Curriculum vitae (abbreviated)

View: PDF of full CV | Publications (on separate page)

Education


2017Ph.D., Chemical Oceanography, MIT/WHOI Joint Program
Thesis title: "The remineralization of marine organic matter by diverse biological and abiotic processes"
Advisor: Dr. Ben Van Mooy
» Access to: PDF of thesis | code and data | LaTeX files to compile from scratch

2011M.E.Sc., Marine Biogeochemistry, Yale School of Forestry & Environmental Studies
Thesis title: "Estimates of new and total productivity in central Long Island Sound from in situ measurements of nitrate and dissolved oxygen"
Advisor: Dr. Pete Raymond

2004B.A., Political Science, Yale College


Professional Scientific Experience


2017 – present     Moore/Sloan & WRF Innovation in Data Science Postdoctoral Fellow, eScience Institute and School of Oceanography, Univ. of Washington

2017 – present     Guest Investigator, Dept. Marine Chemistry & Geochemistry, Woods Hole Oceanographic Inst.

2017                     Postdoctoral Investigator, Dept. Marine Chemistry & Geochemistry, Woods Hole Oceanographic Inst.

2011 – 2016         Research Assistant, Dept. Marine Chemistry & Geochemistry, Woods Hole Oceanographic Inst.

 

Honors and Awards


2017      Moore/Sloan & Washington Research Foundation Innovation Postdoctoral Fellowship in Data Science

2017      Federation of Earth Science Information Partners (ESIP) Student Fellow, Data Stewardship Cluster

2016      Invited Participant, DISCO XXV (Dissertations Symposium on Chemical Oceanography)

2014      U.S. Antarctica Service Medal

2012      EPA Science to Achieve Results (STAR) Graduate Fellowship

2011      Provost's Distinguished Graduate Fellowship, College of Oceanic and Atmospheric Science, Oregon State University (declined)

2009      Post-9/11 G.I. Bill "Yellow Ribbon" Program Recipient, Yale School of Forestry & Environmental Studies
John A. MacLean Scholarship, Yale School of Forestry & Environmental Studies (declined)

2004      Montaigne Prize, Yale College, for excellence in spoken and written French

2000      Golub Foundation Founder's Scholarship, Yale College
William A. Henry III Scholarship, Yale College

 

Professional Publications


Link to: Publications (separate page)

 

Software


Collins, J. R., B. R. Edwards, Helen F. Fredricks, and B. A. S. Van Mooy. 2017. LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences. R package version 1.2.0; Available at https://github.com/vanmooylipidomics/LOBSTAHS (latest beta) or via Bioconductor (production version)

 

Publications (Other; Non-Refereed)


Collins, J.R. 2010. YIBS Center for Field Ecology: Long Island Sound project. Yale Environmental News, Yale Institute for Biospheric Studies 15 (2): 27.

Collins, J. R. 2010. Community respiration in coastal Connecticut: How fast does an aquatic ecosystem breathe? News of the Center for Coastal and Watershed Systems, Yale School of Forestry & Environmental Studies, Spring 2010: 4-5.

 

Invited Talks and Lectures


Collins, J. R., B. R. Edwards, Helen F. Fredricks, K. W. Becker, and B. A. S. Van Mooy. September 2016. "Investigating oxidative stress and metabolic function in marine microbes using new a tool for environmental lipidomics." Bigelow Laboratory for Ocean Sciences, East Boothbay, ME.

Collins, J. R., B. R. Edwards, Helen F. Fredricks, K. W. Becker, and B. A. S. Van Mooy. June 2016. Fort Johnson Marine Science Seminar. "Investigating oxidative stress and metabolic function in marine microbes using new a tool for environmental lipidomics." National Institute of Standards and Technology, Hollings Marine Laboratory, Charleston, SC.

Collins, J. R., B. R. Edwards, K. Thamatrakoln, J. E. Ossolinski, G. R. DiTullio, K. D. Bidle, S. C. Doney, and B. A. S. Van Mooy. September 2015. "Balancing the direct and indirect removal of sinking particles in the North Atlantic Ocean." Departmental Seminar. Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA.

Collins, J. R., and P. A. Raymond. March 2012. "Controls on new production and nitrate inventory in central Long Island Sound." Biogeochemistry Seminar. Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA.

 

Conference Presentations and Posters


Becker, K. W., J. R. Collins, H. F. Fredricks, J. E. Ossolinski, A. E. White, D. J. Repeta, and B. A. S. Van Mooy. February 2017. The microbial lipidome of the oligotrophic North Pacific Subtropical Gyre. Oral presentation. Ocean Sciences Meeting, Honolulu, HI.

Collins, J. R., B. R. Edwards, K. W. Becker, H. F. Fredricks, and B. A. S. Van Mooy. January 2017. Discovery and identification of oxidative stress biomarkers in marine phytoplankton using a new, open-source R package for lipidomics. Poster. Winter meeting of the Federation of Earth Science Information Partners (ESIP), Bethesda, MD. » PDF

Collins, J. R., B. R. Edwards, K. W. Becker, H. F. Fredricks, and B. A. S. Van Mooy. December 2016. Putting the oxylipidome to work: The R-based LOBSTAHS lipidomics software reveals candidate biomarkers for stress in plankton. Poster. Annual meeting of the Simons Collaboration on Ocean Processes & Ecology (SCOPE), New York, NY. » PDF

Collins, J. R., B. R. Edwards, H. F. Fredricks, and B. A. S. Van Mooy. August 2016. Discovery & identification of oxidative stress biomarkers in marine microbes using LOBSTAHS, a new R package for lipidomics. Poster. 16th International Symposium on Microbial Ecology (ISME16), Montreal, Canada. » PDF

Collins, J. R., B. R. Edwards, Helen F. Fredricks, and B. A. S. Van Mooy. January 2016. Discovery and identification of biomarkers for oxidative stress in phytoplankton using LOBSTAHS, a new pipeline for semi-untargeted lipidomics. Poster. EMBO/EMBL Symposium: A New Age of Discovery for Aquatic Microeukaryotes, European Molecular Biology Laboratory, Heidelberg, Germany. » PDF

Becker, K. W., H. F. Fredricks, J. R. Collins, J. E. Ossolinski, J. Wingenroth, D. J. Repeta, D. A. Caron, S. W. Chisholm, and B. A. S. Van Mooy. May 2016. The microbial lipidome of subtropical Pacific surface waters dominated by Prochlorococcus. Poster. 12th Workshop on Cyanobacteria, Arizona State University, Tempe, AZ.

Fredricks, H. F., J. R. Collins, B. R. Edwards, and B. A. S. Van Mooy. June 2015. Lipidomics of marine microorganisms under stress: Solving the needle / haystack problem with a large database and open-source software. Poster. Annual Conference, American Society for Mass Spectrometry, St. Louis, MO.

Collins, J. R., H. F. Fredricks, H. W. Ducklow, and B. A. S. Van Mooy. February 2015. Photochemical production of oxylipin infochemicals in West Antarctica: An approach using new tools for semi-untargeted lipidomics. Poster. ASLO Aquatic Sciences Meeting, Granada, Spain. » PDF

Edwards, B. R., J. R. Collins, H. F. Fredricks, J. E. Ossolinski, H. McNair, M. A. Brzezinski, J. W. Krause, K. Thamatrakoln, K. D. Bidle, and B. A. S. Van Mooy. Comparative lipidomics link bloom decline to infochemical production in the California upwelling zone. Oral presentation. ASLO Aquatic Sciences Meeting, Granada, Spain.

Collins, J. R., B. R. Edwards, K. Thamatrakoln, J. E. Ossolinski, G. R. DiTullio, S. C. Doney, and B. A. S. Van Mooy. July 2014. Constraints on observationally intractable aspects of the mesopelagic carbon cycle: Comparison of direct observations and results from multi-parameter sensitivity analyses. Poster. Ocean Carbon and Biogeochemistry Workshop, Woods Hole, MA. » PDF

Collins, J. R., J. E. Ossolinski, B. R. Edwards, K. Thamatrakoln, J. Tagliaferre and B. A. S. Van Mooy. February 2014. Constraining carbon cycle parameters in the North Atlantic through independent measurements of bacterial production, respiration, and particulate carbon export. Poster. Ocean Sciences Meeting, Honolulu, HI. » PDF

Fulton, J. M., B. A. S. Van Mooy, J. R. Collins, J. E. Hunter, and K. Bidle. February 2014. Lipid connections between viral termination of coccolithophore blooms and carbon export. Poster. Ocean Sciences Meeting, Honolulu, HI.

Collins, J. R., J. R. Valdes, J. E. Ossolinski, R. G. Keil, and B. A. S. Van Mooy. February 2013. The PHORCYS: An autonomous, dual-chamber in situ incubator for the estimation of community metabolism. Oral presentation. ASLO Aquatic Sciences Meeting, New Orleans, LA.

Collins, J. R., P. A. Raymond, W. F. Bohlen, and M. M. Howard-Strobel. November 2011. Metabolism in central Long Island Sound, minute by minute: Estimates from in situ oxygen and nitrate measurements. Poster. Coastal and Estuarine Research Federation (CERF) Biennial Conference, Daytona Beach, FL. » PDF

Collins, J. R., and P. A. Raymond. April 2011. Controls on nutrient flux and productivity over multiple time scales in Long Island Sound. Poster. Master's Student Colloquium, 2011, Yale School of Forestry & Environmental Studies, New Haven, CT.