CS/ST580 - bioinformatics algorithms - Schedule

December 06, 2011, at 09:59 AM MST by 129.82.44.229 -

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Week 15:

Tuesday, 12/6
Lecture: Everything we haven't covered about bioinformatics yet [ slides ].
Tuesday, 12/8
Lecture: No lecture - we will meet instead during finals week for project presentations.

December 01, 2011, at 10:27 AM MST by 129.82.44.229 -

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Jeremy Buhler and Martin Tompa. [[http://www.liebertonline.com/doi/abs/10.1089/10665270252935430 | Finding motifs using random projections ]]. Journal of Computational Biology. April 2002, 9(2): 225-242.

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Jeremy Buhler and Martin Tompa. Finding motifs using random projections. Journal of Computational Biology. April 2002, 9(2): 225-242.

December 01, 2011, at 10:26 AM MST by 129.82.44.229 -

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Reading: Alkes Price, Sriram Ramabhadran and Pavel A. Pevzner. Finding subtle motifs by branching from sample strings.

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Reading: Alkes Price, Sriram Ramabhadran and Pavel A. Pevzner. Finding subtle motifs by branching from sample strings.
Jeremy Buhler and Martin Tompa. [[http://www.liebertonline.com/doi/abs/10.1089/10665270252935430 | Finding motifs using random projections ]]. Journal of Computational Biology. April 2002, 9(2): 225-242.

December 01, 2011, at 10:24 AM MST by 129.82.44.229 -

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Thursday, 12/1
Lecture: Motif finding algorithms (continued).
Reading: Alkes Price, Sriram Ramabhadran and Pavel A. Pevzner. Finding subtle motifs by branching from sample strings.

November 28, 2011, at 10:08 AM MST by 129.82.44.229 -

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Lecture: Motif finding algorithms [ slides ].

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Lecture: Motif finding algorithms [ slides ].

November 28, 2011, at 10:07 AM MST by 129.82.44.229 -

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Lecture: Motif finding algorithms.

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Lecture: Motif finding algorithms [ slides ].

November 21, 2011, at 10:52 AM MST by 129.82.44.229 -

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Week 14:

Tuesday, 11/29
Lecture: Motif finding algorithms.
Reading: Modan K Das and Ho-Kwok Dai. A survey of DNA motif finding algorithms.

November 17, 2011, at 09:57 AM MST by 129.82.44.229 -

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Thursday, 11/17
Lecture: Motif finding [ slides ].

November 16, 2011, at 09:27 AM MST by 129.82.44.229 -

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Lecture: Multiple sequence alignment (cont)

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Lecture: Multiple sequence alignment (cont) and whole genome alignment [ slides ].

November 14, 2011, at 07:18 PM MST by 76.25.21.194 -

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Week 12:

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Week 13:

November 14, 2011, at 07:16 PM MST by 76.25.21.194 -

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Week 12:

Tuesday, 11/15
Lecture: Multiple sequence alignment (cont)

November 10, 2011, at 10:04 AM MST by 129.82.44.229 -

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Reading: Chapter 5 in Durbin and Eddy.

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Reading: Chapter 5 in Durbin and Eddy.

November 10, 2011, at 10:03 AM MST by 129.82.44.229 -

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RC Edgar and S Batzoglou. http://ai.stanford.edu/~serafim/Publications/2006_MSA_COSB.pdf ?. Current Opinion in Structural Biology

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RC Edgar and S Batzoglou. Multiple sequence alignment. Current Opinion in Structural Biology

November 10, 2011, at 10:03 AM MST by 129.82.44.229 -

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RC Edgar and S Batzoglou. ai.stanford.edu/~serafim/Publications/2006_MSA_COSB.pdf ?. Current Opinion in Structural Biology

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RC Edgar and S Batzoglou. http://ai.stanford.edu/~serafim/Publications/2006_MSA_COSB.pdf ?. Current Opinion in Structural Biology

November 10, 2011, at 10:03 AM MST by 129.82.44.229 -

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Reading: Chapter 5 in Durbin and Eddy.

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Reading: Chapter 5 in Durbin and Eddy.

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Reading: Chapter 6 in Durbin and Eddy.

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Reading: Chapter 6 in Durbin and Eddy. Two more up-to-date resources:
RC Edgar and S Batzoglou. ai.stanford.edu/~serafim/Publications/2006_MSA_COSB.pdf ?. Current Opinion in Structural Biology Volume 16, Issue 3, June 2006, pages 368-373.
CB Do and K Katoh. Protein multiple sequence alignment. Methods in Molecular Biology, 2008, Volume 484, IV, pages 379-413.

November 10, 2011, at 09:16 AM MST by 129.82.44.229 -

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Thursday, 11/10
Lecture: Multiple sequence alignment [ slides ].
Reading: Chapter 6 in Durbin and Eddy.

November 07, 2011, at 05:55 PM MST by 76.25.21.194 -

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Week 12:

Tuesday, 11/8
Lecture: Applications of HMMs - describing gene families with profile HMMs.
Reading: Chapter 5 in Durbin and Eddy.

November 02, 2011, at 01:38 PM MST by 76.25.21.194 -

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Lecture: Applications of HMMs [ slides ].

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Lecture: Applications of HMMs - gene finding [ slides ].

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Lecture: Applications of HMMs (cont).

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Lecture: Applications of HMMs - pairwise alignment (slides continued). Reading: Chapter 4 in Durbin and Eddy.

October 31, 2011, at 09:02 PM MST by 76.25.21.194 -

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Tuesday, 11/1'

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Tuesday, 11/1

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Tuesday, 11/3'

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Tuesday, 11/3

October 31, 2011, at 09:02 PM MST by 76.25.21.194 -

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Week 11:

Tuesday, 11/1'
Lecture: Applications of HMMs [ slides ].
Reading: Chapter 4 in Durbin and Eddy.

Tuesday, 11/3'
Lecture: Applications of HMMs (cont).

October 27, 2011, at 09:48 AM MST by 129.82.44.229 -

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Lecture: Learning hidden Markov models - continuing with slides that discuss [ HMMs ].

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Lecture: Learning hidden Markov models - continuing with slides that discuss HMMs.

October 27, 2011, at 09:48 AM MST by 129.82.44.229 -

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Lecture: Learning hidden Markov models - continuing with the HMM [ slides ].

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Lecture: Learning hidden Markov models - continuing with slides that discuss [ HMMs ].

October 27, 2011, at 09:47 AM MST by 129.82.44.229 -

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Lecture: Discussion of the projects. Learning hidden Markov models - continuing with the HMM [ slides ].

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Lecture: Discussion of the projects.

Thursday, 10/27
Lecture: Learning hidden Markov models - continuing with the HMM [ slides ].

October 24, 2011, at 08:55 PM MST by 76.25.21.194 -

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Tuesday, 10/15

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Tuesday, 10/25

October 24, 2011, at 08:55 PM MST by 76.25.21.194 -

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'Lecture:'' Discussion of the projects. Learning hidden Markov models - continuing with the HMM [ slides ].

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Lecture: Discussion of the projects. Learning hidden Markov models - continuing with the HMM [ slides ].

October 24, 2011, at 08:55 PM MST by 76.25.21.194 -

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Week 10:

Tuesday, 10/15
'Lecture: Discussion of the projects. Learning hidden Markov models - continuing with the HMM [ slides ].
Reading:'' Chapter 3 in Durbin and Eddy.

October 18, 2011, at 09:54 AM MST by 129.82.44.229 -

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Lecture: Nathan will present BWA.

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Nathan will present BWA.

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Lecture: Zhisheng will present Gsnap.

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Zhisheng will present Gsnap.

October 18, 2011, at 09:54 AM MST by 129.82.44.229 -

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Thursday, 10/13'

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Thursday, 10/13

October 18, 2011, at 09:53 AM MST by 129.82.44.229 -

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Week 9:

Tuesday, 10/18
Lecture: Nathan will present BWA. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010;26(5):589-95.
Arpita will present SOAPsplice. Huang S, Zhang J, Li R, Zhang W, He Z, Lam T-W, Peng Z and Yiu S-M. SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data. Frontiers in Genomic Assay Technology (2010) 2:46.

Thursday, 10/13'
Lecture: Zhisheng will present Gsnap. T.D. Wu and S. Nacu. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (2010) 26: 873-881.
Indika will present RUM. Gregory R. Grant, Michael H. Farkas, Angel D. Pizarro, Nicholas F. Lahens, Jonathan Schug, Brian P. Brunk, Christian J. Stoeckert, John B. Hogenesch, and Eric A. Pierce. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics (2011) 27(18): 2518-2528.

October 11, 2011, at 09:36 AM MST by 129.82.44.229 -

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Tuesday, 10/11

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Thursday, 10/13

October 11, 2011, at 09:35 AM MST by 129.82.44.229 -

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Reading:: Trapnell C, Pachter L, and Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 25 (9): 1105-1111.

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Reading: Trapnell C, Pachter L, and Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 25 (9): 1105-1111.

Tuesday, 10/11
Lecture: Fayyaz will present PalMapper; Mo will present SpliceMap. Reading: De Bona, F. et al., Optimal spliced alignments of short sequence reads. ECCB08/Bioinformatics, 24 (16):i174, 2008.
and
Kin Fai Au, Hui Jiang, Lan Lin, Yi Xing, and Wing Hung Wong. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research (2010).

October 11, 2011, at 09:31 AM MST by 129.82.44.229 -

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Reading:: Trapnell C, Pachter L, and Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 25 (9): 1105-1111.

October 11, 2011, at 09:31 AM MST by 129.82.44.229 -

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Week 8:

Tuesday, 10/11
Lecture: Jeremy will present the TopHat spliced alignment program.

October 05, 2011, at 01:48 PM MST by 129.82.44.229 -

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Lecture: Hidden Markov models (cont).

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Lecture: Hidden Markov models - the Viterbi, forward and backward algorithms. Reading: Section 3.2 in Durbin and Eddy.

October 03, 2011, at 04:03 PM MST by 129.82.44.229 -

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Reading: Chapter 3 in Durbin and Eddy; another classical resource is Rabiner's tutorial. The notation in the slides follows the textbook.

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Reading: Section 3.2 in Durbin and Eddy; another classical resource is Rabiner's tutorial. The notation in the slides follows the textbook.

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Reading: Chapter 3 in Durbin and Eddy; another classical resource is Rabiner's tutorial. The notation in the slides follows the textbook.

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Reading: Section 3.1 in Durbin and Eddy; another classical resource is Rabiner's tutorial. The notation in the slides follows the textbook.

October 03, 2011, at 01:33 PM MST by 129.82.44.229 -

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Thursday, 10/6
Lecture: Hidden Markov models (cont).

October 03, 2011, at 01:32 PM MST by 129.82.44.229 -

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Week 7:

Tuesday, 10/4
Lecture: Hidden Markov models [ slides ]
Reading: Chapter 3 in Durbin and Eddy; another classical resource is Rabiner's tutorial. The notation in the slides follows the textbook.

September 28, 2011, at 09:00 PM MST by 76.25.21.194 -

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Lecture: Hidden Markov models - an introduction.

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Lecture: Hidden Markov models - an introduction [ slides ].
Reading: Chapter 3 in Durbin and Eddy; another classical resource is Rabiner's tutorial. The notation in the slides follows the textbook.

September 28, 2011, at 02:33 PM MST by 76.25.21.194 -

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Lecture: Multiple sequence alignment [ slides ]
Reading: Chapter 6 in Durbin, Eddy, Krogh, Mitchison (6.1 - 6.4). A recent review of MSA methods is found e.g. in:
W. Pirovano and J. Heringa. Multiple sequence alignment. In: Methods Mol Biol. 2008;452:143-61.

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Lecture: Hidden Markov models - an introduction.

September 28, 2011, at 11:48 AM MST by 129.82.46.175 -

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W. Pirovano and J. Heringa. [[http://www.ncbi.nlm.nih.gov/pubmed/18566763

 | Multiple sequence alignment]]. In:  Methods Mol Biol. 2008;452:143-61.

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W. Pirovano and J. Heringa. Multiple sequence alignment. In: Methods Mol Biol. 2008;452:143-61.

September 28, 2011, at 11:47 AM MST by 129.82.46.175 -

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Thursday, 9/29
Lecture: Multiple sequence alignment [ slides ]
Reading: Chapter 6 in Durbin, Eddy, Krogh, Mitchison (6.1 - 6.4). A recent review of MSA methods is found e.g. in:
W. Pirovano and J. Heringa. [[http://www.ncbi.nlm.nih.gov/pubmed/18566763

 | Multiple sequence alignment]]. In:  Methods Mol Biol. 2008;452:143-61.

September 26, 2011, at 01:21 PM MST by 129.82.46.175 -

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Week 6:

Tuesday, 9/27
Lecture: Guest lecture on using RNA-seq data for prediction of alternative splicing [ slides ]
Reading: SpliceGrapher manuscript will be provided by email.

September 22, 2011, at 10:23 AM MST by 129.82.46.175 -

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Thursday, 9/22
Lecture: Using next generation sequencing technology for studying the transcriptome. The spliced alignment problem [ slides ].
Reading: Davide Campagna, Alessandro Albiero, Alessandra Bilardi, Elisa Caniato, Claudio Forcato, Svetlin Manavski, Nicola Vitulo, and Giorgio Valle. PASS: a program to align short sequences. Bioinformatics (2009) 25(7): 967-968.
Section 6.14 in Jones and Pevzner.

September 20, 2011, at 08:47 AM MST by 129.82.46.175 -

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Next generation sequencing technology [ slides ]
Reading: Elaine R. Mardis. A decade�s perspective on DNA sequencing technology. Nature 470:198�203,2011.

September 19, 2011, at 10:01 AM MST by 129.82.46.175 -

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Week 5:

Tuesday, 9/20
Lecture: linear-space alignment [ slides ]
Reading: Linear space alignment is presented in Chapter 7 of Bioinformatics algorithms. The original paper is:
E.W. Myers and W. Miller. Optimal alignments in linear space. Computer Applications in Biosciences, 4:11-17, 1988 [ pdf ].

September 15, 2011, at 07:47 AM MST by 76.25.21.194 -

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Lecture: Local alignment - the Smith-Waterman algorithm; substitution matrices (slide set continued)

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Lecture: Local alignment - the Smith-Waterman algorithm; substitution matrices ) [ slides ]

September 14, 2011, at 10:50 AM MST by 129.82.44.191 -

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Thursday, 9/15
Lecture: BLAST (continued) and linear-space alignment [ slides ]
Reading: Linear space alignment is presented in Chapter 7 of Bioinformatics algorithms. The original paper is:
E.W. Myers and W. Miller. Optimal alignments in linear space. Computer Applications in Biosciences, 4:11-17, 1988 [ pdf ].

September 12, 2011, at 08:38 PM MST by 76.25.21.194 -

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Lecture: More substitution matrices - Markov models and PAM matrices (slide set continued); heuristic alignment algorithms: Fasta and BLAST [ slides ]

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Lecture: More substitution matrices - Markov models and PAM matrices (slide set continued).
heuristic alignment algorithms: Fasta and BLAST [ slides ]

September 12, 2011, at 08:38 PM MST by 76.25.21.194 -

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Lecture: More substitution matrices - Markov models and PAM matrices (slide set continued)

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Lecture: More substitution matrices - Markov models and PAM matrices (slide set continued); heuristic alignment algorithms: Fasta and BLAST [ slides ]

September 12, 2011, at 12:51 PM MST by 129.82.44.191 -

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Week 4:

Tuesday, 9/13
Lecture: More substitution matrices - Markov models and PAM matrices (slide set continued)
Reading: Chapter 6 of Bioinformatics algorithms.

Week 3:

Tuesday, 9/6
Lecture: Local alignment - the Smith-Waterman algorithm; substitution matrices (slide set continued)
Reading: Chapter 6 of Bioinformatics algorithms.

September 01, 2011, at 02:30 PM MST by 129.82.44.191 -

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Lecture: Pairwise sequence alignment - introduction to dynamic programming algorithms [ slides ]

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Lecture: Pairwise sequence alignment - introduction to dynamic programming algorithms [ slides ]

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Global pairwise alignment - longest common subsequence and global alignment using the Needleman Wunsch algorithm [ Path:../../pdfs/alignment2.pdf ]

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Global pairwise alignment - longest common subsequence and global alignment using the Needleman Wunsch algorithm [ slides ]

September 01, 2011, at 02:30 PM MST by 129.82.44.191 -

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Lecture: Pairwise sequence alignment [ slides ]

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Lecture: Pairwise sequence alignment - introduction to dynamic programming algorithms [ slides ]

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Thursday, 9/1
Lecture: Global pairwise alignment - longest common subsequence and global alignment using the Needleman Wunsch algorithm [ Path:../../pdfs/alignment2.pdf ]

August 24, 2011, at 11:44 AM MST by 129.82.44.191 -

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Lecture: Course introduction (cont). Gene finding in prokaryotes [ slides ]. Assignment 1 is posted.

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Lecture: Course introduction (cont). Gene finding in prokaryotes [ slides ].

August 24, 2011, at 11:27 AM MST by 129.82.44.191 -

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Week 2:

Tuesday, 8/30
Lecture: Pairwise sequence alignment [ slides ]
Reading: Chapter 6 of Bioinformatics algorithms [ pdf ].

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Week 2:

Tuesday, 8/30
Lecture: Pairwise sequence alignment [ slides ]
Reading: Chapter 6 of Bioinformatics algorithms [ pdf ].

August 24, 2011, at 11:26 AM MST by 129.82.44.191 -

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Lecture: Course introduction (cont). Gene finding in prokaryotes [ slides. Assignment 1 is posted.

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Lecture: Course introduction (cont). Gene finding in prokaryotes [ slides ]. Assignment 1 is posted.

August 24, 2011, at 11:26 AM MST by 129.82.44.191 -

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Lecture: Course introduction (cont). Assignment 1 is posted.

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Lecture: Course introduction (cont). Gene finding in prokaryotes [ slides. Assignment 1 is posted.

August 24, 2011, at 11:01 AM MST by 129.82.44.191 -

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Week 2:

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Thursday, 8/25
Lecture: Course introduction (cont). Assignment 1 is posted.
Tuesday, 8/30
Lecture: Pairwise sequence alignment [ slides ]
Reading: Chapter 6 of Bioinformatics algorithms [ pdf ].

August 22, 2011, at 09:50 AM MST by 129.82.44.191 -

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Done.

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Week 1:

Tuesday, 8/23
Lecture: Course introduction [ slides ]
Reading: Alex Zien's A primer on molecular biology [ pdf ].
Martin Tompa's notes [ pdf ].

May 03, 2011, at 10:38 AM MST by 129.82.44.191 -

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Week 1: 1/21 - 1/23

Lectures: Course overview, biological preliminaries
Reading: Here are some "biology for computer scientists" pointers:

The first chapter of the book Kernel methods in computational biology pdf
Book chapter from Larry Hunter pdf
Notes from Martin Tompa pdf
And a paper from Sean Eddy about the nature of research in bioinformatics link

Week 2: 1/26 - 1/30

Lectures: Gene finding in prokaryotes, intro to sequence alignment
Reading: ch 6 in Jones and Pevzner.

Week 3: 2/2 - 2/6

Lectures: Dynamic programming and methods for pairwise sequence alignment: global and local. Reading: ch 6 in Jones and Pevzner

Week 4: 2/9 - 2/13

Lectures: Sequence alignment: Amino acid scoring matrices, handling affine gap penalties, alignment with linear memory

Week 5: 2/16 - 2/20

Lectures: Heuristic alignment methods - FASTA and BLAST. Spliced alignment

Week 6: 2/23 - 2/27

Lectures: Multiple sequence alignment

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Done.

February 27, 2009, at 08:39 AM MST by Asa -

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Spliced alignment

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Spliced alignment

Week 6: 2/23 - 2/27

Lectures: Multiple sequence alignment

February 18, 2009, at 10:35 AM MST by Asa -

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Lectures: Course overview, biological preliminaries, gene finding in prokaryotes

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Lectures: Course overview, biological preliminaries

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And a paper from Sean Eddy about the nature of research in bioinformatics link

to:

And a paper from Sean Eddy about the nature of research in bioinformatics link

Week 2: 1/26 - 1/30

Lectures: Gene finding in prokaryotes, intro to sequence alignment
Reading: ch 6 in Jones and Pevzner.

Week 3: 2/2 - 2/6

Lectures: Dynamic programming and methods for pairwise sequence alignment: global and local. Reading: ch 6 in Jones and Pevzner

Week 4: 2/9 - 2/13

Lectures: Sequence alignment: Amino acid scoring matrices, handling affine gap penalties, alignment with linear memory

Week 5: 2/16 - 2/20

Lectures: Heuristic alignment methods - FASTA and BLAST. Spliced alignment

January 15, 2009, at 06:39 PM MST by Asa -

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The first chapter of the book Kernel methods in computational biology ]

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The first chapter of the book Kernel methods in computational biology pdf

January 15, 2009, at 06:39 PM MST by Asa -

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The first chapter of the book Kernel methods in computational biology [ pdf ]

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The first chapter of the book Kernel methods in computational biology ]

January 15, 2009, at 06:38 PM MST by Asa -

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The first chapter of the book Kernel methods in computational biology pdf

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The first chapter of the book Kernel methods in computational biology [ pdf ]

January 15, 2009, at 06:37 PM MST by Asa -

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The first chapter of the book Kernel methods in computational biology pdf

Book chapter from Larry Hunter pdf

Notes from Martin Tompa pdf

A paper from Sean Eddy about the nature of research in bioinformatics link

to:

The first chapter of the book Kernel methods in computational biology pdf
Book chapter from Larry Hunter pdf
Notes from Martin Tompa pdf
And a paper from Sean Eddy about the nature of research in bioinformatics link

January 15, 2009, at 06:36 PM MST by Asa -

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Lectures: Course overview, biological preliminaries, gene finding in prokaryotes

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Lectures: Course overview, biological preliminaries, gene finding in prokaryotes

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A paper from Sean Eddy about the nature of research in bioinformatics [[link]]

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A paper from Sean Eddy about the nature of research in bioinformatics link

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A paper from Sean Eddy about the nature of research in bioinformatics link

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A paper from Sean Eddy about the nature of research in bioinformatics [[link]]

January 15, 2009, at 06:35 PM MST by Asa -

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Lectures: Course overview, biological preliminaries, gene finding in prokaryotes

Reading: Here are some "biology for computer scientists" pointers:

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Lectures: Course overview, biological preliminaries, gene finding in prokaryotes Reading: Here are some "biology for computer scientists" pointers:

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A paper from Sean Eddy about the nature of research in bioinformatics

link

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A paper from Sean Eddy about the nature of research in bioinformatics link

January 15, 2009, at 06:34 PM MST by Asa -

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The first chapter of the book Kernel methods in computational biology

pdf

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The first chapter of the book Kernel methods in computational biology pdf

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link

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link

January 15, 2009, at 06:33 PM MST by Asa -

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Coming soon!

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Week 1: 1/21 - 1/23

Lectures: Course overview, biological preliminaries, gene finding in prokaryotes

Reading: Here are some "biology for computer scientists" pointers:

The first chapter of the book Kernel methods in computational biology

pdf

Book chapter from Larry Hunter pdf

Notes from Martin Tompa pdf

A paper from Sean Eddy about the nature of research in bioinformatics

link

December 31, 2008, at 03:43 PM MST by Asa -

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Coming soon!

Main.Schedule History

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Week 14:

Week 12:

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Week 10:

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Week 7:

Week 6:

Week 5:

Week 4:

Week 3:

Week 2:

Week 2:

Week 2:

Week 1:

Week 1: 1/21 - 1/23

Week 2: 1/26 - 1/30

Week 3: 2/2 - 2/6

Week 4: 2/9 - 2/13

Week 5: 2/16 - 2/20

Week 6: 2/23 - 2/27

Week 6: 2/23 - 2/27

Week 2: 1/26 - 1/30

Week 3: 2/2 - 2/6

Week 4: 2/9 - 2/13

Week 5: 2/16 - 2/20

Week 1: 1/21 - 1/23