Bioinformatics and Health Informatics Materials
A collection of labs, MOOCs, Websites on Bioinformatics. This article will be updated regularly.
Websites
1. Persagen
My favorite page on:
- Biology-related topics: molecular genetics, cancer molecular biology, personalized and precision medicine, bioinformatics.
- Informatics-related topics: natural language processing, computational linguistics, information retrieval | extraction, machine learning, knowledge stores, graphical models (Apache Solr | PostgreSQL | Neo4j | Cypher), knowledge discovery and data mining.
2. Rosalind
A platform for learning bioinformatics through problem solving.
3. OMGenomics
A great website by Maria Nattestad, which focus on data visualization for genomics.
Labs
1. Imaging and Modeling lab, Instut Pasteur
A lab from the Institut Pasteur. Focuses: Medical images
2. Myers Research Group
A group from the University of Utah. Focuses: Genetics
3. Computational Phenomics & Machine Learning
This group has developed Human Phenotype Oncology and applications of this ontology to differential diagnostics and genomics analysis.
MOOCs
1. Open Source Society University
Path to a free self-taught education in Bioinformatics.
Bioinformatics Database
1. Reactome
An open source, open access, manually curated and peer-review pathway database.
2. Mouse Phenotype
The International Mouse Phenotyping Consortium (IMPC) is an international effort by 19 research institutions to identify the function of every protein-coding gene in the mouse genome.
3. OpenfMRI
A project dedicated to free and open sharing of raw magnetic resonance images (MRI) datasets.
4. UCI Machine Learning Repository
A collection of databases, domain theories, and data generators.
5. SciLifeLab
Science for Life Laboratory is an institution for the advancement of molecular biosciences in Sweden.
6. Genomic Data Commons (GDC)
“The Genomic Data Commons (GDC) is a research program of the National Cancer Institute (NCI). The mission of the GDC is to provide the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine.”
7. Proteomic Data Commons (PDC)
“Proteomic and phosphoproteomic analyses of brain tumor samples included in the Kids First PBTA cohort and represent 199 patients analyzed, integrating the proteomic and genomic molecular characterization across seven pediatric and AYA (adolescent and young adult) histologies: Low Grade Glioma, High Grade Glioma, Ependymoma, Ganglioglioma, Craniopharyngioma, Atypical Teratoid Rhabdoid Tumor (ATRT), and Medulloblastoma”
8. The Cancer Genome Atlas Program
The Cancer Genome Atlas Program (TCGA) is a large database of cancer genomics and is public to the community.
Ontologies
1. Unified Medical Language System (UMLS)
“The UMLS integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records.”