CSE549: Computational Biology

Professor: Rob Patro

Office: 1422 Computer Science
Email: rob.patro@cs.stonybrook.edu
My Office Hours: Tu/Th 3:00 4:30. If you really cannot make the scheduled office hours and you need
to meet with me, send me an e-mail to set up an appointment.
Lectures: 205 Frey Hall, Tu/Th 5:30 6:50 (sorry; I didnt choose this time /)
TA: To be determined.
Website: The website for this course is www.cs.stonybrook.edu/~rp/class/549f14. Currently, it contains
nothing of interest beyond what is in this syllabus. However, it will be updated throughout the semester
with relevant announcements, references, and course material.
Textbook(s): The book Understanding Bioinformatics (Zvelebil and Baum 2008) is the officially listed text
for this course. The lectures given in class and the material on the exams will not necessarily follow this book.
Rather, this book acts as a good, broad, practical introduction Bioinformatics and Computational Biology
and it provides a nice supplement to the in-class material (i.e. Im not requiring that you buy this book, but
you may find it to be an excellent reference). There are two other exceptional introductory texts that I can
recommend if you want to do some external study / reading. They are An Introduction to Bioinformatics
Algorithms (Jones and Pevzner 2004) and Bioinformatics Algorithms: An Active Learning Approach (Compeau
and Pevzner 2014). The latter book (Compeau and Pevzner 2014) is very new. In addition to the book, the
accompanying website (http://bioinformaticsalgorithms.com) has videos, slides and integrated set of small
programming assignments (http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track)
that some may find very helpful practice.
Finally, if youre from a discipline where youve not had a formal algorithms course, I find Algo-
rithms(Dasgupta, Papadimitriou, and Vazirani 2006) PDF available at (http://beust.com/algorithms.pdf)
to be a nice introduction to the basics. I also recommend Algorithm Design(Kleinberg and Tardos 2006)
and, of course, The Algorithm Design Manual(Skiena 2008) ,.
As we cover different material in the course, the course website will be updated with references to other texts
and articles relevant to the topics covered in the lectures.
Course Objectives: The main objective of this course will be to provide a broad overview of the major
areas of Bioinformatics and Computational Biology (B/CB). Our perspective will be a computational and
algorithmic one, though we will take the time to understand the necessary Biology and motivation for the
problems we discuss. We will touch upon many areas of B/CB, including phylogenetics, genome structure
and Biological network analysis. However, there will be a significant concentration on genomics and related
problems such as high-throughput read alignment, gene finding, genome assembly and transcriptome assembly
and analysis. At the end of this course, you should have a good understanding of the types of problems
people work on in B/CB, and a fairly in-depth knowledge of the computational tools and techniques used to
address some foundational problems in the field.

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Course Work (& grading):
Homework(s) 10% (I anticipate 1 or 2 of these)
Midterm 20%
Final 20%
Course Project 50%

proposal 5%
progress report 10%
final report & deliverables 35%

These percentages are tentative and may vary by some reasonably small amount. The final course project
since it constitutes a significant fraction of the grade should represent a substantial investment of
time. I expect that this project will be done in small groups. The deliverables will include a short (8
10 page) writeup, which should be a publishable quality document, even if we do not end up publishing it.
The deliverables will also include any related software (if applicable) and / or analysis scripts & data (if
applicable). Students are encouraged to come up with their own project ideas (we can discuss which ideas
are feasible / appropriate). I will also distribute a list of potential project ideas in a couple of weeks. As in
previous versions of this course, there will be a proposal and progress report due prior to the final project
writeup. Both of these will be graded. The purpose of this is to help set project expectations, allow me to
advise you on any stumbling blocks you may encounter, and to provide real motivation to not leave work on
the project until the last couple weeks of the course.

Course-specific policy

Excused Absences: If you miss a class for a medical or health-related reason, please provide me with a
record of this in writing or via e-mail (I do not need to know the specifics, just the date of your absence and
that it was for a medical or health reason). If, for a health-related or medical reason, you will miss two or
more consecutive classes, or will miss class on a recurring basis, or were unable to meet a particular academic
obligation of this course, I will require a written note from the Student Health Service or a healthcare provider
documenting the range of dates for which you were unable to meet your academic obligations. This note
need not contain any diagnostic information.
If you will miss any classes or scheduled exams as a result of religious observances, you must submit this
information to me, in writing, within the first two weeks of the semester to make necessary accommodations
to complete the work that will be missed.
Final Grades: The grade you receive in this class will reflect, as much as possible, the degree to which you
have mastered the necessary material. How much somebody needs an A will have no bearing on whether
or not (s)he receives an A, other than how this need or desire is reflected in the work that (s)he does. I
want everyone to do well in this course, and will make every reasonable effort to help you understand the
material as well as possible. However, barring errors in the grading of assignments, the grades you receive at
the end of the semester are final, and I will not alter them for personal or non-academic reasons, so please do
not ask me to!
Enjoy: The purpose of this class (and, ideally, any graduate-level class) is for you to learn. Computational
Biology is an active, vibrant, and exciting field of research. It concerns a broad array of interesting problems
that stretch from the primarily theoretical to the eminently practical. This course aims to introduce you to
this exciting field and helps prepare you, should you choose to do so, to perform research in Computational
Biology and tackle some of these interesting problems. Try to be inquisitive, engaged, and interested; try to
enjoy learning about this exciting field.

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University policy

Academic integrity: From the Universitys Academic Integrity Syllabus Statement http://www.stonybrook.
edu/commcms/academic_integrity/syllstate.html:

Each student must pursue his or her academic goals honestly and be personally accountable
for all submitted work. Representing another persons work as your own is always wrong. Any
suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more
comprehensive information on academic integrity, including categories of academic dishonesty,
please refer to the academic judiciary website at www.stonybrook.edu/academicintegrity.

Academic integrity is a very serious issue. Any assignment, project or exam you complete in this course is
expected to be your own work. If you are allowed to discuss the details of or work together on an assignment,
this will be made explicit. Otherwise, you are expected to complete the work yourself. It is always much
better to turn in an incorrect or incomplete assignment representing your own efforts than to attempt to pass
off the work of another as your own. I have a lot of tolerance for those who are making a significant effort
but may be having trouble understanding a particular concept or completing a certain assignment. However,
there will be no tolerance of academic dishonesty.
Learning disabilities: If you have a physical, psychological, medical or learning disability that may impact
your course work, please contact Disability Support Services, ECC (Educational Communications Center)
Building, room 128, (631) 632-6748. They will determine with you what accommodations, if any, are necessary
and appropriate. All information and documentation is confidential.

Bibliography
Compeau, Phillip, and Pavel Pevzner. 2014. Bioinformatics Algorithms: An Active Learning Approach.
Active Learning Publishers.
Dasgupta, Sanjoy, Christos H Papadimitriou, and Umesh Vazirani. 2006. Algorithms. McGraw-Hill, Inc.
Jones, Neil C, and Pavel Pevzner. 2004. An Introduction to Bioinformatics Algorithms. MIT press.
Kleinberg, Jon, and va Tardos. 2006. Algorithm Design. Pearson Education.
Skiena, Steven S. 2008. The Algorithm Design Manual. 2nd ed. Springer Publishing Company, Incorporated.
Zvelebil, Marketa J, and Jeremy O Baum. 2008. Understanding Bioinformatics. Garland Science.