Dr. Natasa Przulj

E-mail: natasha [at] imperial [dot] ac [dot] uk

Office: 407 A Huxley

Lecture time: *Fridays, 2 – 5 pm (2 hours of lecture and 1 hour of tutorial)*

Location: *145 Huxley*

Office hours: *Fridays, 5 pm, 407 A Huxley*

The course will cover basic biological concepts behind biological **networks**, fundamental graph theoretic algorithms, computational complexity and challenges in network analysis, existing post-genomic approaches for analyzing, modeling, and comparing biological networks, and applications of these approaches to understanding biological function, disease, and evolution.

For information about course goals, topics, organization, grading scheme, textbooks and readings, etc., please see the course syllabus.

- Lecture 1: Course overview and Introduction to Biology
- Lecture 2: Sequencing and Genomics (Prof. Guo)
- Lecture 3: Sequence Analysis (Prof. Guo)
- Lecture 4: Sequence Analysis (Prof. Guo)
- Tutorial 1 questions; Tutorial 1 answers.
- Lecture 5: Functional Genomics and Microarray Analysis (Prof. Guo)
- Lecture 6: Functional Genomics and Microarray Analysis continued (Prof. Guo)
- Tutorial 2 questions; Tutorial 2 answers.
- Lectures 7 and 8: Introduction to biological networks
- Tutorial 3: Using BLAST; Tutorial 3: Hands-on microarray analysis.
- Lectures 9 and 10: Introduction to graph theory
- OPTIONAL: Review of more graph algorithms; after slide 11 is optional reading and will not be assessed.
- Tutorial 4 questions; Tutorial 4 answers.
- Coursework 1 — due on March 4 at 2pm.Sample Data for Coursework 1.
- Lectures 11, 12 and 13: Network properties
- Tutorial 5 questions; Tutorial 5 answers.
- Lectures 13 and 14: Network properties and models
- Tutorial 6 questions; Tutorial 6 answers; Answers spreadsheet.
- Tutorial 6: Cytoscape demo notes; Tutorial 6: GraphCrunch demo notes.
- Coursework 2 — due on March 18 at 2pm.
- Lectures 15 and 16: Network comparisons and alignments
- Lecture 16a: Software tools for network analysis and modeling
- Tutorial 7 questions; Tutorial 7 answers.
- Lectures 17 and 18: Graph clustering; interplay of network topology and biological function.
- Coursework 1 and Coursework 2 model solutions: CW1_Q1,CW1_Q2,CW1_Q2_plot,CW1_Q3-5.

- Survey: “Graph-theoretic approaches for studying biological networks“, Tijana Milenkovic, PhD advancement, Univeristy of California, Irvine, 2008.
- Natasa Przulj and Tijana Milenkovic, “Computational Methods for Analyzing and Modeling Biological Networks“, a chapter in “
**Biological Data Mining**”, edited by Jake Chen and Stefano Lonardi, Chapman & Hall/CRC; 1 edition, September 1, 2009. - Sequence alignment (pdf, doc)

- Homework 1

(Given out on February 25, 2011. Due on March 4, 2011 at 2pm.) - Solutions to homework 1
- Homework 2

(Given out on March 4, 2011. Due on March 18, 2011 at 2pm. No late submissions will be allowed.) - Solutions to homework 2
- Exam (Date to be determined.)