Course meets Tuesdays and Thursdays 2:00-3:15 Tuesday/Thursday in 1304 SC.

*Office hours*: Tu 3:15-4:15 PM in Siebel Center 3235

**Teaching Assistant**: Sarah Christensen (sac2@illinois.edu)
(webpage),
Office hours: Wednesdays 11AM to noon, in 4105 Siebel Center.

** Course description**:
This is a course on applied algorithms, focusing on the use of
discrete mathematics, graph theory, probability theory,
statistics, machine learning,
and simulations, to
design and analyze algorithms for
phylogeny (evolutionary tree) estimation,
multiple sequence alignment, genome-scale phylogenetics,
genome assembly and annotation, and metagenomics.
Each of these biological problems is important and unsolved,
so that new methods are needed.
Hence, this course will provide opportunities for
computer scientists, mathematicians, and statisticians, to
do original and important research that can have an
impact on biology.
Every year, two or more students from this course have
done final projects that were subsequently
published in major scientific journals; you can
be one of them!
For examples of these papers,
see Mirarab et al., Bioinformatics 2014,
Zimmermann et al.,
BMC Genomics 2014,
Davidson
et al., BMC Genomics 2015,
Chou et al., BMC Genomics 2015,
Vachaspati and Warnow, BMC Genomics 2015,
and
Nute and Warnow, BMC Genomics 2016.

**Who should take this class:**
The course is designed for
graduate students in computer science, computer
engineering, bioengineering, mathematics,
and statistics, and does not depend on any prior background
in biology.

**Biology graduate students:**
Every year, biology graduate students have taken the course
for credit and done well.
Therefore, if you are a
biology graduate student
where these questions are relevant to your research
(especially if using phylogeny estimation or
multiple sequence alignments), you are very welcome in the class!
However, please meet with me to
discuss my expectations regarding homework and exams for
biology students.

**
Pre-requisites**:
CS 374 and CS 361/STAT 361, or consent of
the instructor;
no biology background is required.
If you did not take these pre-requisites at UIUC but have
equivalent coursework in algorithms and probability/statistics,
you will probably do fine.
If you are a biologist without this background but you are
working on problems where phylogeny estimation or multiple
sequence alignment are important, you may be able to
take the course as well with some extra work.
Please see me if you have any questions about whether the
course is suitable for you!

**Course Textbook: **
*Computational Phylogenetics*:
An introduction to designing methods for phylogeny
estimation, published by Cambridge University Press.
Errata are posted as I find them.
You can get the hardcopy
at the university bookstore (it is supposed to be there) or
on
Amazon.
You can also get the E-book at Google Play.
The image of the Monterey Cypress is there because of
the NSF-funded CIPRES project,
whose purpose was to develop the methods and computational
infrastructure to improve large-scale phylogeny estimation.

** Other course materials**:
Approximately the first half of the course is based on phylogenomics and
multiple sequence alignment, and is based on the textbook.
The second half of the course will cover
genome assembly and annotation, comparative
genomics, and metagenomics, and will be based
on the scientific literature.
You are
expected to do all assigned reading (whether from
the textbook or of published papers)
in advance of coming to class.

**
Grading**:

- Homeworks: 25% (two worst homework grades dropped)
- Take home midterm: 40%
(handed out Thursday April 19 in class, due
**Tuesday April 24 noon, via Moodle**) - Final Project: 25%
- Course Participation and paper presentation: 10%

** Homeworks**:
Homeworks need to be submitted to MOODLE in
PDF format; these
are due at 2 PM on the due date, which
will normally be on Thursdays.
Except as indicated,
homeworks can be submitted
up to 48 hours past the deadline for reduced
credit (80% if within 24 hours
and 60% if within 48 hours).
The single worst homework grade will be dropped.

** Final Project**:
The course requires a final project of each student, and is
due in class on the last day the class meets.
Please provide
hardcopy to
me directly - in class or in my office hours.
You are strongly encouraged to do a research project, but you can also do a survey paper on some topic relevant to the course material. In both cases, your project should be a paper (of about 15 pages) in a format and style appropriate for submission to a journal. Research projects can involve two students, but survey papers must be done by yourself.
Grades on the final project depend upon the kind of project you do. For a research paper, your grade will be 30% writing, 40% scientific/algorithmic rigor, and 30% impact. If you do a survey paper, the grade will be 30% writing, 30% summary of the literature you discuss, and 40% commentary (i.e., insight, critical and thoughtful discussion of the issues that come up).
See the chapter on Projects from the course textbook
for possible research projects.
You might also want to look at
this list of suggested
final projects.
*You will need to submit a 1-2 page proposal for your final project
by March 9 (via Moodle).
You should meet with me to discuss this proposal before you submit it,
and then again meet with me after I have given you feedback about
the proposal.
An approved proposal is required by March 16 (via Moodle).
*

** Class Presentation**:
All students will present research papers from
the recent scientific literature.
The presentation of scientific papers is
a major part of the course, and all students
are expected to participate actively
in discussing these papers.

*If you are presenting the paper:*You will select a paper from the recent scientific literature (related to the course material); these papers will be distributed to the entire class, and all students will read all the papers and submit questions to you in advance to help you prepare the presentation. You will have 15 minutes for the presentation, followed by 15 minutes of Q&A from the other students. You will send the PDF of your presentation to me at least 48 hours before the presentation (to receive feedback from me, submit it at least 72 hours before).-
*If you are not presenting the paper:*You are expected to read and understand the paper, and to participate actively in the discussion. You will submit a one paragraph summary of the paper and two questions about the paper to the professor at least 72 hours before the presentation; these will be forwarded to the student doing the presentation. This will count as one of your homeworks in the course, and will be graded. You should ask at least one question during the Q&A period. The questions you ask count towards the course participation grade.

**Course Participation:**
Your course participation will be evaluated in terms of
how you
participate in the in-class discussions of the scientific literature
we are reading, and also of the presentations
of scientific papers given
by the other students.

**Emergency response recommendations**

Please see webpage for CS 581 from Spring 2017, which has substantial overlap with this year's course.