Jun10 Annual Schedule

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Schedule for the iSEEM Jun10_Annual meeting.

Thursday June 24

9:00 - 9:30 Introductions, etc.

9:30 - 10:45 Protein Family (Guillaume, Morgan, Tom)

Guillaume's Presentation

Morgan's Presentation


  • Discussion will center around the recent creation of protein families for all completed genomes led by Guillaume.

10:45 - 11:00 Break

11:00 - 12:00 Ecotype Simulation (Alex Koeppel)


If there are no objections I'd like to use this session to discuss the results of our Ecotype Simulation analysis of the GOS Prochlorococcus sequences. I don't think I will necessarily need the full hour (maybe 20-30 minutes).

Presentation Slides. File:ISEEM Talk 2010.pdf

12:00 - 13:00 Lunch

13:00 - 14:00 Taxonomic Diversity Discussion (Tom)

Audio (includes audio for Aaron's presentation as well)

I'd like to have a session about characterizing microbial taxonomic diversity. At the very least:

  • PHYLOTU presentation (brief)
  • Where we can take PHYLOTU with future work (Discussion)
  • What improvements can we make to more accurately describe taxonomic diversity (strict PD, maybe something here by Steve?)
  • How can we incorporate Alex's work on the ecotype model of speciation for this purpose (something here by Alex)
  • Microbial biodiversity map (with Josh?)

14:00 - 15:00 Phylogenetic cobinning (Aaron Darling)

Recent progress on binning and linkage estimation in next-generation metagenomes (30 minutes + 15-30 minutes discussion)

Talk slides

15:00 - 15:15 Break

15:15 - 16:15 Characterization of unknown genes (Morgan Langille)


Morgan's Presentation

  • Planning on about 20 minute presentation leaving 25 minutes for questions/discussion
  • Will discuss some of the ranking metrics and results for gene families with unknown function (universality, pathogen, habitat, etc.)for completed genomes.
  • Discuss expansion of characterization metrics to metagenomic datasets.
  • Discuss methods for using metagenomic datasets to predict function for families of unknown function.

16:15 - 17:00 Paper discussions


Friday June 25

9:00 - 11:00 Diversity and Distance-Decay Relationships (Josh & James)

Josh's Presentation

Audio (includes audio for Sam's presentation as well)

  • Update on range estimation
  • The Minkowski-Steiner formula
  • Alpha diversity estimates from distance-decay?

James's Presentation pptx

James's Presentation pdf

  • I will present some slides briefly summarizing the theoretical models we've developed
  • I would like to extend these models to take into account environmental heterogeneity (see also here)
  • These ideas are at very early stages, so I will plan to talk for about 15-20 minutes. After that I'd appreciate feedback/discussion about what people consider most interesting questions/best directions to proceed in

11:00-11:15 Break

11:15 - 12:30 Impact of simulation studies on our phylogenetic analyses (Sam Riesenfeld)


  • Effect of read length, reference sequences, choice in phylogenetic inference method.
  • Doing round 2 simulations now -- what should we include?

12:30 - 14:00 Lunch (ordered in) + Paper discussions

  • Josh's papers
  • Steve's resubmission to PLoS
  • ZORRO revisions?

14:00 - 14:45 Measuring phylogenetic diversity with multiple marker genes (Steve)

Steve's Presentation

  • Discussion of results from analysis of GOS data based on multiple bacterial and archaeal marker genes (with Dongying & Guillaume)
  • How to choose and compare marker genes, identify organisms from different clades (i.e. what's an 'archaeal marker gene', how do we make sure it's capturing the groups we want?).
  • Guidelines for quality control (which sequences can we throw out - Sam, Tom, others have suggestions?)
  • How could this approach to measure diversity be combined with taxonomic, functional gene analyses by others?

14:45 - 15:45 Bioinformatics Discussion (Guillaume)

  • Current projects
  • Future: Supporting bioinformatics needs for different projects

15:45 - 16:00 Break

16:00 - 16:45 Grants and Funding (Josh)


1) finding funding for research that does not involve data collection

2) finding funding for development of general methods -- specific systems wanted


1) add a data collection element -- but preliminary data needed

2) add human/biomedical aspect

3) software development


1) NIH

2) NSF -- ecology, may be willing to fund pure theory (+)

3) NSF -- oceanography, oil spill

4) NSF -- statistics

5) NSF -- mathematical biology (+)

6) private sources

7) Joint NSF/NIH -- mathematical biology (+)

8) DARPA -- may be a stretch, funding less pure science recently

9) NSF -- bioinformatics postdoctoral fellowship (+)

(+) = most promising


  • may need to break into smaller groups for new grants
  • talk to SFI people about doing pure theory
  • grant proposal should reflect future plans, anticipated future directions
  • want to appear on job market as an expert in one field, even if interdisciplinary
  • non-faculty jobs: jobs at centers (e.g., SFI, Davis Genome Center, informaticist at cancer centers)
  • faculty jobs: group size highly dependent on location

16:45 - onward Papers in Prep Loose Ends