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

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

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

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

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

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

por de Boer, Jan M, Datema, Erwin, Tang, Xiaomin, Borm, Theo J A, Bakker, Erin H, van Eck, Herman J, van Ham, Roeland C H J, de Jong, Hans, Visser, Richard G F, Bachem, Christian W B
Publicado 2015

A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network

por Leal Valentim, Felipe, van Mourik, Simon, Posé, David, Kim, Min C., Schmid, Markus, van Ham, Roeland C. H. J., Busscher, Marco, Sanchez-Perez, Gabino F., Molenaar, Jaap, Angenent, Gerco C., Immink, Richard G. H., van Dijk, Aalt D. J.
Publicado 2015

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

por Nijkamp, Jurgen F, van den Broek, Marcel, Datema, Erwin, de Kok, Stefan, Bosman, Lizanne, Luttik, Marijke A, Daran-Lapujade, Pascale, Vongsangnak, Wanwipa, Nielsen, Jens, Heijne, Wilbert HM, Klaassen, Paul, Paddon, Chris J, Platt, Darren, Kötter, Peter, van Ham, Roeland C, Reinders, Marcel JT, Pronk, Jack T, de Ridder, Dick, Daran, Jean-Marc
Publicado 2012

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

por Bolger, Anthony, Scossa, Federico, Bolger, Marie E, Lanz, Christa, Maumus, Florian, Tohge, Takayuki, Quesneville, Hadi, Alseekh, Saleh, Sørensen, Iben, Lichtenstein, Gabriel, Fich, Eric A, Conte, Mariana, Keller, Heike, Schneeberger, Korbinian, Schwacke, Rainer, Ofner, Itai, Vrebalov, Julia, Xu, Yimin, Osorio, Sonia, Aflitos, Saulo Alves, Schijlen, Elio, Jiménez-Goméz, José M, Ryngajllo, Malgorzata, Kimura, Seisuke, Kumar, Ravi, Koenig, Daniel, Headland, Lauren R, Maloof, Julin N, Sinha, Neelima, van Ham, Roeland C H J, Lankhorst, René Klein, Mao, Linyong, Vogel, Alexander, Arsova, Borjana, Panstruga, Ralph, Fei, Zhangjun, Rose, Jocelyn K C, Zamir, Dani, Carrari, Fernando, Giovannoni, James J, Weigel, Detlef, Usadel, Björn, Fernie, Alisdair R
Publicado 2014

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

por de Wit, Pierre J. G. M., van der Burgt, Ate, Ökmen, Bilal, Stergiopoulos, Ioannis, Abd-Elsalam, Kamel A., Aerts, Andrea L., Bahkali, Ali H., Beenen, Henriek G., Chettri, Pranav, Cox, Murray P., Datema, Erwin, de Vries, Ronald P., Dhillon, Braham, Ganley, Austen R., Griffiths, Scott A., Guo, Yanan, Hamelin, Richard C., Henrissat, Bernard, Kabir, M. Shahjahan, Jashni, Mansoor Karimi, Kema, Gert, Klaubauf, Sylvia, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Mehrabi, Rahim, Ohm, Robin A., Owen, Timothy J., Salamov, Asaf, Schwelm, Arne, Schijlen, Elio, Sun, Hui, van den Burg, Harrold A., van Ham, Roeland C. H. J., Zhang, Shuguang, Goodwin, Stephen B., Grigoriev, Igor V., Collemare, Jérôme, Bradshaw, Rosie E.
Publicado 2012

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

por de Wit, Pierre J. G. M., van der Burgt, Ate, Ökmen, Bilal, Stergiopoulos, Ioannis, Abd-Elsalam, Kamel A., Aerts, Andrea L., Bahkali, Ali H., Beenen, Henriek G., Chettri, Pranav, Cox, Murray P., Datema, Erwin, de Vries, Ronald P., Dhillon, Braham, Ganley, Austen R., Griffiths, Scott A., Guo, Yanan, Hamelin, Richard C., Henrissat, Bernard, Kabir, M. Shahjahan, Jashni, Mansoor Karimi, Kema, Gert, Klaubauf, Sylvia, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Mehrabi, Rahim, Ohm, Robin A., Owen, Timothy J., Salamov, Asaf, Schwelm, Arne, Schijlen, Elio, Sun, Hui, van den Burg, Harrold A., van Ham, Roeland C. H. J., Zhang, Shuguang, Goodwin, Stephen B., Grigoriev, Igor V., Collemare, Jérôme, Bradshaw, Rosie E.
Publicado 2015

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

por Goodwin, Stephen B., Ben M'Barek, Sarrah, Dhillon, Braham, Wittenberg, Alexander H. J., Crane, Charles F., Hane, James K., Foster, Andrew J., Van der Lee, Theo A. J., Grimwood, Jane, Aerts, Andrea, Antoniw, John, Bailey, Andy, Bluhm, Burt, Bowler, Judith, Bristow, Jim, van der Burgt, Ate, Canto-Canché, Blondy, Churchill, Alice C. L., Conde-Ferràez, Laura, Cools, Hans J., Coutinho, Pedro M., Csukai, Michael, Dehal, Paramvir, De Wit, Pierre, Donzelli, Bruno, van de Geest, Henri C., van Ham, Roeland C. H. J., Hammond-Kosack, Kim E., Henrissat, Bernard, Kilian, Andrzej, Kobayashi, Adilson K., Koopmann, Edda, Kourmpetis, Yiannis, Kuzniar, Arnold, Lindquist, Erika, Lombard, Vincent, Maliepaard, Chris, Martins, Natalia, Mehrabi, Rahim, Nap, Jan P. H., Ponomarenko, Alisa, Rudd, Jason J., Salamov, Asaf, Schmutz, Jeremy, Schouten, Henk J., Shapiro, Harris, Stergiopoulos, Ioannis, Torriani, Stefano F. F., Tu, Hank, de Vries, Ronald P., Waalwijk, Cees, Ware, Sarah B., Wiebenga, Ad, Zwiers, Lute-Harm, Oliver, Richard P., Grigoriev, Igor V., Kema, Gert H. J.
Publicado 2011