CPBS 7711 readings

Introduction

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

Molecular Biology Databases

• The Molecular Biology Database Collection: 2009 update. Nucleic Acids Research 2009 37(Database Issue):D1-D4
• The NCBI tutorial, Entrez: Making Use of Its Power

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)

PyCogent

• Please read Knight 2007
• Please additionally review the PyCogent project page and in particular look at the Application Controller Framework documentation.
• I also encourage you to download and install the PyCogent toolkit from the developer site (so you have access to the latest code) before the lecture, and begin experimenting.
• Use case 1: tol_example.py This illustrates how to apply pycogent to evaluate the idea that life on Earth clusters into three related domains, which are detectable by distances between their rRNA sequences. Using sequences collections derived from the Silva database (filtered with cd-hit-est so the max pairwise identity between any two sequences is 97%), I randomly select sequences, build a tree, and then visualize the tree. Note that you'll need muscle, fasttree, and matplotlib installed to run this example.
• Use case 2: applying_an_existing_appc.txt This illustrates three different ways to apply the RDP classifier application controller: via the RDPController object, via the assign_taxonomy convenience function, and via the command line interface to the python module.
• Use case 3: defining_a_new_appc.txt, minimal_formatdb.py This discusses how to define a new application controller class to wrap the formatdb program packages with NCBI's blast package. (I had Blast-2.2.20 install when we ran through this in class.) As I mentioned, I frequently use formatdb to create temporary blast databases which I to clean up after using. So, I designed this new app controller for class and will be added an extended version, including some convenience functions, to PyCogent soon. The code I wrote in class is attached as minimal_formatdb.py

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.

Research plans and reviews of same

• NIH's application forms and instructions
• NIH's general review criteria for all grants.
• The forms and review criteria for NIH changed on September 16, 2009. A document explaining the changes is important because it shows how the new forms align with the review criteria.
• The instructions for completing a biosketch are in the process of being revised. I have excerpted what I think are the most current instructions from the revised instructions for a non-competing renewal. Here are blank forms in MS word and PDF formats.

Hidden Markov Models

• The HMM chapter in a textbook (The Ewans and Grant book is particularly good here).
• 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.

Reviewing Research Proposals

• NIH Reviewer Orientation
• NIH Scoring System
• NIH Research Project Review Criteria and Considerations
• NIH Review Template (in MS word format)
• NIH provided Example review (in MS word format)

Sequence Assembly

• Gene Myers, Whole Genome DNA Sequencing, IEEE Computational Engineering and Science 3, 1 (1999), 33-43. [Only available to UCHSC IP addresses.]
• Huang, et al. PCAP: A Whole-Genome Assembly Program. Genome Research, 13: 2164-2170 (2003)
• Warren, et al, Physical map-assisted whole-genome shotgun sequence assemblies. Genome Research 16(6):768-75. (2006)
• Gordon, et al. Consed: a graphical tool for sequence finishing. Genome Research 8:195-202 (1998).

Computational Phylogeny

• Kim & Warnow's ISMB '99 tutorial on phylogenetic inference.
• Huelsenbeck, et al, Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology Science 14 December 2001: Vol. 294. no. 5550, pp. 2310 - 2314 DOI: 10.1126/science.1065889
• Edgar and Sjolander SATCHMO: Sequence alignment and tree construction using hidden Markov models, Bioinformatics 19(11), 1404-1411. 2003

Protein Protein Interactions and networks

• Barabási and Oltvai, Network Biology: Understanding the Cell's Functional Organization Nature Reviews Genetics 5:101-113, February 2004
• Sharan, Ulitsky and Shamir, Network-based prediction of protein function Molecular Systems Biology 3:88 2007

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.

Protein Structure Prediction

• A book length treatment: Brandon and Tooze, Introduction to Protein Structure, second edition
• Hasegawa and Holm, Advances and Pitfalls of protein structural alignment Current Opinion in Structural Biology, 19(3):341-348, June 2009.
• Murzin, Brenner, Hubbard and Chothia, SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Molecular Biology, 247(4):536-540

Reviewing Research Manuscripts

• Elsevier's Reviewer's information pack (Pay particular attention to "Duties of Reviewers" and "A Brief Guide to Reviewing")
• Searls and Tanaka, Manuscript Peer Review: A Helpful Checklist for Students and Novice Reviewers Advances in Physiology Education 23:52-58, 2000
• Sara Rockwell's Ethical Issues in Peer Review

Mechanics, Dynamics & Docking

• Karplus & McCammon's Molecular dynamics simulations of biomolecules Nature: Structural Biology 2002 Sep;9(9):646-52.
• Nussinov, et al, Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 2002 Jun 1;47(4):409-43
• Gerstein & Echols' Exploring the range of protein flexibility, from a structural proteomics perspective. Curr Opin Chem Biol. 2004 Feb;8(1):14-9.

Genetic Analysis

• Short and opinionated overview of linkage and association analysis by Robert Elston, one of the founders of the field. Genetic Epidemiology 15(6):565-576, 1998. This was the 1997 International Genetic Epidemiology Society Presidential Address [NB: only works from UCHSC IP address.]
• The slides and notes, from the first lecture in Gil McVean's outstanding course on population genetics at Oxford (slides from 2004, notes from 2002 version). I strongly recommend reviewing the rest of the notes and slides from the population genetics course. Kent Holsinger also has produced a good set of lecture notes in population genetics (the PDFs have amusing footnotes missing in the HTML versions). The Holsinger notes are from an undergraduate course, and are easier to follow if you've never had any population genetics before.
• Slides from Terry Speed's outstanding 2007 ISMB keynote
• Lin and Zou, Assessing genomewide statistical significance in linkage studies. Genet Epidemiol. 2004 Nov;27(3):202-14.
• Marchini, et al, Genome-wide strategies for detecting multiple loci that influence complex diseases, Nature Genetics 37:413 - 417 (2005)
• The Introduction to the 14th Genetic Analysis Workshop. You can review the entire collection of associated papers for ones of particular interest to you. GAW 15 happened in 2006, but the papers aren't published yet; some results are available.
• Mailund, et al, Whole genome association mapping by incompatibilities and local perfect phylogeniesBMC Bioinformatics 2006, 7:454
• Wang, et al., Genome-wide Association Studies: Theoretical and Practical Concerns Nature Reviews Genetics 6, 109-118 (2005)
• The International HapMap Consortium, A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861. 2007.
• Barrett, et al, Haploview: analysis and visualization of LD and haplotype maps Bioinformatics 21:2(263-265), 2005.
• Optional:
  
  • Kruglyak, et al's Parametric and nonparametric linkage analysis: a unified multipoint approach. American Journal of Human Genetics 58(6):1347 (1996). You have to go to the library to get a copy.
  • The lectures on the coalescent, either from the 2002 Oxford population genetics course or from Holsinger's course
  • Simone Tavaré, et al report on a Markov Chain Monte Carlo method finding disease genes by coalescence, I see dead people: Gene Mapping Via Ancestral Inference from the 12th Genetic Analysis Workshop
  • Nicolas, et al, A model-based approach to selection of tag SNPs BMC Bioinformatics. 2006; 7: 303.

Presenting research

There are many places to get advice about presenting research results on-line. A few that you could look at:
• Tips from Tia Newhall, Swarthmore College
• Tips from Jeff Radel at the KU Medical Center
• Gratuitous advice on giving a talk by Colin Purrington at Swarthmore
• Video: a Humorous, but insightful, take on PowerPoint presentations
• Janet Conrad's slides, originally linked to above.

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.