Author details

Full Name

Jacques van Helden

Affiliation

ORCID

Career Start Year

1995

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
35544234	RSAT 2022: regulatory sequence analysis tools.	Nucleic Acids Res	2022
34543608	An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2.	Lancet, The	2021
33744946	Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.	Plant Physiology	2021
33531884	COVID-19 epidemiologic surveillance using wastewater.	Environmental Chemistry Letters	2021
33558807	Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review.	Environmental Chemistry Letters	2021
32773024	[Tracing the origins of SARS-COV-2 in coronavirus phylogenies].	Medecine/Sciences	2020
33250866	RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach.	Frontiers in Microbiology	2020
32924924	Ancestral state reconstruction of metabolic pathways across pangenome ensembles.	Microbial genomics	2020
32753646	In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication.	Scientific Reports	2020
32665585	Redefining fundamental concepts of transcription initiation in bacteria.	Nat Rev Genet	2020
30836060	Sub-microscopic Plasmodium falciparum infections in matched peripheral, placental and umbilical cord blood samples from asymptomatic Congolese women at delivery.	Acta Tropica	2019
31871587	RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.	Comput Struct Biotechnol J	2019
31405382	The bio.tools registry of software tools and data resources for the life sciences.	Genome Biol	2019
30786165	Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.	Current Protocols in Bioinformatics	2019
29361152	Sequanix: a dynamic graphical interface for Snakemake workflows.		2018
29722874	RSAT 2018: regulatory sequence analysis tools 20th anniversary.	Nucleic Acids Res	2018
29176637	Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide.	Scientific Reports	2017
28591841	RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.	Nucleic Acids Res	2017
28804485	Transcriptional Profiling of Midguts Prepared from -Positive Collected from Two Distinct Cameroonian Foci: Coordinated Signatures of the Midguts' Remodeling As -Supportive Niches.	Frontiers in Immunology	2017
28581502	Genome-wide characterization of mammalian promoters with distal enhancer functions.	Nature Genetics	2017
27557774	RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.	Methods in Molecular Biology	2016
27264199	Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses.	Environmental Microbiology Reports	2016
27467719	Confidence intervals are no salvation from the alleged fickleness of the P value.	Nature Methods	2016
27557775	RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.	Methods in Molecular Biology	2016
26560631	The chromatin environment shapes DNA replication origin organization and defines origin classes.	Genome Res	2015
25904632	RSAT 2015: Regulatory Sequence Analysis Tools.	Nucleic Acids Res	2015
25477382	Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape.	Nucleic Acids Research	2015
23560912	Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis.	BMC Genomics	2013
22144145	Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling.	Methods Mol Biol	2012
22836136	A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.	Nat Protoc	2012
22156162	RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.	Nucleic Acids Res	2012
22144151	Predicting metabolic pathways by sub-network extraction.	Methods in Molecular Biology	2012
21645586	Prediction of metabolic pathways from genome-scale metabolic networks.	BioSystems	2011
20923783	Theoretical and empirical quality assessment of transcription factor-binding motifs.	Nucleic Acids Research	2011
21572103	Unraveling networks of co-regulated genes on the sole basis of genome sequences.	Nucleic Acids Research	2011
21715389	RSAT 2011: regulatory sequence analysis tools.	Nucleic Acids Res	2011
21912665	Clusters of conserved beta cell marker genes for assessment of beta cell phenotype.	PLoS ONE	2011
20215436	Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data.	Nucleic Acids Research	2010
20228128	Pathway discovery in metabolic networks by subgraph extraction.		2010
20023717	The powerful law of the power law and other myths in network biology.	Molecular BioSystems	2009
19450688	Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements.	Methods	2009
19689955	info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling.		2009
19720677	Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.		2009
19281817	Metabolic pathfinding using RPAIR annotation.	Journal of Molecular Biology	2009
19776213	In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'.		2009
19226437	Integrating sequence, evolution and functional genomics in regulatory genomics.	Genome Biol	2009
18802439	Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.		2008
19091052	Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae.	BMC Proceedings	2008
18524799	NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.	Nucleic Acids Research	2008
18238785	Prophinder: a computational tool for prophage prediction in prokaryotic genomes.		2008