MATH 6685 - Computer Applications in Biology - Spring 2017

University of Puerto Rico
Rio Piedras Campus
College of Natural Sciences
Department of Computer Science

Professor

Field Value
Name Humberto Ortiz-Zuazaga
Office NCL A-159
Laboratory NCL A-158
Telephone 787-764-0000 x88363
email humberto.ortiz@upr.edu
Web page https://ccom.uprrp.edu/~humberto/
Office hours Monday, Wednesday 8:00-9:30 AM
or by appointment

Credits

3 credits

Description

Introductory graduate course in bioinformatics to be offered Spring 2017 in UPR-RP. Topics covered will include biological sequences, programming in python, UNIX, sequence alignments, sequence phylogeny, sequence database searches, and gene expresion analysis, including microarray and RNA-Seq analysis, and gene set or pathway analysis.

We will emphasize the fundamental theory behind the analysis, and also present practical problems and their solutions. The course will use open-source bioinformatics tools such as bioconductor, and show how to construct such tools using python, R, or other languages.

Prerequisites

MATE 3026 or MATE 3028 or CCOM 3033

The course is designed for graduate and advanced undergraduate students in biology or computer science. Students should have some familiarity with programming.

Course schedule

The course will meet Monday and Wednesdays from 1:00-2:20PM in room CNL A-143, Natural Sciences, Rio Piedras Campus, University of Puerto Rico.

Objectives

Introduce students to fundamental concepts in bioinformatics, programming, algorithm design and analysis. After completing the course, students should be able to select tools and programs to solve bioinformatic problems and participate in their development.

Calendar

The proposed schedule of lectures, subject to change:

Date Topic Reading
Jan 18 Introduction: History of Bioinformatics Chapter 1, 2
Jan 23 Ethical Issues in Bioinformatics web page
Jan 25, 30 Sequences: Nucleic Acids and Proteins Chapter 3
Feb 1, 6 Computer platforms used in sequence analysis
Feb 8, 13 Brute force - Restriction mapping Chapter 4
Feb 15, 20 Greedy algorithms - Gene order Chapter 5
Feb 22 - Mar 1 Dynamic Programming - Pairwise Sequence Alignment Chapter 6
Mar 6 First Partial Exam
Mar 8-15 Graph Algorithms - Sequence Assembly Chapter 8
Mar 20-22 Combinatorial Pattern Matching - Fasta and BLAST Chapter 9
Mar 27 - Apr 3 Clustering and Trees- Phylogeny Chapter 10
Apr 5 Functional Genomics: Microarrays
Apr 10-17 Statistical Methods for Analysis of Microarray Data
Apr 19-26 Gene Regulatory Networks: Reverse Engineering
May 1 Second Partial Exam

Instructional strategies

The professor will discuss each topic, students will complete a practical excercise for each bioinformatic technique discussed in class.

Instructional resources

The course will be hosted on the UPRRP Moodle. Register and stay tuned for our polls and forum postings.

Textbook:

An Introduction to Bioinformatics Algorithms Neil C. Jones and Pavel A. Pevzner ISBN-10: 0-262-10106-8 ISBN-13: 978-0-262-10106-6

Evaluation

Students work will be evaluated on a 100% basis with the standard curve.

  • Participation in course forums (online, classroom), 25% final grade
  • Homework, 25% final grade
  • Two partial exams, 50% final grade

Reasonable accomodations for students

Students with disabilities properly registered with the Office of Affairs for Persons with Disabilities Oficina de Asuntos para la Persona con Impedimento (O.A.P.I.) should notify the professor at the start of the semester. The professor will make reasonable accommodations to support the student, in consultation with OAPI.

Academic integrity

The University of Puerto Rico promotes the highest standards of academic and scientific integrity. Article 6.2 of the UPR Student Bylaws (Certification JS 13 2009–2010) states that “academic dishonesty includes but is not limited to: fraudulent actions, obtaining grades or academic degrees using false or fraudulent simulations, copying totally or partially academic work from another person, plagiarizing totally or partially the work of another person, copying totally or partially responses from another person to examination questions, making another person to take any test, oral or written examination on his/hers behalf, as well as assisting or facilitating any person to incur in the aforementioned conduct”. Fraudulent conduct refers to “behavior with the intent to defraud, including but not limited to, malicious alteration or falsification of grades, records, identification cards or other official documents of the UPR or any other institution.” Any of these actions shall be subject to disciplinary sanctions in accordance with the disciplinary procedure, as stated in the existing UPR Student Bylaws.

DISCLAIMER: The above statement is an English translation, prepared at the Deanship of Academic Affairs of the Medical Sciences Campus, of certain parts of Article 6.2 of the UPR Student Bylaws “Reglamento General de Estudiantes de la Universidad de Puerto Rico”, (Certificación JS 13 2009-2010). It is in no way intended to be a legal substitute for the original document, written in Spanish.

References

  1. Neil C. Jones and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms. The MIT Press, Cambridge, Massachusetts,

  2. ISBN-10: 0-262-10106-8 ISBN-13: 978-0-262-10106-6.

  3. Introduction to Computational Biology: Maps, sequences and genomes. Michael S. Waterman. Chapman & Hall/CRC. 1995.

  4. Bioinformatics: Seqence and Genome Analysis, Second Edition. David W. Mount. Cold Spring Harbor Laboratory Press, 2004.

  5. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Dan Gusfield, Cambridge University Press, 1997.

  6. Bioinformatics for Biologists. Pavel A. Pevzner and Ron Shamir. Cambridge University Press, 2011.

  7. H. Ortiz-Zuazaga, Bioinformatics: Principles and Applications, http://www.hpcf.upr.edu/~humberto/presentations/bioinfo-pucpr.html

  8. H. Ortiz-Zuazaga, Notas de la clase, presentaciones, 2009, http://moodle.hpcf.upr.edu/course/view.php?id=10