Aphaenofest 2014 - Talk on Network Inference Ideas

[MKLau]

Priority = understand genomic and proteomic changes over time of treatment

http://harvardforest.fas.harvard.edu/ellison/current-research/ants/harvard-climate-response

Why use networks?

What do gene networks mean?

How do you model and compare networks?

• Test and compare multiple methods and perspectives (distance, correlation, LASSO, Poly. Dyn. Sys.)
• Use network distance to measure multivariately
• Look at structural summary stats at multiple scales
• Can we parameterize flows? If so, we can apply ENA and systems theory.
• networkDynamic package in R
• WGCNA

What can you look at?

• Euclidean distance between edges
• Edge variances
• Matrix power series to look at paths of N length

What are the computational challenges?

• Harvard?
• iPlant?
• Amazon Web Services?

NimBios Working Group

• Stuart Borrett
• Ann Stapleton
• Heather Passmore
• DNAC

[MKLau]

Bonneau Lab - Network Inference

Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments

Genome Medicine | Full text | Gene regulatory network inference- evaluation and application to ovari…

http--citeseerx.ist.psu.edu-viewdoc-download?doi=10.1.1.18.3853&rep=rep1&type=pdf

http--cran.r-project.org-web-packages-GeneNet-GeneNet.pdf.webloc

Inference of gene regulatory networks from ge... [Bioinformatics. 2013] - PubMed - NCBI

PLOS Computational Biology- Inference of Gene Regulatory Networks with Sparse Structural Equation Mo…

Protein network inference from multiple genomic data- a supervised approach

Structural influence of gene networks on their inference- analysis of C3NET - Springer

WGCNA- R package for performing Weighted Gene Co-expression Network Analysis

[MKLau]

Hi all:

Aaron and I are organizing the schedule for Aphaenofest III, and we are setting up for the first day for presentations that summarize data and results by different group members. You are on this list because we think you are in this category! If you are willing to give a presentation, here are our thoughts on what you might want to cover:

Matt (new post-doc in Aaron's lab) a presentation to introduce yourself and some aspect of your research that you think would be interesting to the group and relevant to this project. Katie - Summary of stable isotope work done in collaboration with Menisha at HF Clint - Summary of trait data from last year's phytotron experiments Sara, Bryan - Review of basic principles and data stream for -omics in this study (remember, we ecologists are still uneducated newbies), overview of -omics results to date Bernice - Update on Aphaenogaster phylogeny and population genetics structure Andrew - Evolution of heat shock proteins, and summary of summer's work with Joel and Skyler on effects of starvation, dessication, and heat shock on protein expression Lacy - New updates on CT max data? John - update on transcriptome work, Aphaenogaster genome, RAD-tag, DGE data

With 9 presentations, these updates and progress reports will effectively fill our first day, leaving Sunday for planning of new experiments and data collection for 2014, as well as discussion of manuscripts and projected time lines.

At this stage, we are reluctant to prescribe precise times for your presentation because you all have differing amounts of material to report on. We anticipate relatively short talks (15 - 30 minutes) by Matt, Katie, and Lacy, and longer talks (30 - 50 minutes) by Sara, Bryan, John, Andrew, Bernice, and Clint. John's presentation will probably be the longest, given the Big Data he has been working with.

Send us your feedback on this proposal (including a rough estimate of how much time you would like), and we will organize the schedule. Of course we will leave plenty of time for questions and discussion after each presentation. We will ask Matt to give the first presentation in the morning because he has to leave Saturday mid-day.

Best,

Nick & Aaron

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Nicholas J. Gotelli Office Phone: 802-656-0450 Department of Biology Lab Phone: 802-656-0451
University of Vermont Fax: 802-656-2914 Burlington, VT 05405 e-mail: ngotelli@uvm.edu

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Home Page (with manuscript pdfs): http://www.uvm.edu/~ngotelli/homepage.html

Musician's Corner (with mp3s): http://www.uvm.edu/~ngotelli/musicpage/music.html

NEW: EcoSimR (free software for null model analysis): http://www.uvm.edu/~ngotelli/EcoSim/EcoSim.html

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[MKLau]

Mushroom photos!

[MKLau]

About Me

• A bit of personal info (California, HF-2003, Arizona, Boston, running, mushroom hunting, music)
• Long interest in species interactions (ant-plant-animal)
• Community ecology (mycorrhizae, foliar endophytes, lichen, ants, arthropods)
• Genes to Ecosystems - IGERT
• Analytics and Computation (Bayesian methods, R, Informatics, modeling)

[MKLau]

Surprises can occur at the network scale, with a good example being:

Bondavalli, C. & Ulanowicz, R.E. (1999) Unexpected effects of predators upon their prey: The case of the American alligator. Ecosystems, 2, 49–63.