User profiles for Aalt D.J van Dijk

Aalt DJ van Dijk

Professor Data Analysis in the Life Sciences, University of Amsterdam
Verified email at uva.nl
Cited by 7080

Data‐driven docking for the study of biomolecular complexes

ADJ Van Dijk, R Boelens, AMJJ Bonvin - The FEBS journal, 2005 - Wiley Online Library
With the amount of genetic information available, a lot of attention has focused on systems
biology, in particular biomolecular interactions. Considering the huge number of such …

The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history

…, Y Van de Peer, ADJ Van Dijk… - Journal of …, 2014 - academic.oup.com
Successful plant reproduction relies on the perfect orchestration of singular processes that
culminate in the product of reproduction: the seed. The floral transition, floral organ …

Cross-family transcription factor interactions: an additional layer of gene regulation

M Bemer, ADJ van Dijk, RGH Immink… - Trends in plant …, 2017 - cell.com
Specific and dynamic gene expression strongly depends on transcription factor (TF) activity
and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the …

HADDOCK versus HADDOCK: new features and performance of HADDOCK2. 0 on the CAPRI targets

…, ADJ Van Dijk, M Krzeminski, M van Dijk… - Proteins: structure …, 2007 - Wiley Online Library
Here we present version 2.0 of HADDOCK, which incorporates considerable improvements
and new features. HADDOCK is now able to model not only protein–protein complexes but …

[HTML][HTML] A large-scale evaluation of computational protein function prediction

…, S Džeroski, T Šmuc, YAI Kourmpetis, ADJ Van Dijk… - Nature …, 2013 - nature.com
Automated annotation of protein function is challenging. As the number of sequenced
genomes rapidly grows, the overwhelming majority of protein products can only be annotated …

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

…, M Mesiti, G Valentini, JW Bargsten, ADJ van Dijk… - Genome biology, 2016 - Springer
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 …

Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis

Y Zhang, ADJ Van Dijk, A Scaffidi, GR Flematti… - Nature chemical …, 2014 - nature.com
Strigolactones (SLs) are a class of phytohormones and rhizosphere signaling compounds
with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and …

Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically

…, R Waites, S de Folter, A Bimbo, ADJ van Dijk… - Plant …, 2012 - academic.oup.com
Aalt DJ van Dijk , Aalt DJ van Dijk … Selahattin Danisman, Froukje van der Wal, Stijn Dhondt,
Richard Waites, Stefan de Folter, Andrea Bimbo, Aalt DJ van Dijk, Jose M. Muino, Lucas Cutri…

[HTML][HTML] SEPALLATA3: the'glue'for MADS box transcription factor complex formation

…, S de Folter, A Shchennikova, ADJ van Dijk… - Genome biology, 2009 - Springer
Background Plant MADS box proteins play important roles in a plethora of developmental
processes. In order to regulate specific sets of target genes, MADS box proteins dimerize and …

Characterization of SOC1's central role in flowering by the identification of its upstream and downstream regulators

…, S de Folter, F van der Wal, ADJ van Dijk… - Plant …, 2012 - academic.oup.com
The transition from vegetative to reproductive development is one of the most important
phase changes in the plant life cycle. This step is controlled by various environmental signals …