CSE 527,  Au '07:  Approximate Schedule

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Schedule details will evolve as we go; please check back here every week or so to see the latest updates.

Textbook:

1. Richard Durbin, Sean R. Eddy, Anders Krogh and Graeme Mitchison, Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids, Cambridge, 1998. (U. Book Store, Amazon) Errata.

References:  Papers not explicitly listed as "Read" in each section are optional, good supplementary references, recommended if you want more depth in any of the areas.

  Electronic access to journals is generally free from on-campus computers. For off-campus access, follow the "[offcampus]" links or look at the library "proxy server" instructions.  

References -- Introduction & Overview: Read #2; a bit dated, but a good overview. Optional: If you want more biology, former students have recommended Gonick, (also a bit dated, but cheap). Alberts is a popular undergrad textbook, very comprehensive and very well written.

2. Lawrence Hunter, "Molecular Biology for Computer Scientists," Chapter 1 of Artificial Intelligence and Molecular Biology Lawrence Hunter, ed. AAAI press, 1993. (Also here.)
3. Larry Gonick, Mark Wheelis, "The Cartoon Guide to Genetics" (Updated Edition, 1991) ISBN 0062730991, Collins. (Amazon)
4. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, "Molecular Biology of the Cell", Fourth Edition, 2002, ISBN 0815332181, Garland (Amazon. This book is also available online, although the web version is somewhat hard to navigate.)

References -- Sequence Alignment, Search & Scoring: Read #5, 6, 8. The Myers review is a bit dated, but still a good overview of algorithms and algorithmic issues.

5. SR Eddy, "What is dynamic programming?" Nat. Biotechnol., 22, #7 (2004) 909-10. [offcampus]
6. SR Eddy, "Where did the BLOSUM62 alignment score matrix come from?" Nat. Biotechnol., 22, #8 (2004) 1035-6. [offcampus]
7. SR Eddy, "What is Bayesian statistics?" Nat. Biotechnol., 22, #9 (2004) 1177-8. [offcampus]
8. A Pertsemlidis, JW Fondon, "Having a BLAST with bioinformatics (and avoiding BLASTphemy)." Genome Biol., 2, #10 (2001) REVIEWS2002. [offcampus]
9. SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman, "Basic local alignment search tool." J. Mol. Biol., 215, #3 (1990) 403-10. [offcampus]
10. SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res., 25, #17 (1997) 3389-402. [offcampus]
11. Stephen Altschul, "The Statistics of Sequence Similarity Scores," http://www.ncbi.nlm.nih.gov/blast/tutorial/Altschul-1.html [offcampus]
12. Myers, E. (1991) "An overview of sequence comparison algorithms in molecular biology", Tech. Rep. TR-91-29, Dept. of Computer Science, Univ. of Arizona.

References -- Sequence Motif Modeling & Discovery: Read #14, 15, 17. Dempster et al. is the "classic" paper on EM. Tompa et al. is a comprehensive comparison of several motif finding methods. Blanchette et al. is an important example of use of comparitive genomics for this problem.

13. AP Dempster, NM Laird, DB Rubin, "Maximum Likelihood from Incomplete Data via the EM Algorithm," Journal of the Royal Statistical Society. Series B (Methodological), Vol. 39, No. 1. (1977), pp. 1-38. Available here. [offcampus]
14. GD Stormo, "DNA binding sites: representation and discovery." Bioinformatics, 16, #1 (2000) 16-23. [offcampus]
15. TL Bailey, C Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers." Proc Int Conf Intell Syst Mol Biol, 2, (1994) 28-36. [offcampus] Available here. See also http://meme.sdsc.edu/meme/ [offcampus] for related papers and resources.
16. TL Bailey, C Elkan, "The value of prior knowledge in discovering motifs with MEME." Proc Int Conf Intell Syst Mol Biol, 3, (1995) 21-9. [offcampus]
17. CE Lawrence, SF Altschul, MS Boguski, JS Liu, AF Neuwald, JC Wootton, "Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment." Science, 262, #5131 (1993) 208-14. [offcampus] Available here. [offcampus]
18. FP Roth, JD Hughes, PW Estep, GM Church, "Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation." Nat. Biotechnol., 16, #10 (1998) 939-45. [offcampus]
19. M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, MC Frith, Y Fu, WJ Kent, VJ Makeev, AA Mironov, WS Noble, G Pavesi, G Pesole, M Régnier, N Simonis, S Sinha, G Thijs, J van Helden, M Vandenbogaert, Z Weng, C Workman, C Ye, Z Zhu, "Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol., 23, #1 (2005) 137-44. [offcampus]
20. Emily Rocke and Martin Tompa An Algorithm for Finding Novel Gapped Motifs in DNA Sequences RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology, New York, NY, March 1998, 228-233.
21. M Blanchette, B Schwikowski, M Tompa, "Algorithms for phylogenetic footprinting." J. Comput. Biol., 9, #2 (2002) 211-23. [offcampus]
22. M Blanchette, M Tompa, "FootPrinter: A program designed for phylogenetic footprinting." Nucleic Acids Res., 31, #13 (2003) 3840-2. [offcampus]

References -- HMMs & Gene Finding: Read #23, 25. The Rabiner tutorial is a very good intro to HMMs if you want a different perspective from the text. Claverie is a good survey of computational gene finding. Burget and Guigo is a careful comparison of leading programs of its day. Lander et al. and Venter are the landmark initial human genome sequence papers. Klein et al. is an interesting application of HMMs relevant to RNA gene finding, our next topic.

23. SR Eddy, "What is a hidden Markov model?" Nat. Biotechnol., 22, #10 (2004) 1315-6. [offcampus]
24. LR Rabiner, "A Tutorial on Hidden Markov Models and Selected Application in Speech Recognition," Proceedings of the IEEE, v 77 #2,Feb 1989, 257-286. here.
25. C Burge, S Karlin, "Prediction of complete gene structures in human genomic DNA." J. Mol. Biol., 268, #1 (1997) 78-94. [offcampus]
26. M Burset, R Guigó, "Evaluation of gene structure prediction programs." Genomics, 34, #3 (1996) 353-67. [offcampus]
27. JM Claverie, "Computational methods for the identification of genes in vertebrate genomic sequences." Hum. Mol. Genet., 6, #10 (1997) 1735-44. [offcampus]
28. An extensive online bibliography
29. ES Lander, LM Linton, B Birren, C Nusbaum, MC Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh, R Funke, D Gage, K Harris, A Heaford, J Howland, L Kann, J Lehoczky, R LeVine, P McEwan, K McKernan, J Meldrim, JP Mesirov, C Miranda, W Morris, J Naylor, C Raymond, M Rosetti, R Santos, A Sheridan, C Sougnez, N Stange-Thomann, N Stojanovic, A Subramanian, D Wyman, J Rogers, J Sulston, R Ainscough, S Beck, D Bentley, J Burton, C Clee, N Carter, A Coulson, R Deadman, P Deloukas, A Dunham, I Dunham, R Durbin, L French, D Grafham, S Gregory, T Hubbard, S Humphray, A Hunt, M Jones, C Lloyd, A McMurray, L Matthews, S Mercer, S Milne, JC Mullikin, A Mungall, R Plumb, M Ross, R Shownkeen, S Sims, RH Waterston, RK Wilson, LW Hillier, JD McPherson, MA Marra, ER Mardis, LA Fulton, AT Chinwalla, KH Pepin, WR Gish, SL Chissoe, MC Wendl, KD Delehaunty, TL Miner, A Delehaunty, JB Kramer, LL Cook, RS Fulton, DL Johnson, PJ Minx, SW Clifton, T Hawkins, E Branscomb, P Predki, P Richardson, S Wenning, T Slezak, N Doggett, JF Cheng, A Olsen, S Lucas, C Elkin, E Uberbacher, M Frazier, RA Gibbs, DM Muzny, SE Scherer, JB Bouck, EJ Sodergren, KC Worley, CM Rives, JH Gorrell, ML Metzker, SL Naylor, RS Kucherlapati, DL Nelson, GM Weinstock, Y Sakaki, A Fujiyama, M Hattori, T Yada, A Toyoda, T Itoh, C Kawagoe, H Watanabe, Y Totoki, T Taylor, J Weissenbach, R Heilig, W Saurin, F Artiguenave, P Brottier, T Bruls, E Pelletier, C Robert, P Wincker, DR Smith, L Doucette-Stamm, M Rubenfield, K Weinstock, HM Lee, J Dubois, A Rosenthal, M Platzer, G Nyakatura, S Taudien, A Rump, H Yang, J Yu, J Wang, G Huang, J Gu, L Hood, L Rowen, A Madan, S Qin, RW Davis, NA Federspiel, AP Abola, MJ Proctor, RM Myers, J Schmutz, M Dickson, J Grimwood, DR Cox, MV Olson, R Kaul, C Raymond, N Shimizu, K Kawasaki, S Minoshima, GA Evans, M Athanasiou, R Schultz, BA Roe, F Chen, H Pan, J Ramser, H Lehrach, R Reinhardt, WR McCombie, M de la Bastide, N Dedhia, H Blöcker, K Hornischer, G Nordsiek, R Agarwala, L Aravind, JA Bailey, A Bateman, S Batzoglou, E Birney, P Bork, DG Brown, CB Burge, L Cerutti, HC Chen, D Church, M Clamp, RR Copley, T Doerks, SR Eddy, EE Eichler, TS Furey, J Galagan, JG Gilbert, C Harmon, Y Hayashizaki, D Haussler, H Hermjakob, K Hokamp, W Jang, LS Johnson, TA Jones, S Kasif, A Kaspryzk, S Kennedy, WJ Kent, P Kitts, EV Koonin, I Korf, D Kulp, D Lancet, TM Lowe, A McLysaght, T Mikkelsen, JV Moran, N Mulder, VJ Pollara, CP Ponting, G Schuler, J Schultz, G Slater, AF Smit, E Stupka, J Szustakowski, D Thierry-Mieg, J Thierry-Mieg, L Wagner, J Wallis, R Wheeler, A Williams, YI Wolf, KH Wolfe, SP Yang, RF Yeh, F Collins, MS Guyer, J Peterson, A Felsenfeld, KA Wetterstrand, A Patrinos, MJ Morgan, P de Jong, JJ Catanese, K Osoegawa, H Shizuya, S Choi, YJ Chen, J Szustakowki, International Human Genome Sequencing Consortium: "Initial sequencing and analysis of the human genome." Nature, 409, #6822 (2001) 860-921. [offcampus]
30. JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, GG Sutton, HO Smith, M Yandell, CA Evans, RA Holt, JD Gocayne, P Amanatides, RM Ballew, DH Huson, JR Wortman, Q Zhang, CD Kodira, XH Zheng, L Chen, M Skupski, G Subramanian, PD Thomas, J Zhang, GL Gabor Miklos, C Nelson, S Broder, AG Clark, J Nadeau, VA McKusick, N Zinder, AJ Levine, RJ Roberts, M Simon, C Slayman, M Hunkapiller, R Bolanos, A Delcher, I Dew, D Fasulo, M Flanigan, L Florea, A Halpern, S Hannenhalli, S Kravitz, S Levy, C Mobarry, K Reinert, K Remington, J Abu-Threideh, E Beasley, K Biddick, V Bonazzi, R Brandon, M Cargill, I Chandramouliswaran, R Charlab, K Chaturvedi, Z Deng, V Di Francesco, P Dunn, K Eilbeck, C Evangelista, AE Gabrielian, W Gan, W Ge, F Gong, Z Gu, P Guan, TJ Heiman, ME Higgins, RR Ji, Z Ke, KA Ketchum, Z Lai, Y Lei, Z Li, J Li, Y Liang, X Lin, F Lu, GV Merkulov, N Milshina, HM Moore, AK Naik, VA Narayan, B Neelam, D Nusskern, DB Rusch, S Salzberg, W Shao, B Shue, J Sun, Z Wang, A Wang, X Wang, J Wang, M Wei, R Wides, C Xiao, C Yan, A Yao, J Ye, M Zhan, W Zhang, H Zhang, Q Zhao, L Zheng, F Zhong, W Zhong, S Zhu, S Zhao, D Gilbert, S Baumhueter, G Spier, C Carter, A Cravchik, T Woodage, F Ali, H An, A Awe, D Baldwin, H Baden, M Barnstead, I Barrow, K Beeson, D Busam, A Carver, A Center, ML Cheng, L Curry, S Danaher, L Davenport, R Desilets, S Dietz, K Dodson, L Doup, S Ferriera, N Garg, A Gluecksmann, B Hart, J Haynes, C Haynes, C Heiner, S Hladun, D Hostin, J Houck, T Howland, C Ibegwam, J Johnson, F Kalush, L Kline, S Koduru, A Love, F Mann, D May, S McCawley, T McIntosh, I McMullen, M Moy, L Moy, B Murphy, K Nelson, C Pfannkoch, E Pratts, V Puri, H Qureshi, M Reardon, R Rodriguez, YH Rogers, D Romblad, B Ruhfel, R Scott, C Sitter, M Smallwood, E Stewart, R Strong, E Suh, R Thomas, NN Tint, S Tse, C Vech, G Wang, J Wetter, S Williams, M Williams, S Windsor, E Winn-Deen, K Wolfe, J Zaveri, K Zaveri, JF Abril, R Guigó, MJ Campbell, KV Sjolander, B Karlak, A Kejariwal, H Mi, B Lazareva, T Hatton, A Narechania, K Diemer, A Muruganujan, N Guo, S Sato, V Bafna, S Istrail, R Lippert, R Schwartz, B Walenz, S Yooseph, D Allen, A Basu, J Baxendale, L Blick, M Caminha, J Carnes-Stine, P Caulk, YH Chiang, M Coyne, C Dahlke, A Mays, M Dombroski, M Donnelly, D Ely, S Esparham, C Fosler, H Gire, S Glanowski, K Glasser, A Glodek, M Gorokhov, K Graham, B Gropman, M Harris, J Heil, S Henderson, J Hoover, D Jennings, C Jordan, J Jordan, J Kasha, L Kagan, C Kraft, A Levitsky, M Lewis, X Liu, J Lopez, D Ma, W Majoros, J McDaniel, S Murphy, M Newman, T Nguyen, N Nguyen, M Nodell, S Pan, J Peck, M Peterson, W Rowe, R Sanders, J Scott, M Simpson, T Smith, A Sprague, T Stockwell, R Turner, E Venter, M Wang, M Wen, D Wu, M Wu, A Xia, A Zandieh, X Zhu, "The sequence of the human genome." Science, 291, #5507 (2001) 1304-51. [offcampus]
31. RJ Klein, Z Misulovin, SR Eddy, "Noncoding RNA genes identified in AT-rich hyperthermophiles." Proc. Natl. Acad. Sci. U.S.A., 99, #11 (2002) 7542-7. [offcampus]
32. Phillip A. Sharp, Split Genes and RNA Splicing, Nobel Lecture, December 8, 1993, http://nobelprize.org/nobel_prizes/medicine/laureates/1993/sharp-lecture.pdf [offcampus]
33. JP Staley, C Guthrie, "Mechanical devices of the spliceosome: motors, clocks, springs, and things." Cell, 92, #3 (1998) 315-26. [offcampus]
34. Cute animation of the splicing process. Not as detailed as the "Motors" paper above, but you might like it: http://vcell.ndsu.nodak.edu/animations/mrnasplicing/movie.htm [offcampus]

References -- RNA Structure, Alignment, & Search: Read #38, 42, 44, 46-48. Optional: Refs 35-37 are good surveys of recent surprising discoveries about the roles of non-coding RNA. Refs 53-55 might give you some picture of one nice biological example and how computational approaches are useful in this arena.

35. G Storz, "An expanding universe of noncoding RNAs." Science, 296, #5571 (2002) 1260-3. [offcampus]
36. SR Eddy, "Computational genomics of noncoding RNA genes." Cell, 109, #2 (2002) 137-40. [offcampus]
37. A Hüttenhofer, P Schattner, N Polacek, "Non-coding RNAs: hope or hype?" Trends Genet., 21, #5 (2005) 289-97. [offcampus]
38. SR Eddy, "How do RNA folding algorithms work?" Nat. Biotechnol., 22, #11 (2004) 1457-8. [offcampus]
39. JS McCaskill, "The equilibrium partition function and base pair binding probabilities for RNA secondary structure." Biopolymers, 29, #6-7 (1990 May-Jun) 1105-19. [offcampus]
40. RB Lyngsø, M Zuker, CN Pedersen, "Fast evaluation of internal loops in RNA secondary structure prediction." Bioinformatics, 15, #6 (1999) 440-5. [offcampus]
41. PP Gardner, R Giegerich, "A comprehensive comparison of comparative RNA structure prediction approaches." BMC Bioinformatics, 5, (2004) 140. [offcampus]
42. SR Eddy, R Durbin, "RNA sequence analysis using covariance models." Nucleic Acids Res., 22, #11 (1994) 2079-88. [offcampus]
43. SR Eddy, "A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure." BMC Bioinformatics, 3, (2002) 18. [offcampus]
44. S Griffiths-Jones, A Bateman, M Marshall, A Khanna, SR Eddy, "Rfam: an RNA family database." Nucleic Acids Res., 31, #1 (2003) 439-41. [offcampus]
45. S Griffiths-Jones, S Moxon, M Marshall, A Khanna, SR Eddy, A Bateman, "Rfam: annotating non-coding RNAs in complete genomes." Nucleic Acids Res., 33, #Database issue (2005) D121-4. [offcampus]
46. B Knudsen, J Hein, "RNA secondary structure prediction using stochastic context-free grammars and evolutionary history." Bioinformatics, 15, #6 (1999) 446-54. [offcampus]
47. B Knudsen, J Hein, "Pfold: RNA secondary structure prediction using stochastic context-free grammars." Nucleic Acids Res., 31, #13 (2003) 3423-8. [offcampus]
48. Z Weinberg, WL Ruzzo, "Faster Genome Annotation of Non-coding RNA Families Without Loss of Accuracy." Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004) , pp 243-251, March 2004, San Diego, CA. Preprint.
49. Z Weinberg, WL Ruzzo, "Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy." Bioinformatics, 20 Suppl 1, (2004) I334-I341. [offcampus]
50. Z Weinberg, WL Ruzzo, "Sequence-based heuristics for faster annotation of non-coding RNA families." Bioinformatics, 22, #1 (2006) 35-9. [offcampus]
51. M Mandal, M Lee, JE Barrick, Z Weinberg, GM Emilsson, WL Ruzzo, RR Breaker, "A glycine-dependent riboswitch that uses cooperative binding to control gene expression." Science, 306, #5694 (2004) 275-9. [offcampus]
52. JE Barrick, N Sudarsan, Z Weinberg, WL Ruzzo, RR Breaker, "6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter." RNA, 11, #5 (2005) 774-84. [offcampus]
53. AE Trotochaud, KM Wassarman, "A highly conserved 6S RNA structure is required for regulation of transcription." Nat. Struct. Mol. Biol., 12, #4 (2005) 313-9. [offcampus]
54. DK Willkomm, J Minnerup, A Hüttenhofer, RK Hartmann, "Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog." Nucleic Acids Res., 33, #6 (2005) 1949-60. [offcampus]
55. T Babak, BJ Blencowe, TR Hughes, "Considerations in the identification of functional RNA structural elements in genomic alignments." BMC Bioinformatics, 8, (2007) 33. [offcampus]

References -- : Optional: Recent papers mentioned in the last few lectures, mostly related to noncoding RNAs. Refs 56-58 describe CMfinder and our applications of it to riboswitch discovery. Refs 59-62 describe RNAz and Evofold and their application to genome-wide discovery in humans, and 63 is our recent paper in this area. Ref 64-65 describes approaches to identifying evolutionary conservation in noncoding regions.

56. Z Yao, Z Weinberg, WL Ruzzo, "CMfinder--a covariance model based RNA motif finding algorithm." Bioinformatics, 22, #4 (2006) 445-52. [offcampus]
57. Z Yao, J Barrick, Z Weinberg, S Neph, R Breaker, M Tompa, WL Ruzzo, "A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes." PLoS Comput Biol, 3, #7 (2007) e126. [offcampus]
58. Z Weinberg, JE Barrick, Z Yao, A Roth, JN Kim, J Gore, JX Wang, ER Lee, KF Block, N Sudarsan, S Neph, M Tompa, WL Ruzzo, RR Breaker, "Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline." Nucleic Acids Res., 35, #14 (2007) 4809-19. [offcampus]
59. S Washietl, IL Hofacker, PF Stadler, "Fast and reliable prediction of noncoding RNAs." Proc. Natl. Acad. Sci. U.S.A., 102, #7 (2005) 2454-9. [offcampus]
60. S Washietl, IL Hofacker, M Lukasser, A Hüttenhofer, PF Stadler, "Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome." Nat. Biotechnol., 23, #11 (2005) 1383-90. [offcampus]
61. JS Pedersen, G Bejerano, A Siepel, K Rosenbloom, K Lindblad-Toh, ES Lander, J Kent, W Miller, D Haussler, "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput. Biol., 2, #4 (2006) e33. [offcampus]
62. S Washietl, JS Pedersen, JO Korbel, C Stocsits, AR Gruber, J Hackermüller, J Hertel, M Lindemeyer, K Reiche, A Tanzer, C Ucla, C Wyss, SE Antonarakis, F Denoeud, J Lagarde, J Drenkow, P Kapranov, TR Gingeras, R Guigó, M Snyder, MB Gerstein, A Reymond, IL Hofacker, PF Stadler, "Structured RNAs in the ENCODE selected regions of the human genome." Genome Res., 17, #6 (2007) 852-64. [offcampus]
63. Torarinsson, Yao, Wiklund, Bramsen, Hansen, Kjems, Tommerup, Ruzzo and Gorodkin. Comparative genomics beyond sequence based alignments: RNA structures in the ENCODE regions. Genome Research, To Appear.
64. G Lunter, CP Ponting, J Hein, "Genome-wide identification of human functional DNA using a neutral indel model." PLoS Comput. Biol., 2, #1 (2006) e5. [offcampus]
65. J Ponjavic, CP Ponting, G Lunter, "Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs." Genome Res., 17, #5 (2007) 556-65. [offcampus]

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