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 [ [[Path:../../pdfs/conclusions.pdf | 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.

to:

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 10:26 AM MST by 129.82.44.229 -

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''Reading:'' Alkes Price, Sriram Ramabhadran and Pavel A. Pevzner. [[http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii149.short | Finding subtle motifs by branching from sample strings]].

to:

''Reading:'' Alkes Price, Sriram Ramabhadran and Pavel A. Pevzner. [[http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii149.short | 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. [[http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii149.short | 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 [ [[Path:../../pdfs/~~motifFinding~~.pdf | slides]] ].\\

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''Lecture:'' Motif finding algorithms [ [[Path:../../pdfs/motifFinding2.pdf | 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 [ [[Path:../../pdfs/motifFinding.pdf | 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.
[[http://www.biomedcentral.com/1471-2105/8/S7/S21 |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 [ [[Path:../../pdfs/motifFinding.pdf | slides]] ].

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

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''Lecture:'' Multiple sequence alignment (cont)

to:

''Lecture:'' Multiple sequence alignment (cont) and whole genome alignment [ [[Path:../../pdfs/msa_genomic.pdf | 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. [[~~Multiple sequence alignment |~~ http://ai.stanford.edu/~serafim/Publications/2006_MSA_COSB.pdf]]. Current Opinion in Structural Biology

to:

RC Edgar and S Batzoglou. [[http://ai.stanford.edu/~serafim/Publications/2006_MSA_COSB.pdf | 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. [[Multiple sequence alignment | ai.stanford.edu/~serafim/Publications/2006_MSA_COSB.pdf]]. Current Opinion in Structural Biology

to:

RC Edgar and S Batzoglou. [[Multiple sequence alignment | 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.

to:

''Reading:'' Chapter 6 in Durbin and Eddy. Two more up-to-date resources:\\
RC Edgar and S Batzoglou. [[Multiple sequence alignment | 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. [[http://www.springerlink.com/content/kp41118876120w06/#section=89635&page=1 |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 [ [[Path:../../pdfs/msa.pdf | 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 [ [[Path:../../pdfs/hmmApplications.pdf | slides]] ]. \\

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''Lecture:'' Applications of HMMs - gene finding [ [[Path:../../pdfs/hmmApplications.pdf | 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 [ [[Path:../../pdfs/hmmApplications.pdf | 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 [ [[Path:../../pdfs/hmms.pdf | HMMs]] ]. \\

to:

''Lecture:'' Learning hidden Markov models - continuing with slides that discuss [[Path:../../pdfs/hmms.pdf | 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 [~~ [[Path:../../pdfs/hmms.pdf | ~~slides~~]] ]. \\

to:

''Lecture:'' Learning hidden Markov models - continuing with slides that discuss [ [[Path:../../pdfs/hmms.pdf | 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 [ [[Path:../../pdfs/hmms.pdf | slides]] ]. \\

to:

''Lecture:'' Discussion of the projects.

'''Thursday, 10/27'''\\
''Lecture:'' Learning hidden Markov models - continuing with the HMM [ [[Path:../../pdfs/hmms.pdf | 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 [ [[Path:../../pdfs/hmms.pdf | slides]] ]. \\

to:

''Lecture:'' Discussion of the projects. Learning hidden Markov models - continuing with the HMM [ [[Path:../../pdfs/hmms.pdf | 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 [ [[Path:../../pdfs/hmms.pdf | 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 [[http://bio-bwa.sourceforge.net/ | BWA]].

to:

Nathan will present [[http://bio-bwa.sourceforge.net/ | BWA]].

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~~''Lecture:''~~ Zhisheng will present [[http://research-pub.gene.com/gmap/ | Gsnap]].

to:

Zhisheng will present [[http://research-pub.gene.com/gmap/ | 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 [[http://bio-bwa.sourceforge.net/ | BWA]].
Li H, Durbin R. [[http://bioinformatics.oxfordjournals.org/content/26/5/589.full | Fast and accurate long-read alignment with Burrows-Wheeler transform]]. Bioinformatics 2010;26(5):589-95.\\
Arpita will present [[ http://soap.genomics.org.cn/soapsplice.html | SOAPsplice]].
Huang S, Zhang J, Li R, Zhang W, He Z, Lam T-W, Peng Z and Yiu S-M. [[ http://www.frontiersin.org/genomic_assay_technology/10.3389/fgene.2011.00046/abstract | 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 [[http://research-pub.gene.com/gmap/ | Gsnap]].
T.D. Wu and S. Nacu. [[http://bioinformatics.oxfordjournals.org/content/26/7/873.full | Fast and SNP-tolerant detection of complex variants and splicing in short reads]]. Bioinformatics (2010) 26: 873-881.\\
Indika will present [[http://www.cbil.upenn.edu/RUM/userguide.php | 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. [[ http://bioinformatics.oxfordjournals.org/content/27/18/2518.full| 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. [[http://bioinformatics.oxfordjournals.org/content/25/9/1105.full | TopHat: discovering splice junctions with RNA-Seq]]. Bioinformatics (2009) 25 (9): 1105-1111.

to:

''Reading:'' Trapnell C, Pachter L, and Salzberg SL. [[http://bioinformatics.oxfordjournals.org/content/25/9/1105.full | 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., [[http://bioinformatics.oxfordjournals.org/content/24/16/i174.full | 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. [[http://nar.oxfordjournals.org/content/early/2010/04/05/nar.gkq211.full | 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. [[http://bioinformatics.oxfordjournals.org/content/25/9/1105.full | 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)~~.

to:

''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 [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.131.2084&rep=rep1&type=pdf | tutorial]]. The notation in the slides follows the textbook.

to:

''Reading:'' Section 3.2 in Durbin and Eddy; another classical resource is Rabiner's [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.131.2084&rep=rep1&type=pdf | 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 [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.131.2084&rep=rep1&type=pdf | tutorial]]. The notation in the slides follows the textbook.

to:

''Reading:'' Section 3.1 in Durbin and Eddy; another classical resource is Rabiner's [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.131.2084&rep=rep1&type=pdf | 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 [ [[Path:../../pdfs/hmms.pdf | slides]] ] \\
''Reading:'' Chapter 3 in Durbin and Eddy; another classical resource is Rabiner's [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.131.2084&rep=rep1&type=pdf | 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.

to:

''Lecture:'' Hidden Markov models - an introduction [ [[Path:../../pdfs/hmmIntro.pdf | slides]] ]. \\
''Reading:'' Chapter 3 in Durbin and Eddy; another classical resource is Rabiner's [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.131.2084&rep=rep1&type=pdf | 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 [ [[Path:~~../../pdfs/msa.pdf | 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.

to:

''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.

to:

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

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'''Thursday, 9/29'''\\
''Lecture:'' Multiple sequence alignment [ [[Path:../../pdfs/msa.pdf | 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 [ [[Path:../../pdfs/splice_grapher.pdf | 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 [ [[Path:../../pdfs/spliced_alignment_alternative_splicing.pdf | slides]] ]. \\
''Reading:'' Davide Campagna, Alessandro Albiero, Alessandra Bilardi, Elisa Caniato, Claudio Forcato, Svetlin Manavski, Nicola Vitulo, and Giorgio Valle.
[[http://bioinformatics.oxfordjournals.org/content/25/7/967 |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 [ [[Path:../../pdfs/NGS.pdf | slides]] ]\\
''Reading:'' Elaine R. Mardis. [[ http://www.nature.com/nature/journal/v470/n7333/full/nature09796.html | 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 [ [[Path:../../pdfs/alignment3.pdf | 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 [ [[http://research.janelia.org/myers/Papers/linear.pdf | 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)~~ \\

to:

''Lecture:'' Local alignment - the Smith-Waterman algorithm; substitution matrices ) [ [[Path:../../pdfs/alignment2.pdf | 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 [ [[Path:../../pdfs/alignment3.pdf | 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 [ [[http://research.janelia.org/myers/Papers/linear.pdf | 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 [ [[Path:../../pdfs/blast.pdf | slides]] ] \\

to:

''Lecture:'' More substitution matrices - Markov models and PAM matrices (slide set continued).\\ heuristic alignment algorithms: Fasta and BLAST [ [[Path:../../pdfs/blast.pdf | 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) \\

to:

''Lecture:'' More substitution matrices - Markov models and PAM matrices (slide set continued); heuristic alignment algorithms: Fasta and BLAST [ [[Path:../../pdfs/blast.pdf | 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 [ [[Path:../../pdfs/alignment.pdf | slides]] ]

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''Lecture:'' Pairwise sequence alignment - introduction to dynamic programming algorithms [ [[Path:../../pdfs/alignment.pdf | slides]] ] \\

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

to:

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

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

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''Lecture:'' Pairwise sequence alignment [ [[Path:../../pdfs/alignment.pdf | slides]] ] \\

to:

''Lecture:'' Pairwise sequence alignment - introduction to dynamic programming algorithms [ [[Path:../../pdfs/alignment.pdf | 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 [ [[Path:../../pdfs/prokaryote_gene_finding.pdf | slides]] ]~~. Assignment 1 is posted~~.\\

to:

''Lecture:'' Course introduction (cont). Gene finding in prokaryotes [ [[Path:../../pdfs/prokaryote_gene_finding.pdf | 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 [ [[Path:../../pdfs/alignment.pdf | slides]] ] \\
''Reading:'' Chapter 6 of ''Bioinformatics algorithms'' [ [[http://bix.ucsd.edu/bioalgorithms/book/excerpt-ch6.pd | pdf]] ].\\

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!!Week 2:

'''Tuesday, 8/30'''\\
''Lecture:'' Pairwise sequence alignment [ [[Path:../../pdfs/alignment.pdf | slides]] ] \\
''Reading:'' Chapter 6 of ''Bioinformatics algorithms'' [ [[http://bix.ucsd.edu/bioalgorithms/book/excerpt-ch6.pd | 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 [ [[Path:../../pdfs/prokaryote_gene_finding.pdf | slides]]. Assignment 1 is posted.\\

to:

''Lecture:'' Course introduction (cont). Gene finding in prokaryotes [ [[Path:../../pdfs/prokaryote_gene_finding.pdf | 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.\\

to:

''Lecture:'' Course introduction (cont). Gene finding in prokaryotes [ [[Path:../../pdfs/prokaryote_gene_finding.pdf | slides]]. Assignment 1 is posted.\\

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

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!!Week 2:

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

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'''Thursday, 8/25'''\\
''Lecture:'' Course introduction (cont). Assignment 1 is posted.\\

'''Tuesday, 8/30'''\\
''Lecture:'' Pairwise sequence alignment [ [[Path:../../pdfs/alignment.pdf | slides]] ] \\
''Reading:'' Chapter 6 of ''Bioinformatics algorithms'' [ [[http://bix.ucsd.edu/bioalgorithms/book/excerpt-ch6.pd | 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 [ [[Path:../../pdfs/intro.pdf | slides]] ] \\
''Reading:'' Alex Zien's ''A primer on molecular biology'' [ [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf | pdf]] ].\\ Martin Tompa's notes [ [[http://www.cs.washington.edu/homes/tompa/papers/molbio.pdf |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'' [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]
* Book chapter from Larry Hunter [[http://www.cs.colostate.edu/~asa/courses/cs580/spr08/reading/hunterBioForCS.pdf | pdf]]
* Notes from Martin Tompa [[http://www.cs.washington.edu/homes/tompa/papers/molbio.pdf | pdf]]
* And a paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|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

to:

Done.

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

Changed lines 27-31 from:

Spliced ~~alignment~~

to:

Spliced alignment

!!!Week 6: 2/23 - 2/27
''Lectures:'' Multiple sequence alignment

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

Changed line 3 from:

''Lectures:'' Course overview, biological preliminaries~~, gene finding in prokaryotes~~\\

to:

''Lectures:'' Course overview, biological preliminaries\\

Changed lines 8-27 from:

* And a paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

to:

* And a paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|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 -

Changed line 5 from:

* The first chapter of the book ''Kernel methods in computational biology'' [[[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]]

to:

* The first chapter of the book ''Kernel methods in computational biology'' [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]

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

Changed line 5 from:

* The first chapter of the book ''Kernel methods in computational biology'' [ [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]] ]

to:

* The first chapter of the book ''Kernel methods in computational biology'' [[[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]]

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

Changed line 5 from:

* The first chapter of the book ''Kernel methods in computational biology'' [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]

to:

* The first chapter of the book ''Kernel methods in computational biology'' [ [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]] ]

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

Changed lines 5-8 from:

-> The first chapter of the book ''Kernel methods in computational biology'' [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]
-> Book chapter from Larry Hunter [[http://www.cs.colostate.edu/~asa/courses/cs580/spr08/reading/hunterBioForCS.pdf | pdf]]
-> Notes from Martin Tompa [[http://www.cs.washington.edu/homes/tompa/papers/molbio.pdf | pdf]]
~~-> A~~ paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

to:

* The first chapter of the book ''Kernel methods in computational biology'' [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]
* Book chapter from Larry Hunter [[http://www.cs.colostate.edu/~asa/courses/cs580/spr08/reading/hunterBioForCS.pdf | pdf]]
* Notes from Martin Tompa [[http://www.cs.washington.edu/homes/tompa/papers/molbio.pdf | pdf]]
* And a paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

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

Changed lines 3-4 from:

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

to:

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

Changed line 8 from:

-> A paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|[[link]]]]

to:

-> A paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

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

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Changed line 9 from:

-> A paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

to:

-> A paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|[[link]]]]

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

Changed lines 3-4 from:

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

to:

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

Changed lines 8-9 from:

-> A paper from Sean Eddy about the nature of research in bioinformatics
[[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

to:

-> A paper from Sean Eddy about the nature of research in bioinformatics [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

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

Changed lines 5-6 from:

-> The first chapter of the book ''Kernel methods in computational biology''
[[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf | pdf]]

to:

-> The first chapter of the book ''Kernel methods in computational biology'' [[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf|pdf]]

Changed line 9 from:

[[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006 | link]]

to:

[[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006|link]]

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

Changed lines 1-2 from:

~~Coming soon~~!

to:

!!!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''
[[http://www.kyb.mpg.de/publications/pdfs/pdf2503.pdf | pdf]]
-> Book chapter from Larry Hunter [[http://www.cs.colostate.edu/~asa/courses/cs580/spr08/reading/hunterBioForCS.pdf | pdf]]
-> Notes from Martin Tompa [[http://www.cs.washington.edu/homes/tompa/papers/molbio.pdf | pdf]]
-> A paper from Sean Eddy about the nature of research in bioinformatics
[[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006 | link]]

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

Added lines 1-2:

Coming soon!

Main.Schedule History