René L. Warren

According to our database, René L. Warren authored at least 24 papers between 2007 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

GoldPolish-target: targeted long-read genome assembly polishing.

Emily Zhang, Lauren Coombe, Johnathan Wong, René L. Warren, Inanç Birol

BMC Bioinform., December, 2025

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., November, 2022

ntHash2: recursive spaced seed hashing for nucleotide sequences.

Parham Kazemi, Johnathan Wong, Vladimir Nikolic, Hamid Mohamadi, René L. Warren, Inanç Birol

Bioinform., October, 2022

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

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

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

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

2020

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs.

Lauren Coombe, Vladimir Nikolic, Justin Chu, Inanç Birol, René L. Warren

Bioinform., 2020

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

2018

Visualizing genome synteny with xmatchview.

René L. Warren

J. Open Source Softw., 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

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

ARCS: scaffolding genome drafts with linked reads.

Sarah Yeo, Lauren Coombe, René L. Warren, Justin Chu, Inanç Birol

Bioinform., 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

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

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

2016

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences.

René L. Warren

J. Open Source Softw., 2016

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

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

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

Spaced seed data structures.

Inanç Birol, Hamid Mohamadi, Anthony Raymond, Karthika Raghavan, Justin Chu, Benjamin P. Vandervalk, Shaun D. Jackman, René L. Warren

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2011

Parallelization of the SSAKE Genomics Application.

Daniele D'Agostino, Ivan Merelli, René L. Warren, Alessandro Guffanti, Luciano Milanesi, Andrea Clematis

Proceedings of the 19th International Euromicro Conference on Parallel, 2011

2009

Profiling model T-cell metagenomes with short reads.

René L. Warren, Brad H. Nelson, Robert A. Holt

Bioinform., 2009

2007

Assembling millions of short DNA sequences using SSAKE.

René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt

Bioinform., 2007

THOR: targeted high-throughput ortholog reconstructor.

Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones

Bioinform., 2007