A5004336328- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- Biomedical Text Mining and Ontologies
- COVID-19 Clinical Research Studies
- Long-Term Effects of COVID-19
- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Machine Learning in Bioinformatics
- Semantic Web and Ontologies
- Animal Genetics and Reproduction
- COVID-19 diagnosis using AI
- Hepatitis B Virus Studies
- Genomics and Rare Diseases
- Hepatitis C virus research
- Hydrocarbon exploration and reservoir analysis
- RNA and protein synthesis mechanisms
- Liver Disease Diagnosis and Treatment
- Computational Drug Discovery Methods
- HIV, Drug Use, Sexual Risk
- Gene expression and cancer classification
- Geological and Geophysical Studies
- Scientific Computing and Data Management
- Opioid Use Disorder Treatment
- Plant Virus Research Studies
University of Delaware
2015-2024
Shenzhen Third People’s Hospital
2017-2024
Southern University of Science and Technology
2019-2024
European Bioinformatics Institute
2023-2024
SIB Swiss Institute of Bioinformatics
2024
Hainan General Hospital
2022-2023
Hainan Medical University
2022-2023
Machine Science
2013-2021
South China University of Technology
2021
University of Macau
2019-2021
When compared to Sanger sequencing technology, next-generation (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo reference-based assembly, introducing artifacts errors that may contribute incorrect interpretation data. Although many tools have been developed for control pre-processing NGS data, none them provide...
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication, we describe ongoing changes our production pipeline limit available in UniProtKB high-quality, non-redundant reference proteomes. We continue manually curate scientific literature add latest data use machine learning techniques. also encourage community curation...
The UniProt knowledgebase is a public database for protein sequence and function, covering the tree of life over 220 million entries. Now, whole community can use new crowdsourcing annotation system to help scale up curation receive proper attribution their biocuration work.
The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization annotation systematic detection errors, PIR has extended its superfamily concept developed SuperFamily (PIRSF) classification system. Based on evolutionary relationships whole proteins, this system allows both specific biological generic biochemical functions. adopts a network structure for from to subfamily levels. family members are...
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation protein data to support genomic/proteomic research and scientific discovery. PIR, in collaboration with the Munich Center for Sequences (MIPS) Japan International Database (JIPID), produces PIR-International Sequence (PSD), major annotated sequence database domain, containing about 250 000 proteins. To improve coverage experimentally validated data, a bibliography submission system is...
We have developed a new web application for peptide matching using Apache Lucene-based search engine. The Peptide Match service is designed to quickly retrieve all occurrences of given query from UniProt Knowledgebase (UniProtKB) with isoforms. matched proteins are shown in summary tables rich annotations, including sequence region(s) and links corresponding number proteomic/peptide spectral databases. results grouped by taxonomy can be browsed organism, taxonomic group or tree. supports...
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific taxon-neutral protein-related entities in three major areas: proteins related by evolution; produced from a given gene; protein-containing complexes. PRO thus serves as tool for referencing protein at any level of specificity. To enhance this ability, to facilitate the comparison such described different resources, we developed standardized representation proteoforms using UniProtKB...
Abstract Background Thousands of Coronavirus Disease 2019 (COVID-19) patients have been discharged from hospitals Persistent follow-up studies are required to evaluate the prevalence post-COVID-19 fibrosis. Methods This study involves 462 laboratory-confirmed with COVID-19 who were admitted Shenzhen Third People’s Hospital January 11, 2020 April 26, 2020. A total 457 underwent thin-section chest CT scans during hospitalization or after discharge identify pulmonary lesion. 287 followed up 90...
The accelerating growth in the number of protein sequences taxes both computational and manual resources needed to analyze them. One approach dealing with this problem is minimize proteins subjected such analysis a way that minimizes loss information. To end we have developed set Representative Proteomes (RPs), each selected from Proteome Group (RPG) containing similar proteomes calculated based on co-membership UniRef50 clusters. A proteome can best represent all its group terms majority...
Identifier (ID) mapping establishes links between various biological databases and is an essential first step for molecular data integration functional annotation. ID allows diverse on genes proteins to be combined mapped pathways ontologies. We have developed comprehensive protein-centric services providing mappings 90 IDs derived from genes, proteins, pathways, diseases, structures, protein families, interaction, literature, ontologies, etc. The are widely used been regularly updated since...
<ns4:p>Chondrichthyan fishes are a diverse class of gnathostomes that provide valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies phylogeny, species diversity, population structure, conservation, physiology accelerated genomic, transcriptomic protein sequence data. These data widely available for many sarcopterygii (coelacanth, lungfish tetrapods) actinoptergii (ray-finned fish including teleosts) taxa, but limited chondrichthyan fishes. In...
Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result genome sequencing and prediction protein-coding genes. Providing functional annotation for these proteins presents significant continuing challenge. Results In response this challenge, has developed method annotation, known UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) by members...
The Kuqa depression along the northern flank of Tarim basin is filled with a thick sequence Neogene and Quaternary coarse elastic continental sediments. This structural part large foreland that lies south Tianshan—an orogenic belt intracontinental convergence resulting from northward propagation stress following collision India southern margin Eurasia.
Iron–sulfur (Fe-S) clusters are ancient enzyme cofactors found in virtually all life forms. We evaluated the physiological effects of chronic Fe-S cluster deficiency human skeletal muscle, a tissue that relies heavily on cluster-mediated aerobic energy metabolism. Despite greatly decreased oxidative capacity, muscle from patients deficient scaffold protein ISCU showed predominance type I fibers and higher capillary density, enhanced expression transcriptional co-activator PGC-1α increased...
Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood sequence data has made it critically important to train the next generation scientists handle inherent bioinformatic challenges. North East Bioinformatics Collaborative (NEBC) is undertaking genome and annotation little skate (Leucoraja erinacea) promote advancement bioinformatics infrastructure our region, an emphasis on...
Genetic selection for enhanced growth rate in meat-type chickens (Gallus domesticus) is usually accompanied by excessive adiposity, which has negative impacts on both feed efficiency and carcass quality. Enhanced visceral fatness several unique features of avian metabolism (i.e., fasting hyperglycemia insulin insensitivity) mimic overt symptoms obesity related metabolic disorders humans. Elucidation the genetic endocrine factors that contribute to could also advance our understanding human...
SLC10A1 codes for the sodium-taurocholate cotransporting polypeptide (NTCP), which is a hepatocellular transporter bile acids (BAs) and receptor hepatitis B D viruses. NTCP also target of multiple drugs. We aimed to evaluate medical consequences loss function mutation p.Ser267Phe in SLC10A1. identified eight individuals with homozygous followed up 8-90 months. compared their total serum BAs 6 species 170 wild-type 107 heterozygous healthy individuals. performed in-depth examinations exome...
Nicotine is one of the primary components in cigarettes, which responsible for addiction. Numerous studies have investigated effects nicotine on pulmonary disease. The health epithelial cells important development chronic obstructive disease (COPD). Accumulating evidence has suggested that cell death may initiate or contribute to progression a number lung diseases via airway remodeling. Pyroptosis unique form inflammatory mediated by activation caspase‑1 and NOD‑like receptor protein‑3...
Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map pathways induced in liver during embryo-to-hatchling transition. Furthermore, we know very little about regulatory factors regulate lipid metabolism late embryos or newly-hatched chicks. In present study, examined hepatic transcriptomes of 12 hatchling chicks peri-hatch period-or switch from chorioallantoic pulmonary respiration.Initial...
Coffee leaf rust caused by the fungus Hemileia vastatrix is one of most important diseases coffee plantations worldwide. Current knowledge H. genome limited and only a small fraction total fungal secretome has been identified. In order to obtain more comprehensive understanding its secretome, we aimed sequence assemble entire using two next-generation sequencing platforms hybrid assembly strategy. This resulted in 547 Mb race XXXIII (Hv33), with 13,364 predicted genes that encode 13,034...
Abstract Summary The global response to the COVID-19 pandemic has led a rapid increase of scientific literature on this deadly disease. Extracting knowledge from biomedical and integrating it with relevant information curated biological databases is essential gain insight into etiology, diagnosis treatment. We used Semantic Web technology RDF integrate mined by iTextMine, PubTator SemRep formalized in standardized computable Knowledge Graph (KG). published KG via SPARQL endpoint support...
Among 417 COVID-19 patients in Shenzhen, demographic characteristics, clinical manifestations and baseline laboratory tests showed significant differences between mild-moderate cohort severe-critical cohort.Based on these differences, a convenient mathematical model was established to predict the illness severity of COVID-19. The includes four parameters: age, BMI, CD4+ lymphocytes IL-6 levels. AUC is 0.911.The high risk factors for developing severe are: age ≥ 55 years, BMI > 27 kg / m2, 20...
Abstract Late recurrences of breast cancer are hypothesized to originate from disseminated tumor cells that re‐activate after a long period dormancy, ≥5 years for estrogen‐receptor positive (ER+) tumors. An outstanding question remains as what the key microenvironment interactions regulate this complex process, and well‐defined human model systems needed probing this. Here, robust, bioinspired 3D ER+ dormancy culture is established utilized probe effects matrix properties common sites late...