Denis Bertrand

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

The paper uses long-read and Hi-C technologies to analyze gut microbiomes from Southeast Asians, revealing novel species, improved references, and uncharacterized biosynthetic gene clusters.

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

The paper characterizes the ecological and evolutionary dynamics of gut microbiomes colonized by carbapenemase-producing Enterobacteriaceae (CPE) using longitudinal metagenomics and whole genome sequencing.

Learning phenotypic patterns in genetic disease by symptom interaction modeling

This paper develops a symptom interaction model to address heterogeneous phenotype reporting in genetic disease, improving gene prioritization by 42%.

Critical Assessment of Metagenome Interpretation - the second round of challenges

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Genome Alert!: a standardized procedure for genomic variant reinterpretation and automated genotype-phenotype reassessment in clinical routine

Genome Alert! automatically detects changes in variant classifications and gene-disease associations over time, improving clinical interpretation of genomic data with minimal human effort.

Large-scale whole-genome sequencing of three diverse Asian populations in Singapore

This study presents whole-genome sequencing data from 4,810 Singaporeans across three ethnic groups, revealing genetic structure, admixture, and improved imputation for Asian and Oceanian populations.

A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction

The paper presents a large-scale cancer pharmacogenomic screen with 11,576 experiments on 910 drug combinations across 85 cancer cell lines, enabling crowd-sourced prediction of synergistic drug pairs and biomarkers.

Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome

This paper introduces a hybrid metagenomic assembler that improves assembly quality and enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome.

Predicting Cancer Drug Response Using a Recommender System

This paper introduces a recommender system approach to predict cancer drug responses using pharmacogenomic data and demonstrates its effectiveness across multiple datasets.

A MinION-based pipeline for fast and cost-effective DNA barcoding

The paper develops a MinION-based pipeline for DNA barcoding that generates accurate barcodes for up to 1000 specimens per flowcell at a low cost.

ConsensusDriver Improves Upon Individual Algorithms For Predicting Driver Alterations In Different Cancer Types And Individual Patients -- A Toolbox For Precision Oncology

ConsensusDriver improves driver alteration prediction by combining multiple methods, increasing sensitivity by 20% across cancer types and individual patients.

Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.

OPERA-LG: Efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees

OPERA-LG improves scaffold correctness and contiguity for large, repeat-rich eukaryotic genomes by combining short and long-read sequencing data efficiently.