Introduction to Genomics
BL 3300/FW 3300
Syllabus available at http://forest.mtu.edu/faculty/joshi/web/course%20Fall%202008.html
Who is your instructor?
• Shekhar Joshi (Chandrashekhar P. Joshi)
• Dr. Joshi
• Professor of Plant Molecular Genetics, SFRES
• Over 20 years of research experience
– Molecular Genetics, Biotechnology, Bioinformatics
• 45 papers, 16 book chapters,80 presentations
• Teaching molecular genetics at MTU since 1998
• This class is offered since 2001.
Where and when can you find me?
• Room # 168, Forestry Building
• Office Hours: I am generally available between
9 am to 6 pm on all weekdays except
– MWF between 3-4 pm when I teach this
BL3300/FW3300 class (better to take my
• Phone: 906-487-3480
• Email: email@example.com
• Web site: http://forest.mtu.edu/faculty/joshi/
• For those who walk up from the main campus: Do call
me or email me before walking up the hill to meet me!
Why was this course proposed?
Genomics is the study of genome structure and
function. This is a new and exciting area that has
recently witnessed many conceptual and
technical advances. This information is vital to
our day-to-day living in this century. Such a
course would also make our students
competitive in current job market
Bioinformatics majors needed this type of class
and now all molecular biology major students will
need this class too.
The main purpose of this course is to introduce concepts
of human genomics that can also be applied to microbial,
plant and animal genomes. The topics covered are:
• Genes and genome organization
• Genome mapping
• DNA fingerprinting
• Gene tagging
• Legal and Ethical aspects of genomics
• Genome evolution
• Credits: 3
• Time: Monday, Wednesday and Friday
3 pm-4 pm
• Place: Forestry G002
• Class Paper:
– Genomics meets Hollywood! (more on this
• Note: Class paper presentations will be held
between December 8th and 12th, 2008.
Required Text Book
– Philip N. Benfey and Alexander D. Protopapas
(Pearson Prentice Hall)
(For 2006 updates go to
– Recent book
– Up to date
– Real genomics book
– Ready made slides and space for notes
– Updates available
• Optional Reading material (No need to buy it)
• Genomes by T.A. Brown, 1999, John Wiley & Sons, NY
• Genes VIII by Benjamin Lewin, 2003, Oxford University Press
• Molecular Biology by Robert F. Weaver, 1999, McGraw-Hill
• Genome by Matt Ridley, Harper Collins, 2000
Grading Point System
• 100-95 A
• 94-90 AB
• 89-85 B
• 84-80 BC
• 79-75 C
• 74-70 CD
• 69-60 D
• < 59 F
• Course point distribution
• Class participation 10% (attendance and attention)
• Home work, quizzes etc 20%
• Class paper 10% (essay and Powerpoint presentation)
• Mid-term exam 30% (October 27th or 29th, 2008)
• Final exam 30% (during December 15-19, 2008)
• Each discussion group will consist of four-five students (you form your own
• Each of you will see a movie that uses DNA, genes, genomics or genetic
engineering as a theme (e.g. Jurassic park) and write a 3-5 page overview
of that movie and submit to me electronically by November 7, 2008.
• You will discuss the movie that you selected with the group
• You ALL will select one movie that you want to present to the class and one
of you will present it
• Tell the class about your movie selection: its main theme, the plot and how it
fits with the topic of the class.
• Provide your interpretations about accuracies and discrepancies of science
depicted in those movies.
• If you were the writer/director, how would you improve it to portray the
science more accurately (but not making it a complete flop)
• One representative per group will present a 10 minute powerpoint talk
sometime between December 8-12, 2008.
or student handbook
– Academic Integrity: plagiarism
– Attendance Policy: email me if absent
– Code of Conduct: follow the laws of the land
– Computer Use Policy: use responsibly
Please visit this site and make sure that all your actions
in the class are within the bounds of these policies.
• Chapter 1: Introduction
• Chapter 2: Technical Foundations of Genomics
• Chapter 3: Fundamentals of Genome Mapping and Sequencing
• Chapter 4: Genome sequencing
• Chapter 5: RNA expression analysis
• Chapter 6: The Computational Foundations of Genomics
• Chapter 7: High-Throughput Genetics
• Chapter 8: Proteomics
• Chapter 13: The Structure of Genomes
• Chapter 15: Genomics and Medicine
• Chapter 19: Genomics and Agriculture
• Chapter 20: Ethical issues of genomics
• Advanced genomics
• Remaining chapters of this book plus
• Sequenced genomes and what we learnt
• Future of genomics
What is the genome?
Entire genetic compliment of an
How many types of genomes
Why we should study genomes?
• Life’s little book of instructions
• DNA blue print of life!
• Human body has 1013
cells and each cell
has 6 billion base pairs (A, C, G, T)
• A hidden language determines which
proteins should be made and when
• This language is common to all organisms
What can genome sequence tell
• Everything about organism's life
• Its developmental program
• Disease resistance or susceptibility
• Where you are going?
How are human genomes
• 3% coding and rest of it junk (repetitive
• Nuclear and mitochondrial
• You are 99.99% similar to your neighbor
Why human genome?
• We want to know about ourselves
• How do we develop?
• How do we struggle, survive and die?
• Where are we going and where we came
• How similar are we to apes, trees, and
How will we change in this century
because of the Genomics?
• You will control the destiny of this planet
• Big changes in our life
• Biotechnology: more products
• GMOs: More food-More problems?
• Our society will not be the same!
• Individualized medicine
• Gene therapy
• Immortality? Disease free life?
Are we playing GOD?
Central dogma in Molecular Biology