A5103164604- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Glycosylation and Glycoproteins Research
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Research Data Management Practices
- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Genetic factors in colorectal cancer
- Computational Drug Discovery Methods
- Microbial Community Ecology and Physiology
- Gene Regulatory Network Analysis
- Algorithms and Data Compression
- Gene expression and cancer classification
- RNA modifications and cancer
- Advanced Proteomics Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- RNA Research and Splicing
- Genetic diversity and population structure
- Cooperative Studies and Economics
- Cancer-related gene regulation
Vrije Universiteit Amsterdam
2015-2024
Amsterdam UMC Location Vrije Universiteit Amsterdam
2009-2023
GGD Amsterdam
2018
Institute of Bioinformatics
2004-2017
Center for Life Sciences
2016
Academic Center for Dentistry Amsterdam
2013-2014
University of Amsterdam
2003-2014
Netherlands Bioinformatics Centre
1987-2014
Amsterdam UMC Location University of Amsterdam
2013
University of Cambridge
2013
There is an urgent need to improve the infrastructure supporting reuse of scholarly data. A diverse set stakeholders-representing academia, industry, funding agencies, and publishers-have come together design jointly endorse a concise measureable principles that we refer as FAIR Data Principles. The intent these may act guideline for those wishing enhance reusability their data holdings. Distinct from peer initiatives focus on human scholar, Principles put specific emphasis enhancing ability...
PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment application. In addition to number of available strategies, PRALINE can integrate information from database homology searches generate homology-extended alignment. also provides choice seven different secondary structure prediction programs that be used individually or in combination as consensus for integrating structural into the process. The program through two separate interfaces: one has been designed cater...
Recent advances in protein engineering have come from creating multi-functional chimeric proteins containing modules various proteins. These are typically joined via an oligopeptide linker, the correct design of which is crucial for desired function protein. Here we analyse properties naturally occurring inter-domain linkers with aim to domain fusion. Two main types linker were identified; helical and non-helical. Helical thought act as rigid spacers separating two domains. Non-helical rich...
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
Abstract Motivation: In this paper, we present a secondary structure prediction method YASPIN that unlike the current state-of-the-art methods utilizes single neural network for predicting elements in 7-state local scheme and then optimizes output using hidden Markov model, which results providing more information prediction. Results: was compared with top-performing methods, such as PHDpsi, PROFsec, SSPro2, JNET PSIPRED. The overall accuracy on independent EVA5 sequence set is comparable of...
New findings are presented for the ~ 50 residue KH motif, a domain recently discovered in RNA‐binding proteins. The conserved sequence is 10 residues larger than previously reported. Profile searches have revealed new members of this family, including two, E. coli NusA and human GAP‐associated p62 phosphoprotein, which data exists. A nus homolog was detected RNA polymerase gene complex six archaebacterial species may encode an antiterminator. All KH‐containing proteins linked with motif most...
Mycobacterial pathogens use specialized type VII secretion (T7S) systems to transport crucial virulence factors across their unusual cell envelope into infected host cells. These lack classical signals and the mechanism of substrate recognition is not well understood. Here we demonstrate that model T7S substrates PE25/PPE41, which form a heterodimer, are targeted pathway ESX-5 by signal located in C terminus PE25. Site-directed mutagenesis residues within this resulted identification highly...
Abstract Motivation: Internal repeats in coding sequences correspond to structural and functional units of proteins. Moreover, duplication fragments is known be a mechanism facilitate evolution. Identification crucial shed light on the function structure proteins, explain their evolutionary past. The task difficult because during course evolution many diverged beyond recognition. Results: We introduce new method TRUST, for ab initio determination internal It provides an improvement...
Abstract Motivation: Membrane-bound proteins are a special class of proteins. The regions that insert into the cell-membrane have profoundly different hydrophobicity pattern compared with soluble Multiple alignment techniques use scoring schemes tailored for sequences and therefore in principle not optimal to align membrane-bound Results: Transmembrane (TM) protein can be reliably recognized using state-of-the-art sequence prediction techniques. Furthermore, membrane-specific matrices...
Abstract Motivation: Combinatorial interactions of transcription factors with cis-regulatory elements control the dynamic progression through successive cellular states and thus underpin all metazoan development. The construction network models elements, therefore, has potential to generate fundamental insights into fate differentiation. Haematopoiesis long served as a model system study mammalian differentiation, yet modelling based on experimentally informed so far been restricted pairs...
Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in such annotations. One key challenge remains the prediction amino acids a given sequence that involved protein-protein interactions. Such typically based on machine learning methods take advantage properties positions known to be interaction. In this paper, we...
Pseudoknots are abundant in RNA structures. Many computational analyses require pseudoknot-free structures, which means that some of the base pairs knotted structure must be disregarded to obtain a nested structure. There is surprising diversity methods perform this pseudoknot removal task, but these often poorly described and studies can therefore difficult reproduce (in part, because different procedures may intuitively obvious investigators). Here we provide variety algorithms for...
Abstract Motivation: Identification of residues that account for protein function specificity is crucial, not only understanding the nature functional specificity, but also engineering experiments aimed at switching an enzyme, regulator or transporter. Available algorithms generally use multiple sequence alignments to identify residue positions conserved within subfamilies divergent in between. However, many biological examples show a much subtler picture than simple intra-group conservation...
Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in protein–protein interactions. A small number of amino acids generally determine specificity. The identification these residues can aid the understanding function and help finding targets for experimental analysis. Here, we present multi-Harmony, an interactive web sever detecting sub-type-specific sites proteins starting from a multiple sequence alignment....
Abstract Hyperactivation of Wnt and Ras-MAPK signalling are common events in development colorectal adenomas. Further progression from adenoma-to-carcinoma is frequently associated with 20q gain overexpression Aurora kinase A (AURKA). Interestingly, AURKA has been shown to further enhance signalling. However, the molecular details these interactions driving carcinogenesis remain poorly understood. Here we first performed differential expression analysis (DEA) knockdown two cancer (CRC) cell...