• Our report on the HLA profiles of COVID-19 patients at the early stage of the 2020 pandemic, now published in Bioinformatics

    news  · 27 Aug 2020

    Our Letter to the Editor, just published in the peer-reviewed journal Bioinformatics, reports on the HLA profiles derived from the metatranscriptomic RNA-Seq samples of eight COVID-19 patients at the pandemic onset. Our study highlights the central role of HLA in vaccine development and host immunity in the current context, and adds perspective to host susceptibility to SARS-CoV-2, the coronavirus...

  • Manuscript describing RNA-Bloom, single-cell transcriptome assembler, just published at Genome Research

    news  · 17 Aug 2020

    Our study describing RNA-Bloom, a utility for reference-free and reference-guided sequence assembly of single-cell transcriptomes, was just published in the peer-reviewed journal Genome Research.

  • Multiindex Bloom Filter (miBF) data structure manuscript published in PNAS

    news  · 08 Jul 2020

    Our manuscript describing miBF, a probabilistic data structure we developed for alignment-free sequence classification tasks, was published in PNAS. Alignment-free methods, including miBF, have applications ranging from transcript expression analysis, metagenome characterization, to de novo assembly to name a few. They are usually faster than alignment-based methods, but often limited in their sensitivity and memory requirements. In the manuscript...

  • Meta-NanoSim, ntJoin, Physlr, RNA-Scoop and RResolver at ISMB 2020

    conference  · 01 Jul 2020

    The annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2020) is held online July 13-16 and the BTL group will be there, presenting several new bioinformatics technologies developed by our lab and including Meta-NanoSim, ntJoin, Physlr, RNA-Scoop and RResolver.

  • Transcriptome long read simulator trans-NanoSim published in GigaScience

    news  · 10 Jun 2020

    This is our second publication on the NanoSim tool, describing a functionality to simulate nanopore reads for transcriptome sequencing experiments. Trans-NanoSim was published in GigaScience and is an integral part of the NanoSim project, freely available from GitHub.

  • P. sitchensis (Sitka spruce) mitonchondrial genome published in Genome Biology and Evolution

    news  · 25 May 2020

    Our study describing the genome sequencing of the Sitka spruce mitochondrial genome was accepted for publication in Genome Biology and Evolution. In the manuscript we present the complete 5.5 Mb genome, one of the largest mitochondrial genome of a gymnosperm, assembled from Oxford Nanopore long reads and describe its complex physical structure.

  • Reference-guided scaffolder ntJoin published in Bioinformatics

    news  · 04 May 2020

    Our manuscript describing ntJoin, a fast and lightweight reference-guided scaffolder, was published in Bioinformatics. Instead of alignments, ntJoin uses a mapping approach based on a graph data structure generated from ordered minimizer sketches. ntJoin can be used in a variety of different research applications, including improving a draft assembly with a reference-grade genome, a short-read assembly with a draft...

  • Manuscript describing FusionBloom for detecting transcript fusions, just published

    news  · 02 Dec 2019

    Our study describing FusionBloom, a utility for detecting transcript fusions with utility in cancer diagnostics, was just published in the peer-reviewed journal Bioinformatics.

  • Spruce chloroplast genome manuscripts published

    news  · 06 Jun 2019

    Two studies reporting on the complete chloroplast genomes and gene annotations of white and Engelmann spruce are now published in the peer-reviewed journal Microbiology Resource Announcements.

  • Manuscript describing our fast genome polishing tool ntEdit published

    news  · 16 May 2019

    Our study describing ntEdit, a fast and scalable technology to polish and ‘haploidize’ genome sequences, was just published in the peer-reviewed journal Bioinformatics.

  • Bioinformatics container environment for education and research (ORCA), published

    news  · 20 Apr 2019

    We introduce ORCA, a Docker image with hundreds of bioinformatics tools/dependencies, simplifying software installs. ORCA was recently published in the peer-reviewed journal Bioinformatics.

  • Study on bullfrog antimicrobial peptides discovery published

    news  · 06 Feb 2019

    Our latest work on antimicrobial peptide (AMP) discovery in bullfrogs was just published in the peer-reviewed journal Scientific Reports The paper describes the AMP discovery bioinformatics pipeline and functional assays to test their efficacy against microbes.

  • Genome misassembly correction using linked reads (tigmint), published

    news  · 26 Oct 2018

    Our study presenting Tigmint, a bioinformatics utility to detect and correct errors in genome assemblies using linked reads is published in the peer-reviewed journal BMC Bioinformatics.

  • ARKS, linked read kmer genome scaffolder, published

    news  · 20 Jun 2018

    Our latest genome assembly scaffolder, ARKS, was just published in the peer-reviewed journal BMC bioinformatics The paper describes a new read alignment-free methodology that employs kmer-based read mapping and improves assembly runtime. In the paper we present benchmarks on human genome draft assemblies and show how linked reads can improve drafts assembled with the same sequencing data further.

  • Research Programmer (C++) position available

    jobs  · 15 Jun 2018

    The Research Programmer: •Develops and implements new algorithms •Works with the BTL’s large C/C++ code base (improve existing modules, create new ones, etc.) •Works on complex biological problems in which analysis of sequence data requires in-depth evaluation More info available here

  • ABySS 2.0, Tigmint, ARKS, and Bloom Filters at RECOMB-Seq

    conference  · 19 Apr 2018

    RECOMB 2018 will be taking place in Paris, France, from April 21-24th. RECOMB-Seq is one of its four satellite workshops this year, taking place from April 19-20th, bringing together researchers in computational genomics and bioinformatics to discuss new frontiers in gene sequencing.