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View article: Accurate hybrid plasmids assembly with HyPlAs
Accurate hybrid plasmids assembly with HyPlAs Open
Summary The increasing availability of hybrid sequencing datasets comprising both short and long reads, is radically transforming microbial genomics, with the prospect of obtaining routinely near-complete bacterial genome assemblies. Howev…
View article: On the size of the neighborhoods of a word
On the size of the neighborhoods of a word Open
The d-neighborhood of a word W in the Levenshtein distance is the set of all words at distance at most d from W. Generating the neighborhood of a word W, or related sets of words such as the condensed neighborhood or the super-condensed ne…
View article: Pangebin: improving plasmid binning in bacterial isolates using pangenome-assembly graphs
Pangebin: improving plasmid binning in bacterial isolates using pangenome-assembly graphs Open
Short-read genome assemblies typically consist of many contigs of variable lengths and their putative connections represented as an assembly graph. Assembly graphs produced by different tools from the same data may differ significantly, po…
View article: A vector representation for phylogenetic trees
A vector representation for phylogenetic trees Open
Good representations for phylogenetic trees and networks are important for enhancing storage efficiency and scalability for the inference and analysis of evolutionary trees for genes, genomes and species. We propose a new representation fo…
View article: Undesignable motifs in structural RNAs and combinatorial consequences
Undesignable motifs in structural RNAs and combinatorial consequences Open
International audience
View article: Plaseval: a framework for comparing and evaluating plasmid detection tools
Plaseval: a framework for comparing and evaluating plasmid detection tools Open
Background Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active r…
View article: A Vector Representation for Phylogenetic Trees
A Vector Representation for Phylogenetic Trees Open
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We introdu…
View article: PlasEval: a framework for comparing and evaluating plasmid detection tools
PlasEval: a framework for comparing and evaluating plasmid detection tools Open
Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research are…
View article: TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator Open
Motivation Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools have been developed to tackle various transcriptomic sequencing tasks (e.g. isoform and gene …
View article: plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph
plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph Open
Identification of plasmids from sequencing data is an important and challenging problem related to antimicrobial resistance spread and other One-Health issues. We provide a new architecture for identifying plasmid contigs in fragmented gen…
View article: TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator Open
Motivation Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools have been developed to tackle various transcriptomic sequencing tasks (e.g. isoform and gene …
View article: PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning Open
Motivation The analysis of bacterial isolates to detect plasmids is important due to their role in the propagation of antimicrobial resistance. In short-read sequence assemblies, both plasmids and bacterial chromosomes are typically split …
View article: PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning
PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning Open
PlasBin-flow is a method for detecting plasmid contigs bins from the assembly graph for a given bacterial sample. The method is based on a Mixed-Integer Linear Programming (MILP) formulation. The data shared consists of output files of Pla…
View article: PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning
PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning Open
PlasBin-flow is a method for detecting plasmid contigs bins from the assembly graph for a given bacterial sample. The method is based on a Mixed-Integer Linear Programming (MILP) formulation. The data shared consists of output files of Pla…
View article: Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing Open
Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective targ…
View article: plASgraph - using graph neural networks to detect plasmid contigs from an assembly graph
plASgraph - using graph neural networks to detect plasmid contigs from an assembly graph Open
Identification of plasmids from sequencing data is an important and challenging problem related to antimicrobial resistance spread and other One-Health issues. In our work, we provide a new architecture for identifying plasmid contigs in f…
View article: scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments
scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments Open
Summary Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level. However, because of its use of short-reads, it is severely limited at detecting full-length features of transcripts such as …
View article: Small parsimony for natural genomes in the DCJ-indel model
Small parsimony for natural genomes in the DCJ-indel model Open
The Small Parsimony Problem (SPP) aims at finding the gene orders at internal nodes of a given phylogenetic tree such that the overall genome rearrangement distance along the tree branches is minimized. This problem is intractable in most …
View article: Automated identification of maximal differential cell populations in flow cytometry data
Automated identification of maximal differential cell populations in flow cytometry data Open
We introduce a new cell population score called SpecEnr (specific enrichment) and describe a method that discovers robust and accurate candidate biomarkers from flow cytometry data. Our approach identifies a new class of candidate biomarke…
View article: Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms
Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms Open
Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective targ…
View article: Geographic heterogeneity impacts drug resistance predictions in<i>Mycobacterium tuberculosis</i>
Geographic heterogeneity impacts drug resistance predictions in<i>Mycobacterium tuberculosis</i> Open
The efficacy of antibiotic drug treatments in tuberculosis (TB) is significantly threatened by the development of drug resistance. There is a need for a robust diagnostic system that can accurately predict drug resistance in patients. In r…
View article: HASLR: Fast Hybrid Assembly of Long Reads
HASLR: Fast Hybrid Assembly of Long Reads Open
Third-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and potentially gap-free assemblies. The larger effective length of their reads has pro…
View article: The distance and median problems in the single-cut-or-join model with single-gene duplications
The distance and median problems in the single-cut-or-join model with single-gene duplications Open
Background. In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem i…
View article: The Distance and Median Problems in the Single-Cut-or-Join model with Single-Gene Duplications
The Distance and Median Problems in the Single-Cut-or-Join model with Single-Gene Duplications Open
Background: In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, it is NP-comp…
View article: HASLR: Fast Hybrid Assembly of Long Reads
HASLR: Fast Hybrid Assembly of Long Reads Open
Third generation sequencing technologies from platforms such as Oxford Nanopore Technologies and Pacific Biosciences have paved the way for building more contiguous assemblies and complete reconstruction of genomes. The larger effective le…