drafts with linked reads. Bioinform. 34 (5) (2018)
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)
René L. Warren
RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences. J. Open Source Softw. 1 (7) (2016)
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)
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)
Daniele D'Agostino, Ivan Merelli, René L. Warren, Alessandro Guffanti, Luciano Milanesi, Andrea Clematis
Parallelization of the SSAKE Genomics Application. PDP (2011)
René L. Warren, Brad H. Nelson, Robert A. Holt
Profiling model T-cell metagenomes with short reads. Bioinform. 25 (4) (2009)
Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones
THOR: targeted high-throughput ortholog reconstructor. Bioinform. 23 (19) (2007)
René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt
Assembling millions of short DNA sequences using SSAKE. Bioinform. 23 (4) (2007)