Search Results - "VAN HAM, Roeland C. H. J"

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network by Leal Valentim, Felipe, Mourik, Simon van, 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

“…Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of…”
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Bayesian Markov Random Field analysis for protein function prediction based on network data by 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

“…Inference of protein functions is one of the most important aims of modern biology. To fully exploit the large volumes of genomic data typically produced in…”
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Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis by Goodwin, Stephen B, M'barek, Sarrah Ben, 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

“…The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the…”
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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 by 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

“…We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum…”
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Mutational robustness of gene regulatory networks by van Dijk, Aalt D J, van Mourik, Simon, van Ham, Roeland C H J

“…Mutational robustness of gene regulatory networks refers to their ability to generate constant biological output upon mutations that change network structure…”
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Predicting the impact of alternative splicing on plant MADS domain protein function by Severing, Edouard I, van Dijk, Aalt D J, Morabito, Giuseppa, Busscher-Lange, Jacqueline, Immink, Richard G H, van Ham, Roeland C H J

“…Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of…”
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Reductive Genome Evolution in Buchnera aphidicola by Roeland C. H. J. van Ham, Kamerbeek, Judith, Palacios, Carmen, Rausell, Carolina, Abascal, Federico, Bastolla, Ugo, Fernández, Jose M., Jiménez, Luis, Postigo, Marina, Silva, Francisco J., Tamames, Javier, Viguera, Enrique, Latorre, Amparo, Valencia, Alfonso, Morán, Federico, Moya, Andrés

“…We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80-150 million years ago…”
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Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function by Villegas-Morcillo, Amelia, Makrodimitris, Stavros, van Ham, Roeland C H J, Gomez, Angel M, Sanchez, Victoria, Reinders, Marcel J T

“…Abstract Motivation Protein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence…”
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Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction by van Dijk, Aalt D J, Morabito, Giuseppa, Fiers, Martijn, van Ham, Roeland C H J, Angenent, Gerco C, Immink, Richard G H

“…Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of…”
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Metric learning on expression data for gene function prediction by Makrodimitris, Stavros, Reinders, Marcel J T, van Ham, Roeland C H J

“…Abstract Motivation Co-expression of two genes across different conditions is indicative of their involvement in the same biological process. However, when…”
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The quest for orthologs: finding the corresponding gene across genomes by Kuzniar, Arnold, van Ham, Roeland C.H.J, Pongor, Sándor, Leunissen, Jack A.M

“…Orthology is a key evolutionary concept in many areas of genomic research. It provides a framework for subjects as diverse as the evolution of genomes, gene…”
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Evolution of the Leucine Gene Cluster in Buchnera aphidicola: Insights from Chromosomal Versions of the Cluster by SABATER-MUNOZ, Beatriz, VAN HAM, Roeland C. H. J, MOYA, Andrés, SILVA, Francisco J, LATORRE, Amparo

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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A Comparison of Global Sensitivity Analysis Methods for Explainable AI With an Application in Genomic Prediction by Stein, Bas Van, Raponi, Elena, Sadeghi, Zahra, Bouman, Niek, Van Ham, Roeland C. H. J., Back, Thomas

“…Explainable Artificial Intelligence (XAI) is an increasingly important field of research required to bring AI to the next level in real-world applications…”
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The Genome Sequence of Blochmannia floridanus: Comparative Analysis of Reduced Genomes by Gil, Rosario, Silva, Francisco J., Zientz, Evelyn, Delmotte, François, González-Candelas, Fernando, Latorre, Amparo, Rausell, Carolina, Kamerbeek, Judith, Gadau, Jürgen, Hölldobler, Bert, Roeland C. H. J. van Ham, Gross, Roy, Moya, Andrés

“…Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence…”
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Molecular Characterization of the Leucine Cluster in Buchnera sp. Strain PSY, a Primary Endosymbiont of the Aphid Pemphigus spyrothecae by Sabater-Muñoz, Beatriz, Gómez-Valero, Laura, van Ham, Roeland C. H. J., Silva, Francisco J., Latorre, Amparo

“…Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit…”
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High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6 by Szinay, Dóra, Chang, Song-Bin, Khrustaleva, Ludmila, Peters, Sander, Schijlen, Elio, Bai, Yuling, Stiekema, Willem J, van Ham, Roeland C.H.J, de Jong, Hans, Klein Lankhorst, René M

“…Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a…”
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Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin by 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

“…In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable…”
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Genome-Wide Computational Function Prediction of Arabidopsis Proteins by Integration of Multiple Data Sources by Kourmpetis, Yiannis A.I, van Dijk, Aalt D.J, van Ham, Roeland C.H.J, ter Braak, Cajo J.F

“…Although Arabidopsis (Arabidopsis thaliana) is the best studied plant species, the biological role of one-third of its proteins is still unknown. We developed…”
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The genome of the stress-tolerant wild tomato species Solanum pennellii by 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

“…Björn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii . The authors identify genes important for stress…”
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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 by Visser, R.G.F, Bachem, C.W.B, Boer, J.M. de, Bryan, G.J, Chakrabati, S.K, Feingold, S, Gromadka, R, Ham, R.C.H.J. van, Huang, S, Jacobs, J.M.E, Kuznetsov, Boris, Melo, P. de, Milbourne, D, Orjeda, G, Sagredo, Boris, Tang, X

“…Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and…”
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