The following Genomics-oriented Workshops are offered by the University Library this fall.

For more information or to register, go to http://library.stonybrook.edu/events/

Bioinformatics Series

·         Intro to Bioinformatics Resources – Jennifer Lyon

o   HSL EBM Room, Monday, 9/12/16, 9-10:30am

o   Melville, Classroom A, Tuesday, 9/13/16, 9-10:30am

o   There are a vast number of bioinformatics databases, software tools, and resources available on the web. This workshop will help you get started by identifying key ‘entrance’ points and high quality resources for specific research areas and purposes.

·         BLAST Sequence Similarity Searching – Jennifer Lyon

o   HSL EBM Room, Monday, 10/17/16, 9-11am

o   Melville, Classroom A, Tuesday, 10/18/16, 9-11am

o   The NCBI’s Basic Local Alignment Search Tool (BLAST). BLAST allows rapid, easy sequence similarity searching online. However, use of BLAST is only truly effective when you understand what it does – and doesn’t do. This workshop will introduce how sequence similarity searching works and demonstrate some of the various BLAST search options.

·         Molecular Structure Viewing with Cn3D – Jennifer Lyon

o   HSL EBM Room, Monday, 11/14/16, 3-5pm

o   Melville, Classroom A, Tuesday, 11/15/16, 9-11am

o   This workshop will introduce the primary databases, PDB & MMDB, which archive the molecular structures of proteins and other molecules, and will demonstrate the NCBI’s Cn3D software tool for viewing and manipulating those structures.

·         Clinical Genetics Resources – Jennifer Lyon

o   HSL EBM Room, Thursday, 12/1/16, 9-10:30am

o   Melville, Classroom A, Tuesday, 11/29/16, 9-10:30am

o   This workshop will introduce resources focused on the relationship between human disease and genetics, such as OMIM, GeneReviews, and MedGen.

Scholarly Communications Issues Series

·         Organizing Your Publications: Author IDs and Profiles – Jennifer Lyon & Clara Tran

o   Monday, 10/3/16, HSL EBM Room, 2-3pm

o   Organizing and managing your publications, particularly for grant biosketches, can be a challenge. The ORCID project is an international effort to provide every scholarly author with a unique identifier. SciENcv is a new tool from the NCBI that allows researchers to create and store biosketches specifically formatted for NIH and NSF grants, including an automated import function from ORCID. These resources will be demonstrated.

·         My NCBI: My Bibliography, SciENcv Biosketches, & Managing Search Results – Jennifer Lyon & Clara Tran

o   Thursday 10/6/16, HSL EBM Room, 9-10am

o   The National Center for Biotechnology Information (NCBI) at the National Library of Medicine provides access to a wide range of databases and resources including PubMed. The website offers a free user account (My NCBI) which allows the researcher to save searches, collections of articles & other database records, set up alerts, manage their own publications, and create grant biosketches. This course will demonstrate the My NCBI account features.

·         NIH Public Access Policy – Jennifer Lyon

o   Tuesday, 10/11/16, HSL EBM Room, 1-2pm

o   Compliance with the NIH Public Access Policy is a requirement for all published peer-reviewed papers based on NIH funding; failure to comply can delay or stop further funding. So what is the policy and how is compliance managed?

On April 22nd, 2016, Students enrolled in the Collegiate Science and Technology Entry Program (C-STEP) have be given the chance to meet and discuss with Stony Brook University Genomics Researchers.

The C-STEP program “encourages and prepares more historically underrepresented and economically disadvantaged Stony Brook University students for entry into scientific, technical, health, and health related professions.”

During this event, students have discussed the wide variety of career opportunities provided by Genomics, from mathematics, to computer science, personalized medicine, genetics and marine sciences. Nine departments and Centers from Stony Brook University were represented.

Volunteering Genomics Researchers:

School of Marine and Atmospheric Sciences : Jackie Collier (microbiology), Nolwenn Dheilly (parasitology), Sleiman Bassim (bioinformatics) and Elizabeth Suther (microbiology)
Department of Applied Mathematics and Statistics : Pei Fen Kuan (statistics and computation)
Department of Ecology and Evolution: Jesse Hollister (plant biology), Brenna Henn (human populations)
Department of Biochemistry and Cell Biology and Laufer Center: Sasha Levy (cell behavior)
Department of Computer Sciences: Robert Patro (algorithms and methods development)
Department of Anesthesiology and Center for Nervous system Disorder Center: Kevin Czaplinski (gene expression in the nervous system)
Biomedical Engineering Department: Eric Brouzes (single cell biology)

Hosts:
Nolwenn M. Dheilly – SOMAS
Office Location: 107A Dana Hall
Office Phone: (631) 632-3088
Fax: (631) 632-8915
E-mail: Nolwenn.Dheilly@stonybrook.edu
Laboratory: http://you.stonybrook.edu/dheilly/

Christine Veloso – STEP-CSTEP
Office Location: 358 Harriman Hall
Office Phone: (631) 632-3205
Fax: (631) 632-7809
E-mail: Christine.Veloso@stonybrook.edu

From SBU Happenings – November 13, 2015 – SoMAS’ Jackie Collier Receives Funding from Moore Foundation for Microbial Ecology Research

Associate Professor Jackie Collier

Jackie Collier, an associate professor in the School of Marine and Atmospheric Sciences (SoMAS) at Stony Brook University, is studying tiny organisms called labyrinthulomycetes with the hope of making a big impact on understanding how the smallest marine life in our oceans affects the global carbon cycle. Collier is principal investigator on an experimental model system that has received funding from The Gordon and Betty Moore Foundation’s (GBMF) Marine Microbiology Initiative (MMI). Her team includes Joshua Rest, Department of Ecology and Evolution, Stony Brook University; Daiske Honda, Department of Biology, Konan University, Japan; and Thorsten Reusch, Helmhotlz Centre for Ocean Research, Germany.

The grant is part of The Moore Foundation’s overall $8 million investment to support scientists worldwide to accelerate development of experimental model systems in marine microbial ecology. Collier is among more than 100 scientists across 33 institutions to collectively tackle the challenge of developing methods to bring experimental model systems to the ocean. The genetic tools generated in this effort will allow researchers to more easily disrupt the activities of microbial genes to understand how these organisms function in marine ecosystems and provide the capability to ask scientific questions in ways not currently possible.

Model systems, such as the mammalian gut bacterium E. coli for microbiology and the fruit fly for biomedicine, have been invaluable for deciphering complex biology. But in the world of marine microbial ecology, there are very few model systems that enable scientists to deeply explore the physiology, biochemistry and ecology of marine microbes, which are key drivers of the ocean’s elemental cycles, influence greenhouse gas levels and support marine food webs.

Collier explained that oceanographers understand relatively well the “light side” of the marine carbon cycle: photosynthesis performed by microscopic phytoplankton that convert inorganic carbon dioxide into the organic carbon that provides food for marine food webs, including all the fish we eat. It is the “dark side” — respiration of heterotrophic marine organisms that returns carbon from organic forms back to carbon dioxide — that requires much more research.

Just like in photosynthesis, many diverse microorganisms are responsible for remineralizing marine carbon. Collier and her team will study labyrinthulomycetes, which are fungus-like single-cell microorganisms. They can be found everywhere in the oceans and can reach similar total biomass as bacteria, so they are likely to make a major contribution to the ‘dark side’ of the carbon cycle. “But we know very little about labyrinthulomycete ecology or physiology. The long-term goal of our GBMF EMS project is to develop the tools we need to learn enough about labyrinthulomycetes so that we can understand and model their role in the marine carbon cycle and food webs, and eventually predict how that may change as the climate and oceans change.”

Collier and her team will attempt to determine the functions of specific genes by manipulating their expression and/or activity in the lab. They will use genome sequences to identify elements that can be used to regulate the expression of reporter and marker genes, and will find the best way to introduce foreign DNA into diverse labyrinthulomycetes.

“Moore Foundation funding for this work is crucial,” Collier stressed, “it’s the kind of very basic effort that’s pretty much impossible to get funded by regular mechanisms. We greatly appreciate their support.”

Official Job Title: Instructional Support Associate
Job Field: Administrative & Professional (non-Clinical)
Primary Location: US-NY-Stony Brook
Department/Hiring Area: Ecology & Evolution-Stony Brook University
Schedule: Part-time Day Shift 1:00pm – 4:00pm Pass Days: Sat, Sun
Posting Start Date: Dec 14, 2015
Posting End Date: Jan 13, 2016
Salary: $27,500 – $29,000 at 0.5 FTE
Salary Grade: SL2
Appointment Type:Temporary

Details on the required qualifications and description of duties are available here

Assistant Professor Nolwenn M. Dheilly received an award of nearly $25,000 from the Eppley Foundation of Research to develop a model system to study microbiome-parasite interactions. The grant will allow the comparative analysis of the microbiome of healthy and parasitized Threespine Sticklebacks and of its tapeworm parasite Schistocephalus solidus, collected from lakes in Anchorage, Alaska this autumn. This is the first necessary step to her long-term goal to investigate the impact of microbe interactions with parasite on the parasite fitness, and on the evolution of virulence strategies. Dr. Dheilly says that this research will be complementary to ongoing research on the role of microbes in host defense systems and as such it will provide a foundation to develop new therapeutic design strategies. This grant will also allow students working on the project with the unique opportunity to carry out viral and bacterial metagenomics analyses.

Incorporated in 1947, the Eppley Foundation for Research funds projects “increasing knowledge in pure or applied science…in chemistry, physics and biology through study, research and publication.” Particular areas of interest include innovative medical investigations and applications, endangered animals and ecosystems, and climate change.  The Foundation was established by Captain Marion Eppley, a Princeton-educated physical chemist, who founded the Eppley Laboratory in Newport, RI, in 1917 to manufacture standard cells.