RenéWarren.ca
ACCOLADES
2019 -resource- Scalable de novo genome assembly
2018 -resource- Genome Assembly Toolkit
2016 - SSAKE manuscript cited over 500 times
2015 - Speaker/Mentor at BC Student Biotech Network SBN
2011 - Fuso discovery on TIME magazine's top ten medical breakthroughs of the year
2011 - Interviewed with newspaper for Fusobacterium discovery
2011 - Interviewed with TV channel for Fusobacterium discovery
2009 - Interviewed with The Scientist for work on profiling T cell metagenomes
2009 - SSAKE packaged in the Debian operating system
2009 - SSAKE short-listed in the editorial of the scientific journal Bioinformatics
2008 - One of 6 experts invited to discuss NGS bioinformatics
2006|14 - SSAKE one of four 3rd-party genomics application recommended by Illumina Ltd.
2008 - SSAKE recognized by Russ Altman, MD PhD as one of 27 publication with most impact
2007 - Interviewed by GenomeWeb for the release of SSAKE
2002|04 - Interviewed with french CBC about the GSC and bovine genome release
2004 - 'faculty of 1000' recognizes paper "Warren et al. 2004. Functional characterization.."
2001 - Engineered a gene switch (BRI-NRC) - work was patented, sold to QBIOgene
1998 - Awarded University of British Columbia Graduate Fellowship (UGF)
1997 - Recipient of excellence award from the FRSQ for Honor's thesis
1996 - Scholarship recipient from Fonds de la recherche en sante Quebec (FRSQ)
1995 - Worked at NASA with the purpose of crystallizing proteins under microgravity
PUBLICATIONS
2019 -meeting- ISMB, Basel - ntEdit: scalable genome sequence polishing
2019 -paper- Complete chloroplast genome sequence of an Engelmann spruce from western Canada
2019 -paper- Complete chloroplast genome sequence of a white spruce from eastern Canada
2019 -paper- ntEdit: scalable genome sequence polishing
2019 -paper- Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identifcation of novel forms from tadpoles
2018 -paper- Tigmint: correcting assembly errors using linked reads from large molecules
2018 -paper- Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes
2018 -paper- ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
2018 -meeting- RECOMB, Paris - Chromosome-scale scaffolding human genomes with linked read kmers
2018 -paper- Visualizing genome synteny with xmatchview
2018 -paper- ChopStitch: exon annotation and splice graph construction
2017 -paper- The Genome of the Northern Sea Otter
2017 -paper- The Genome of the Beluga Whale
2017 -paper- The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
2017 -paper- Complete Genome Sequence of Mycobacterium chimaera SJ42
2017 -paper- ARCS: Scaffolding Genome Drafts with Linked Reads
2017 -talk- RECOMB-Seq, Hong Kong - Scaffolding with linked reads
2017 -paper- NanoSim: nanopore sequence read simulator based on statistical characterization
2017 -paper- Kollector: transcript-informed, targeted de novo assembly of gene loci
2017 -paper- Innovations and challenges in detecting long read overlaps
2016 -paper- RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences
2016 -meeting- ASHG, Vancouver Canada - HLAminer
2016 -paper- ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter
2016 -paper- Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10x Genomics GemCode Sequencing Data
2016 -paper- XLF deficiency affects TCR V(D)J recombination
2016 -talk- ISMB2016, Orlando, Florida USA - Genome Assembly Toolkit
2015 -paper- Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation
2015 -paper- Konnector v2.0: pseudo-long reads from paired-end sequencing data
2015 -paper- Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism
2015 -paper- LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads
2015 -paper- Sealer: a scalable gap-closing application for finishing draft genomes
2015 -paper- Spaced Seed Data Structures for De Novo Assembly
2015 -paper- Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma
2015 -talk- ISMB2015, Dublin, Ireland - Scaffolding Genome Assemblies with Nanopore Reads
2015 -meeting- Pacific Symposium on Biocomputing, Hawaii, USA - High-Performance Computing for Assembly and Analysis of Big Genomics Data
2015 -paper- Sequencing the human IG light chain
2014 -paper- Konnector: Connecting paired-end reads using a Bloom filter de Bruijn graph
2014 -paper- Spaced seed data structures
2014 -paper- Neo-antigens from tumor genome meta-analysis correlate with survival
2013 -paper- Co-occurrence of anaerobic bacteria in colorectal carcinomas
2013 -paper- Brain microbial populations in HIV/AIDS: α-proteobacteria predominate independent of host immune status
2013 -paper- Complete haplotype sequence of human IgH
2012 -paper- Derivation of HLA types from shotgun sequence datasets
2012 -meeting- Pacific Symposium on Biocomputing, Hawaii, USA - Computational HLA prediction
2012 -patent- Fusobacterium for colon cancer diagnosis
2012 -paper- Fusobacterium infection is prevalent in human colorectal carcinoma
2011 -paper- Identifying microbes with short reads
2011 -paper- Targeted Assembly of Sequence Reads
2011 -paper- HERV expression in brain
2011 -paper- Exhaustive T cell Repertoire Sequencing
2011 -paper- Genome Variation in Cryptococcus gattii
2010 -talk- SFAF2010, Santa Fe, USA - Sequencing human IgH from H.mole
2010 -paper- A census of predicted mutational epitopes
2009 -paper- Mutational evolution in a lobular breast tumour
2009 -paper- Profiling the T-cell receptor beta-chain
2009 -paper- Unique parameter for separation of biomolecules
2009 -meeting- AGBT, Florida, USA - Profiling model TCRb
2009 -meeting- AGBT, Florida, USA - SSAKE 3.2.1
2009 -paper- Profiling model T cell metagenomes
2008 -paper- Transcription of foreign DNA in Escherichia coli
2008 -paper- Constructing large DNA segments by clone recombination
2008 -meeting- Pacific Symposium on Biocomputing, Hawaii, USA - SSAKE 3.0
2007 -talk- Synthetic Biology 3.0, Zurich, Switzerland -Genome reconstruction
2007 -paper- Rebuilding microbial genomes
2007 -paper- Assembling millions of short DNA sequences using SSAKE
2006 -paper- The Cumate gene-switch
2006 -paper- Analysis of the prostate cancer cell line LNCaP transcriptome
2006 -paper- THOR: Targeted high-throughput ortholog reconstructor
2006 -paper- The complete genome of Rhodococcus sp. RHA1
2006 -paper- Physical map-assisted WGSS assemblies
2006 -paper- Mating factor linkage and genome evolution in pathogens of cereals
2005 -paper- Management of WGSS assemblies using SAM
2005 -meeting- Genome Informatics, CSHL NY
2004 -paper- Characterization of a catabolic plasmid from Rhodococcus RHA1
2004 -meeting- Computational Genomics, VA USA - Rhodococcus WGA
2004 -meeting- Genomes 2004, Hinxton UK - WGA of Rhodococcus sp. RHA1
2003 -meeting- Genome Informatics, CSHL NY
2002 -paper- Regulation of the rod photoreceptor cGMP channel
2000 -paper- Biochemical analysis of cGMP channels of rods
1999 -paper- cGMP channels and peripherin complex of rod cells
1999 -thesis- Insights on the regulation of the rod cgmp-gated channel in vision
1997 -paper- The cardiac transcription factors Nkx2-5+GATA-4 are cofactors