CS612: Algorithms in Bioinformatics

 Fall 2017

Mo We 5:30-6:45, M-2-207



Course Description



Homework and Term Projects

Coursework (Links and PDF slides are posted here)



Student Conduct


Nurit Haspel
Office: S-3-071
Office Hours: Monday, Wednesday 2:30-4:00pm or by appointment
Office Phone: 617-287-6414
e-mail: nurit.haspel@umb.edu
Homepage: http://www.cs.umb.edu/~nurith

Course Description

This course will introduce students to bioinformatics - the area concerning the development and application of computational methods to address key problems in biology. It will introduce the students to a variety of methods and skills required to conduct research in this highly rising field. The emphasis of the course is structural bioinformatics with focus on various computational methods to simulate, analyze and model protein structure, dynamics and function. Other subjects such as systems biology, genomics and interaction networks will be introduced as well. The course is designed first and foremost for computer scientists but is also open to biology majors with adequate computational/mathematical background.

See the course syllabus for a detailed list of topics.

Prerequisites are CS210 (Intermediate Computing) and MATH 260 (Linear Algebra) or permission from the instructor.

Recommended Textbooks

Introduction to Bioinformatics, Arthur M. Lesk, Oxford, 4th edition.

Structural Bioinformatics, edited by Jenny Gu and Phillip E. Bourne, Willey Blackwell, 2nd edition.

Grade Evaluation

Homework assignments: 40-50% (4-5 homework assignments will be given)
Project and Final Presentation: 50-60%

Homework assignments

Assignment (PDF) Posted/Given on Due Date Handouts Sample Solution





Book Chapters

Session Dates

Session Info



basic concepts


September 6


Notes - introduction


Finish up intro
Sequence Alignment

Lesk: Chapter 4

September 11

Finish up introduction,
sequence comparison

September 13

Sequence alignment, BLAST

Notes - sequences

CS310 DP class notes



Accommodations:  Section 504 of the Americans with Disabilities Act of 1990 offers guidelines for curriculum modifications and adaptations for students with documented disabilities. If applicable, students may obtain adaptation recommendations from the Ross Center for Disability Services, Campus Center, UL Room 211, (617-287-7430). The student must present these recommendations and discuss them with each professor within a reasonable period, preferably by the end of Drop/Add period.

Student Conduct:  Students are required to adhere to the University Policy on Academic Standards and Cheating, to the University Statement on Plagiarism and the Documentation of Written Work, and to the Code of Student Conduct as delineated in the catalog of Undergraduate Programs. The Code is available online at: http://www.umb.edu/life_on_campus/policies/code/