PAPER LIST

A. Introduction

1.      Primer on Molecular Genetics

2.      Chapter 1 from Molecular Biology for Computer Scientists

3.      The Neutral Theory is Dead. Long Live the Neutral Theory. M. Kreitman, Bioessays, vol. 8, no. 8.

4.      Molecular biology database collection, Nucleic Acids Research, 36, Jan. 2008.

5.      List of sequenced genomes

6.      Interrelating genomic data

7.      Defining bioinformatics

8.      Bioinformatics in the Post-sequence Era, M. Kanehisa and P. Bork, Nature Genetics, 33, March 2003.

9.      Data Management for the Biosciences, Report of the NSF/NLM Workshop of Data Management for Molecular and Cell Biology, Feb. 2003

10.  Bionformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine?, V. Maojo and C.A. Kulikowski, JAMIA, 10(6), Nov/Dec 2003, pp. 515-522.

11.  Pharmacogenetics and Drug Development: The Path to Safer and More Effective Drugs, A.D. Roses, Nature Reviews, Genetics, 5, September 2004, pp. 645-656.

12.  What is the relevance of bioinformatics to pharmacology?, P. A. Whittaker, Trends in Pharmacological Sciences, 24(8), August 2003, pp. 434-439.

13.  Plant Bioinformatics: from Genome to Phenome, D. Edwards and J. Batley, Trends in Biotechnology, 22(5), May 2004, pp. 323-237.

 

 

B. Sequence analysis

 

  1. A model of evolutionary change in proteins, M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt
  2. Homology, a personal view on some of the problems, W.M. Fitch, TIG, 16(5), May 2000, pp. 227-231.
  3. The modern molecular clock, L. Bromham and D. Penny, Nature Genetics Review, March 2003.

4.      Where did the BLOSUM62 alignment score matrix come from?, S.R. Eddy, Nature Biotechnology, 22(8), August 2004.

5.      Amino Acid substitution matrices from Protein Blocks, Heinkoff and Heinkoff, PNAS, 89(22):10915-10919, November 1992.

  1. Protein sequence comparison and protein evolution, W.R. Pearson, Tutorial, ISMB 2000.
  2. Initial sequencing and comparative analysis of the mouse genome, Mouse Genome Sequencing Consortium, Nature, vol. 402, Dec. 2002.
  3. Gapped Blast and PSI-Blast: a new generation of protein database search programs, Altschul et al, Nucleic Acids Research, 25(17), pp. 3389-3402.
  4. The statistics of sequence similarity scores, NCBI.
  5. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Nucleic Acids Research, 22:4673-4680.
  6. Alignment of Whole Genomes, Delcher A. L., Kasif S., Fleischmann R. D., Peterson J, White O., Salzberg S.L., Nucleic Acids Research, 27:11, 2369-2376. (1999).
  7. Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction, Batzoglou S., Pachter L, Mesirov J., Berger, B., Lander E. S., Genome Research, 10:950. (2000).

 

 

 

READING ASSIGNMENT

October 1: Papers 1 and 2 from Introduction

I only need a critique of Paper 2.

There are 7 sections that contain material. You can choose to direct your comments at any one of the sections. Some questions to consider:

·         Is the material well presented?

·         Was it appropriate for your background?

·         What would you have changed?

·         Did it inspire you to read further?

Remember not to write a summary.  I am interested in your reaction in 1-2 paragraphs.

Please email it by Monday October 6.

October 18: Papers 2 and 3 from Sequence analysis

I only need a critique of Paper 3. Please email it to me by October 24. Again, I need 1-2 paragraphs.