Welcome to the web-site for
Current Research in Statistical Genomics, Spring 2006
Meetings: alternate Thurs
(starting Jan 12), from 12.00noon to approximately 1.30pm.
Location: the Video-Conferencing room on the 5th floor of Wartik (519)
Instructor: Francesca Chiaromonte, Statistics, firstname.lastname@example.org , 505 Wartik, ph 5-7075.
Office Hours: Wed 1.30-3.30pm (or
Description: this 1-credit course will continue along the lines established by IBIOS 598E/STAT 598A in the Fall 2005. We will gather for a period of approximately 1.5 hours starting at 12.00noon on alternate Thursdays, and present and discuss recent Genomics articles with high computational and statistical content. Borrowing strength from the activities and research pursued in the Center for Comparative Genomics and Bioinformatics of Penn State, topics selection for Spring 2006 will focus on Comparative Genomics. Students enrolled for credit will be divided in groups and asked to present an article.
the second meeting has been moved from Thur Jan 26 to Tue Jan 24 (noon to 1.30pm)
ARTICLES and PRESENTATIONS
Please always read articles prior to our meeting dates. Links to pdf files are provided below.
Jan 12: Comparative Genomics and function: Conservation and beyond (I)
Taylor et al. Phylogeny-based encoding of genomic sequence alignments to investigate functional elements. (in revision). Presenter: J. Taylor.
Related reference: Kolbe, D. et al. (2004) Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Research 14:700-707.
Jan 24: Comparative Genomics and function: Conservation and beyond (II)
Siepel et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research, Aug 2005; 15: 1034-1050. Presenter: S. Tyekucheva.
Related reference: Siepel, A. and Haussler, D. (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J. Comput. Biol. 11(2-3):413-28.
Feb 9: Primate Genomes and Human Variation (I)
Hellmann et al. Why do human diversity levels vary at a megabase scale? Genome Research, Sept 2005; 15: 1222-1231. Presenters: E. Kvikstad and J. Skinner.
Related references: (1) Gaffney, D. and Keightley, P. (2005) The scale of mutational variation in the murid genome. Genome Research 15:1086-1094. (2) Hardison, R.C. et al. (2003) Co-variation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution. Genome Research 13:13-26.
For this general topic see also: (1) Chimpanzee Sequencing and Analysis Consortium article, Nature 437:69-87, Sept 2005. (2) International HapMap Consortium article, Nature 437:1299-1320, Oct 2005. (3) Special issue of Genome Research, Nov 2005; 15
Feb 23: Primate Genomes and Human Variation (II)
Schaffner et al. Calibrating a coalescent simulation of human genome sequence variation. Genome Research, Nov 2005; 15:1576-1583. Presenter: S. Sinha.
Mar 23: Reconstructing Ancestral Genomes
Blanchette et al. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Research, Dec 2004; 14:2412-2423. Presenter: J. Ma.
Also: J. Ma, L. Zhang, B. Suh, B. Raney, M. Blanchette, D. Haussler, and W. Miller (2006) Reconstructing contiguous regions of an ancestral genome (in preparation).
Apr 6: Comparative Genomics and function: Conservation and beyond (III)
Lunter et al. Genome-wide identification of human functional DNA using a neutral indel model. PLoS Computational Biology, Jan 2006; 2:2-12. Presenters: K.D. Ko and S.M. Liao.
Related reference: Chiaromonte et al. (2004) The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harbor Symposia in Quantitative Biology: The Genome of Homo Sapiens, 68:245-255.
Apr 20: Primate Genomes and Human Variation (III)
Raina et al.: Evolution of base-substitution gradients in primate mitochondrial genomes. Genome Research, May 2005; 15:665-673. Presenters: Y. Kelkar and D. Kim.
An additional paper of interest concerning Primate Genomes and Human Variation:
Nielsen et al. Genomic scans for selective sweeps using SNP data. Genome Research, Nov 2005; 15:1566-1575.