Search filters

Authors whose works are in public domain in at least one jurisdiction

List of works by Jacques van Helden

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

scientific article

A web site for the computational analysis of yeast regulatory sequences

article

An Overview of Data Models for the Analysis of Biochemical Pathways

An overview of data models for the analysis of biochemical pathways

scientific article

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data

scientific article

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer

Assessing computational tools for the discovery of transcription factor binding sites

scientific article

Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling

scientific article published on January 2012

Cis-regulatory Element

article

Cis-regulatory Module (CRM)

Cis-regulatory Module Prediction

Clusters of conserved beta cell marker genes for assessment of beta cell phenotype

scientific article

Combining pattern discovery and discriminant analysis to predict gene co-regulation

article

Confidence intervals are no salvation from the alleged fickleness of the P value

scientific article

Contribution of the geneextramacrochaetae to the precise positioning of bristles inDrosophila

scientific article published on 01 May 1995

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

scientific article published on 24 November 2017

Correction: Clusters of Conserved Beta Cell Marker Genes for Assessment of Beta Cell Phenotype.

scientific article

Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses

scientific article published on 6 June 2016

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads

scientific article published on April 2000

Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes

scientific article published on 01 January 2007

Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes

Discovery of Motifs in Promoters of Coregulated Genes

article

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

scientific article

Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae

scientific article published on 16 February 2007

Establishment of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis

scientific article published in December 1997

Evaluation of clustering algorithms for protein-protein interaction networks

scientific article published on 6 November 2006

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

scientific article

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

scientific article

Fine-tuning enhancer models to predict transcriptional targets across multiple genomes

scientific article

From molecular activities and processes to biological function

scientific article

Genome-wide characterization of mammalian promoters with distal enhancer functions

scientific article published on 5 June 2017

In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'.

scientific article published on 23 September 2009

In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells

scientific article published on 15 February 2007

In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis

scientific article published in May 2003

Inferring meaningful pathways in weighted metabolic networks

scientific article

Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks

scientific article published on 20 February 2019

Integrating sequence, evolution and functional genomics in regulatory genomics

scientific article published on 30 January 2009

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

scientific article

Interactive visualization and exploration of relationships between biological objects.

scientific article

Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements

scientific article published on 18 May 2009

Metabolic PathFinding: inferring relevant pathways in biochemical networks

scientific article

Metabolic Pathfinding Using RPAIR Annotation

Metrics for comparing regulatory sequences on the basis of pattern counts

scientific article published on 5 February 2004

Modularity of the transcriptional response of protein complexes in yeast

scientific article published on 03 July 2006

Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns

scientific article

Motif Discovery

Motif Enrichment Analysis

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

scientific article published on 4 June 2008

Network Analysis Tools: from biological networks to clusters and pathways

scientific article published in January 2008

Pathway discovery in metabolic networks by subgraph extraction

scientific article published on 12 March 2010

Phylogenetic Footprint

scholarly article published 15 October 2004

Phylogenetic Footprint Detection

scholarly article published 15 October 2004

Position Weight Matrix

Predicting Metabolic Pathways by Sub-network Extraction ⬇️

scientific article published on January 1, 2012

Prediction of metabolic pathways from genome-scale metabolic networks.

scientific article published on 27 May 2011

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

scientific article published on 30 January 2008

RSAT 2011: regulatory sequence analysis tools.

scientific article

RSAT 2015: Regulatory Sequence Analysis Tools.

scientific article published on 22 April 2015

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

scientific article published in July 2018

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

scientific article published on 07 June 2017

RSAT peak-motifs: fast extraction of transcription factor binding motifs from full-size ChIP-seq datasets

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

scientific article published on 8 December 2011

RSAT: regulatory sequence analysis tools

scientific article published on 21 May 2008

RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes

scientific article published in January 2016

RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes

scientific article published on January 2016

Redefining fundamental concepts of transcription initiation in bacteria

scientific article published on 14 July 2020

Regulatory Region

Regulatory sequence analysis tools

scientific article

RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli

scientific article published on January 1999

Reticulate representation of evolutionary and functional relationships between phage genomes

scientific article published on 29 January 2008

Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl

scientific article published on 31 August 2009

Retrouver les origines du SARS-CoV-2 dans les phylogénies de coronavirus

scientific article published on 10 August 2020

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

scientific article published on 19 January 2018

SnakeChunks: modular blocks to build Snakemake workflows for reproducible NGS analyses

Software Suites for Regulatory Sequences

scholarly article published 15 October 2004

Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals

scientific article published on February 2000

Sub-microscopic Plasmodium falciparum infections in matched peripheral, placental and umbilical cord blood samples from asymptomatic Congolese women at delivery

scientific article published on 02 March 2019

The bio.tools registry of software tools and data resources for the life sciences

article

The chromatin environment shapes DNA replication origin organization and defines origin classes

scientific article published on 11 November 2015

The iroquois complex controls the somatotopy of Drosophila notum mechanosensory projectionss ⬇️

scientific article published on September 1, 1998

The powerful law of the power law and other myths in network biology

scientific article published on 02 October 2009

Theoretical and empirical quality assessment of transcription factor-binding motifs

scientific article

Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

scholarly article

Transcription Factor

Transcription Factor Binding Motif (TFBM)

Transcription Factor Binding Site

article

Transcription Factor Database

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

scientific article

Transcriptional Profiling of Midguts Prepared from Trypanosoma/T. congolense-Positive Glossina palpalis palpalis Collected from Two Distinct Cameroonian Foci: Coordinated Signatures of the Midguts' Remodeling As T. congolense-Supportive Niches

scientific article published on 28 July 2017

Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis

scientific article

Transcriptional regulation of protein complexes in yeast

scientific article

Unraveling networks of co-regulated genes on the sole basis of genome sequences

scientific article

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences

scientific article

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

scientific article

info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling.

scientific article

Paulina is supported by:

About Paulina

Help