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

por Makrodimitris, Stavros, Reinders, Marcel, van Ham, Roeland
Publicado 2020

Conserved and variable correlated mutations in the plant MADS protein network

por van Dijk, Aalt DJ, van Ham, Roeland CHJ
Publicado 2010

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

por Severing, Edouard I, van Dijk, Aalt DJ, van Ham, Roeland CHJ
Publicado 2011

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

por Makrodimitris, Stavros, van Ham, Roeland C H J, Reinders, Marcel J T
Publicado 2019

Automatic Gene Function Prediction in the 2020’s

por Makrodimitris, Stavros, van Ham, Roeland C. H. J., Reinders, Marcel J. T.
Publicado 2020

Metric learning on expression data for gene function prediction

por Makrodimitris, Stavros, Reinders, Marcel J T, van Ham, Roeland C H J
Publicado 2020

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

por Severing, Edouard I, van Dijk, Aalt DJ, Stiekema, Willem J, van Ham, Roeland CHJ
Publicado 2009

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

por van der Burgt, Ate, Fiers, Mark WJE, Nap, Jan-Peter, van Ham, Roeland CHJ
Publicado 2009

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

por Muiño, Jose M, Kaufmann, Kerstin, van Ham, Roeland CHJ, Angenent, Gerco C, Krajewski, Pawel
Publicado 2011

Correlated mutations via regularized multinomial regression

por Sreekumar, Janardanan, ter Braak, Cajo JF, van Ham, Roeland CHJ, van Dijk, Aalt DJ
Publicado 2011

Mutational Robustness of Gene Regulatory Networks

por van Dijk, Aalt D. J., van Mourik, Simon, van Ham, Roeland C. H. J.
Publicado 2012

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

por Muiño, Jose M., Hoogstraat, Marlous, van Ham, Roeland C. H. J., van Dijk, Aalt D. J.
Publicado 2011

High-throughput bioinformatics with the Cyrille2 pipeline system

por Fiers, Mark WEJ, van der Burgt, Ate, Datema, Erwin, de Groot, Joost CW, van Ham, Roeland CHJ
Publicado 2008

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

por Fiers, Mark WEJ, Kleter, Gijs A, Nijland, Herman, Peijnenburg, Ad ACM, Nap, Jan Peter, van Ham, Roeland CHJ
Publicado 2004

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

por Villegas-Morcillo, Amelia, Makrodimitris, Stavros, van Ham, Roeland C H J, Gomez, Angel M, Sanchez, Victoria, Reinders, Marcel J T
Publicado 2020

Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato

por Datema, Erwin, Mueller, Lukas A, Buels, Robert, Giovannoni, James J, Visser, Richard GF, Stiekema, Willem J, van Ham, Roeland CHJ
Publicado 2008

Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

por van Dijk, Aalt D. J., Morabito, Giuseppa, Fiers, Martijn, van Ham, Roeland C. H. J., Angenent, Gerco C., Immink, Richard G. H.
Publicado 2010

Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function

por Severing, Edouard I., van Dijk, Aalt D. J., Morabito, Giuseppa, Busscher-Lange, Jacqueline, Immink, Richard G. H., van Ham, Roeland C. H. J.
Publicado 2012

Continuous-time modeling of cell fate determination in Arabidopsis flowers

por van Mourik, Simon, van Dijk, Aalt DJ, de Gee, Maarten, Immink, Richard GH, Kaufmann, Kerstin, Angenent, Gerco C, van Ham, Roeland CHJ, Molenaar, Jaap
Publicado 2010

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data

por Kourmpetis, Yiannis A. I., van Dijk, Aalt D. J., Bink, Marco C. A. M., van Ham, Roeland C. H. J., ter Braak, Cajo J. F.
Publicado 2010