IRIDA's Genomic epidemiology application ontology (GenEpiO): Genomic, clinical and epidemiological data standardization and integration

GenEpiO: The Genomic Epidemiology Application Ontology for the Standardization and Integration of Microbial Genomic, Clinical and Epidemiological Data

http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/ Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.

A presentation introducing genomic epidemiology and its application in public health. It also explains the need for standards to support the Canadian Integrated Rapid Infectious Disease Analysis platform which implements genomic epidemiology analyses for detection and investigation of infectious disease outbreaks caused by food-borne pathogens.

This document discusses the GenEpiO (Genomic Epidemiology Application Ontology) project. GenEpiO aims to standardize terms used to describe genomic, laboratory, clinical, and epidemiological data related to foodborne pathogen outbreak investigations. This will help integrate these different types of data and allow researchers to more easily identify relationships between genomic clusters, exposures, locations, and other factors. The document provides examples of how GenEpiO could automatically generate case definitions and help facilitate data sharing between organizations. Development of GenEpiO focuses on ontologies for food, antimicrobial resistance, and disease surveillance.

The document summarizes a study on the use of empirical antibiotics for patients with signs of clinical infection but persistently negative cultures. The study was a prospective study conducted over two months at an ICU in New Delhi, India. It analyzed 200 consecutive patient samples based on criteria for clinical infection and response. Results found the median GCS was 11 and mean ventilated days was 7. 90% of cases were operated on and 90% improved and were discharged. The study concluded that empirical antibiotics can play a role for such patients and use of them could be reduced if better methods existed to differentiate infection from inflammatory response.

Poster presentation at the Rare Disease Symposium at Oregon Health & Science University in Portland, Oregon, 2015. http://openwetware.org/wiki/OHSU_Rare_Disease_Research_Consortium_Symposium_2015

Designing ICT location-aware recommender for mobile health information system Design science research method

IUPHAR Guide to IMMUNOPHARMACOLOGY poster. Presented at the BSI Congress 2017, Brighton, UK (6th December 2017) and at Pharmacology 2017, London, UK (13th December 2017.

Romain Banchereau is a computational biologist and translational immunologist focused on analyzing immune cell populations and transcriptional profiles from human disease cohorts. He has expertise in genomics analysis of blood and immune cells from infectious and autoimmune disease patients. Through bioinformatics analysis, he identifies biomarkers for disease diagnosis, prognosis, and response to treatment. He currently works as a research associate applying these skills to study lupus, juvenile arthritis, and complications during pregnancy with SLE.

The MiBio project aims to create a free online platform for sperm analysis across species. It provides a high reliability computer-assisted sperm analysis (CASA) system with species-specific knowledge bases and reference values developed from shared data. The platform allows automated batch analysis of biological samples with customizable settings. Researchers can contribute data to expand the knowledge bases and reference values or explore applying the technology to new areas like cell analysis.

Molecular biomarkers can be used for several purposes in infectious disease research and clinical practice. These include detecting pathogens, measuring antibody responses, identifying markers of virulence, resistance, and disease severity, and understanding human immune responses and genetic susceptibility. Challenges include lack of sensitivity, mobile genetic elements, and changes in RNA sequences. Whole genome sequencing allows investigation of microbial phylogeny, evolution, and virulence factors.

Case study and analysis of Targeted Genetics' adeno-associated virus, tgAAC94. Includes overview of clinical trial design, FDA action, NIH investigation, and outcomes surrounding the death of a patient enrolled in the investigational trial.

This document discusses the application of whole genome sequencing in infectious disease diagnostics. It provides examples of how genome sequencing has been used to identify bacterial species, detect antibiotic resistance genes, and study outbreaks. The document also discusses challenges around regulatory approval of genomic tests, data sharing policies, and database management. Overall, it argues that whole genome sequencing is a valuable tool but that standards must be developed to ensure high quality data.

The document discusses the intersection of precision medicine, biomarkers, and healthcare policy. It describes how biomarkers and -omics data can be used for precision medicine to improve diagnostic accuracy, deliver targeted therapies, and stratify patient populations. However, clinical validation of biomarkers now requires large datasets and years of studies due to regulatory and payer requirements. This has reduced incentives for diagnostic innovation. The document also discusses challenges around clinical interpretation of complex multi-omic tests, evolving medical training and workflows, and disconnects between patent and reimbursement policies.

This document presents a computational method for estimating the population structure of viruses using pyrosequencing reads. The method involves four steps: 1) aligning reads to a reference genome, 2) correcting sequencing errors in the reads, 3) reconstructing haplotypes consistent with the reads, and 4) estimating the frequency of each haplotype in the population. The method is validated on pyrosequencing data from four HIV populations, with over 5000 reads each, by comparing the estimated populations to those obtained from clonal sequencing.

Exploiting These are the slides from my talk at the Department of Computer Science at Sheffield University. The talk covers broad ground in my experience of applying natural language processing to knowledge discovery from various media including social media, news and the scientific literature.

An Introduction to Bioinformatics Drexel University INFO648-900-200915 A Presentation of Health Informatics Group 5 Cecilia Vernes Joel Abueg Kadodjomon Yeo Sharon McDowell Hall Terrence Hughes

Grand Challenges in Genomics A Joint NHGRI and Wellcome Trust Strategic Meeting 25 and 26 February 2019 https://www.wellcomeevents.org/WELLCOME/media/uploaded/EVWELLCOME/event_661/Draft_agenda_for_WT_December_2018.pdf Join lecture: Nicky Mulder, Han Brunner and Joaquin Dopazo