Reading List for Stat 315

 

  1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. H. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Research 25, no. 17 (1997): 3389-3402.

 

  1. Krogh, A., M. Brown, I. S. Mian, K. Sjolander, and D. Haussler. “Hidden Markov-Models in Computational Biology : Applications to Protein Modeling.” Journal of Molecular Biology 235, no. 5 (1994): 1501-1531.
  2. Baldi, P., Y. Chauvin, T. Hunkapiller, and M. A. McClure. “Hidden Markov-Models of Biological Primary Sequence Information.” Proceedings of the National Academy of Sciences of the United States of America 91, no. 3 (1994): 1059-1063.
  3. Lawrence, C. E., S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, and J. C. Wootton. “Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.” Science 262, no. 5131 (1993): 208-14.
  4. Sonnhammer, E. L. L., S. R. Eddy, E. Birney, A. Bateman, and R. Durbin. “Pfam: multiple sequence alignments and HMM-profiles of protein domains.” Nucleic Acids Research 26, no. 1 (1998): 320-322.

 

  1. Zuker, M., and P. Stiegler. “Optimal Computer Folding of Large Rna Sequences Using Thermodynamics and Auxiliary Information.” Nucleic Acids Research 9, no. 1 (1981): 133-148.
  2. Zuker, M. “On Finding All Suboptimal Foldings of an Rna Molecule.” Science 244, no. 4900 (1989): 48-52.
  3. Jaeger, J. A., D. H. Turner, and M. Zuker. “Improved Predictions of Secondary Structures For Rna.” Proceedings of the National Academy of Sciences of the United States of America 86, no. 20 (1989): 7706-7710.
  4. Lowe, T. M., and S. R. Eddy. “tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence.” Nucleic Acids Research 25, no. 5 (1997): 955-964.
  5. Lowe, T. M., and S. R. Eddy. “A computational screen for methylation guide snoRNAs in yeast.” Science 283, no. 5405 (1999): 1168-1171.
  6. Pedersen, A. G., P. Baldi, Y. Chauvin, and S. Brunak. “DNA structure in human RNA polymerase II promoters.” Journal of Molecular Biology 281, no. 4 (1998): 663-673.

 

 

  1. Burge, C., and S. Karlin. “Prediction of complete gene structures in human genomic DNA.” Journal of Molecular Biology 268, no. 1 (1997): 78-94.
  2. Burge, C. B., and S. Karlin. “Finding the genes in genomic DNA.” Current Opinion in Structural Biology 8, no. 3 (1998): 346-354.
  3. Krogh, A., I. S. Mian, and D. Haussler. “A Hidden Markov Model That Finds Genes in Escherichia-Coli Dna.” Nucleic Acids Research 22, no. 22 (1994): 4768-4778.

 

 

  1. Ewing, B., and P. Green. “Base-calling of automated sequencer traces using phred. II. Error probabilities.” Genome Research 8, no. 3 (1998): 186-194.
  2. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. “Base-calling of automated sequencer traces using phred. I. Accuracy assessment.” Genome Research 8, no. 3 (1998): 175-185.
  3. Gordon, D., C. Abajian, and P. Green. “Consed: A graphical tool for sequence finishing.” Genome Research 8, no. 3 (1998): 195-202.

 

  1. Koonin, E. V., R. L. Tatusov, and K. E. Rudd. “Protein sequence comparison at genome scale.” Computer Methods For Macromolecular Sequence Analysis 266 (1996): 295-322.
  2. Koonin, E. V., A. R. Mushegian, M. Y. Galperin, and D. R. Walker. “Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.” Molecular Microbiology 25, no. 4 (1997): 619-637.
  3. Koonin, E. V., and M. Y. Galperin. “Prokaryotic genomes: the emerging paradigm of genome-based microbiology.” Current Opinion in Genetics & Development 7, no. 6 (1997): 757-763.
  4. Tatusov, R. L., E. V. Koonin, and D. J. Lipman. “A genomic perspective on protein families.” Science 278, no. 5338 (1997): 631-637.
  5. Jain R, Rivera, M. C., Lake, J. A . “Horizontal gene transfer among genomes: The complexity hypothesis.”  Proceedings of the National Academy of Science 96, no. 7 (1999): pp. 3801-3806.

 

  1. Roth, F. P., J. D. Hughes, P. W. Estep, and G. M. Church. “Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.” Nature Biotechnology 16, no. 10 (1998): 939-945.
  2. Hughes, J. D., P. W. Estep, S. Tavazoie, and G. M. Church. “Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.” Journal of Molecular Biology 296, no. 5 (2000): 1205-1214.
  3. Johnson, J. M., and G. M. Church. “Alignment and structure prediction of divergent protein families: Periplasmic and outer membrane proteins of bacterial efflux pumps.” Journal of Molecular Biology 287, no. 3 (1999): 695-715.

 

  1. Salamov, A. A., and V. V. Solovyev. “Prediction of Protein Secondary Structure By Combining Nearest-Neighbor Algorithms and Multiple Sequence Alignments.” Journal of Molecular Biology 247, no. 1 (1995): 11-15.
  2. Frishman, D., and P. Argos. “Seventy-five percent accuracy in protein secondary structure prediction.” Proteins-Structure Function and Genetics 27,  3 (1997): 329-335.
  3. Yi, T. M., and E. S. Lander. “Protein Secondary Structure Prediction Using Nearest-Neighbor Methods.” Journal of Molecular Biology 232, no. 4 (1993): 1117-1129.
  4. Rost, B., and C. Sander. “Prediction of Protein Secondary Structure At Better Than 70-Percent Accuracy.” Journal of Molecular Biology 232, no. 2 (1993): 584-599.

 

  1. Felsenstein, J. “Distance Methods For Inferring Phylogenies : a Justification.” Evolution 38, no. 1 (1984): 16-24.
  2. Felsenstein, J. “Inferring phylogenies from protein sequences by parsimony ; distance ; and likelihood methods.” Computer Methods For Macromolecular Sequence Analysis 266 (1996): 418-427.
  3. Graur, D., W. A. Hide, and W. H. Li. “Is the Guinea-Pig a Rodent.” Nature 351, no. 6328 (1991): 649-652.
  4. Gu, X., Y. X. Fu, and W. H. Li. “Maximum-Likelihood-Estimation of the Heterogeneity of Substitution Rate Among Nucleotide Sites.” Molecular Biology and Evolution 12, no. 4 (1995): 546-557.
  5. Li, W. H. “Unbiased Estimation of the Rates of Synonymous and Nonsynonymous Substitution.” Journal of Molecular Evolution 36, no. 1 (1993): 96-99.
  6. Shyue, S. K., D. Hewettemmett, H. G. Sperling, D. M. Hunt, J. K. Bowmaker, J. D. Mollon, and W. H. Li. “Adaptive Evolution of Color-Vision Genes in Higher Primates.” Science 269, no. 5228 (1995): 1265-1267.
  7. Zharkikh, A., and W. H. Li. “Statistical Properties of Bootstrap Estimation of Phylogenetic Variability From Nucleotide-Sequences .1. 4 Taxa With a Molecular Clock.” Molecular Biology and Evolution 9, no. 6 (1992): 1119-1147.