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

Related Work

Netflix Prize


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

Sample Result

Side Projects

PubMed Author Analysis - TF author results
TF list


Bioinformatics Tools
Shell Scripting
Text Manipulation
R statistics Snippets
Chromosome Location to Features
MySQL Snippets

Journals to Submit to


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



  1. transcription factor genes from Entrez Gene (genes)
  2. brain disease publications from PubMed (disease term, pubmedID)
  3. brain disease verification set from OMIM (genes, disease)
  4. brain disease list/ontology (disease) - UMLS (MeSH + Neuronames + SnoMed + …), ?
  5. GeneRIF (gene,pubmedID)
  6. get (gene) mapping to (disease)
  7. 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)

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