• Manuscript describing Physlr, a tool to generate next-generation physical maps of genomes, published today

  news  · 10 Jun 2022

  Our manuscript, published in the peer-reviewed journal DNA, presents Physlr, a tool that leverages long-range information provided by linked read sequencing technologies to construct next-generation physical maps. These maps have many potential applications in genome assembly and analysis, including, but not limited to, scaffolding. In our study, using experimental linked-read datasets from two humans, we used Physlr to construct...

• Scientific abstracts describing long sequencing read genome assembler GoldRush and data structure Stash, accepted for oral presentations at ISMB 2022

  conference  · 19 May 2022

  The 30th conference on Intelligent Systems for Molecular Biology (ISMB 2022) is taking place in Madison, WI (USA) July 10-14, 2022 and the BTL group will attend in person to showcase our work on de novo long read genome assembler with linear time complexity, GoldRush, and its key components (golden path algorithm GoldRush-Path, long read scaffolder GoldRush-Link and long...

• Manuscript describing the genome polishing protocol ntEdit+Sealer, just published

  news  · 14 May 2022

  Our manuscript, published in the peer-reviewed journal Current Protocols, presents a fast, scalable and memory-efficient methodology for targeted error resolution and automated finishing of long-read genome assemblies. The ntEdit+Sealer protocol, available on GitHub, was initially designed to polish (any) draft genome assemblies with short sequencing reads. It is being extended to also work with k-mers sourced from erroneous...

• Spruce weevil genome published

  news  · 04 Mar 2022

  In our peer-reviewed manuscript, just published in the journal G3: Genes, Genomes, Genetics, we present the nuclear and mitochondrial genomes and associated annotations of the forest insect pest Pissodes strobi, commonly known as the spruce weevil or white pine weevil, a major pest of spruce and pine forests in North America. We also describe the genome of an apparent...

• AMPlify, our machine learning method for predicting putative antimicrobial peptides is published

  news  · 25 Jan 2022

  In our peer-reviewed manuscript, just published in the journal BMC Genomics, we present a novel and robust attentive deep learning model, named AMPlify. In the research manuscript, we show how AMPlify was used to predict antimicrobial peptides (AMPs) from the Rana [Lithobates] catesbeiana (bullfrog) genome and demonstrate the bioactivity of these AMPs against multiple species of bacteria, including multi-drug...

• RNA-Scoop, our interactive visualization tool for transcripts in single-cell transcriptomes, published in NAR Genomics and Bioinformatics

  news  · 30 Nov 2021

  Our manuscript describing an interactive visualization tool for transcripts in single-cell transcriptomes, RNA-Scoop, was just published in NAR Genomics and Bioinformatics. In the manuscript, we show that RNA-Scoop allows users to examine differential transcript expression across clusters and investigate how usage of specific transcript expression mechanisms varies across cell groups. RNA-Scoop is freely available from GitHub.

• LongStitch, our pipeline for correcting and scaffolding genome assemblies using long reads, published in BMC Bioinformatics

  news  · 01 Nov 2021

  Our manuscript describing the newly developed long read correction and scaffolding pipeline, LongStitch, was just published in BMC Bioinformatics. LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively,...

• Manuscript reporting associations between COVID-19 disease severity and the human leukocyte antigen (HLA) published.

  news  · 15 Oct 2021

  In our peer-reviewed manuscript, just published in the journal PeerJ, we report on observations linking host HLA alleles with COVID-19 disease severity in a New York cohort, some of which (eg. C04:01 and HLA11:01) are corroborated by different research groups and in different COVID-19 patient cohort transcriptome data.

• Our peer-reviewed research on the application of deep learning approaches to the gap-filling problem in genome assembly (GapPredict) was just published

  news  · 07 Sep 2021

  In our peer-reviewed manuscript, just published in the journal IEEE-TCBB, we report on a novel application, GapPredict, for resolving gaps in genome sequence assemblies. This proof-of concept study demonstrates the practical utility of deep-learning machine learning models for this task.

• Manuscript describing Straglr, a tool for detecting tandem repeat expansion using long-read sequences, just published at Genome Biology

  news  · 13 Aug 2021

  Our manuscript describing Straglr, a tool for both targeted tandem repeat genotyping and novel expansion detection using long-read sequences, was just published in the peer-reviewed journal Genome Biology.

• Genome assembly repeat resolution, long read genome scaffolding & polishing, AMP discovery and SARS-CoV-2 variant time maps at ISMB/ECCB 2021

  conference  · 21 Jul 2021

  The joint 29th conference on Intelligent Systems for Molecular Biology and the 20th European Conference on Computational Biology (ISMB/ECCB 2021) meeting is held online July 25-30 and the BTL group is presenting several new bioinformatics technologies and analysis workflow developed by our lab. These include ABySS 2.5 genome assembly, LongStitch genome scaffolding, ntEdit/Sealer genome polishing,

• Interactive SARS-CoV-2 mutation timemaps, published at F1000research and available online

  news  · 01 Jan 2021

  A report describing our SARS-CoV-2 variant analysis and interactive SVG mutation maps freely available to the community for browsing and sharing was just published at F1000research. It was announced earlier at arXiv. The maps report nucleotide changes in over 2.5 million SARS-CoV-2 coronavirus genomes (and their effect on gene products) over time and in different continents and...

• 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.