A5090122303- Machine Learning in Bioinformatics
- Evolution and Genetic Dynamics
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Malaria Research and Control
- Insect Resistance and Genetics
- Enzyme Structure and Function
- Mosquito-borne diseases and control
- Invertebrate Immune Response Mechanisms
- Insect symbiosis and bacterial influences
- Glycosylation and Glycoproteins Research
- Traumatic Brain Injury and Neurovascular Disturbances
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Species Distribution and Climate Change
- Viral Infectious Diseases and Gene Expression in Insects
- Genomics and Chromatin Dynamics
- Monoclonal and Polyclonal Antibodies Research
- Forensic Entomology and Diptera Studies
- Evolutionary Algorithms and Applications
- Evolutionary Game Theory and Cooperation
- Sepsis Diagnosis and Treatment
- Acute Ischemic Stroke Management
- Forest Insect Ecology and Management
Imperial College London
2008-2023
Vector (United States)
2018
University of Crete
2011
University of Notre Dame
2011
Wellcome Trust
2011
European Bioinformatics Institute
2011
Stockholm University
2003-2007
University of Geneva
2007
Johns Hopkins University
2007
University of California, Riverside
2007
Mosquitoes are vectors of parasitic and viral diseases immense importance for public health. The acquisition the genome sequence yellow fever Dengue vector, Aedes aegypti (Aa), has enabled a comparative phylogenomic analysis insect immune repertoire: in Aa, malaria vector Anopheles gambiae (Ag), fruit fly Drosophila melanogaster (Dm). Analysis signaling pathways response modules reveals both conservative rapidly evolving features associated with different functional gene categories...
VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors human pathogens. Now in its 11th year, currently hosts the genomes 35 organisms including number non-vectors comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript protein expression to population genetics variation insecticide-resistance phenotypes. Here we describe improvements our resource set tools...
Fourteen models were constructed and analyzed for the comparative modeling section of Critical Assessment Techniques Protein Structure Prediction (CASP4). Sequence identity between each target best possible parent(s) ranged 55 13%, root-mean-square deviation model was from 0.8 to 17.9 Å. In fold recognition section, 10 11 remote homologues recognized. The protocols are a combination automated computer algorithms, 3D-JIGSAW (for modeling) 3D-PSSM recognition), with human intervention at...
Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of explore new avenues vector control, we sequenced genomes 16 anopheline from diverse locations spanning ~100 million years evolution. Comparative analyses show faster rates gene gain loss, elevated shuffling on X chromosome, more intron losses, relative to Drosophila. Some determinants capacity,...
Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with EuPathDB projects. As a Bioinformatics Center funded by National Institutes Health, additional support from Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists fungi) relevant free-living or non-pathogenic species hosts. Designed to empower researchers access Omics data...
Abstract Summary: NucPred analyzes patterns in eukaryotic protein sequences and predicts if a spends at least some time the nucleus or no all. Subcellular location of proteins represents functional information, which is important for understanding interactions, diagnosis human diseases drug discovery. novel web tool based on regular expression matching multiple program classifiers induced by genetic programming. A likelihood score derived from programs each input sequence residue position....
In modern societies, cultural change seems ceaseless. The flux of fashion is especially obvious for popular music. While much has been written about the origin and evolution pop, most claims its history are anecdotal rather than scientific in nature. To rectify this we investigate US Billboard Hot 100 between 1960 2010. Using Music Information Retrieval (MIR) text-mining tools analyse musical properties ~17,000 recordings that appeared charts demonstrate quantitative trends their harmonic...
Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Center funded by the National Institutes of Health with additional funding from Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists fungi) relevant free-living or non-pathogenic species hosts. Since 2004, has analyzed omics data public domain using contemporary bioinformatic workflows, including...
VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, contains genome information three mosquito species: Aedes aegypti, Anopheles gambiae Culex quinquefasciatus, body louse Pediculus humanus tick species Ixodes scapularis. Since our last report has initiated community annotation...
VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) tsetse fly (Glossina morsitans). Hosted range from genomic features expression to population genetics ontologies. We describe improvements integration new that...
Traumatic brain injury (TBI) is responsible for up to 45% of in-hospital trauma mortality. Computed tomography (CT) central acute TBI diagnostics, and millions CT scans are conducted yearly worldwide. Though many studies have addressed individual predictors outcome from findings on scans, few done so a multivariate perspective. As these parameters interrelated in complex manner, there need better understanding them this context. 861 patients were reviewed according an extensive protocol. An...
The results of the first Critical Assessment Fully Automated Structure Prediction (CAFASP-1) are presented. objective was to evaluate success rates fully automatic web servers for fold recognition which available community. This study based on targets used in third meeting Techniques Protein (CASP-3). However, unlike CASP-3, not a blind trial, as it held after structures were known. aim assess performance methods without user intervention that several groups their CASP-3 submissions....
VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. annotates and maintains vector genomes providing an integrated resource the research community. Currently, contains genome two organisms: Anopheles gambiae, Plasmodium protozoan agent causing malaria, Aedes aegypti, flaviviral agents Yellow fever Dengue fever.
Music evolves as composers, performers, and consumers favor some musical variants over others. To investigate the role of consumer selection, we constructed a Darwinian music engine consisting population short audio loops that sexually reproduce mutate. This evolved for 2,513 generations under selective influence 6,931 who rated loops’ aesthetic qualities. We found quickly into attributable, in part, to evolution aesthetically pleasing chords rhythms. Later, however, slowed. Applying Price...
Here we present the evaluation results of Critical Assessment Protein Structure Prediction (CASP6) contact prediction category. Contact was assessed with standard measures well known in field and performance specialist groups evaluated alongside that submitted models 3D coordinates. The mainly focused on long range predictions for set new fold targets, although analyzed all targets. Three similar levels accuracy coverage performed a little better than others. Comparisons three best methods...
Current approaches to contact map prediction in proteins have focused on amino acid conservation and patterns of mutation at sequentially distant positions. This sequence information is poorly understood very little progress has been made this area during recent years.In study, an observation 'striped' across beta-sheets prompted the development a new type predictor. Computer program code was evolved with evolutionary algorithm (genetic programming) select residues residue pairs likely make...
The African mosquito Anopheles gambiae is the major vector of human malaria. We report a genome-wide survey gene expression profiles clustered temporally into developmental programs and spatially adult tissue-specific patterns. Global analysis shows that genes belong to related functional categories or encode same functionally linked protein domains are associated with characteristic tissue Comparative our data together published from Drosophila melanogaster reveal an overall strong positive...
Anopheles gambiae is a major mosquito vector responsible for malaria transmission, whose genome sequence was reported in 2002. Genome annotation continuing effort, and many of the approximately 13,000 genes listed VectorBase are predictions that have still not been validated by any other method. To identify protein-coding An. based on its genomic sequence, we carried out deep proteomic analysis using high-resolution Fourier transform mass spectrometry both precursor fragment ions. Based...
Cerebral microdialysis (MD) is used to monitor local brain chemistry of patients with traumatic injury (TBI). Despite an extensive literature on cerebral MD in the clinical setting, it remains unclear how individual levels real-time data are be interpreted. Intracranial pressure (ICP) and perfusion (CPP) important continuous monitors neurointensive care. They as surrogate blood flow have established relation outcome. The purpose this study was investigate relations between parameters ICP...
This paper reports an analysis of the encoded proteins (the proteome) genomes human, fly, worm, yeast, and representatives bacteria archaea in terms three-dimensional structures their globular domains together with a general sequence-based study. We show that 39% human proteome can be assigned to known structures. estimate for 77% proteome, there is some functional annotation, but only 26% standard sequence motifs characterize function. Of protein sequences, 13% are transmembrane proteins,...