This is a graduate course on
a hot topic where current issues and technologies are changing rapidly. It is
also intended to accommodate students with diverse backgrounds in computer
science and biology. Therefore, I expect you to be resourceful about finding
the reading materials that are most appropriate for you. Do not just sit and
wait for me to tell you what to read – if there is a term or concept you don’t
understand or want to understand better, try searching on Google,
going to the library to get a
reference book, or looking up a review article in Pubmed.
I will do my best to provide you with starting points and key terms/concepts
that will allow you to look things up quickly.
Biological
Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids by Durbin, Eddy, Krogh, and Mitchison
is a required text. It has been ordered by the
Genomes, 2nd
Edition, By T.A. Brown is a
useful reference. It is available online.
I strongly suggest that, if
your background in molecular biology is limited, you purchase or otherwise get
access to a serious introductory textbook on molecular biology or cell and
molecular biology. There are a number of good ones around, and it doesn’t much
matter which one you use --- they all contain pretty much the same basic facts.
I will not be referring to such a textbook explicitly in lecture, but I suggest
you read a few choice chapters. For
example, I use
Molecular Cell
Biology, by Harvey Lodish, et al., 4th
Edition. New York: W.H. Freeman and Company.
NEW The full text is available through PubMed!
This book is expensive but
everyone interested enough to take this course should own this book or one like
it. This book is also on reserve at the Hilltop library. There is a good
supplementary website for the book,
but looking at the site is no substitute for owning the book. For CS587 I would
particularly recommend the following chapters:
Chapter 1: The Dynamic Cell
Chapter 4: Nucleic Acids,
the Genetic Cod, and the Synthesis of Macromolecules
Chapter 7: Recombinant DNA
and Genomics
Chapter 9: Molecular
Structure of Genes and Chromosomes
Chapter 11: RNA Processing,
Nuclear Transport, and Transcriptional Control
Also of interest, though
less central to the lecture topics, are:
Chapter 6: Manipulating
Cells and Viruses in Culture
Chapter 8: Genetic Analysis
in Cell Biology
Chapter 10: Regulation of Transcription
Initiation
There are vast treasure
troves of biology information, including complete courses, available for free
on the web. For example, I just typed “molecular biology textbooks” into Google
and the top hit was this valuable
page. I have checked out one site linked from it, which I can recommend: the
MIT online biology textbook. However, I still think it is worth having your
own hardcopy molecular biology text, as it will provide lots more information
and probably better indexing.
A number of lectures will be
based on specific journal papers. Here is a list that will probably grow as the
semester progresses, with links to online copies where possible.
Durbin, R & Dear,
S (1998). Base qualities help sequencing software. Genome Research,
8, 161-162.
(Note: This paper is
challenging but at least the part up through Section 2.1 and Section 6, the
experiments, should be accessible.)
Mullikin, J.C.
and Z. Ning. 2003. The Phusion assembler. Genome
Res 13: 81-90.
Burge, C.
1997. Identification of Genes in Human Genomic DNA. Stanford University,
Stanford, CA.
(This is actually a dissertation but it is the best
available source on HMM Gene
Finding.)
Many journals provide all
their articles on line. Some are free to anyone and many others are free if you
access them through the library’s
Full Text Sources list. Among the completely free journals, the most
important for this class is Genome Research. It
is well worth browsing for final project/paper ideas.