CS 262 Handouts Computational Genomics Winter 2004

---

Homeworks and Logistics

• Course Information (HTML)
• Course Syllabus (HTML)
• Course Staff (HTML)

This year's lecture notes

---

• Lecture 1: Jan 6 (Introduction to the Course and Basics of Molecular Biology).

  Serafim's Slides: (PPT).

  Omkar Deshpande's Slides on Biology For CS262: (PPT).

  Animation shown by Omkar on Protein Synthesis: (swf).

  Scribed notes (PDF - I)

  Scribed notes (PDF - II) .

  ---

• Lecture 2: Jan 8 (Pairwise Sequence Alignment).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 3: Jan 13 (Linear Space Alignment and Four-Russian Algorithm).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 4: Jan 15 (Heuristic Aligners & Introduction to HMMs).

  Serafim's Slides: (PPT).

  Scribed notes (DOC)

  ---

• Problem Set 1 (DOC) . (PDF).

  ---

• Discussion section 1: Jan 16.

  Omkar's Slides: (PPT).

  ---

• Lecture 5: Jan 20 (Hidden Markov Models, contd).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 6: Jan 22 (Training of HMMs).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Discussion section 2: Jan 23.

  Omkar's Slides: (PPT).

  ---

• Lecture 7: Jan 27 (HMM wrapup & Pair HMMs for Pairwise Alignment).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 8: Jan 29 (Connection between Alignments and Pair HMMs & DNA sequencing).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Problem Set 2 (DOC) .

  ---

• Discussion section 3: Jan 30.

  Omkar's Slides: (PPT).

  Animation on Sanger's Dideoxy Method: (swf).

  ---

• Lecture 9: Feb 3 (DNA sequencing, contd).

  Serafim's Slides: (PPT).

  Scribed notes (DOC)

  ---

• Lecture 10: Feb 5 (Whole Genome Shotgun Sequencing).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Discussion section 4: Feb 6.

  Omkar's Slides: (PPT).

  ---

• Lecture 11: Feb 10 (Suffix Trees & Rapid Genomic Global Alignments).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 12: Feb 12 (Multiple Sequence Alignments).

  Serafim's Slides: (PPT).

  Scribed notes (PDF - I)

  ---

• Problem Set 3 (DOC) .

  ---

• No Discussion section on Feb 13.

  ---

• Lecture 13: Feb 17 (Multiple Alignments and Gene Recognition).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 14: Feb 19 (Gene Recognition).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 15: Feb 24 (Gene Regulation & Microarray Analysis).

  Serafim's Slides: (PPT).

  Scribed notes (DOC - I)

  Scribed notes (DOC - II)

  ---

• Lecture 16: Feb 26 (Motif Finding).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 17: Mar 2 (Gibbs Sampling and Introduction to RNA structure prediction).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Problem Set 4 (DOC) .

  ---

• Lecture 18: Mar 4 (RNA secondary structure prediction).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

• Lecture 19: Mar 9 (Modeling of Evolutionary Trees).

  Lecture taken by Omkar on blackboard: no slides.

  Scribed notes (PDF)

  ---

• Lecture 20: Mar 11 (Phylogenetic Trees).

  Serafim's Slides: (PPT).

  Scribed notes (PDF)

  ---

Papers and Other Reference Materials

• Genscan: Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
• Transcriptional Regulation of the Stem Cell Leukemia Gene (PDF)
• T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment (PDF)
• LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (PDF)
• Glocal Alignment: Finding Rearrangements During Alignment (PDF)
• AVID: A Global Alignment Program (PDF)
• BLAT: The BLAST-Like Local Alignment Tool (PDF)
• Gapped BLAST and PHI-BLAST (PDF)
• Pattern Hunter: Faster and more sensitive homology search (PDF)
• The estimation of statistical parameters for local alignment score distributions (PDF)
• ARACHNE 2: Whole-genome sequence assembly for Mammalian Genomes (PDF)
• The Eulerian path approach to DNA fragment assembly (PDF)
• EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance (PDF)
• Exploring the conditional co-regulation of yeast gene expression through fuzzy k-means clustering (PDF)
• Systematic determination of genetic network architecture (PDF)
• A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition (PDF)
• ARACHNE: A Whole-Genome Shotgun Assembler (PDF)
• Genome Sizes (HTML)
• Transposons (HTML)
• Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
• SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model (PDF)
• Integrating Genomic Homology into Gene Structure Prediction (PDF)
• Christopher Burge's PhD Thesis (PS) (PDF)
• Identifying DNA and Protein Patterns with Statistically Significant Alignments of Multiple Sequences (PDF)
• Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment (PDF)

Viewing PostScript and PDF

• PostScript viewer
• PDF viewer

---