Andrew Nightingale
A5027873927- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Embedded Systems Design Techniques
- Genomics and Rare Diseases
- Computational Drug Discovery Methods
- Interconnection Networks and Systems
- Gene expression and cancer classification
- Corneal surgery and disorders
- VLSI and Analog Circuit Testing
- Enzyme Structure and Function
- Genomic variations and chromosomal abnormalities
- Scientific Computing and Data Management
- Advanced Proteomics Techniques and Applications
- Hereditary Neurological Disorders
- Genetic Associations and Epidemiology
- Digital Humanities and Scholarship
- Phytoplasmas and Hemiptera pathogens
- Data Mining Algorithms and Applications
- Neurological diseases and metabolism
- Cellular transport and secretion
- RNA and protein synthesis mechanisms
- Research Data Management Practices
- Evolution and Genetic Dynamics
European Bioinformatics Institute
2015-2021
New York Eye and Ear Infirmary
2014-2018
Protein Information Resource
2017
SIB Swiss Institute of Bioinformatics
2017
Columbia University
2007
ARM (United Kingdom)
2003-2006
American Rock Mechanics Association
2005
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this article, we describe significant updates that have made over last two years resource. number in UniProtKB has risen approximately 190 million, despite continued work reduce sequence redundancy at proteome level. We adopted new methods assessing completeness quality. continue extract detailed annotations from...
Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication we describe enhancements made our data processing pipeline website adapt an ever-increasing information content. number in UniProtKB has risen over 227 million are working towards including reference proteome for each taxonomic group. We continue extract detailed annotations from literature...
Abstract Motivation To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities Biological Interest), to better support efforts study and predict functionally interactions between protein sequences structures small molecule ligands. Results We structured data model cognate ligand site annotations performed a complete reannotation all stable unique identifiers from...
The Proteins API provides searching and programmatic access to protein associated genomics data such as curated sequence positional annotations from UniProtKB, well mapped variation proteomics large scale sources (LSS). Using the coordinates service, researchers are able retrieve genomic for proteins in UniProtKB. This, LSS UniProt is programmatically only available through this service. A Swagger UI has been implemented provide documentation, an interface users, with little or no...
Abstract Motivation Understanding the protein structural context and patterning on proteins of genomic variants can help to separate benign from pathogenic reveal molecular consequences. However, mapping coordinates structures is non-trivial, complicated by alternative splicing transcript evidence. Results Here we present VarMap, a web tool for list chromosome canonical UniProt sequences associated 3D structures, including validation checks, annotating them with information. Availability...
Understanding the association of genetic variation with its functional consequences in proteins is essential for interpretation genomic data and identifying causal variants diseases. Integration protein function knowledge genome annotation can assist rapidly comprehending within complex biological processes. Here, we describe mapping UniProtKB human sequences positional annotations, such as active sites, binding to (GRCh38) release a public track hub browsers. To demonstrate power combining...
Abstract Systemic analysis of available large-scale biological/biomedical data is critical for studying biological mechanisms, and developing novel effective treatment approaches against diseases. However, different layers the are produced using technologies scattered across individual computational resources without any explicit connections to each other, which hinders extensive integrative multi-omics-based analysis. We aimed address this issue by a new integration/representation...
J. Neurochem .(2008) 104, 1536–1552. Abstract Charcot‐Marie‐Tooth disease (CMT) is an inherited peripheral neuropathy that has been linked to mutations in multiple genes. Mutations the neurofilament light ( NFL ) chain gene lead CMT2E form whereas myotubularin‐related protein 2 and 13 MTMR2 MTMR13 genes CMT4B form. These two forms share characteristic pathological hallmarks on nerve biopsies including concentric sheaths (‘onion bulbs’) and, at least one case, myelin loops. In addition, shown...
UniProt continues to support the ongoing process of making scientific data FAIR. Here we contribute this with a FAIRness assessment our UniProtKB dataset followed by critical reflection on challenges and future directions adoption validation FAIR principles metrics.
We describe how system design consistency can be maintained across multiple levels of abstraction using a modular verification IP strategy. This strategy involves delivery in an environment independent manner, utilizing standard architecture that leverages re-usable component drivers, transaction-based interfaces, and synchronization through system-verification master. enables single test-bench to applied for systems modeled both SystemC, as well at the RT level. The configuration testbench...
Abstract Systemic analysis of available large-scale biological and biomedical data is critical for developing novel effective treatment approaches against both complex infectious diseases. Owing to the fact that different sections produced by organizations/institutions using various types technologies, are scattered across individual computational resources, without any explicit relations/connections each other, which greatly hinders comprehensive multi-omics-based data. We aimed address...
ABSTRACT Motivation Studying the pattern of genetic variants is a primary step in deciphering basis biological diversity, identifying key ‘driver variants’ that affect disease states and evolution species. Catalogs contain vast numbers are growing at an exponential rate, but lack interactive exploratory interface. Results We present BioJS-HGV Viewer, BioJS component to represent visualize pooled from different sources. The tool displays sequences levels detail, facilitating representation...
Abstract Understanding the association of genetic variation with its functional consequences in proteins is essential for interpretation genomic data and identifying causal variants diseases. Integration protein function knowledge genome annotation can assist rapidly comprehending within complex biological processes. Here, we describe mapping UniProtKB human sequences positional annotations such as active sites, binding to (GRCh38) release a public track hub browsers. To demonstrate power...