Nicola Mulder
A5080377820- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Genomics and Rare Diseases
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Genetic Associations and Epidemiology
- Tuberculosis Research and Epidemiology
- Biomedical and Engineering Education
- Computational Drug Discovery Methods
- Malaria Research and Control
- Advanced Proteomics Techniques and Applications
- vaccines and immunoinformatics approaches
- Mycobacterium research and diagnosis
- Gut microbiota and health
- Ethics in Clinical Research
- Cancer Genomics and Diagnostics
- Reproductive tract infections research
- Nutrition, Genetics, and Disease
- Research Data Management Practices
- Scientific Computing and Data Management
- Biotechnology and Related Fields
- Hemoglobinopathies and Related Disorders
University of Cape Town
2016-2025
Wellcome Centre for Infectious Diseases Research in Africa
2016-2025
Université d'Abomey-Calavi
2023-2024
Centers for Disease Control and Prevention
2023-2024
Kenya Medical Research Institute
2023-2024
St. Jude Children's Research Hospital
2022-2023
University of Antwerp
2022-2023
University of Miami
2022-2023
Arizona State University
2023
VIB-UAntwerp Center for Molecular Neurology
2022-2023
This study describes comprehensive polling of transcription start and termination sites analysis previously unidentified full-length complementary DNAs derived from the mouse genome. We identify 5' 3' boundaries 181,047 transcripts with extensive variation in arising alternative promoter usage, splicing, polyadenylation. There are 16,247 new protein-coding transcripts, including 5154 encoding proteins. Genomic mapping transcriptome reveals transcriptional forests, overlapping on both...
InterProScan [E. M. Zdobnov and R. Apweiler (2001) Bioinformatics, 17, 847-848] is a tool that combines different protein signature recognition methods from the InterPro [N. J. Mulder, Apweiler, T. K. Attwood, A. Bairoch, Bateman, D. Binns, P. Bradley, Bork, Bucher, L. Cerutti et al. (2005) Nucleic Acids Res., 33, D201-D205] consortium member databases into one resource. At time of writing there are 10 distinct publicly available in application. Protein as well DNA sequences can be analysed....
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY TIGRFAMs. Integration is performed manually approximately half of the total 58,000 signatures available in databases belong to an entry. Recently, we have started also display remaining un-integrated via our web...
InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, makes it freely available to the public via Web-based interfaces services. Central are diagnostic models, known as signatures, against which sequences can be searched determine their potential function. has utility in large-scale analysis of whole genomes meta-genomes, well characterizing individual sequences. Herein we give an overview new...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means amalgamating the major signature databases into one comprehensive resource.PROSITE, Pfam, PRINTS, ProDom, SMART TIGRFAMs have been manually curated are available InterPro for text-and sequence-based searching.The results provided single format that rationalises would be obtained by searching member individually.The latest release contains 5629 entries describing...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF SUPERFAMILY. Signatures are manually into InterPro entries that curated provide biological information. Annotation is provided in abstract, Gene Ontology mapping links specialized New features include extended match views, taxonomic range information 3D structure...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D PANTHER. The latter two new member databases have been since last publication in this journal. There several developments InterPro, including additional reading field, database links, extensions to web interface match XML files. has always provided matches UniProtKB proteins on...
InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as means of rationalising the complementary efforts PROSITE, PRINTS, Pfam ProDom database projects.Merged annotations from PROSITE form core. Each combined entry includes descriptions literature references, links are made back to relevant parent database(s), allowing users see at glance whether particular family or domain has associated patterns, profiles, fingerprints,...
Gene Ontology Annotation (GOA) is a project run by the European Bioinformatics Institute (EBI) that aims to provide assignments of terms from (GO) resource gene products in number its databases ( http://www.ebi.ac.uk/GOA ). In first stage this project, GO have been applied data set representing complete human proteome combination electronic mappings and manual curation. This vocabulary has also nonredundant sets for all other completely sequenced organisms as well proteins wide range where...
The human genome sequence defines our inherent biological potential; the realization of biology encoded therein requires knowledge function each gene. Currently, in this area is still limited. Several lines investigation have been used to elucidate structure and genes genome. Even so, gene prediction remains a difficult task, as varieties transcripts may vary great extent. We thus performed an exhaustive integrative characterization 41,118 full-length cDNAs that capture complete functional...
We present here the annotation of complete genome rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions identified or inferred in 19,969 (70%) proteins, 131 possible npRNAs (including 58 antisense transcripts) found. Almost 5000 annotated protein-coding genes found to be disrupted insertional mutant lines, which will accelerate future experimental validation annotations....
Young African females are at an increased risk of HIV acquisition, and genital inflammation or the vaginal microbiome may contribute to this risk. We studied these factors in 168 HIV-negative South adolescent aged 16 22 years. Unsupervised clustering 16S rRNA gene sequences revealed three clusters (subtypes), one which was strongly associated with inflammation. In a multivariate model, compositional subtype hormonal contraception were significantly identified 40 taxa inflammation, including...
Early life microbiota is an important determinant of immune and metabolic development may have lasting consequences. The maternal gut during pregnancy or breastfeeding for defining infant microbiota. We hypothesized that a critical immunity. To test this, pregnant BALB/c dams were fed vancomycin 5 days prior to delivery (gestation; Mg), 14 postpartum nursing (Mn), gestation (Mgn), no (Mc). analyzed adaptive immunity in pups at various times after delivery. In addition direct alterations...
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does aim to propose new development best practices, but rather provide simple recommendations encourage the adoption of existing practices. Software promote better improves reproducibility reusability research. These are designed around Open Source values, practical suggestions contribute making source code more discoverable,...
The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping sequencing improved data analysis capabilities. Some the greatest genetic diversity among humans, animals, plants, microbiota occurs Africa, yet genomic outputs from continent are limited. Human Heredity Health Africa (H3Africa) initiative was established drive development for human health through recognition critical role bioinformatics...
Abstract The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern populations for better understanding human diversity. In this pilot study characterizes genomes 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total ~16 million variants are identified. Despite shallow time depth since divergence between two main Bantu-speaking groups (Nguni Sotho-Tswana),...
InterPro amalgamates predictive protein signatures from a number of well-known partner databases into single resource. To aid with interpretation results, entries are manually annotated terms the Gene Ontology (GO). The InterPro2GO mappings comprised cross-references between these two resources and largest source GO annotation predictions for proteins. Here, we describe protocol by which curators integrate database. We discuss unique challenges involved in integrating specific that may...
Bioinformatics is recognized as part of the essential knowledge base numerous career paths in biomedical research and healthcare. However, there little agreement field over what that entails or how best to provide it. These disagreements are compounded by wide range populations need bioinformatics training, with divergent prior backgrounds intended application areas. The Curriculum Task Force International Society Computational Biology (ISCB) Education Committee has sought a framework for...
Abstract Given that the biological processes governing oncogenesis of pancreatic cancers could present useful therapeutic targets, there is a pressing need to molecularly distinguish between different clinically relevant cancer subtypes. To address this challenge, we used targeted proteomics and other molecular data compiled by The Cancer Genome Atlas reveal tumours can be broadly segregated into two distinct Besides being associated with substantially clinical outcomes, belonging each these...