Search results for: Aalt D. J. van Dijk

Items from 1 to 8 out of 8 results

article

Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Niels Aerts, Suzanne de Bruijn, Hilda van Mourik, Gerco C. Angenent, more

BMC Plant Biology > 2018 > 18 > 1 > 1-16

Background Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. The canonical DNA binding motif for this transcription factor family is the CArG-box, which has the consensus CC(A/T)₆GG. However, so...

article

Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade

Hilda van Mourik, Aalt D. J. van Dijk, Niek Stortenbeker, Gerco C. Angenent, more

BMC Plant Biology > 2017 > 17 > 1 > 1-14

Background Small Auxin-Upregulated RNA (SAUR) genes encode growth regulators that induce cell elongation. Arabidopsis contains more than 70 SAUR genes, of which the growth-promoting function has been unveiled in seedlings, while their role in other tissues remained largely unknown. Here, we focus on the regulatory regions of Arabidopsis SAUR genes, to predict the processes in which they play a role,...

article

Sequence‐based analysis of protein degradation rates

Miguel Correa Marrero, Aalt D. J. van Dijk, Dick de Ridder

Proteins: Structure, Function, and Bioinformatics > 85 > 9 > 1593 - 1601

Protein turnover is a key aspect of cellular homeostasis and proteome dynamics. However, there is little consensus on which properties of a protein determine its lifetime in the cell. In this work, we exploit two reliable datasets of experimental protein degradation rates to learn models and uncover determinants of protein degradation, with particular focus on properties that can be derived from the...

article

An interactomics overview of the human and bovine milk proteome over lactation

Lina Zhang, Aalt D. J. van Dijk, Kasper Hettinga

Proteome Science > 2016 > 15 > 1 > 1-14

Background Milk is the most important food for growth and development of the neonate, because of its nutrient composition and presence of many bioactive proteins. Differences between human and bovine milk in low abundant proteins have not been extensively studied. To better understand the differences between human and bovine milk, the qualitative and quantitative differences in the milk proteome as...

article

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu

BMC Bioinformatics > 2016 > 17 > 16 > 51-52

article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, more

Genome Biology > 2016 > 17 > 1 > 1-19

Background A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking...

article

Solvated protein–protein docking using Kyte‐Doolittle‐based water preferences

Panagiotis L. Kastritis, Koen M. Visscher, Aalt D. J. van Dijk, Alexandre M. J. J. Bonvin

Proteins: Structure, Function, and Bioinformatics > 81 > 3 > 510 - 518

HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on water‐mediated contact probabilities. The latter were derived from an analysis of water contact frequencies...

article

Modeling Protein−Protein Complexes Involved in the Cytochrome c Oxidase Copper-Delivery Pathway

Aalt D. J. van Dijk, Simone Ciofi-Baffoni, Lucia Banci, Ivano Bertini, more

Journal of Proteome Research > 2007 > 6 > 4 > 1530 - 1539

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