Topics and reading list
Fall 2018
BNFO 591 Proteins
G, W: General reading for all students (W = Wikipedia)
S: student specific material.
Each student will need to read 2 or 3 papers about a specific project, including 1-2 reviews and an original research papers, and give a short presentation about that topic.
Aug 28 Intro: Proteins and resources
- G: Proteins (Wikipedia)
- G: How many genes do we have?
- W(ikipedia): Bioinformatics
Sep 4: Protein resources
Sep 11 Mass spec (cancelled) now Nov 6
Sep 18: protein feature analysis
Sep 25: protein structure
- G: Protein structure (Wikipedia)
- G: Pymol intro, Pymol for beginners
- S: Covering complete genomes with X-ray structures
Oct 9: protein evolution, protein families
- W: protein evolution, protein families (Pfam tour)
- W: homology, sequence homology, sequence alignments
Oct 16: proteomes
W: Proteome
- W: Proteomics (Wikipedia)
- S: A subcellular map of the human proteome
- G: The human canonical protein count
- S: The human proteome
- S: Coding status of human genes
Types of proteins: membrane proteins
Oct 23: midterm quiz
Oct 30: Protein synthesis: translation, regulation
- W: Transcription, gene regulation, transcription factors
- W: Protein synthesis, regulation of translation
Nov 6: Mass spectrometry and protein analysis
- Kristina Nelson, Mass spec core facility, VCU
Nov 13: Signaling, protein interaction networks
- W: PPIs, Y2H and other PPI methods
- W: protein complexes, EBI complex portal (tour)
- W: signal transduction, PPI importance (1 h course)
- PPI databases: Intact (short, middle, long webinar) BioGRID
Nov 20: function prediction, disease
- W: Protein function prediction
- SMART
- W: Human genetics, human genetic variation
- Databases: OMIM (online), ClinVar, dbSNP info (human genetic diseases)
Nov 27: Protein/proteome evolution
- W: Molecular evolution (not great, so feel free to ignore)
- Directed evolution of proteins
- How do new proteins arise?
- Evolution of new protein functions
Dec 4: enzymology and metabolic networks
- W: enzymes, EC numbers
- W: Metabolic network modeling (metabolic reconstruction)
- S: Computational methods for metabolic reconstruction
Dec 11: Final exam