Analysis Working Groups

GeneLab is a science collaboration initiative and data system effort that provides a workspace with tools to analyze and visualize omics data. GeneLab has established four different Analysis Working Groups with the goal of maximizing the generation of new knowledge from these rare and complex spaceflight-relevant omics datasets within the GeneLab Data System.

About & Charter |  How to join an AWG |  Internship opportunity |  AWG workshop

Members –
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Plants
Name Affiliation
Matt Geniza, Ph.D. NASA Ames Research Center
Stephanie Richards NASA Kennedy Space Center
Howard Levine, Ph.D. NASA Kennedy Space Center
Sarah Wyatt, Ph.D. Ohio University
Colin P.S. Kruse Ohio University
Chris (Scot) Wolverton, Ph.D. Ohio Wesleyan University
Simon Gilroy, Ph.D. University of Wisconsin, Madison
Alexander Gabel University of Halle, Germany
Lasse Feldhahn University of Halle, Germany
John Kiss, Ph.D. UNC-Greensboro
Richard Barker, Ph.D. University of Wisconsin, Madison (Gilroy Lab)
Javier Medina, Ph.D. Centro de Investigaciones Biológicas
Alicia Villacampa Centro de Investigaciones Biológicas
Pankaj Jaiswal, Ph.D. Oregon State University
Federica Brandizzi, Ph.D. Michigan State University
Evan Angelos Michigan State University
Stanley Roux, Ph.D. The University of Texas at Austin
Eric Scott Land North Carolina State University
Austin Meier, Ph.D. Oregon State University
Matthew Martin Oregon State University
Norman Lewis, Ph.D. Pacific Northwest National Lab/Washington State University
Kim Nixon Pacific Northwest National Lab/Washington State University
Imara Perera, Ph.D. North Carolina State University
Ivo Grosse, Ph.D. Martin-Luther-University Halle-Wittenberg
Raul Herranz, Ph.D. Centro de Investigaciones Biológicas
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Multi-Omics/System Biology
Name Affiliation
Afshin Beheshti, Ph.D. NASA Ames Research Center
Daniel Berrios, MD, Ph.D., MPH NASA Ames Research Center
Sylvain Costes, Ph.D. NASA Ames Research Center
Homer Fogle, Ph.D. NASA Ames Research Center
Marianne Sowa, Ph.D. NASA Ames Research Center
Yared Kidane, Ph.D. Texas Scottish Rite Hospital for Children & KBRwyle
Susana (Susi) Zanello, Ph.D. NASA Johnson Space Center
Daniel Gallahan, Ph.D. NCI / NIH
Michael Reich, Ph.D. University of California San Diego
John (Ted) Theodore Liefeld, Ph.D. University of California San Diego
Thorin Miles Tabor, Ph.D. University of California San Diego
Sucharita Dutta, Ph.D. Beth Israel Deaconess Medical Center / Harvard Medical School
Yang Xie, Ph.D. UT Southwestern
Lin Xu, Ph.D. UT Southwestern
J. Tyson McDonald, Ph.D. Hampton University
Josh Vandenbrink, Ph.D. The University of North Carolina at Greensboro
Deborah Hung, MD Ph.D. Massachusetts General Hospital / Broad Institute / Harvard Medical School
Gerard (Gary) Hardiman, Ph.D. Medical University of South Carolina
Charles (Chuck) Vanderburg, Ph.D. Broad Institute
Dongjun Chung, Ph.D. Medical University of South Carolina
Edward Starr Hazard, Ph.D. Medical University of South Carolina
Willian Abraham da Silveira, Ph.D. Medical University of South Carolina
Ludvine Renaud, Ph.D. Medical University of South Carolina
William Bailey Glen Jr., Ph.D. Medical University of South Carolina
Deanne M. Taylor, Ph.D. University of Pennsylvania / The Children’s Hospital of Philadelphia
Cem Meydan, Ph.D. Weill Cornell Medical College
David Danko Weill Cornell Medical College
Daniel Stephan Couch Medical University of South Carolina
Ramgopal Mettu, Ph.D. Tulane University
Helio Costa, Ph.D. Stanford Medical School
Katharine Rosalie Grabek Stanford University
Kathleen (Katie) Fisch, PhD University of California San Diego, Center for Computational Biology & Bioinformatics
Sara Brin Rosenthal, Ph.D. University of California San Diego, Center for Computational Biology & Bioinformatics
Christopher Mason, Ph.D. Weill Cornell Medical College
Hossein Fazelinia University of Pennsylvania / The Children’s Hospital of Philadelphia
Tessa (Tess) Morris-Paterson English Institute of Sport / Centre of Human Aerospace Physiology at King's College London
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Microbes
Name Affiliation
Jonathan Galazka, Ph.D. NASA Ames Research Center
Sam Gebre NASA Ames Research Center
Egle Cekanaviciute, Ph.D. NASA Ames Research Center
Nancy Keller, Ph.D. University of Wisconsin-Madison
Luis Zea University of Colorado Boulder
Hernan Lorenzi, Ph.D. J. Craig Venter Institute
Adam Arkin, Ph.D. University of California, Berkeley
A. Murat Eren, Ph.D. University of Chicago
Ozcan Esen University of Chicago
Crystal Jaing, Ph.D. Lawrence Livermore National Laboratory
Michale Strong, Ph.D. National Jewish Health & University of Colorado, Denver
Ashkaan Fahimipour, Ph.D. University of Oregon
Daniela Bezdan, Ph.D. Weill Cornell Medicine
Stefan Green, Ph.D. University of Illinois at Chicago
Kasthuri Venkateswaran, Ph.D. NASA Jet Propulsion Laboratory (JPL)
Jason Wood, Ph.D. NASA Jet Propulsion Laboratory (JPL)
Nitin Singh, Ph.D. NASA Jet Propulsion Laboratory (JPL)
Silvio Weging Martin-Luther-University Halle-Wittenberg
Mike Lee University of Southern California
Ivo Grosse, Ph.D Martin-Luther-University Halle-Wittenberg
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Animals

Mammals

Name Affiliation
Sylvain Costes, Ph.D. NASA Ames Research Center
Candice Tahimic, Ph.D. NASA Ames Research Center
Shayoni Ray, Ph.D. NASA Ames Research Center
Afshin Beheshti, Ph.D. NASA Ames Research Center & Rutgers Cancer Institute of New Jersey
Ann-Sofie Schreurs, Ph.D. NASA Ames Research Center
Elizabeth Blaber, Ph.D. NASA Ames Research Center
Honglu Wu, Ph.D. NASA Johnson Space Center
Jeffery Willey, Ph.D. Wake Forest School of Medicine
Andy Tsing-ho Kwok Wake Forest School of Medicine
Christopher Mason, Ph.D. Weill Medical College of Cornell University
Susan Bailey, Ph.D. Colorado State University - Environmental & Radiological Health Sciences (ERHS).
Alexander Wassel Colorado State University
Marc Salit, Ph.D. National Institute of Standards and Technology (NIST) - Stanford University
Christopher Porada, Ph.D. Wake Forest School of Medicine
David Weinstock, MD Dana-Farber Cancer Institute, Harvard Medical School
Richard A. Britten, Ph.D. Eastern Virginia Medical School
Brinda Rana, Ph.D. University of California, San Diego
Tejaswini Mishra, Ph.D. Stanford University
Eliah Overbey University of Washington
Stanley M. Walls Jr. SBP Medical Discovery Inst.
Helio Costa, Ph.D. Stanford Medical School
Katharine Rosalie Grabek Stanford University
Yared Kidane, Ph.D. Texas Scottish Rite Hospital for Children & KBRwyle
Cem Meydan, Ph.D. Weill Cornell Medical College
Amanda Saravia-Butler, Ph.D. NASA Ames Research Center
Jared James Luxton Colorado State University 

Non-mammals

Name Affiliation
Sigrid Reinsch, Ph.D NASA Ames Research Center
Soda Balla Diop, Ph.D. Sanford Burnham Prebys Medical Discovery Institute
Homer Fogle, Ph.D. NASA Ames Research Center
Sharmila Bhattacharya, Ph.D. NASA Ames Research Center
Amber Paul, Ph.D. NASA Ames Research Center
Rachel Gilbert, Ph.D. NASA Ames Research Center
Siddhita Mhatre, Ph.D. NASA Ames Research Center
Brin Rosenthal, Ph.D. UC San Diego Health
Rolf Bodmer, Ph.D Sanford Burnham Prebys Medical Discovery Institute
Thomas Boothby, Ph.D University of North Carolina Chapel Hill
Susan Celniker, Ph.D LBNL
Ann Hammonds, Ph.D. UC Berkeley
Gary Karpen, Ph.D. LBNL
Karen Ocorr, Ph.D Sanford Burnham Prebys Medical Discovery Institute
Anjali Gupta Sanford Burnham Prebys Medical Discovery Institute
Ludivine Renaud, Ph.D. Medical University of South Carolina
Chandran Sabanayagam, Ph.D. University of Delaware
Paul Sternberg, Ph.D. Caltech
Nathaniel Szewczyk, Ph.D. University of Nottingham
Robert Waterston, MD, Ph.D. University of Washington
Raul Herranz, Ph.D Centro de Investigaciones Biológicas
Willian Abraham da Silveira, Ph.D. Medical University of South Carolina
Latest News —
April 2018 –
 

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Analysis Working Groups Reach Consensus on Pipelines Needed to Generate Higher-order Data

The GeneLab Project hosted its first Analysis Working Group (AWG) workshop in Orlando, FL on April 23-24, 2018. Workshop participants comprised 65 of the 114 AWG members and included principal investigators, post-docs and students from three NASA centers, as well as from universities and institutes in the U.S. and internationally.

Members gathered for the two-day workshop to discuss and reach consensus on the analysis pipelines necessary to process raw data from the GeneLab Data Repository into higher-order data. The workshop also featured presentations by members on their analysis tools and platforms, and the results of analysis of GeneLab datasets.

Members of the Microbes AWG Members of the Microbes Analysis Working Group (Left to right: Luis Zea, Michael Lee, Crystal Jainh, Silvio Weging, Jonathan Galazka, Samrawit Gebre, Egle Cekanaviciute, Daniela Bezdan, and Michael Strong)

Day 1:

Opening the workshop, GeneLab Project Manager Sylvain Costes presented the project’s vision, the AWGs’ efforts and accomplishments to date, and summarized recent publications from GeneLab. Following Costes, four AWG members presented their tools and platforms:

  • TOAST (Test Of Arabidopsis Space Transcriptome) Database - Richard Barker, Ph.D., University of Wisconsin, Madison
  • Integrative Genomics for Single Cells, Cities, and Space Stations - Cem Meydan, Ph.D., Weill Cornell Medical College
  • Visualizing Multi-Omics Data for Biological Discovery - Katie Fisch, Ph.D,. University of California San Diego
  • Toward Reproducible GeneLab Analyses with GenePattern Notebook - Ted Liefeld, Ph.D., University of California San Diego.

Day 2:

In the first session of the day, AWG members presented current data analysis efforts and results:

  • From Molecules to the Eyes: Physical alterations of cell properties impacting astronauts’ health problems - Willian Abraham da Silveira, Ph.D., Medical University of South Carolina
  • Differential gene expression of Arabidopsis seedlings grown in a continuum of gravity - Josh Vandenbrink, Ph.D., University of North Carolina at Greensboro
  • Genomic approaches to investigate clinical and environmental microorganisms capable of impacting human health - Michael Strong, Ph.D., National Jewish Health & University of Colorado, Denver
  • Using C. elegans to understand muscle adaptation to spaceflight - Nate Szewczyk, Ph.D., University of Nottingham
  • Galaxy on GeneLab: A preliminary look at the effects of spaceflight on plant roots - Colin Kruse, Ph.D., Ohio University; Matthew Geniza, Ph.D., NASA Ames Research Center.

GeneLab’s Afshin Beheshti and Jonathan Galazka presented the tools and pipelines provided by each AWG and led a discussion to propose the concensus pipelines for generating higher-order data for genomic, transcriptomic, proteomic and metabolomic data types. Members provided feedback and reached consensus on the pipelines needed to generate higher-order data.

The workshop divided into breakout sessions for each of the four AWG groups.  The groups discussed metadata requirements and data organization of the GeneLab data repository, expectations of the analysis and higher-order data to be processed by GeneLab, future visualization capabilities, and the upcoming integrated Galaxy analysis platform which will be released to the public in Fall 2018. Members also attended several special sessions focused on publications, maximizing scientific discovery using multiple model organisms, interactions between microbes and their hosts (plants and animals), and a tutorial of the integrated Galaxy analysis platform.

To close the workshop, each group presented their discussions and results from the breakout sessions. In summary, key accomplishments from the workshop included:

  • Consensus on the pipelines to generate higher-order data
  • Extensive input on visualization requirements and implementation strategies
  • Input on metadata and data organization
  • Requirement that all processed data and intermediate data products be made available
  • Excitement about Galaxy as a working and teaching tool
  • Appreciation for the AWG and meeting structure
  • Collaborative work among AWG members and NASA centers
  • Identification of new datasets to be added to the GeneLab repository.

GeneLab will continue working with AWG members to implement the new features discussed, improve on current data organization, process raw data into higher-order data, and continue developing the Galaxy Platform.

February 2018 –
 

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Apply Today! Join us this summer in analyzing spaceflight omics data in the GeneLab Data Repository!

Thank you to all who applied for the summer internship. Applications are now closed. To receive AWG updates and information about other opportunities at GeneLab, subscribe to the Newsletter.

Analysis of Spaceflight Omics Data Using the GeneLab Data System

Spaceflight places unique stresses on living systems and understanding how biological systems sense and respond to these stresses is a requisite for an expanded human presence in space. However, the enormous complexity of biological systems means that the precise nature of these responses remain unclear. In response, NASA is developing an open platform for storing and analyzing biological datasets called GeneLab (genelab.nasa.gov).

By gathering genomic, transcriptomic, proteomic and metabolomic datasets together, GeneLab will allow these datasets to be compared, integrated and analyzed together, increasing the likelihood that important patterns of adaptation to space environments will be discovered. Currently, the GeneLab data system houses raw unprocessed data (e.g. fastq files), however GeneLab will soon offer tools for analysis of this data. To ensure that these tools meet the needs of the space biology community, GeneLab is assembling Analysis Working Groups (AWGs) charged with identifying essential tools, constructing canonical analysis pipelines and generating processed data. These AWGs will be led by subject matter experts from various domains (plant biology, microbiology, vertebrate and invertebrate physiology), however it is expected that many of the tasks identified by these AWGs will be carried out by a group of 10 - 20 interns recruited through this opportunity.

Interns will work with GeneLab and AWG scientists, as well as other interns, to develop computational pipelines for the analysis of biological data housed within GeneLab. Interns will utilize these within the GeneLab analysis framework to make discoveries about how biological systems react to spaceflight. Internships are for 10 weeks and will take place at NASA Ames Research Center in Silicon Valley. Students will be provided a stipend and offered affordable housing at NASA Ames.

For more information on the summer program and application process, please visit the NASA OSSI web page at https://ossi.nasa.gov/.

  1. Scroll to the bottom of the page and enter GeneLab in the 'Enter keywords for opportunity descriptions' field. screenshot
  2. The opportunity title is Analysis of Spaceflight Omics Data Using the GeneLab Data System. screenshot
  3. Create an OSSI account to apply for the position. screenshot
January 2018 –
 

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GeneLab is recruiting members for Analysis Working Groups to analyze NASA omics data!

NASA’s GeneLab Project is recruiting investigators, bioinformaticians, graduate students, and postdocs to participate in Analysis Working Groups (AWGs) that will investigate specific subsets of omics data from experiments conducted onboard the International Space Station, the Space Shuttle, as well as ground-based research with relevance to spaceflight (e.g. radiation or unloading/weightlessness).

GeneLab is a science collaboration initiative and data system effort that provides a workspace with tools to analyze and visualize omics data. GeneLab has established the AWGs with the goal of maximizing the generation of new knowledge from these rare and complex spaceflight datasets.

The project has established four AWGs – scientific groups of excellence focused on analyzing spaceflight-relevant omics data within the GeneLab Data System (GLDS). Below is a list of the groups and their leads:

  • Animals (Mammals and Non-mammals) – Sylvain Costes
  • Plants (Arabidopsis, Mizuna) – Matthew Geniza
  • Microbes (eukaryotic, prokaryotic) – Jonathan Galazka
  • Multi-omics strategies – Afshin Beheshti

The primary activity of each AWG will be to establish analytical processes to generate higher-order data from data in the GLDS, with relevance to one or more specific application areas. For example, the AnimalAWG will analyze all data relevant to mammalian systems (human, mouse, rat, etc.). The multi-omics group will focus on gaining new knowledge using systems biology approaches: e.g. how do transcriptomics and proteomics compare within the same dataset? What are the common molecular signals induced by spaceflight across the various species?

The AWG participants will help assess and improve the effectiveness of GeneLab through intensive utilization of data analysis tools. These investigations are anticipated to lead to one or more scientific publications, as well as implementation of specific data visualization strategies to disseminate new knowledge from these analyses.

A kick-off meeting for the AWG was held January 25, 2018 at the Human Research Program Investigators’ Annual Workshop in Galveston, TX, and virtually. Members from all five AWGs met in this first session. Following, each AWG has met separately in monthly teleconferences to become familiar with datasets and tools in the GLDS, and to provide initial feedback on how to gain new knowledge from the data. In April 2018, all AWGs met in-person for a two-day workshop to finalize the establishment of processing pipelines. The GLDS data processing will take place during summer 2018 with GeneLab hosting 10 student interns at NASA Ames Research Center. Students will be encouraged to submit their most significant findings to the annual meeting of the American Society for Gravitation and Space Research, October 31 – November 3, 2018, and to join the conference to support training sessions for the introduction of the GeneLab toolshed. We anticipate the most exciting results to also be submitted for publication.

If you are interested in participating, and/or if you have students with strong bioinformatics skills who might also be interested, please review the GeneLab Analysis Working Groups Charter and send an email to arc-dl-genelab-awg@mail.nasa.gov with name of the group (see list above) in the subject line. Interested scientists having the required specialized capabilities/qualifications to support the work described in AWG charter are asked to submit a capability/qualification statement. There is no required font size and/or type designated for this Capability/Qualification Statement. Submit your response electronically in PDF format. The response must include the following: 1) Contact: name, affiliation, address, phone, e-mail, and website (if applicable). 2) Subject area expertise. Please provide a concise description of your expertise in terms of omics analyses including a list of relevant work and publications performed in the past five years. Looking forward to hearing from you!

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GeneLab Analysis Working Groups Charter

Purpose

The purpose of the GeneLab Analysis Working Groups (AWGs) is to optimize the processing of raw omics data from the GeneLab repository in order to maximize the gain of new knowledge from such complex datasets. The AWGs will also assess and improve the effectiveness of the GeneLab Data System (GLDS) through intensive utilization of the analytics to be deployed therein.

Organization and Function

The AWGs aspire to scientific excellence, and participation in AWGs is strictly on a volunteer basis. The primary activity of each AWG is to establish analytical processes to generate higher order data from data housed in the GLDS with relevance to one or more specific application areas. For example, a mammalian AWG would analyze all data relevant to mammalian systems (human, mouse, rat, etc.). The GeneLab AWGs aspire to yield:

  1. Canonical data analysis pipelines. The interpretation of analysis results is too often confounded by variability in data-processing protocols. This can make comparison of results between studies even more difficult. By developing canonical analysis pipelines, the AWGs will help speed the harmonization of results across space biology experiments.
  2. Processed (“higher-order”) space biology data. The AWGs will work with GeneLab staff to generate processed data using the canonical analysis pipelines. This higher-order data will be made available to the broader scientific community through the GLDS. This data will serve as a reference to the community on use of the pipelines, and will be fully reproducible using the GLDS and referenced pipelines. Optimal strategies regarding the display of processed data to the scientific community will also be discussed.
  3. Critiques of the GLDS. The value of the GLDS to the scientific community is best judged through extensive use of the systems. As the AWGs will be using the GLDS intensively (see 1 and 2 above), they will be poised to give valuable feedback to GeneLab on its strengths and weaknesses.
  4. Scientific communication of available analyses and interpretations. The AWGs are expected to communicate the development and application of the canonical data analysis pipelines with the broader scientific community. Such communications could take the form of self-published white papers, newsletters, or peer-review publications and conference presentations. These communications will also serve to catalyze the generation of new hypotheses for further experimentation.

Precisely how each AWG reaches these goals will be determined by the AWGs themselves, but, in general, AWGs should hold frequent in-person or virtual meetings to organize work and review progress. The schedule for delivering the above products is set by the Chair in consultation with GeneLab and the other AWG participants.

Participation

The constitution of each AWG must meet the following criteria: (1) have at least one participant who possesses application area expertise; (2) have at least one participant who possesses bioinformatics expertise; (3) have at least one representative from GeneLab. AWG participants are chosen based on a candidate’s ability to provide the scientific or data analysis insight necessary to achieve the AWG goals. AWG participation is entirely voluntary and participants will not be compensated.

Chairs - All AWGs will have a chair (or co-chairs) selected by GeneLab, with input from the scientific community and/or participants of the AWG. Chairs will lead the AWGs and will draft a schedule and review progress of each AWG towards achieving their goals. Chairs will serve for the life of the AWGs, unless they decide to step down, at which time GeneLab or the remaining participants of the AWG will appoint a new Chair.

GeneLab Representative - Each AWG will have a designated representative from GeneLab to help ensure outcomes of the work meet GeneLab criteria and to otherwise support the work of the AWG. A GeneLab representative can also be chair of an AWG.

Coordinators – The following Coordinators will be selected on a volunteer basis by each AWG. Multiple coordinating functions may be performed by a single Coordinator.

  • Analysis Coordinator - The analysis coordinator tracks the progress of individual analyses, ensuring that analyses are done in a consistent and reproducible manner, sets deadlines for completion of individual analyses, and collects and organizes interim and final analysis results.
  • Communication Coordinator – Assembles information for newsletter or manuscript sections, ensures consistency in writing and figure styles, and sets goals for the completion of articles or newsletter.

Expectations for AWG Participation

Participation in GeneLab AWGs is open to all investigators (academic, government, private sector); however participants must be willing to:

  1. Contribute significantly to the goals of the AWG.
  2. Take part in group activities including periodic teleconferences. Participants are expected to actively contribute to the group goals (see above).
  3. Share AWG products with other AWG participants via the collaborative workspace provided by the GLDS.

An investigator that would like to take part in any AWG(s) should provide a description of their expertise in the relevant area of analysis to GeneLab, and must sign a statement of acknowledgement of the Expectations for AWG Participation (see above). Requests for participation in AWGs will be reviewed by GeneLab and the AWG chairs who must reach a consensus to allow the applicant to participate. The AWG chair(s) and GeneLab will review participation in each group yearly.

Benefits of AWG Participation

By participating within a GeneLab AWG, investigators will join a group of scientific excellence and may co-author a landmark paper. They will help set data and analysis standards for the community, and may develop relationships that could lead to additional collaborations.