CPBS 7711 readings

Introduction

• The Computational Bioscience Program educational mission statement.
• Sample preliminary exam short essay questions.

Planning a course project

• Advice on preparing a research plan (read: grant) from NINDS

Database Search and Sequence Alignment

• A textbook chapter on dynamic programming alignments.
• A textbook chapter on BLAST.
• (Chapter 2 of Durbin, Eddy, Krogh, Mitchison, "Biological Sequence Analysis" addresses both of the above)
• Per Kraulis' Lecture Notes on Dynamic Programming alignments, particularly the simple example and the more complex example
• The NCBI BLAST education pages (all sections).
• Altschul, et al on PSI-BLAST and on improving PSI-BLAST (using ROC curves)

Multiple Sequence Alignment

• Edgar & Batzoglou, Multiple Sequence Alignment, Current Opinion in Structural Biology 16(3):368-373, June 2006
• Thompson, et al, CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Res. 1994 November 11; 22(22): 4673
• The ClustalW2 FAQ
• Wrabi & Grishin, Gaps in structurally similar proteins: Towards improvement of multiple sequence alignment Proteins: Structure, Function, and Bioinformatics 2003 54(1): 71 - 87
• Sauder, et al, Large-scale comparison of protein sequence alignment algorithms with structure alignments.Proteins. 2000 Jul 1;40(1):6-22.

Hidden Markov Models

• Rabiner's classic tutorial on Hidden Markov Models, and erratum.
• Sean Eddy's Review article on HMMs, Bioinformatics 14:755-763 (1998).
• A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Research, 2002, Vol. 30, No. 19 4321-4328
• Rachel Karchin's ISMB'99 HMM tutorial "Making the Most of your HMM"
• The PFAM article in the 2006 NAR Database issue.

Sequence Assembly and Next-Gen Sequencing

• Drosophila genome paper
• Next-Gen Sequencing review

Molecular Biology Databases

• The Molecular Biology Database Collection: 2010 update. Nucleic Acids Research 2010 38(Database Issue):D1-D4
• The NCBI tutorial, Entrez: Making Use of Its Power

NIH materials on Reviewing Research Proposals

• Peer Review Policies and Practices
• Reviewer Orientation
• Scoring System
• Research Project Review Criteria and Considerations
• Review criteria at a glance for all different sorts of grants
• Review Template (in MS word format)
• Example review from NIH (in MS word format)

Reporting on your research

• Robert Day and Barbara Gastel's How to Write and Publish a Scientific Paper. This is a book that is worth owning, but most of the relevant parts are available on google books for free. It's a little old, but almost all of it is still true. You should know all of this stuff well.
• Kaj Sand-Jensen, How to write consistently boring scientific literature. A tongue-in-cheek, but useful article about scientific writing, aimed largely at ecologists, but still valuable to you.
• Janet Conrad's slides on how to write and give a good scientific talk are full of good advice, despite being a little physics-centric.

Biomedical Language Processing

• Altman et al, Text mining for biology - the way forward: opinions from leading scientists. Genome Biology 2008, 9(Suppl 2):S7.
• Renear and Palmer, Strategic Reading, Ontologies, and the Future of Scientific Publishing Science, Vol. 325, no. 5942, 14 August 2009.
• Shotton, Portwin, Klyne, and Miles. Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article PLoS Computational Biology, Vol. 5, no. 4, April 2009.
• Hunter and Cohen, Biomedical Language Processing: What's Beyond PubMed? Molecular Cell 2006 Mar 3;21(5):589-94.