Project Resource

Genetics and Molecular Biology

• An Introduction to Genetic Analysis.

Bioinformatics

• Bioinformatics Methods I, Coursera.
• Bioinformatics Methods II, Coursera.
• Concepts of Bioinformatics, ICAR.
  

Programming

• Applied Statistics for Bioinformatics using R, Wim P. Krijnen, 2009.
• R Tutorials, MarinStatsLectures, 2016.

Text Mining & Biopathways

• Getting Started in Biological Pathway Construction and Analysis, Ganesh A. Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C. Sealfon, 2008 
• A framework for the development of Biomedical Text Mining software tools,  Anália Lourenço, Rafael Carreira, Sónia Carnei ro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez- Riverola, Eugénio C. Ferreira, Isabel Rocha and Miguel Rocha, 2008 
• What the papers say: Text mining for genomics and systems biology, Nathan Harmston, Wendy Filsell and Michael PH Stumpf, Human Genomics, 2010.
• Integrated Bio-Entity Network- A System for Biological Knowledge Discovery,  Lindsey Bell, Rajesh Chowdhary, Jun S. Liu, Xufeng Niu, Jinfeng Zhang, 2011
• IMID: integrated molecular interaction database, Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S. Liu and Jinfeng Zhang, 2012

Lyme Disease

• RNA-Seq-based analysis of changes in Borrelia burgdorferi gene expression linked to pathogenicity,  Wu Q, Guan G, Liu Z, Li Y, Luo J, Yin H, Parasites & Vectors, 2015 

Tools/Database

• BioGRID: An interaction repository with data compiled through comprehensive curation efforts. 
• IntAct: Molecular Interaction Database.
• NCBI Gene: Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
• STITCH 4.0: A resource to explore known and predicted interactions of chemicals and proteins.
• IBN: Integrated bio-entity network for automatic biological knowledge discovery. 
• IMID: Integrated Molecular Interaction Database.
• PubMed: Comprises more than 26 million citations for biomedical literature. 
• KEGG: KEGG PATHWAY Database. 
• PID: NCI - Pathway Interaction Database.
• Reactome: A free, open-source, curated and peer reviewed pathway database.
• AmiGO 2: Allows users to query, browse and visualize ontologies and related gene product annotation (association) data.
• UniProt-GOA: Provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).