Journal Club

Journal Club

In 2009, the journal club will be folded into the lab meeting.

Calendar

(Also shows lab meeting)

Edit this list to add date, name and paper:

Past papers (2008):

• 17 Oct 2008 - Lars - Worobey et al.: Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 2008;455:661-4.
• 24 Oct 2008 - Oscar - Bacolla et al.: Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Res. 2008;18:1545-53.
• 31 Oct 2008 - Ian - Blouin et al.: Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain. Protein Sci. 2004;13:608-16.
• 21 Nov 2008 - Mitch - Koonin &: Evolution of genome architecture. Int. J. Biochem. Cell Biol. 2009;41:298-306.
• 5 Dec 2008 - Oscar - Mossel &: On the impossibility of reconstructing ancestral data and phylogenies. J. Comput. Biol. 2003;10:669-76.

Proposed papers

General theme for fall 2008: evolutionary origins & reconstruction.

= already done

Algorithms

• Haussler reconstruction papers
  • Ma et al.: The infinite sites model of genome evolution. Proc. Natl. Acad. Sci. U.S.A. 2008;105:14254-61.
  • Ma et al.: DUPCAR: reconstructing contiguous ancestral regions with duplications. J. Comput. Biol. 2008;15:1007-27.

• Theoretical limits of reconstruction accuracy
  • Li et al.: More taxa are not necessarily better for the reconstruction of ancestral character states. Syst. Biol. 2008;57:647-53.
  • Mossel &: On the impossibility of reconstructing ancestral data and phylogenies. J. Comput. Biol. 2003;10:669-76.
  • http://front.math.ucdavis.edu/0406.5447
  • http://www.stat.berkeley.edu/~mossel/publications/second.pdf

The oldest genes

• Gutell, Smith et al -- origins of the ribosome
  • Smith et al.: The origin and evolution of the ribosome. Biol. Direct 2008;3:16.
• Primordial genes
  • Isenbarger et al.: The most conserved genome segments for life detection on Earth and other planets. Orig Life Evol Biosph 2008;38:517-33.

Disease & biomedical applications

Viruses

• Worobey et al -- origins of HIV
  • Worobey et al.: Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 2008;455:661-4.

• Quasispecies & error thresholds
  • Bull et al.: Quasispecies made simple. PLoS Comput. Biol. 2005;1:e61.
  • http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010061

• Selection in viruses
  • de Groot et al.: Investigating selection on viruses: a statistical alignment approach. BMC Bioinformatics 2008;9:304.
• Rate variation in HIV
  • Penn et al.: Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput. Biol. 2008;4:e1000214.

Other pathogens

• Origin and evolution of M. tuberculosis
  • 9000 year old M. tuberculosis DNA?!
  • Article

Repetitive sequence

• Microsatellite dynamics
  • Bacolla et al.: Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Res. 2008;18:1545-53.
  • Tanay & Siggia: Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol. 2008;9:R37.
• Prions
  • Ahn & Son: Comparative bioinformatics analysis of prion proteins isolated from reptile, rodent, ruminant, and human species. Exp. Mol. Med. 2007;39:769-77.
  • Lupi et al.: Did the first virus self-assemble from self-replicating prion proteins and RNA?. Med. Hypotheses 2007;69:724-30.
  • Lupi et al.: Are prions related to the emergence of early life?. Med. Hypotheses 2006;67:1027-33.

Pharmacognosy

• Antimicrobial peptides
  • Zhu & Gao: A fossil antibacterial peptide gives clues to structural diversity of cathelicidin-derived host defense peptides. FASEB J. 2009;23:13-20.

Background reading:

• Wikipedia:Pharmacognosy
• First example of pharmacognosy: discovery of penicillin

Cell biology

• Evolution of phospholipid signaling
  • Phosphatidylinositols form an important membrane-based signaling code and inositol-based probes are an emerging area at the interface of proteomics & chemical biology. This review outlines a very interesting evolutionary connection to Wikipedia:Symbiogenesis
  • Michell &: Inositol derivatives: evolution and functions. Nat. Rev. Mol. Cell Biol. 2008;9:151-61.
• Denker et al -- horizontal gene transfer and the evolution of cnidarian stinging cells
  • only two pages, but looks like there's a lot of fun stuff to dig in to in the supplemental
  • Denker et al.: Horizontal gene transfer and the evolution of cnidarian stinging cells. Curr. Biol. 2008;18:R858-9.

Transposons

See also Transposon Papers.

• horizontal transfer of DNA transposons in mammals
  • simultaneous transposon transfers in multiple distinct lineages, presumably the result of a virus
  • article

• Selfish elements & the evolution of genome architecture
  • Koonin &: Evolution of genome architecture. Int. J. Biochem. Cell Biol. 2009;41:298-306.

Experimental Validation of Reconstruction

• Resurrecting ancestral alcohol dehydrogenases from yeast

See also...

See also

• Lab Meeting
• Reconstruction Targets
• Old Journal Club Info

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Lab meeting events (included from Lab Meeting page):

• 17 Sep - joint BBOP/HL meeting - 381 Stanley
• 29 Oct - Le Petit Cheval
• 5 Nov - Chris Nasrallah - 421 Stanley