Old Lab Meeting Info
Past lab meetings
- 28 Jan - Soeren - Biolog: Probabilistic Logic Programming for Bioinformatics
- 4 Feb - Ian - recent enhancements to phylocomposer/handalign
- 11 Feb - Peter Schattner - Implementation of xrate on parallel compute-clusters and application to RNA structure prediction
- 18 Feb - Mitch - JBrowse
- 25 Feb - Oscar - Examining viral quasispecies evolution using microarrays: technical, experimental, and statistical perspectives.
- 4 Mar - CANCELED (Ian @Duke)
- 11 Mar - CANCELED (Ian @Pythium workshop)
- 18 Mar (relocated to 381 Stanley) - Benedict - Evolutionary chains and genomic cacti: a recursive method for homology mapping based upon chains of evolutionary conserved homology.
- 25 Mar - CANCELED (Spring break)
- 1 Apr - Oscar - Quasispecies array progress
- 8 Apr - Alexandre Bouchard-Cфtй
- 15 Apr - Oscar/everyone: discuss this paper: link
- 27 May Erick Matsen
- 9 Oct - internal group meeting
- 16 Oct - Transducer Meeting - Michael Hoffman - GCONSTRUCTOR
- 23 Oct - internal meeting - Soeren Moerk - Probabilistic Toolbox and PRISM
- 30 Oct - internal meeting - Oscar Westesson - Rec HMM
- 13 Nov - Internal meeting - Mitch Skinner - JBrowse
- 20 Nov - Transducer Meeting - Lars Barquist - Reconstruction Benchmarks
Spring 2007 lab meetings are held on alternate Wednesdays, from 12-1:30pm, in 381 Stanley Hall. Each lab meeting will focus on a particular topic in bioinformatics algorithms or software. One goal of this format is to work out ideas for new projects.
Prior to the meeting, one or two related papers will be assigned to each group member. Each person will present a quick summary of their assigned paper(s) and will then lead a short discussion of the work. These paper summaries will lead into an ad hoc summary of the state of the field in this area & a discussion of open questions and possible future projects.
The style is very informal; no powerpoint presentations or any of that rubbish; just "whiteboards, banter and the occasional URL". [tm]
To give people time to read & prepare I suggest we meet every 2-4 weeks.
When we're not holding a formal lab meeting we will try to meet at the same time/place for some kind of mini-jamboree, Wikipedia:Hackathon or other collective activity, or just to chat. Guests are always welcome.
Please note that dates marked "provisional" are subject to change!
|3/7/2007||noon||Gene species tree reconciliation lab meeting|
|4/4/2007||noon||Makefile lab meeting|
|4/18/2007||noon||Gene family evolution lab meeting|
|5/2/2007||noon||Ontology modeling lab meeting|
|5/23/2007||noon||Metagenomics clustering lab meeting|
|6/13/2007||noon||Genome assembly lab meeting|
|6/27/2007||noon||HIV fitness landscape lab meeting|
Future meeting dates...
|?||noon||Fungal genome mini-hackathon|
|? (provisional)||noon||Metagenomics workshop review lab meeting - take 2|
|? (provisional)||noon||Automated ortholog database lab meeting|
|? (provisional)||noon||Pathway evolution lab meeting|
Suggested future topics:
Some other ideas we might consider covering
- Ancestral gene & genome reconstruction
- Simultaneous alignment & folding of noncoding RNA
- Transposon annotation, classification & detection (see also Transposon Papers)
- Pseudogene detection & analysis
- Annotation pipeline architecture (largely covered by Makefile Lab Meeting; more specific topics might work, e.g. Automated Ortholog Database Lab Meeting)
Population genetics is of course a huge beast of a topic but a few semi-manageable entry points might include
- Heuristic alignment with recombination
- e.g. multi-tree phylo-HMMs, Spang et al.: A novel approach to remote homology detection: jumping alignments. J. Comput. Biol. 2002;9:747-60., jpHMMs
- main uses? (e.g. population subtyping in HIV)
- what (if anything) do these tell us about the recombination rate?
- what about adaptive versions to estimate the local rate?
- Heuristic & principled methods for sampling the Ancestral Recombination Graph
- e.g. Minichiello & Durbin: Mapping trait loci by use of inferred ancestral recombination graphs. Am. J. Hum. Genet. 2006;79:910-22. (heuristic), Song & Hein: Constructing minimal ancestral recombination graphs. J. Comput. Biol. 2005;12:147-69. (exhaustive), Song et al.: Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Bioinformatics 2005;21 Suppl 1:i413-22. (minimal), Fearnhead & Donnelly: Estimating recombination rates from population genetic data. Genetics 2001;159:1299-318. (exact sampling)...
- Population structure
- e.g. Pritchard et al.: Inference of population structure using multilocus genotype data. Genetics 2000;155:945-59. (and Pritchard et al.: Association mapping in structured populations. Am. J. Hum. Genet. 2000;67:170-81.), ...
For reference, presentation titles & other notes for previous lab meetings are preserved below.
|09/08||Andrew Uzilov, Gabriel Wu, Yuri Bendana, Robert Bradley, Ian Holmes||Overview of ongoing projects and opportunities||Yuri Bendana|
|09/22||Andreas Heger||Fruitfly CDS alignments and resources||Andrew Uzilov|
|10/20||Gabriel Wu||Protein structure annotation with xrate||Yuri Bendana|
|11/03||Robert Bradley||Phylogenetic SCFG composition||Gabriel Wu|
|11/10||Yuri Bendana||Genome annotation with xrate||Andrew Uzilov|
|11/17||Ian Holmes||String transducers||TBA|
Possible future speakers to invite for Fall 2006 - Spring 2007:
- Simon Prochnik
- Marcin Joachimiak
- Jason Stajich
- Dan Pollard
- Chris Smith
- Serafim Batzoglou, Chuong Do -- the people behind CONTRAfold (see: Do et al.: CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 2006;22:e90-8.)
Ideas for future lab meetings
- Tree-adjoining grammars
- Langevin equations and Markov models for ion channels
- A journal club is now in full effect
- See Teaching.CompbioTeaching for lecture and lab times
Spring 2006 speakers:
|02/24||Ian Holmes||Overview of fruitfly comparative genomics||Andrew Uzilov|
|03/03||Andrew Uzilov||Sixty Four Bit Cluster||Ian Holmes|
|03/10||Ian Holmes||Evolutionary grammars and xgram (ppt)||Sharon Chao|
|03/17||Andrew Uzilov||Generic Genome Browser||Yuri Bendana|
|03/24||Yuri Bendana||Drosophila noncoding RNA genes||Sharon Chao|
|03/31||n/a||(adjourned for Drosophila Research Conference, 2006)||n/a|
|04/07||Ian Holmes||Fly genome annotation||Robert Bradley|
|04/14||Robert Bradley||Drosophila transposons||Andrew Uzilov|
|04/21||Ian Holmes||informal wiki review (posted at lab news)||Robert Bradley|
|04/28||n/a||(adjourned for QB3/Designated Emphasis in Compbio Seminar, UCSF)||n/a|
|05/05||n/a||(adjourned for CSHL Biology of Genomes Meeting)||n/a|
|05/12||n/a||(adjourned for CSHL Biology of Genomes Meeting)||n/a|
|05/19||Chris Smith||Drosophila heterochromatin||Ian Holmes|
-- Created by: Ian Holmes on 04 Dec 2005