Papers for Computational Biology

These papers are provided for the use of CS 6104, summer, 2000.

• Steven E. Brenner, Cyrus Chothia, and Tim J. P. Hubbard
  Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
  PNAS 95, May 26, 1998, 6073-6078.

• Martijn A. Huynen and Erik van. Nimwegen
  Power-Laws in the Size Distribution of Gene Families in Complete Genomes: Biological Interpretations
  Technical report of the Santa Fe Institute

• Samuel Karlin and Stephen F. Altschul
  Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes
  PNAS 87, May, 1990, 2264-2268.

• Samuel Karlin, Amir Dembo, and Tsutomu Kawabata
  Statistical Composition of High-Scoring Segments from Molecular Sequences
  Annals of Statistics 18, June, 1990, 571-581.

• Atsushi Kasuya and Janet M. Thornton
  Three-dimensional Structure Analysis of PROSITE Patterns

• William R. Pearson, Todd Wood, Zheng Zhang, and Webb Miller
  Comparison of DNA Sequences with Protein Sequences
  Genomics 46, 1997, 24-36.

• Steven Salzberg, Arthur L. Delcher, Kenneth H. Fasman, John Henderson
  A Decision Tree System for Finding Genes in DNA
  This technical report is found at the MORGAN home page.
  A version of the technical report suitable to print in duplex and bind on the left is here.

• Jorg Schultz, Frank Milpetz, Peer Bork, and Chris P. Ponting
  SMART, a simple modular architecture research tool: Identification of signaling domains
  PNAS 95, May 1998, 5857-5864.

• Eugene G. Shpaer, Max Robinson, David Yee, James D. Candlin, Robert Mines, and Tim Hunkapiller
  Sensitivity and Selectivity in Protein Similarity Searches: A Comparison of Smith-Waterman in Hardware to BLAST and FASTA
  Genomics 38, 1996, 179-191.

• Michael S. Waterman and Martin Vingron
  Rapid and accurate estimates of statistical significance for sequence data base searches
  PNAS 91, May 1994, 4625-4628.

• Michael S. Waterman and Martin Vingron
  Sequence Comparison Significance and Poisson Approximation
  Statistical Science 9, August 1994, 367-381.

• G. ALastair Young
  Bootstrap: More than a Stab in the Dark?
  Statistical Science 9, August 1994, 382-395.

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