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BIOS 692 - Topics in Computational Biology
Topics in Computational Biology is a seminar/reading group that meets once a week to discuss current issues in bioinformatics
| DATE | PRESENTER | CATEGORY | PAPER TITLE | DOWNLOAD |
|---|---|---|---|---|
| Jan. 21 | Mike Thomas | Sequence searching | "PhyloBLAST: Facilitating phylogenetic analysis of BLAST results" by Brinkman et al. Bioinformatics 17: 385-387, 2001 | |
| Jan. 28 | Mike Thomas | Homologs, orthlogs, and paralogs...oh my | "Orthologs & paralogs - we need to get it right" by R.A. Jensen, Genome Biology 2:interactions1002.1-1002.3, 2001; AND "OrthoMCL: Identification of ortholog groups for eukaryotic genomes" by Li et al., Genome Research 13:2178-2189, 2003 | PDF1, PDF2 |
| Feb. 4 | Eric Waltari | shotgun assembly | "An intro to shotgun sequencing" by G Gibson & SV Muse, pages 84-91 in A Primer of Genome Science; AND "Hierarchical Scaffolding With Bambus" by Pop et al., Genome Research 14:149-159, 2004 | PDF1, PDF2 |
| Feb. 11 | Quinn Shurtliff | gene expression analysis | "Serial Analysis of Gene Expression" by VE Velculescu et al. Science 270: 484-487, 1995; AND "Gene expression analysis of plant host–pathogen interactions by SuperSAGE" by H Matsumura et al., PNAS 100:15718-15723, 2003 | PDF1, PDF2 |
| Feb. 18 | Quinn Shurtliff & Mike Thomas | Bioinformatics approaches to SAGE tag annotation | "Assessment of SAGE in Transcript Identification" by VE Pleasance et al. Genome Res. 13(6):1203-1215, 2003 AND "Genome annotation by high-throughput 5' RNA end determination" by BJ Hwang et al., PNAS 101(6):1650-1655, 2004 | PDF1, PDF2 |
| Feb. 25 | Deborah Johnson | Chromosome evolution | John H. Postlethwait, et al. 2000. Zebrafish Comparative Genomics and the Origins of Vertebrate Chromosomes. Genome Research 10: 1890-1902 AND Anne E. Kwitek, et al. 2001. Automated Construction of High- Density Comparative Maps Between Rat, Human, and Mouse. Genome Research 11:1935–1943 | PDF1, PDF2 |
| Mar. 3 | Deborah Johnson & Mike Thomas | Chromosome evolution: informatics tools & approaches | ||
| Mar. 10 | Amy Runck | Whole genome phylogenetics | Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature, Vol. 425, 798-804 by Antonis Rokas et al. 2003. The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Boostrap Support, Mol. Biol. Evol. 19(4) 394-405 by Thomas R. Buckley and Clifford W. Cunningham 2002. |
Rokas.pdf, Buckley.pdf |
| Mar. 17 | Spring Break | |||
| Mar. 24 | Mitch Day | Horizontal Gene Transfer | Primary Paper "Ancient Horizontal Gene Transfer" by J R Brown "Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect" by Kondo, et al |
HGT HGT in Wolbachia |
| Mar. 31 | Tejaswita Karve | Computational identification of Drosophila microRNA genes | MicroRNA targets in Drosophila; Anton J Enright et al., Genome Biology 2003,5:RI; Computational identification of Drosophila microRNA genes. Eric C Lai et al. Genome Biology 2003,4:R42 | Enright, Lai |
| Apr. 7 | Lynn Durtschi | Informatics of gene prediction | Current methods of gene prediction, their strengths and weaknesses, Mathe' et al., Nucleic Acids Research, 2002, Vol. 30 No. 19 | Mathe' |
| Apr. 14 | Joy Olbertz | Microarray data analysis | Cluster analysis and display of genome-wide expression patterns, M. Eisen et al., PNAS 95:14863; Global functional profiling of gene expression, S Draghici, Genomics 81: 98 | Eisen, Onto |
| Apr. 28 | Mike Thomas | Microarray data analysis | More microarray gene expression experimental data analysis - a closer look at the Eisen paper | |
| May 3 | Luobin Yang | Data mining | Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology, June 2004, Volume 2, Issue 6 | H-inv |