The MarineOmics working group is part of the RCN for Evolution in Changing Seas, and was formed to promote reproducible and robust genomic research in nonmodel species, but especially marine and aquatic studies. Methods in next generation sequencing and bioinformatics advance at a pace that quickly render any static set of best practices as obsolete. To support robust ’omics research now and moving forward, the working group helps disseminate guidelines through this dynamic, open-sourced website.

Rigorous: following best principles to identify and mitigate sources of error in data generation and analysis

Reproducible: when others can reproduce the results with accessible data, code, and documentation

Guidelines for ’omics analyses

On this website you will find a growing and evolving collection of guidelines, tutorials, recommended readings, and method evaluations for various ’omics analyses that are commonly used in studies of nonmodel systems (particularly marine species). Instead of providing rigid “best practices”, we aim to encourage data exploration and rigorous quality control through “best principles”. The guidelines are written by members of the MarineOmics working group or the community, then shared for peer review. Comments on current website content or suggestions for new content can be made through the Discussion Forum.

Based on the expertise of the MarineOmics working group, the first topics include:

Topics

Functional Genomics

  • Transcriptomics with RNA-Seq (coming soon!)
  • Differential gene expression (coming soon!)

The guidelines portion of the website is still under peer review and should be considered a “preprint”. If you are interested in contributing to the peer review process, check out the Discussion Forum.

Panel Seminars

To facilitate discussions about practices and pitfalls in applying ’omics to non-model systems, we hosted Q & A panel seminars with experts on topics ranging from RADseq, population genomics with WGS, and transcriptomics. Check them out on YouTube!

Reproducibility in Marine Genomics

The working group is also interested in evaluating and improving reproducibility in studies that use genomics to study adaptation in marine systems. utilizing genomics in marine species, through a peer-reviewed literature survey of data availability, code accessibility, and methods reproducibility. In Spring 2021, three undergraduate research interns contributed to this literature survey, with funding from the RCN-ECS.

Working Group Members

Katherine Silliman, PhD, Auburn University - kes0132[at]auburn.edu

Sam Bogan, UC-Santa Barbara -snbogan[at]ucsb.edu

Alan Downey-Wall, Northeastern University

Chris Mantegna, University of Washington

Danielle Davenport, University of Queensland

Hanny Rivera, PhD, Woods Hole Oceanographic Institute

Jecy Klinkam, College of William and Mary

Joe McGirr, PhD, UC-Davis

Kaitlin Macaranas, CSU-Bakersfield

Megan Guidry, University of Rhode Island

Natalie Ameral, University of Rhode Island & RI Dept. of Environmental Management

Nicolas Lou, Cornell University

Sara Schaal, Northeastern University

Sara Wuitchik, PhD, Harvard University

Faculty Advisors

Jon Puritz, PhD, University of Rhode Island

Steven Roberts, PhD, University of Washington

Contact

For more information about the working group or panel seminars, contact Katherine Silliman: kes0132[at]auburn.edu
For more information about the reproducibility review and undergraduate internship, contact Sam Bogan: snbogan[at]ucsb.edu