COURSE

SYLLABUS BIO 493-02/BIO 593-02 FALL 2014

BIO 493-02/BIO 593-02

INTRODUCTION TO GENOMICS

Instructor: Dr. Zhenguo Lin
Office Hour: THUR 10:00-11:30 in MW 323 or by appointment
Office Phone: 314-977-9816
Email: zhenguolin@slu.edu(Please put BIO493 or BIO593 in the subject header so that I can easily find
your email). I will try to respond within 24 hours to your message.

Class Meeting Time/Location:

Time: M 2:10-4:00, R 2:10-4:00
Location: 142 Macelwane Hall

Credits/Pre-requisites:

3 Credits
BIOL 302 (Biochemistry & Molecular Biology) and BIOL 303 (Genetics)

Course Description:
The course introduces students to core concepts in genomics research and the computational
methods used to analyze big data resources. The topics of this course include overviews of genome
projects, genomic architecture, sequence and structural variations,sequencing and data analysis,
fundamental bioinformatic and phylogenetic analyses, comparative genomic studies,and all other
omics studies (transcriptome, proteome, epigenomes and metagenome).

Learning Objectives
After successfully complete this course, studentsare expected:
1) toobtain necessary knowledge to be conversant in all of the areas of genomics
2)toestablish a knowledge base that enables the student to successfully move on and master
advanced topics in genomics
3)toutilize online databases and web resources to research and analyze genomics data using
problem-solving approaches.

Course Textbook (optional):

Jonathan Pevsner 2009 Bioinformatics and Functional Genomics, 2nd Edition
Arthur M Lesk, 2012 Introduction to Genomics 2nd Edition
Greg Gibson and Spencer V. Muse, 2004 A primer of Genome Science, 2nd Edition
TA Brown, 2002 Genomes, 2nd Edition
(free online book http://www.ncbi.nlm.nih.gov/books/NBK21130/)

Assignment and Grades:

Assignments: There will be numerous assignments in a variety of formats such as (but not
exclusively) in-class assignments, Bb online assignments, and take home assignments. At the end of
the semester you will receive a cumulative score for all of these assigned points, minus 10% For
example, if at the end of the semester the total points awarded for Assignments is 1000, the points
you earned will be divided by 900. Anyone who scores 900 points or more over the course of the
semester will receive a 100% for the assignments. If you miss an assignment of any kind (in
class or online) there is NO make-up. However, you can still earn 100% of the Assignments
points because 10% of the total possible points will be dropped at the end of the course. You will


COURSE SYLLABUS BIO 493-02/BIO 593-02 FALL 2014

not receive any credit for assignments turned in late. If you receive a 0 for an assignment due to an
academic integrity violation, that 0 will count toward your final grade and may not be dropped.

Exams:There will be two exams (Midterm and Final). Each exam will cover all material (lecture,
discussion and assigned readings). Final exam coverscontents learned throughout the semester.
The exams will be composed of questions in a variety of formats such as listing terms or concepts,
multiple choice, short answers and essay formats. Attendance to all exams is mandatory. If you must
miss an exam you must contact the instructor and submit a written request for a makeup exam at
least two weeks prior to that exam date. You will need to provide in writing the request that should
include detailed information about the conflict and provide documentation of the conflict and any
relevant contact information. Legitimate conflicts and excuses require written documentation, and
are limited to death or near-death instances in the immediate family, a students illness that
requires immediate doctors care, a University sponsored event (not club sports) and regularly
scheduled religious obligations. Excuses that will NOT be considered include personal travel
arrangements, non-University sponsored events, a conflicting appointment, a previous illness that
interfered with your study time or an illness that does not prevent you from coming to the exam.
Unexcused exam absences will be counted as zero in the calculation of your final grade.

Requirements for 593-02Section

1) Critical review essay and presentation: students enrolled in 593-02 sectionare expected to
complete two short (2-3 page), thoughtful and critical review essayson a research article relating to
genome biology and present the essays in class (10 mins). One essay/presentation is required for
493-02 section students.

2) Term research project and presentation: students enrolled in 593-02 sectionare expected to
complete a research project/proposal and present the project/proposal in-class (15 mins). The
research project provides an opportunity to conduct original research on a subject that interests
you. The instructor will recommend a list of research topics. However, students are encouraged to
provide their own research project. No research project/presentation is required for 493-02
section students.

Grading Scheme
Course Item Percent of Final Grade
493-02 section
593-02 section
Homework Assignments
45%
30%
Critical Review& Presentation
10%
20%
Exams
40%
25%
Participation
5%
5%
Research Project & Presentation
N/A
20%
Total
100%
100%

Final grades for the course will be based on the following scale. The instructor reserve the right to
make adjustments to grades based on overall performance in the course. There will be no
opportunity for extra credit to improve grades that have already been earned. Bargaining for
grades will not be tolerated.

Letter Grade
%

F
<60

D
60
<70

C-
70
<73

C
73
<77

C+
77
<80

B-
80-
<83

B
83
<87

B+
87
<90

A-
90
<93

A
93


COURSE SYLLABUS BIO 493-02/BIO 593-02 FALL 2014

Attendance policy:
You are expected to attend every lecture and take notes.There is no makeup for exams unless you
demonstrate in advance (and I agree) that a significant life-event prevents you from attending class
or if you have a documented emergency. If you schedule something else during a class when you
take an exam, you will get a zero for that grade.

Academic Integrity and Honesty
Saint Louis University is a community of learning in which integrity and mutual trust are vital. Since
the mission of the University is "the pursuit of truth for the greater glory of God and for the service
of humanity," acts of falsehood violate its very reason for existence. They also demean and
compromise the activities of teaching, research, and community service that are the primary
corporate purposes of the institution. Academic dishonesty runs counter to the ethical principles of
Christianity and of other cultural traditions and undercuts the spiritual and intellectual ideals of the
Catholic Church and the Society of Jesus, upon which the University is founded.
The destructive effects of academic dishonesty are many. Not only does it undermine the grading
process, robbing teachers of their ability to assess the accomplishments of their students and to
give proper responses and rewards, but it also impairs the ability of the University to certify to the
outside world the skills and attainments of its graduates. Such dishonesty allows students to take
unfair advantage of their peers and undermines moral character as well as self-respect. It also
damages the bonds of academic trust upon which the entire University rests. Since the College of
Arts and Sciences seeks to prepare students for lives of integrity and for occupations of trust, it
regards all acts of academic dishonesty as matters of serious concern.
In establishing high standards of integrity, the College is not only affirming certain rules students
are to observe in their time as students at Saint Louis University, but giving students ethical
principles and practices to take with them as they move into diverse professions and walks of life
beyond the walls of the University. To this end, the College relies, not merely on the willing
compliance and support of its students, but on the adherence to professional ethics displayed by its
students, but also by its faculty, staff, and administrators as well. Each year, the Committee on
Academic Honesty will pursue a variety of opportunities to heighten awareness of college policy
and the ethical principles on which it is founded. For more information visit the college web site
http://www.slu.edu/x12657.xml
In accordance with this policy the Biology Department has a ZERO TOLERANCE policy for any
violations of academic honesty. This includes plagiarism of any form. Any violations will result in a
zero for the graded material (which will be counted as a zero in your grade calculation), a report to
the Biology Department Chair, and potential for failing the course.

Student Disabilities Services and Accommodations:
Saint Louis University is committed to providing equal educational access for all of its students by
ensuring that students with documented clinical or medical disabilities receive reasonable
accommodations that support effective participation in all aspects of the educational experience. At
Disability Services, students, faculty and staff are welcome to obtain information regarding services
available, procedures, documentation, and best practices.
Students with documented clinical or medical disabilities who anticipate needs for
accommodations in this course should meet with Dr. Lin within the first two weeks of classes in
order for accommodations to be completed before the first exam. All inquiries about the
availability of reasonable university-related accommodations are kept confidential, and should be
addressed to:

Disability Services


COURSE SYLLABUS BIO 493-02/BIO 593-02 FALL 2014

disability_services@slu.edu
Phone: 314-977-3484
Fax: 314-977-3486
Busch Student Center, Suite 331 (part of Student Success Center)
20 North Grand Boulevard
St. Louis, MO 63103

Writing Center
I encourage you to take advantage of the writing services in the Student Success Center; getting
feedback benefits writers at all skill levels. Trained writing consultants can help with any writing,
multimedia project, or oral presentation. During the one-on-one consultations, you can work on
everything from brainstorming and developing ideas to crafting strong sentences and documenting
sources. These services do fill up, so please make an appointment! For more information, or to
make, change, or cancel an appointment, call 977-3484 or visit
http://www.slu.edu/writingservices.xml.

Weather Policy:
Please call 977-SNOW for information about school closure or class cancellations.


COURSE SYLLABUS BIO 493-02/BIO 593-02 FALL 2014

Topic Outline and Schedule(Schedule is tentative and subject to change):

Day
M

Date
08/25

Topic
Introduction, Human Genome Project

R
M

08/28
09/01

Structure and contentof human genome

Labor Day (No Class)

09/04

*Lab: UCSCgenome browser, NCBI

M
R

09/08
09/12

Genetic/PhysicalMapping
Sequencing techniques

09/15

Genome assembly and annotation

09/18

*Lab: Genome sequencing/assembly/annotation

09/22

Bioinformatics: sequence alignment/BLAST

R
M

09/25
09/29

*Lab: sequence alignment/BLAST

Mutations, Phylogenetics I

10/02

Phylogenetics II

10/06

*Lab: Phylogenetic analysis

R
M

10/09
10/13

Genomic variations: SNP, GWAS

Copy Number Variation (CNV)/ Genomic drift

10/16

Mid-Term Exam

10/20

Fall Break (No Class)

10/23

593 Essay presentation

M
R

10/27
10/30

Virus/ prokaryotic genomes

*Lab: Genomic variations

11/03

Fungi/plant genomes

R
M

11/06
11/10

Animal genomes
Evolutionary genomics

11/13

*Lab: Comparative &Evolutionary genomics

11/17

Gene expression and transcriptomes

11/20

493/593 Essay presentation

M
R

11/24
11/27

Proteomics
Thanksgiving (No Class)

12/01

Epigenomics, metagenomics

12/04

*Lab: transcriptomics, proteomics, epigenomics

M
TBA

12/08

593 Project presentation, & reviews

Final Exam