General topic: probabilistic models of the fitness (particularly as regards drug resistance) & mutation/recombination landscapes for the HIV virus genome.

For date/time see LabMeeting.

• MitchSkinner: pairwise amino acid correlations via ratios
  • Pan C, Kim J, Chen L, Wang Q, Lee C.  The HIV positive selection mutation database.  Nucleic Acids Res. 2007 Jan;35(Database issue):D371-5. Epub 2006 Nov 15.
  • http://www.bioinformatics.ucla.edu/HIV
• AndrewUzilov: "mutagenic tree" graphical models for correlated amino acid mutations; mixtures of same
  • Beerenwinkel N, Rahnenfuhrer J, Daumer M, Hoffmann D, Kaiser R, Selbig J, Lengauer T.  Learning multiple evolutionary pathways from cross-sectional data.  J Comput Biol. 2005 Jul-Aug;12(6):584-98.
• AvinashVaradarajan: mutagenic-tree models that include evolutionary time via mutation rates, instead of probabilities
  • Beerenwinkel N, Daumer M, Sing T, Rahnenfuhrer J, Lengauer T, Selbig J, Hoffmann D, Kaiser R.  Estimating HIV evolutionary pathways and the genetic barrier to drug resistance.  J Infect Dis. 2005 Jun 1;191(11):1953-60. Epub 2005 Apr 28.
• RobertBradley: multi-track profile HMMs to detect subtype mixtures and recombination hotspots
  • Schultz AK, Zhang M, Leitner T, Kuiken C, Korber B, Morgenstern B, Stanke M.  A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.  BMC Bioinformatics. 2006 May 22;7:265.

HIV genome diagrams: 1, 2, 3

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Papers for the next meeting on viral phyloinformatics:

• Hein: viral ORF-finding phylogrammars
  • de Groot S, Mailund T, Hein J.  Comparative annotation of viral genomes with non-conserved gene structure.  Bioinformatics. 2007 May 1;23(9):1080-9. Epub 2007 Mar 6.

• Hofacker, Stadler et al: RNA regulatory elements in viruses
  • Hofacker IL, Stadler PF, Stocsits RR.  Conserved RNA secondary structures in viral genomes: a survey.  Bioinformatics. 2004 Jul 10;20(10):1495-9.
  • Thurner C, Witwer C, Hofacker IL, Stadler PF.  Conserved RNA secondary structures in Flaviviridae genomes.  J Gen Virol. 2004 May;85(Pt 5):1113-24.

• Meyer, Hein et al: phylogrammars for RNA structure in exons
  • Pedersen JS, Forsberg R, Meyer IM, Hein J.  An evolutionary model for protein-coding regions with conserved RNA structure.  Mol Biol Evol. 2004 Oct;21(10):1913-22. Epub 2004 Jun 30.
  • Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J.  A comparative method for finding and folding RNA secondary structures within protein-coding regions.  Nucleic Acids Res. 2004 Sep 24;32(16):4925-36. Print 2004.

• Drummond, Rambaut et al: mutation rate predicts disease
  • Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, Taveira N, Rambaut A.  Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.  PLoS Comput Biol. 2007 Feb 16;3(2):e29. Epub 2007 Jan 2.

HIV genome diagrams: 1, 2, 3

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Papers for the next meeting on NucleicAcidEngineering...

• RNA synthetic biology overview
  • Isaacs FJ, Dwyer DJ, Collins JJ.  RNA synthetic biology.  Nat Biotechnol. 2006 May;24(5):545-54.

• Principles of positive and negative RNA design
  • Dirks RM, Lin M, Winfree E, Pierce NA.  Paradigms for computational nucleic acid design.  Nucleic Acids Res. 2004 Feb 27;32(4):1392-403. Print 2004.

• Examples of RNA logic circuits
  • Penchovsky R, Breaker RR.  Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes.  Nat Biotechnol. 2005 Nov;23(11):1424-33. Epub 2005 Oct 23.
    • One-shot YES,NOT,AND,OR gates using hammerhead ribozyme
    • in silico design pipeline using Vienna
      • RNAfold, RNAinverse, RNAheat, kinRNA
  • Seelig G, Soloveichik D, Zhang DY, Winfree E.  Enzyme-free nucleic acid logic circuits.  Science. 2006 Dec 8;314(5805):1585-8.
    • Enzyme-Free Nucleic Acid Logic Circuits (Seelig, Winfree et al)
    • DNA logic gates with no catalysis required -- everything is done by binding and conformational changes.
  • Bayer TS, Smolke CD.  Programmable ligand-controlled riboregulators of eukaryotic gene expression.  Nat Biotechnol. 2005 Mar;23(3):337-43. Epub 2005 Feb 20.
    • ligand-gated riboswitches, GFP reporter

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Papers for the next meeting on viral synthetic biology:

• ViralRiboswitches
  • Wang S, White KA.  Riboswitching on RNA virus replication.  Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10406-11. Epub 2007 Jun 6.

• Synthesis of poliovirus
  • Cello J, Paul AV, Wimmer E.  Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template.  Science. 2002 Aug 9;297(5583):1016-8. Epub 2002 Jul 11.
  • De Jesus N, Franco D, Paul A, Wimmer E, Cello J.  Mutation of a single conserved nucleotide between the cloverleaf and internal ribosome entry site attenuates poliovirus neurovirulence.  J Virol. 2005 Nov;79(22):14235-43.

• HIV gene therapy
  • Weinberger LS, Schaffer DV, Arkin AP.  Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection.  J Virol. 2003 Sep;77(18):10028-36.

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Older list of papers (now superceded by above lists):

• Lengauer, Beerenwinkel et al (geno2pheno; "mutagenic tree" graphical models)
  • Beerenwinkel N, Daumer M, Oette M, Korn K, Hoffmann D, Kaiser R, Lengauer T, Selbig J, Walter H.  Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes.  Nucleic Acids Res. 2003 Jul 1;31(13):3850-5.
  • Beerenwinkel N et al.  Computational methods for the design of effective therapies against drug resistant HIV strains.  Bioinformatics. 2005 Nov 1;21(21):3943-50. Epub 2005 Sep 6.
  • Beerenwinkel N, Rahnenfuhrer J, Daumer M, Hoffmann D, Kaiser R, Selbig J, Lengauer T.  Learning multiple evolutionary pathways from cross-sectional data.  J Comput Biol. 2005 Jul-Aug;12(6):584-98.

• Chris Lee et al
  • Pan C, Kim J, Chen L, Wang Q, Lee C.  The HIV positive selection mutation database.  Nucleic Acids Res. 2007 Jan;35(Database issue):D371-5. Epub 2006 Nov 15.
  • Helweg-Larsen J, Lee CH, Jin S, Hsueh JY, Benfield TL, Hansen J, Lundgren JD, Lundgren B.  Clinical correlation of variations in the internal transcribed spacer regions of rRNA genes in Pneumocystis carinii f.sp. hominis.  AIDS. 2001 Mar 9;15(4):451-9.
  • Park CS, Kim MS, Lee SD, Kim SS, Lee KM, Lee CH.  Molecular phylogenetic analysis of HIV-1 vif gene from Korean isolates.  J Microbiol. 2006 Dec;44(6):655-9.

-- IanHolmes - 20 Jan 2007