Cracking the Code of Life NOVA program.
Requires Quick Time or Real Video Plug-in.
Recommended segments: 1, 2, 6, 9, 10, 12, 13, 14, and 16.
Link to
biotechnology companies in the Bay Area.
Information about the Instructor
Name: Sami Khuri
Office: 207 MacQuarrie Hall
Phone: 924-5081
Office Hours: By appointment
Course Description
Provides business and regulatory perspectives on electronic information
technologies, processes and standards in the conduct of clinical trials.
Special emphasis: data collection, clinical trial & data management
randomization and drug supply, statistical processes, safety databases and
electronic regulatory submission, electronic records and signatures, sys
validation processes, and data standards.
The course also covers the main topics in bioinformatics, such as the
analysis of DNA and protein sequences, building phylogenetic trees,
microarray analysis and pharmacogenomics.
Prerequisites
Admission to the MPDM program and completion of SMPD 286 and
BUS 224C.
Textbooks [No required textbooks]
Recommended (Not Required):
Understanding Bioinformatics
by Marketa Zvelebil and Jeremy Baum,
Garland Science, 2008, ISBN 0-815-34024-9.
Recommended:
Bioinformatics and Functional Genomics
by :
Jonathan Pevsner
Wiley-Blackwell, 2015, Third Edition,
ISBN 978-1-118-58178-0. (BFG)
Recommended:
Discovering Genomics, Proteomics, and Bioinformatics
by : A. Malcolm Campbell and Laurie J. Heyer,
Pearson Benjamin Cummings, 2007, Second Edition,
ISBN 0-8053-8219-4. (DGPB)
Recommended:
Practical Guide to Clinical Data Management
by : Susanne Prokscha,
Taylor and Francis, 2007, Second Edition,
ISBN 0-8493-7615-7. (SP)
- You will find a wealth of information including links, explanations,
lectures, etc... of each chapter of Bioinformatics and Functional
Genomics, at:
http://www.bioinfbook.org/php/?q=book3
- A copy of my powerpoint slides (6 per page) will be available at
Canvas, to the students enrolled in the class.
- We shall have topics in Regulatory Standards, Electronic Data
Capture, and more, covered by guest lecturers,
from the pharmaceutical
industry. Please see the tentative
schedule.
Tentative schedule that will be updated very frequently.
Please, check regularly.
Class |
Date |
Lecturer(s) |
Topics |
One |
March 11, 2019 |
Sami Khuri (4 hours) |
- Green sheet discussion
- Homework One discussion
- Hands-On One: Human Traits
- Chapter One: Molecular Biology (Review)
- Hands-On Two: Transcription-Translation
- Hands-On Three: Interesting Problems
|
Two |
March 18, 2019 |
Sami Khuri (4 hours) |
- Hands-On Three: Interesting Problems (cont.)
- Chapter Two: What is Bioinformatics? (I)
- Why Bioinformatics in SMPD?
- Hands-On Four: Sample Record and Databases
- Four Conventions for DNA, RNA, and proteins
- NCBI Sample Record
- Genomic Variations: SNPs, Haplotypes, CNVs and Indels
- Hands-On Five: Investigating Inherited Diseases (A,B)
- Hands-On Five: Investigating Inherited Diseases (C,D)
- UCSC Human Genome Browser
|
Three |
March 25, 2019 |
Sami Khuri (4 hours) |
- Chapter Two: What is Bioinformatics? (II)
- Submit Homework One
- In-Class, student presentations
- Homework Two Uploaded
- Hands-On Six: PAX6
- Multiple Sequence Alignment (I)
|
Four |
April 1, 2019 |
Sami Khuri (4 hours) |
- What is Bioinformatics? (III)
- Multiple Sequence Alignment (II)
- Why Bioinformatics in SMPD?
- Chapter Three: Beta Thalassemia
- Hemoglobinopathies
- Transitions and Transversions
- Beta Globin Gene
- Hands-On Seven: Beta Thalassemia
- Hands-On Eight: Multiple Sequence Alignment
|
Five |
April 8, 2019 |
Sami Khuri
(4 hours) |
- Submit Homework Two
- Homework Three Uploaded
- Chapter Four: CRISPR
- Gene Editing
- Hands-On Nine: CRISPR Part One
- CRISPR Arrays
- Hands-On Ten: CRISPR Part Two
|
Six |
April 15, 2019 |
Guest lecturers:
Jim Rogers and
James Warren
(4 hours)
|
A) Regulatory Standards
- 21 CFR Part 11: Electronic records and signatures
- FDA Guidance: Computerized systems used in clinical trials
- FDA Guidance: General Principles for software validation
- EU Reflection Paper on Electronic Source Data
- FDA Guidance on Electronic Source Documentation
- FDA Draft Guidance on Electronic Health Record Data in Clinical
Investigations
B) Electronic Data Capture (EDC)
- Evolution of EDC
- Current Technology and Adoption
- EDC Architectures/Hosting
- Points to Consider
C) Electronic Health Record Integration
- Safety Reporting
- Clinical Trial Data Collection
- Other Applications
|
Seven |
April 22, 2019 |
Sami Khuri (4 hours) |
- Chapter Five: Motifs
- Math Minute 2.2 (DGPB)
- Hands-On Eleven: Motifs
- Position Weight Matrices (PWM)
- Hands-On Twelve: PWM
- Hands-On Thirteen: Constructing a PWM (Part A)
|
Eight |
April 29, 2019 |
Sami Khuri (4 hours) |
- Submit Homework Three
- Take-Home Final Uploaded
- General discussion on Take-Home Final
- Hands-On Thirteen: Constructing a PWM (Part B)
- Hands-On Fourteen: Scoring using a PWM (Part A)
|
Nine |
May 6, 2019 |
Sami Khuri
(4 hours)
|
- Hands-On Fourteen: Scoring using a PWM (Part B)
- Motifs and CRISPR
- Further discussion of Take-Home Final
|
Ten |
May 13, 2019 |
Email Final to Sami Khuri |
- Submit Take-Home Final Examination by midnight PST
- Email subject: firstname_familyname_X where X is A, B, or C.
|
Course Requirements
- Problem Sets
Three homework assignments. The purpose of the assignments is to
develop
your understanding of the material and your skills in problem-solving.
Assignments are due in the beginning of the
lecture on the following dates:
-
Homework One
due on Monday, March 25, 2019.
-
Homework Two
due on Monday, April 8, 2019.
-
Homework Three
due on Monday, April 29, 2019.
- Hands-On Exercises
We will have a number of hands-on exercises.
The purpose of the hands-on exercises is to develop your
understanding of the material.
Students get full credit on Hands-On Exercsies as long as they are in
class during the discussion of the solutions of the problems. Students
marked absent will have to hand in a hard copy of detailed solutions of
the hands-on exercises they missed (if they want to get credit for the
exercises that were solved and discussed during their absence). The
submission will have to be done within a week from the absence. It is not
meant to be as a punishment, but rather to make sure that students do not
fall behind.
- Take-Home Final Examination:
Due by midnight (PST) on Monday, May 13, 2019.
Class Attendance
Class attendance is strongly encouraged as it is an integral part
of the learning process.
In class, we shall cover many
topics and examples that are neither in the class notes
nor in the textbook. If you miss a lecture,
it is your responsibility to find out what was covered in
class (this includes: handouts given
out during your absence, corrected typos and errors,
examples discussed in class - that
are neither in the book nor in the notes - clarifications
and changes made to assignments or the take-home exam, etc...).
Grading Policy
The final grade will be computed as shown below:
Homework: 30%
Hands-On Exercises: 40%
Take-Home Final Exam: 30%
[97, 100] A+
[93, 97) A
[90, 93) A-
[87, 90) B+
[82, 87) B
[80, 82) B-
[77, 80) C+
[72, 77) C
[70, 72) C-
[67, 70) D+
[62, 67) D
[60, 62) D-
[0, 60) F
Add/Drop Policy
For those wishing to add this course, the deadline is February 12, 2019.
The last day to drop with a full refund is February 5, 2019.
According to University and Department guidelines, dropping after
February 5, 2018, requires a serious and compelling reason to drop a
course.
Grades alone do not constitute reason to drop a course.
Students who stop attending without officially dropping will
be issued a U at the end of the semester which is counted as
an F in calculations of GPA. See University Catalog.
University Policies
Per University Policy S16-9, university-wide policy information relevant
to all courses, such as academic integrity, accommodations, etc. will be
available on Office of Graduate and Undergraduate Programs’
Syllabus Information web page
at
http://www.sjsu.edu/gup/syllabusinfo/ .
Make sure
to review these policies and resources.