BIO 505: Winter 2008
Current Topics in Biology: Comparative Genomics
Instructor: Dr. Kathy Szick-Miranda
Office: Science I, 316
Phone: 654-6165
Email: kszick-miranda@csub.edu Web: www.csub.edu/~kszick_miranda
Office hours: W 2:00-4:00, and Th 10:30-1:00 or by appointment
Lecture and Discussion: M W 7:00-9:05pm, Sci I 221
Course Description: Current topics of special interest to graduate students in Biology.
Topics and content will vary as announced but will include contemporary or
interdisciplinary areas of interest. Repeatable. Prerequisites: Graduate standing or consent
of instructor. The focus of BIO 505 for the Winter of 2008 will be comparative genomics.
Course Philosophy:
Genomics is the study of an organism's entire genome or complete set of genetic
information encoded in that organisms DNA. This includes both genes and non-coding
sequences. Comparative genomics is the study of relationships between the genomes of
different species or strains. The goal of comparative genomics is to understand the
function and evolutionary processes that act on genomes. Upon completion of this course,
students will possess a thorough understanding of genomic sequencing techniques, public
DNA databases, sequence analysis tools, genome evolution and function/evolution of
regulatory sequences.
Course Format:
The format for this course is quite different from the traditional lecture format. Students
are expected to read all of the assigned literature and be prepared to serve as the
discussion leader for all assigned literature. The discussion leader for each paper will be
chosen at random the day the paper is to be discussed. As the discussion leader, it will be
your responsibility to provide an overview, lead the discussion and summarize the
assigned paper.
Grading: Grades will be based on the percentage of points accumulated in the course
using the scale shown below.
A = 94-100
B- = 80-82.9
D+ = 67-69.9
A-= 90-93.9
C+ = 77-79.9
D = 63-66.9
B+ = 87-89.9
C = 73-76.9
D- = 60-62.9
B = 83-86.9
C- = 70-72.9
F = 0-59.9
Assignment Point Percentages:
Attendance/Participation
Discussion Leader
Final Summary Paper
TOTAL
20%
40%
40%
100%
Academic Policies: It is expected that your work is YOUR work. In the unexpected
event of plagiarism and/or dishonesty during exams or for the research term-paper, the
student will receive a zero on that activity and be referred to the campus administration
for disciplinary action. Please refer to the campus 2007-2009 catalog page 81.
Final Writing Assignment (Due Friday March 15th):
Your final writing assignment is to prepare a clear, concise overview/summary of the
field of comparative genomics. Your target audience is other biology graduate students
who have not taken this specific version of BIO 505. You must include as many of the
assigned articles as possible. In addition you must include 5 additional resources (other
than those we covered in class). This writing assignment will serve as your final exam
and is due at 5pm (preferable sooner!) on Friday March 15th.
Course Schedule:
January 2:
Course introduction and distribution of reading material for lecture on January
7th.
January 7:
Bringing everyone up to speed. Lecture by Dr. Miranda
January 9:
Databases:
Wheeler, D. L., et al. (2007) Database Resources of the National Center for
Biotechnology Information. Nucleic Acids Research 35: 5-12.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. and Wheeler, D. L.
(2007) GenBank. Nucleic Acids Research 35: 21-25.
Crosby, M. A., Goodman, J. L., Strelets, V. B., Zhang, P., Gelbart, W. M., and
The FlyBase Consortium. (2007) FlyBase: Genomes by the Dozen. Nucleic Acids
Research 35: 486-491.
Identifying Genes:
Burge, C. B. and Karlin, S. (1998) Finding the Genes in Genomic DNA. Current
Opinion in Structural Biology. 8:346-354.
January 14:
Comparative Genomics Tools:
Loots, G. G. and Ovcharenko, I. (2005) Dcode.org Anthology of Comparative
Genomics Tools. Nucleic Acids Research 33: 56-64.
Brudno, M., Poliakov, A., Minovitsky, S., Ratnere, I., and Dubchak, I. (2007)
Mulitple Whole Genome Alignments and Novel Biomedical Applications at the
VISTA Portal. Nucleic Acids Research 35: 669-674.
Liolios, K., Mavromatis, K., Tavernarakis, N., and Kyrpides, N. C. (2007) The
Genomes On Line Database (GOLD) in 2007: Status of Genomic and
Metagenomic Projects and their Associated metadata. Nucleic Acids Research
Medigue, C., and Moszer, I. (2007) Annotation, Comparison and Databases for
Hundreds of Bacterial Genomes. Research in Microbiology. 158:724-736.
January 16:
Comparisons (within species):
Fleischmann, R. D., et al. (2002) Whole-Genome Comparison of Mycobacterium
tuberculosis Clinical and Laboratory Strains. Journal of Bacteriology. 184(19),
5479-5490.
Comparisons (minimal genome):
Koonin, E. V. (2003) Comparative Genomics, Minimal Gene-Sets and the Last
Universal Common Ancestor. Nature Reviews Microbiology 1: 127-136
January 21: HOLIDAY, Martin Luther King, Jr. Day
January 23:
Goffeau, A. et al. (1996) Life with 6000 genes. Science. 274:546-567.
Rubin, G. M., et al. (2000) Comparative Genomics of the Eukaryotes. Science.
287:2204-2215.
January 28:
Human Genome:
International Human Genome Sequencing Consortium (2001) Initial Sequencing
and Analysis of the Human Genome. Nature. 409:860-921.
January 30:
Human Genome:
Ventner, J. C., et al. (2001) The Sequence of the Human Genome. Science. 291:
1304-1351.
February 4:
Lindblad-Toh, K., et al. (2005) Genome Sequence, Comparative Analysis and
Haplotype Structure of the Domestic Dog. Nature. 438:803-819.
Putnam, N. H., et al. (2007) Sea Anemone Genome Reveals Ancestral
Eumetazoan Gene Repertoire and Genomic Organization. Science 317: 86-94.
February 6:
Rhesus Macaque Genome Sequencing and Analysis Consortium (2007)
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome.
Science. 316:222-234.
Mikkelsen, T. S. et al. (2007) Genome of the Marsupial Monodelphis domestica
Reveals Innovation in Non-coding Sequences. Nature. 447:167-178.
February 11:
Fitzpatrick, D. A., Logue, M.E., Stajich, J. E. and Butler, G. (2006) A Fungal
Phylogeny Based on 42 Complete Genomes Derived from Supertress and
Combined Gene Analysis. BMC Evolutionary Biology. 6:99-113.
Galagan, J. E., Henn, M. R., Ma, L.-J., Cuomo, C. A. and Birren, B. (2007)
Genomics of the Fungal Kingdom: Insights into Eukaryotic Biology. Genome
Research. 15:1620-1631.
February 13:
Niimura, Y., and Nei, M. (2006) Evolutionary Dynamics of Olfactory and Other
Chemosensory Receptor Genes in Vertebrates. J Hum Genet. 51:505-517.
Vicario, S., Moriyama, E. N., and Powell, J. R. (2007) Codon Usage in Twelve
Species of Drosophila. BMC Evolutionary Biology. 7:226-.
February 18:
Demuth, J. P., De Bie, T., Stajich, J. E., Cristianini, N., and Hahn, M.W. (2006)
The Evolution of Mammalian Gene Families. PLoS One. 1: 1-12.
Hahn, M. W., Han, M. V., and Han, S.-G. (2007) Gene Family Evolution across
12 Drosophila Genomes. PLoS Genetics. 3(11):2135-2146.
February 20:
Comparisons (non-coding DNA):
Dermitzakis, E. T., et al. (2002) Numerous Potentially Functional but Non-genic
Conserved Sequences on Human Chromosome 21. Nature. 420: 578-582.
Cooper, G. M. and Sidow, A. (2003) Genomic Regulatory Regions: Insights from
Comparative Sequence Analysis. Current Opinion in Genetics & Development.
13:604-610.
February 25:
Dermitzakis, E. T., Bergman, C. M., and Clark, A. G. (2003) Tracing the
Evolutionary History of Drosophila Regulatory Regions with Models that Identify
Transcription Factor Binding Sites. Mol. Biol. Evol. 20(5): 703-714.
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E. S. (2003)
Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory
Elements. Nature. 423:241-254.
February 27:
Dermitzakis, E. T., Kirkness, E., Schearz, S., Birney, E., Reymond, A. and
Antonarakis, S. (2004) Comparison of Human Chromosome 21 Conserved
Nongenic Sequences (CNGs) with the Mouse and Dog Genomes Shoes that their
Selective Constraint is Independent of their Genic Environment. Genome
Research 14:852-859.
Dermitzakis, E. T., Reymond, A., and Antonarakis, S. E. (2005) Conserved NonGenic Sequences – an Unexpected Feature of Mammalian Genomes. Nature
Reviews Genetics. 6: 151-157.
March 3:
Bird, C. P., Stranger, B. E., and Dermitzakis, E. T. (2006) Functional Variation
and Evolution of Non-coding DNA. Current Opinion in Genetics & Development.
16: 559-564.
Yamamoto, Y. Y., Ichida, H., Abe, T., Suzuki, Y., Sugano, S. and Obokata, J.
(2007) Differentiation of Core Promoter Architecture between Plants and
Mammals Revealed by LDSS Analysis. Nucleic Acids Research. 35(18): 62196226.
Stark, A., et al. (2007) Discovery of Functional Elements in 12 Drosophila
Genomes using Evolutionary Signatures. Nature. 450:219-232.
March 5: No class, work on papers.
March 10: No class, work on papers.