Author details

Full Name

Denis Bertrand

Affiliation

ORCID

Career Start Year

2005

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
35311657	Genome Alert!: A standardized procedure for genomicÂ variant reinterpretation and automated gene-phenotype reassessment in clinical routine.	Genet Med	2022
36109646	Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects.	Nature Microbiology	2022
36229545	Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians.	Nature Communications	2022
36057769	Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella.		2022
33417711	Household transmission of carbapenemase-producing Enterobacteriaceae: a prospective cohort study.	Journal of Antimicrobial Chemotherapy	2021
33862216	Stool metagenome analysis of patients with Klebsiella pneumoniae liver abscess and their domestic partners.	International Journal of Infectious Diseases	2021
34039264	Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads.	BMC Genomics	2021
32818397	Duration of Carbapenemase-Producing Enterobacteriaceae Carriage in Hospital Patients.	Emerging Infectious Diseases	2020
29259006	ConsensusDriver Improves upon Individual Algorithms for Predicting Driver Alterations in Different Cancer Types and Individual Patients.	Cancer Res	2018
29880655	Immunological corollary of the pulmonary mycobiome in bronchiectasis: the CAMEB study.	European Respiratory Journal	2018
29868820	Predicting Cancer Drug Response using a Recommender System.	Bioinformatics	2018
30096302	Comprehensive Characterization of Cancer Driver Genes and Mutations.	Cell	2018
29673082	A MinIONâ¿¢-based pipeline for fast and cost-effective DNA barcoding.	Molecular Ecology Resources	2018
29625053	Comprehensive Characterization of Cancer Driver Genes and Mutations.	Cell	2018
29625049	Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.	Cell	2018
28874669	Phenotype-driven precision oncology as a guide for clinical decisions one patient at a time.	Nature Communications	2017
28967888	Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.	Nat Methods	2017
27169502	OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.		2016
27428430	Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma.	eBioMedicine	2016
26783136	Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion.	Nature Communications	2016
26146084	Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.	Cell Reports	2015
25572314	Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.	Nucleic Acids Res	2015
26040716	Cloning and variation of ground state intestinal stem cells.	Nature	2015
25007141	The Opisthorchis viverrini genome provides insights into life in the bile duct.	Nat Commun	2014
25186909	Systems consequences of amplicon formation in human breast cancer.	Genome Res	2014
23179022	The draft genome of sweet orange (Citrus sinensis).	Nature Genetics	2013
23066108	LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.	Nucleic Acids Res	2012
22484628	Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes.	Nat Genet	2012
23237666	Whole-genome reconstruction and mutational signatures in gastric cancer.	Genome Biol	2012
21899424	Genome halving and double distance with losses.	Journal of Computational Biology	2011
22152029	Evolution of orthologous tandemly arrayed gene clusters.	BMC Bioinformatics	2011
19903657	Inferring the evolutionary history of gene clusters from phylogenetic and gene order data.	Molecular Biology and Evolution	2010
19754272	Genetic map refinement using a comparative genomic approach.	Journal of Computational Biology	2009
18781832	Inferring ancestral gene orders for a family of tandemly arrayed genes.	Journal of Computational Biology	2008
19017397	The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals.	BMC Mol Biol	2008
17572024	Duplication and inversion history of a tandemly repeated genes family.	Journal of Computational Biology	2007
17044161	Topological rearrangements and local search method for tandem duplication trees.	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2005