Classical papers in bioinformatics

Ph.D. course, Fall 2012,
Scilifelab, Stockholm. Arne Elofsson, 5 ECTS

Course description

The subject of the course is a set of classical articles that contain fundamental contributions to bioinformatics. This includes papers describing results or novel approaches that have influenced the thinking in bioinformatics, or recent papers that are considered particularly important.

Course format

All students must read the given articles before the meeting. Two students will be responsible for presenting the articles, in order to start the discussion about them. These two students are supposed to meet and prepare the presentation together. The two students should be responsible for a subject that is different from the field of their Ph.D. projects.

All students must prepare at least one question about the articles for the presenting students to consider. Send this question to the course organizer (Arne Elofsson ), at the latest the Moday before the meeting, who will forward it to the presenting students.

All students must attend every meeting. If for some reason a student is unable to attend a meeting the student will have to write a one-page summary (A4, own words) of the articles and send it to Arne Elofsson (arne(at)bioinfo.se) by the latest three weeks after the session that was missed. A maximum number of three sessions could be missed.

The senior scientist(s) will not lead the discussion, only participate. That’s why the senior scientist is called ‘sponsor’, not teacher. The presenting students are encouraged to contact the sponsor well in advance of the meeting to discuss the paper(s).

You will have to get copies of the articles yourself. In a few cases (some very old papers), we may provide paper copies or pdfs.

Format of the discussion

Here is a list of questions to discuss.

1. What was novel about these papers ?
2. How has they changed the field ?
3. What has happened with the field since they were published ?

Email List

The email list is accessible by sending an email to classical@sbc.su.se

Meeting date

The meetings are held weekly, Wednesdays, 15:00-18:00, in the Kilsbergen at floor  4 at Scilifelab. There will be 14 meetings during the fall of 2012. Starting from the 19th of Sept until Christmas.

Participants

Sponsors:

• Arne Elofsson
• Bengt Persson
• Erik Lindahl
• Gunnar von Heijne
• Jens Carlsson
• Jens Lagergren
• Lars Arvestad
• Lukas Käll
• Lukasz Humaniecki
• Sara Light

Students:

1. Auwn Muhammad
2. Carlos Talavera-Lopez
3. Frances Vega
4. Ikram Ullah
5. Joel Sjöstrand
6. Karolis Uziela
7. Konstantinos Tsirigos
8. Linus Östberg
9. Luisa Hugerth
10. M Owais Mahmudi
11. Özge Yoluk
12. Oxana Sachenkova
13. Per Warholm
14. Raja Hashim
15. Ranganathan Anirudh
16. Valentine Svensson
17. Viktor Granholm
18. Walter Basile
19. Viveca Lindahl

Schedule

Location: Kilsbergen, Floor 4 Scilifelab.

NOTE THAT PAPERS IN ITALICS ARE ONLY PRELIMINARY SUGGESTIONS AND THAT THEY WILL CHANGE

Date	Topic	Article(s)	Students	Sponsor
120919	Alignments and Homology detection	Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443-53. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195-7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Domains Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. Review. Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005 Apr 1;21(7):951-60. Epub 2004 Nov 5. Erratum in: Bioinformatics. 2005 May 1;21(9):2144.	Carlos Talavera-Lopez, Frances Vega	Arne Elofsson
120926	Phylogenetic inference	Fitch, W.M., Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 20 (1971) 406-416. Felsenstein, J. 1981. Evolutionary Trees From DNA Sequences: a Maximum Likelihood Approach.. Journal of Molecular Evolution 17 (6): 368–376. Huelsenbeck, John P, F Ronquist, R Nielsen, and J P Bollback. 2001. Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology Science (New York, NY) 294 (5550) (December 14): 2310–2314. doi:10.1126/science.1065889. Wong, Karen M, Marc A Suchard, and John P Huelsenbeck. 2008. Alignment Uncertainty and Genomic Analysis Science (New York, NY) 319 (5862) (January 25): 473–476. doi:10.1126/science.1151532. Redelings, Benjamin, and Marc Suchard. 2005. Joint Bayesian Estimation of Alignment and Phylogeny. Systematic Biology 54 (3) (June 1): 401–418. doi:10.1080/10635150590947041	Linus Östberg, Luisa Hugerth, Valentine Svensson	Lars Arvestad
121003	Signal peptides and TM proteins	Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Protein Eng. 1997 Jan;10(1):1-6. A new method for predicting signal sequence cleavage sites. von Heijne G. Nucleic Acids Res. 1986 Jun 11;14(11):4683-90. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. J Mol Biol. 2001 Jan 19;305(3):567-80. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. von Heijne G. J Mol Biol. 1992 May 20;225(2):487-94.	Ikram Ullah, Joel Sjöstrand, Oxana Sachenkova	Gunnar von Heijne
121010	Networks, function predictions and interactions	Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. Probabilistic model of the human protein-protein interaction network. Nat Biotechnol. 2005 Aug;23(8):951-9. Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat. Genet. 2008, 40:181-8 Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL. The human disease network. Proc Natl Acad Sci U S A. 2007 104:8685-90	Karolis Uziela, Per Warholm, Raja Hashim	Bengt Persson
121017	Secondary structure predictions	Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry. 1974 Jan 15;13(2):211-22. Chou PY, Fasman GD. Prediction of protein conformation. Biochemistry. 1974 Jan 15;13(2):222-45. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. Garnier J, Osguthorpe DJ, Robson B. J Mol Biol. 1978 Mar 25;120(1):97-120. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993 Jul 20;232(2):584-99,	Viveca Lindahl , Ranganathan Anirudh, Viktor Granholm	Arne Elofsson
121024	Hidden Markov Models	Hidden Markov models in computational biology. Applications to protein modeling. Krogh A, Brown M, Mian IS, Sjölander K, Haussler D. J Mol Biol. 1994 Feb 4;235(5):1501-31. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. Eddy SR. PLoS Comput Biol. 2008 May 30;4(5):e1000069. A tutorial on hidden Markov models and selected applications in speech recognition. Lawrence R Rabiner,	Raja Hashim, Walter Basile, Auwn Mohammed	Lukas Käll
121031	Expression analysis	A gene atlas of the mouse and human protein-encoding transcriptomes. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Wal ker JR, Hogenesch JB. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. Epub 2004 Apr 9. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467-70. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8. Quackenbush J. Computational analysis of microarray data. Nat Rev Genet. 2001 Jun;2(6):418-27.	Ranganathan Anirudh , Auwn Muhammad, Frances Vega	Lukasz Humaniecki
121107	Genome Assembly and gene annotation	Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. Ronaghi M, Uhlén M, Nyrén P. A sequencing method based on real-time pyrophosphate. Science. 1998 Jul 17;281(5375):363, 365. Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 1998 Feb 15;26(4):1107-15. Anson E & Myers G Algorithms for whole genome shotgun sequencing Annual Conference on Research in Computational Molecular Biology, 1999 Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, Lonardi S, Beasley EM, Brandon RC, Chen L, Dunn PJ, Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter JC.A whole-genome assembly of Drosophila. Science. 2000 Mar 24;287(5461):2196-204.	Oxana Sachenkova, Özge Yoluk, Carlos Talavera-Lopez	Arne Elofsson
121114	Mapping	Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754–1760. Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq Research in Computational Molecular Biology Lecture Notes in Computer Science Volume 7262, 2012, pp 163-164 Trapnell, C., Williams, B., Pertea, G., Mortazavi, A., Kwan, G., Van Baren, M., Salzberg, S., et al. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28(5), 511–515.	Konstantinos Tsirigos, Walter Basile, Per Warholm	Jens Lagergren
121121	Protein design	Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, Montelione GT, Baker D, Principles for designing ideal protein structures, Nature 491, 222-227 (2012) Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, Degrado WF, Computational design of peptides that target transmembrane helices, Science 315, 1817-1822 (2007) Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science. 1997 Oct 3;278(5335):82-7. PubMed	Joel Sjöstrand,Ikram Ullah	Erik Lindahl
121128	Protein Structure prediction	Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature. 1992 Jul 2;358(6381):86-9, Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993 Dec 5;234(3):779-815. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science. 2005 Sep 16;309(5742):1868-71. Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. PLoS One. 2011;6(12):e28766.	Luisa Hugerth, M Owais Mahmudi	Arne Elofsson
121205	Molecular docking: Methods for fast scoring of protein-ligand complexes	Kuntz, ID; Blaney, JM; OAtley, SJ; et al. A geometric approach to macromolecule-ligand interactions Journal of Molecular BIOLOGY Volume: 161 Issue: 2 Pages: 269-288 Meng, EC; SHoichet, BK; Kuntz, ID Automated docking with grid-based energy evaluation JOURNAL OF COMPUTATIONAL CHEMISTRY Volume: 13 Issue: 4 Pages: 505- 524 DOI: 10.1002/jcc.540130412 Published: MAY 1992 BOHM, HJ The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known 3- dimensional structure Journal of Computer-Aided Molecular Design Volume: 8 Issue: 3 Pages: 243-256 DOI: 10.1007/BF00126743 Published: JUN 1994 Muegge, I; Martin, YC A general and fast scoring function for protein-ligand interactions: A simplified potential approach Journal of Medicinal Chemistry Volume: 42 Issue: 5 Pages: 791-804 DOI: 10.1021/jm980536j Published: MAR 11 1999 Warren, Gregory L.; Andrews, C. Webster; Capelli, Anna-Maria; et al. A critical assessment of docking programs and scoring functions Source: JOURNAL OF MEDICINAL CHEMISTRY Volume: 49 Issue: 20 Pages: 5912- 5931 DOI: 10.1021/jm050362n Published: OCT 5 2006	Valentine Svensson,, Viktor Granholm, Konstantinos Tsirigos	Jens Carlsson
121212	Protein Domains	Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997 Jul;28(3):405-20. Gordana Apic, Julian Gough, Sarah A Teichmann, Domain combinations in archaeal, eubacterial and eukaryotic proteomes, Journal of Molecular Biology, Volume 310, Issue 2, 6 July 2001, Pages 311-325, ISSN 0022-2836 Gabrielle A. Reeves, Timothy J. Dallman, Oliver C. Redfern, Adrian Akpor, Christine A. Orengo, Structural Diversity of Domain Superfamilies in the CATH Database Journal of Molecular Biology, Volume 360, Issue 3, 14 July 2006, Pages 725-741 Levy ED, Boeri Erba E, Robinson CV, Teichmann SA. Assembly reflects evolution of protein complexes. Nature. 2008 Jun 26;453(7199):1262-5. Epub 2008 Jun 18.	Linus Östberg, Özge Yoluk	Sara Light
121219	Molecular Dynamics and computational chemistry	Chothia C, Levitt M, Richardson D. Structure of proteins: Packing of alpha-helices and pleated sheets Proc Natl Acad Sci U S A. 1977 Oct;74(10):4130-4. McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature. 1977 Jun 16;267(5612):585-90. Levinthal C. Molecular model-building by computer. Sci Am. 1966 Jun;214(6):42-52.	M Owais Mahmudi, Karolis Uziela	Erik Lindahl

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