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, 39, 2011.
  5. List of sequenced genomes
  6. Bioinformatics in the Post-sequence Era, M. Kanehisa and P. Bork, Nature Genetics, 33, March 2003.
  7. 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.
  8. Pharmacogenetics and Drug Development: The Path to Safer and More Effective Drugs, A.D. Roses, Nature Reviews, Genetics, 5, September 2004, pp. 645-656.
  9. What is the relevance of bioinformatics to pharmacology?, P. A. Whittaker, Trends in Pharmacological Sciences, 24(8), August 2003, pp. 434-439.
  10. 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.
  6. Protein sequence comparison and protein evolution, W.R. Pearson, Tutorial, ISMB 2000.
  7. Initial sequencing and comparative analysis of the mouse genome, Mouse Genome Sequencing Consortium, Nature, vol. 402, Dec. 2002.
  8. Gapped Blast and PSI-Blast: a new generation of protein database search programs, Altschul et al, Nucleic Acids Research, 25(17), pp. 3389-3402.
  9. The statistics of sequence similarity scores, NCBI.
  10. 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.
  11. 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).
  12. 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).
  13. Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals, Nathan L. Nehrt., Wyatt T. Clark., Predrag Radivojac, Matthew W. Hahn, PLoS Computational Biology, Volume 7, Issue 6, June 2011.
  14. Orthology, paralogy and proposed classification for paralog subtypes, Erik L.L. Sonnhammer, TRENDS in Genetics Vol.18 No.12 December 2002.
  15. Average time until fixation of a mutant allele in a finite population under continued mutation pressure: Studies by analytical, numerical, and pseudo-sampling methods,  M. Kimura, Proc. Natl. Acad.  Sci. USA, Vol.  77, No. 1, pp. 522-526, January 1980. 
  16. Genetic Drift and Effective Population Size, Kliman, R., Sheehy, B. & Schultz, J. (2008)  Nature Education 1(3).
  17. Fixation Probabilities and Times, Sarah P Otto, Michael C Whitlock, ENCYCLOPEDIA OF LIFE SCIENCES & 2008, John Wiley & Sons, Ltd. www.els.net.