Agenda - DOE Joint Genome Institute

Poster Session

Day 1 – Wednesday, April 5

SESSION 1 (morning): Understanding phylogenetic novelty of natural microbial communities

This session will focus on the wealth of novel microbial lineages that have recently been identified using metagenomic and single-cell genomic data, and how to define this novelty. Talks will include the current status of the tree of life; approaches to classify and taxonomically define lineages (phyla); tools for measuring phylogenetic distance relative to accepted taxonomic schemes; and efforts towards developing standards to define lineages.

Chairs: Jill Banfield / Tanja Woyke

08:00 – 08:30: AM Refreshments
08:25 – 08:30: Welcome, JGI
08:30 – 09:30: Keynote: Jill Banfield, University of California, Berkeley, “New biology across the tree of life”
09:30 – 09:50: Tandy Warnow, University of Illinois, “Improved techniques to taxonomically characterize metagenomic datasets using ensembles of Hidden Markov Models”
09:50 – 10:00: Questions
10:00 – 10:20: Phil Hugenholtz, University of Queensland, “Calibrating microbial dark matter using a genome-based taxonomy”
10:20 – 10:30: Questions
10:30 – 11:00: Break
11:00 – 11:20: Laura Katz, Smith College, “Insights into the evolution of eukaryotic microbes through single-cell ‘omics”
11:20 – 11:30: Questions
11:30 – 11:50: Ramunas Stepanauskas, Bigelow Laboratory, “Linking genomes and phenomes of individual cells in their environment”
11:50 – 12:00: Questions
12:00 – 12:30: Roundtable Discussion
12:30 – 13:30: Working Lunch “Discussion on the future of Microbial Dark Matter exploration”

SESSION 2 (afternoon): Computational approaches for functional characterization

This session will focus on efforts to functionally characterize MDM and sequence novelty using computational approaches. Talks will include non-homology based predictions and the search for novel biochemistry.

Chairs: Matt Sullivan / Emiley Eloe-Fadrosh

13:30 – 13:50: Thomas Brüls, Genoscope, “Rationale for a “grayscale imaging” of microbial dark matter genes”
13:50 – 14:00: Questions
14:00 – 14:20: Andrew Doxey, University of Waterloo, “Mining genomes for functional novelty: detecting the unexpected”
14:20 – 14:30: Questions
14:30 – 14:50: Katie Pollard, Gladstone Institutes, UCSF, “A “most wanted” list of gene families with unknown function”
14:50 – 15:00: Questions
15:00 – 15:20: Break
15:20 – 15:40: Sergey Ovchinnikov, University of Washington, “Protein structure determination using metagenome sequence data”
15:40 – 15:50: Questions
16:00 – 16:20: Roundtable Discussion
16:45 – 18:30: Poster Session
18:45 – 20:15: Working Dinner
19:15: After dinner talk: Slava Epstein, Northeastern University, “Microbial Stem Cell Hypothesis”

Day 2 – Thursday, April 6

SESSION 3 (morning): Experimental approaches to validate functional predictions

This session will focus on experimental methodologies and advances to test and validate sequence-based functional predictions. Talks will include approaches to experimentally characterize hypothetical proteins; quantitatively measure predicted pathways; high-throughput screening methods; and novel techniques to assign functional “read out” to sequence data of MDM.

Chairs: Jennifer Pett-Ridge / Rex Malmstrom

08:00 – 08:30: AM Refreshments
08:30 – 08:50: Rich Roberts, New England Biolabs, “Characterizing DNA methyltransferases”
08:50 – 09:00: Questions
09:00 – 09:20: Ann Pearson, Harvard University, “Stable isotope fingerprinting: probing metabolisms without the use of labels”
09:20 – 09:30: Questions
09:30 – 09:50: Cheri Ackerman, UC Berkeley, “Mapping static and dynamic metals in living systems: from metabolism to signaling”
09:50 – 10:00: Questions
10:00 – 10:20: Break
10:20 – 11:20: DOE User Facility flash talks (15 min + 5 min for question)
- Carolyn Larabell, LBNL, Advanced Light Source, “3D views of cell organization with soft x-ray tomography”
- Branden Brough, LBNL, Molecular Foundry
- Galya Orr, PNNL, Environmental Molecular Sciences Laboratory, “EMSL capabilities for exploring microbial functions”
11:20 – 11:30: Questions
11:30 – 12:00: Roundtable Discussion
12:00 – 13:00: Working Lunch “Future of NeLLi Workshop, expansion and goals”

SESSION 4 (afternoon): Leveraging improved experimental design for enhanced biological interpretation

This session will focus on how to improve experimental design and new approaches to leverage interpretation of MDM populations. Speakers will explore pitfalls in current experimental designs. Continuing we will have selected poster talks and close out with a brainstorming session on large-scale, community-driven CSP project. The envisioned community-driven CSP would focus on functional aspects of primary MDM lineages and with the potential to draw in other DOE User facilities.

Chairs: Jonathan Eisen / Natalia Ivanova

13:00 – 13:20: Joshua Weitz, Georgia Institute of Technology, “Inferring virus-microbe infections (and more) from environmentally sequenced time-series”
13:20 – 13:30: Questions
13:30 – 13:50: Susan Holmes, Stanford University,”Reproducible research for multi-table data in microbiome studies”
13:50 – 14:00: Questions
14:00 – 14:30: Roundtable Discussion
14:30 – 15:30: Poster talks (4 speakers, 10 min each)
- Mircea Podar, ORNL, “The enigmatic Nanoarchaeota: why we still need to culture microbes”
- Simon Roux, LBNL, Joint Genome Institute, “Exploring viral dark matter through time-series metagenomes: the case of virophages”
- Vivek K. Mutalik, LBNL, “A high-throughput screening platform for assigning function to microbial dark matter”
- Sari Peura, SLU, “Functional phylogeny of superphylum Parcubacteria”
15:30 – 15:50: Break
15:50 – 16:50: CSP Brainstorming session
17:00: Meeting Adjourn