University of Illinois BIOE 582 (Fall 2017)Statistics and Algorithms in Genomic Biology
University of Illinois BIOE 582 (Fall 2017)Sergei Maslov: maslov@illinois.edu
Office: IGB 3406
Office hours: by appointment
Until about mid-November when he will be replaced with
Paul Jensen: pjens@illinois.edu
Tuesdays: 2:00PM - 3:20PM
Thursays: 2:00PM - 3:20PM
305 Material Science and Engineering Building (305 MSE)
Follow links from the Schedule page
WE WANT YOU TO BRING YOUR i-CLICKERS TO THIS CLASS.
WE WANT YOU TO BRING YOUR OWN LAPTOPS.
LAPTOPS SHOULD HAVE MATLAB INSTALLED
INCLUDING STATISTICS... AND BIONFORMATICS TOOLBOXES.
WE KNOW IT IS $100 BUT VIEW IT AS A TEXTBOOK.
THIS CLASS HAS NO REQUIRED TEXTBOOKS...
The course will provide students with the practical knowledge of statistical analysis
and computational modeling techniques relevant for applications in genomics and systems biology.
The focus will be on the fundamental concepts and algorithms for microbial genome assembly and annotation,
gene expression and network analysis, etc.
Topical Outline
Grading: midterm (40%), final project (60%).
Final Project: Teams of students will complete a de novo assembly for an unsequenced bacteria
of clinical relevance. Students will load and run a Oxford Nanopore sequencer and apply standard
tools to assemble, quality control, and annotate a genome. The final sequence will be deposited in
the NCBI genome repository.
Textbooks recommended: Textbooks will not be required for the core classes, but students are
encouraged to review these textbooks for optional information on fundamental concepts that
will be covered during class:
Prerequisites:
STAT 100 or 8equivalent, MCB 250 or equivalent, MATH 220 or equivalent, CS 101 or equivalent
The University's policy on academic integrity can be found in the
Code of Policies and Regulations Applying to All Students under
Article One, Part IV. The following policies support and reinforce that policy.
1. Science cannot exist without honesty. We expect all students, as scientists-in-the-making,
to hold the highest standards of scientific and academic conduct. Any form of cheating on
any graded work in this course is unacceptable, and will be dealt with as outlined below,
and in accordance with the University-wide standards in the Code of Policies and
Regulations Applying to All Students.
2. We require that all graded work be entirely your own, and that anything you write
using the words of other writers be correctly attributed. Some specific points follow:
On assignments, quizzes, and presentations, the answers that you turn in for grading
must be your own understanding of the material. Even working within a group, you must
contribute to the group's effort and not just have one person do all of the work. Since
we cannot monitor you as you complete your work, we have only the appearance of
your work from which to judge. If the work that you submit closely resembles that
of another student/team too closely, we may conclude that it was not your original work.
Failure to adhere to these standards may result in a grade of zero for the entire assignment,
for all persons involved.
On assignments, if you use another source to obtain the facts and/or opinions necessary
to complete your assignment, you must credit the source (see next point below) and rephrase
the information so that your assignment is entirely your own words. A good practice is to
read the source until you have a thorough understanding of the material, and then put it away.
Write your assignment as if you are explaining the information you learned from reading the
source to a classmate, member of your family, or to your teaching assistant. You may wish
to look at the source again for clarification, but be certain that you do not use statements taken
directly from the text in your assignment. Your entire assignment should be in your own words.
Furthermore, paraphrasing does NOT mean replacing key words in a statement with synonyms.
For an example of proper paraphrasing of a statement, consult the University's Code of Policies
and Regulations Applying to All Students. Failure to adhere to these standards may result in zero
credit for the entire assignment.
On assignments, if you use the ideas and/or opinions from another author or source,
you must provide the appropriate citation. That is, you must, using APA format, place a parenthetical
reference to the source that provided you the information necessary to complete that portion of the assignment.
Failure to adhere to these standards may result in zero credit for the entire assignment.
On assignments, if you use a statement taken directly from any book or other publication,
including the course textbook, you must provide a citation. That is, you must put the text in quotes
and, using APA format, place a parenthetical reference to the source at the end of the quote.
Direct quotations should be severely limited in your assignment; they should be used
ONLY in the following situations: