List of works - Roeland C H J van Ham

A genome-wide genetic map of NB-LRR disease resistance loci in potato

scientific article

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network

scientific article published on 26 February 2015

A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins

scientific article published on 25 November 2020

Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

scientific article

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

scientific article

Automatic Gene Function Prediction in the 2020's

scientific article published on 27 October 2020

Bayesian Markov Random Field analysis for protein function prediction based on network data

scientific article

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome.

scientific article

Conserved and variable correlated mutations in the plant MADS protein network.

scientific article

Continuous-time modeling of cell fate determination in Arabidopsis flowers

scientific article

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

scientific article published on 22 December 2015

Correlated mutations via regularized multinomial regression

scientific article

Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster

scientific article (publication date: May 2004)

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

scientific article published on 3 September 2014

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis

scientific article

Genome sequence and analysis of the tuber crop potato

scientific article

Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources ⬇️

scientific article published on November 22, 2010

Genomic determinants of protein folding thermodynamics in prokaryotic organisms.

scientific article published in November 2004

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6.

scientific article

High-throughput bioinformatics with the Cyrille2 pipeline system

scientific article

Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin.

scientific article published on 10 May 2015

Improving protein function prediction using protein sequence and GO-term similarities.

scientific article

In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

scientific article

Metric learning on expression data for gene function prediction

scientific article published on 01 February 2020

Molecular characterization of the leucine cluster in Buchnera sp. strain PSY, a primary endosymbiont of the aphid Pemphigus spyrothecae

scientific article published on May 2002

Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids.

scientific article

Mutational robustness of gene regulatory networks

scientific article

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

scientific article

Post alignment clustering procedure for comparative quantitative proteomics LC-MS data

scientific article

Predicting the impact of alternative splicing on plant MADS domain protein function

scientific article

Reductive genome evolution in Buchnera aphidicola

scientific article

SLIDER: a generic metaheuristic for the discovery of correlated motifs in protein-protein interaction networks.

scientific article published in September 2011

Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction

scientific article

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

article

Solanum lycopersicum cv. Heinz 1706 chromosome 6: distribution and abundance of genes and retrotransposable elements.

scientific article published on 4 February 2009

The genome of the stress-tolerant wild tomato species Solanum pennellii.

scientific article published on 27 July 2014

The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes

scientific article

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

scientific article

The quest for orthologs: finding the corresponding gene across genomes

scientific article

The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation.

scientific article published on January 2007

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function

scientific article published on 14 August 2020

List of works by Roeland C H J van Ham

A genome-wide genetic map of NB-LRR disease resistance loci in potato

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network

A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins

Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

Automatic Gene Function Prediction in the 2020's

Bayesian Markov Random Field analysis for protein function prediction based on network data

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome.

Conserved and variable correlated mutations in the plant MADS protein network.

Continuous-time modeling of cell fate determination in Arabidopsis flowers

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

Correlated mutations via regularized multinomial regression

Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis

Genome sequence and analysis of the tuber crop potato

Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources ⬇️

Genomic determinants of protein folding thermodynamics in prokaryotic organisms.

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6.

High-throughput bioinformatics with the Cyrille2 pipeline system

Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin.

Improving protein function prediction using protein sequence and GO-term similarities.

In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

Metric learning on expression data for gene function prediction

Molecular characterization of the leucine cluster in Buchnera sp. strain PSY, a primary endosymbiont of the aphid Pemphigus spyrothecae

Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids.

Mutational robustness of gene regulatory networks

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Post alignment clustering procedure for comparative quantitative proteomics LC-MS data

Predicting the impact of alternative splicing on plant MADS domain protein function

Reductive genome evolution in Buchnera aphidicola

SLIDER: a generic metaheuristic for the discovery of correlated motifs in protein-protein interaction networks.

Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

Solanum lycopersicum cv. Heinz 1706 chromosome 6: distribution and abundance of genes and retrotransposable elements.

The genome of the stress-tolerant wild tomato species Solanum pennellii.

The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

The quest for orthologs: finding the corresponding gene across genomes

The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation.

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function