Lista de obras - Jacques van Helden - Dominio Público Uruguay

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

artículo científico publicado en 2012

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

artículo científico publicado en 2003

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

artículo científico publicado en 2008

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer

Assessing computational tools for the discovery of transcription factor binding sites

artículo científico publicado en 2005

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

artículo científico

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

artículo científico publicado en 2011

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

artículo científico publicado en 2016

Contribution of the geneextramacrochaetae to the precise positioning of bristles inDrosophila

artículo científico publicado en 1995

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

artículo científico publicado en 2017

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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 2000

Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes

artículo científico publicado en 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

artículo científico publicado en 2007

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

artículo científico publicado en 2005

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

artículo científico publicado en 2007

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

artículo científico publicado en 1997

Evaluation of clustering algorithms for protein-protein interaction networks

artículo científico publicado en 2006

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

artículo científico publicado en 2008

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

artículo científico publicado en 1998

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

artículo científico publicado en 2007

From molecular activities and processes to biological function

artículo científico publicado en 2001

Genome-wide characterization of mammalian promoters with distal enhancer functions

artículo científico publicado en 2017

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

artículo científico publicado en 2009

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

artículo científico publicado en 2007

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

artículo científico publicado en 2003

Inferring meaningful pathways in weighted metabolic networks

artículo científico publicado en 2005

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

artículo científico publicado en 2019

Integrating sequence, evolution and functional genomics in regulatory genomics

artículo científico publicado en 2009

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

artículo científico publicado en 2014

Interactive visualization and exploration of relationships between biological objects.

artículo científico publicado en 2000

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

artículo científico publicado en 2005

Metabolic Pathfinding Using RPAIR Annotation

Metrics for comparing regulatory sequences on the basis of pattern counts

artículo científico publicado en 2004

Modularity of the transcriptional response of protein complexes in yeast

artículo científico

Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns

artículo científico publicado en 2003

Motif Discovery

Motif Enrichment Analysis

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

artículo científico publicado en 2008

Network Analysis Tools: from biological networks to clusters and pathways

artículo científico publicado en 2008

Pathway discovery in metabolic networks by subgraph extraction

artículo científico publicado en 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 ⬇️

artículo científico publicado el 1 de enero de 2012

Prediction of metabolic pathways from genome-scale metabolic networks.

artículo científico publicado en 2011

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

artículo científico publicado en 2008

RSAT 2011: regulatory sequence analysis tools.

artículo científico publicado en 2011

RSAT 2015: Regulatory Sequence Analysis Tools.

artículo científico publicado en 2015

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

artículo científico publicado en 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.

artículo científico publicado en 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

artículo científico publicado en 2011

RSAT: regulatory sequence analysis tools

artículo científico publicado en 2008

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

artículo científico publicado en 2016

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

artículo científico

Redefining fundamental concepts of transcription initiation in bacteria

artículo científico publicado en 2020

Regulatory Region

Regulatory sequence analysis tools

artículo científico publicado en 2003

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

artículo científico publicado en 1999

Reticulate representation of evolutionary and functional relationships between phage genomes

artículo científico publicado en 2008

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

artículo científico

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

artículo científico publicado en 2020

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

artículo científico publicado en 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

artículo científico publicado en 2000

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado el 1 de septiembre de 1998

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

artículo científico publicado en 2009

Theoretical and empirical quality assessment of transcription factor-binding motifs

artículo científico publicado en 2010

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

artículo científico

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

artículo científico publicado en 2010

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

artículo científico

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

artículo científico publicado en 2013

Transcriptional regulation of protein complexes in yeast

artículo científico publicado en 2004

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

artículo científico publicado en 2011

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

artículo científico publicado en 2008

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

artículo científico publicado en 2008

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

artículo científico publicado en 2009

Lista de obras de Jacques van Helden

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

A web site for the computational analysis of yeast regulatory sequences

An Overview of Data Models for the Analysis of Biochemical Pathways

An overview of data models for the analysis of biochemical pathways

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

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer

Assessing computational tools for the discovery of transcription factor binding sites

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

Cis-regulatory Element

Cis-regulatory Module (CRM)

Cis-regulatory Module Prediction

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

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

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

Contribution of the geneextramacrochaetae to the precise positioning of bristles inDrosophila

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

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

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

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

Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes

Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes

Discovery of Motifs in Promoters of Coregulated Genes

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

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

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

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

Evaluation of clustering algorithms for protein-protein interaction networks

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

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

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

From molecular activities and processes to biological function

Genome-wide characterization of mammalian promoters with distal enhancer functions

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

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

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

Inferring meaningful pathways in weighted metabolic networks

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

Integrating sequence, evolution and functional genomics in regulatory genomics

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

Interactive visualization and exploration of relationships between biological objects.

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

Metabolic PathFinding: inferring relevant pathways in biochemical networks

Metabolic Pathfinding Using RPAIR Annotation

Metrics for comparing regulatory sequences on the basis of pattern counts

Modularity of the transcriptional response of protein complexes in yeast

Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns

Motif Discovery

Motif Enrichment Analysis

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

Network Analysis Tools: from biological networks to clusters and pathways

Pathway discovery in metabolic networks by subgraph extraction

Phylogenetic Footprint

Phylogenetic Footprint Detection

Position Weight Matrix

Predicting Metabolic Pathways by Sub-network Extraction ⬇️

Prediction of metabolic pathways from genome-scale metabolic networks.

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

RSAT 2011: regulatory sequence analysis tools.

RSAT 2015: Regulatory Sequence Analysis Tools.

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

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.

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

RSAT: regulatory sequence analysis tools

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

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

Redefining fundamental concepts of transcription initiation in bacteria

Regulatory Region

Regulatory sequence analysis tools

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

Reticulate representation of evolutionary and functional relationships between phage genomes

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

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

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

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

Software Suites for Regulatory Sequences

Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals

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