PhD Research
Mining Brain-Related Transcription Factor-Disease Relationships for Novel Linkages
Overview of PhD Research
PhD Research Proposal - Summer 2007
Committee Meeting - Fall 2008
Blog and Meeting Notes
Moved to a Wordpress Blog
Older entries archived at PhD Research Forum
Results
Research Results: All the Hard Data
Adapt to Muscle
Implementation Details: The Programming Bits
Data Source Analysis: Information about the data sources used
Computational Resources
Scoring Methods
Profile Comparisons
Validation
Side Projects
PubMed Author Analysis - TF author results
TF list
n-SIFT
Miscellaneous Tools
Bioinformatics Tools
Shell Scripting
Text Manipulation
R statistics Snippets
Chromosome Location to Features
MySQL Snippets
Timeline
Notes on Committee Meetings and Qualifying Exam
TODO list
- ROC-style curve analysis/AUC analysis
- Cloud-style Profiles for Diseases
- Committee Report
- Slides for Meeting
Data
Posters/Presentations
- transcription factor genes from Entrez Gene (genes)
- brain disease publications from PubMed (disease term, pubmedID)
- brain disease verification set from OMIM (genes, disease)
- brain disease list/ontology (disease) - UMLS (MeSH + Neuronames + SnoMed + …), ?
- GeneRIF (gene,pubmedID)
- get (gene) mapping to (disease)
- investigate other methods of linking genes to disease - via common (terms)
Exploratory Research Notes: Big list of papers and ideas
Study Notes: Facts to study (comprehensive exam)
Misc
- UBC Thesis Template Source (Feb 21.2007) http://alum.mit.edu/www/mforbes/projects/ubcthesis/
