SHELLY A. TRIGG, Ph.D.

 (339) 368-0029 · shellywanamaker@gmail.com · ORCID ID: 0000-0001-6904-4149 · https://gihub.com/shellytrigg

PROFESSIONAL SUMMARY

Biologist with 9+ years of experience in functional genomics and expertise in:

·       Management and analysis of large, diverse datasets (genomics, epigenomics, proteomics, and metabolomics)

·       Programming, statistical analysis, and network analysis

·       DNA sequencing assay development, optimization, and implementation using liquid handling robots and both Illumina and Oxford Nanopore DNA sequencing platforms

·       Leading and managing complex research projects (staff management, budget preparation, meeting deadlines, writing grants, annual reports, and research publications, etc.)

EDUCATION

Ph.D. in Biological Sciences….……………………………………………………………………………Sept 2018

Cell, molecular, and genetics track, University of California San Diego, La Jolla, CA

 

B.S. in Biochemistry..…………………………………………………………………………….………..May 2010

Magna Cum Laude and honors thesis, Simmons College, Boston, MA

RESEARCH SKILLS

Lab Biology and Automation

-  ocean acidification animal rearing systems

-  sequencing library preparation

-  Illumina and Oxford Nanopore sequencing platform

-  recombinant DNA techniques

-  PCR, qPCR, and oligo design

-  nucleic acid and protein purification

-  ELISA, immuno-blotting and precipitation

-  cell culture and transfection

-  Tecan liquid handling robots and plate readers

 

Bioinformatics and Computing

-    high throughput DNA sequencing data analysis

-    data integration and meta-analysis

-    DNA methylation, proteomics and metabolomics data analysis

-    molecular network analysis (Cytoscape, Qiagen IPA, R)

-    data management

-    R scripting and statistical analysis

-    UNIX/Linux shell scripting

-    Some Python

-    Microsoft Office applications

 

Training Programs

-  LC-MS Data processing and statistics course, UC Davis (Jan 2018)

-  Visiting Scientist Network Analysis Training Program, Broad Institute (Jan-Feb 2016)

-  NSF Graduate Data Science Workshop, University of Washington (Aug 2015)

-  Biostatistics Refresher Course, UC San Diego (Aug 2015)

-  Tecan EVO Training Course (Aug 2012)

 

RESEARCH EXPERIENCE

University of Washington School of Aquatic and Fishery Sciences, Roberts Lab, Seattle, WA

Postdoctoral Research Associate…...……………………..………….…………….………Sept 2018 -  Present

Advisor: Steven Roberts, Ph.D.

·    Perform quality control, statistical, and network analyses of proteomics datasets from oyster larvae exposed to lab-simulated ocean warming conditions

·    Develop and implement differential epigenome analysis bioinformatics pipelines for RRBS and WGBS data

·    Prepare RRBS and WGBS libraries from Atlantic salmon and sea lice exposed to lab-simulated ocean warming conditions

·    Design, build, and implement ocean acidification rearing system for shellfish

·    Lead collaborative engineering and execution of shellfish aquaculture technologies with Jamestown-S’klallam tribal fisheries including field, hatchery, and laboratory work

·    Manage graduate student and support staff research efforts related to research listed above

 

NOAA Northwest Fisheries Science Center, Conservation Genetics, Seattle, WA

Volunteer…...……………………..………….……………………………………………..Jun 2018 - Present

NSF Graduate Research Internship Program Fellow…...………………..………….…….Jun 2017 - May 2018

Project title: Understanding the physiological and genetic impacts of ocean acidification on marine invertebrates

Advisors:  Paul McElhany Ph.D. and Krista Nichols Ph.D.

·    Support development and implementation of NWFSC Ocean Acidification research program

·    Applied statistics, biochemical pathway analyses, and developed analysis pipelines to uncover significantly changed metabolites in complex metabolomics data sets from differentially conditioned invertebrates (Dungeness crab and pteropods)

·    Carried out time-course high throughput ocean acidification exposure experiments on Dungeness crab larvae

·    Did field collection and laboratory rearing of Dungeness crab larvae and adults

 

Salk Institute for Biological Studies, Ecker Lab, Genomic Analysis Section, La Jolla, CA

NSF Graduate Research Fellow………………………………………………….……….…..Aug 2013 - Sept 2018

Ph.D. dissertation:  High-resolution molecular networks from novel ‘omics’ approaches elucidate survival strategies in organisms from land to sea

Advisor: Joseph Ecker, Ph.D.

·     Developed a DNA sequencing assay (CrY2H-seq) for high throughput protein-protein interaction screening and coded an analysis pipeline to identify and quantify interactions from large sequence datasets

·     Validated observed protein interaction network data against network simulations

·     Used model predictions to determine scaled assay performance

·     Performed experimental and computational quality control, in-depth network analysis, data integration, and functional annotation of proteins to interpret biological significance of protein interaction networks

·     Engineered thousands of expression clones and used CrY2H-seq to iteratively screen billions of interactions en masse to generate a comprehensive protein-protein interactome map for Arabidopsis thaliana

·     Manage support staff research efforts related to the CrY2H-seq project

Research Assistant II……………………………….………………………………………….Jul 2012 - Aug 2013

Research Assistant I…………………………………………………………………………..Nov 2011 - Jun 2012

 

Dana Farber Cancer Institute, Center for Cancer Systems Biology, Vidal Lab, Boston, MA

Research Technician I………………………………….……………………………………..Aug 2010 - Oct 2011

·     Generated the most comprehensive human interactome to-date from high throughput yeast two-hybrid screening, protein complementation assay, and from developing and implementing a high throughput well-nucleic-acid-programmable-protein-array validation assay protocol

·     Generated interactomes from high throughput yeast two-hybrid screening of autism genes and isoforms against a human ORFeome

·    Constructed arrayed collections of Kaposi’s Sarcoma and Epstein-Barr viral ORFs by high throughput gateway cloning for yeast two-hybrid screening against a human ORFeome to further define potential cancer driver and passenger proteins

Research Trainee…………………………………………………………………………….....Jan 2010 - Aug 2010

 

Simmons College, Department of Chemistry, Roecklein-Canfield Lab, Boston, MA

Undergraduate Researcher……………………………………………………………………July 2009 - June 2010

·    B.S. Honors Thesis: The effectiveness of the GST fusion system for isolating Epstein-Barr viral thymidine kinase, a potential target for antiviral antitumor therapies.

PUBLICATIONS AND MANUSCRIPTS

Shelly A. Trigg, DS Busch, P McElhany, M Maher, D Perez, C O’Brien, and KM Nichols. (2019) Searching for signs of resilience in over-wintering juvenile pteropods to ocean acidification and deoxygenation. (In preparation).

 

Shelly A. Trigg, KM Mitchell, R Elliot, B Eudeline, B Vadopalas, EB Timmins-Schiffman, SB Roberts. (2019) Temperature-influenced proteomic variation throughout larval development in the Pacific oyster. (In preparation).

 

Shelly A. Trigg. (2019) Temperature-influenced protein network differences in the Pacific oyster (Crassostrea gigas) during larval development. Figshare. Poster. https://doi.org/10.6084/m9.figshare.7853573.v1.

 

Shelly A. Trigg, P McElhany, M Maher, D Perez, DS Busch, and KM Nichols. (2019) Uncovering mechanisms of global ocean change effects on Dungeness crab (Cancer magister) through metabolomics analysis. Scientific Reports. https://doi.org/10.1101/574798.

 

West Coast National Marine Sanctuaries Education Team and NOAA Northwest Fisheries Science Center (Shelly A. Trigg) (2018) Ocean acidification communication toolkit: Dungeness crab case study. https://sanctuaries.noaa.gov/education/crab-toolkit.html.

 

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, A Bartlett, R Castanon, A Goubil, J Feeney, R O’Malley, SC Huang, ZZ Zhang, M Galli, and JR Ecker (2017) CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 14(8):819-825.

 

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, A Bartlett, R Castanon, A Goubil, J Feeney, R O’Malley, SC Huang, ZZ Zhang, M Galli, and JR Ecker (2017) CrY2H-seq interactome screening. Protoc. Exch. doi:10.1038/protex.2017.058.

 

X Yang, [15 others], Shelly A. Trigg, [20 others], and M Vidal. (2016) Widespread expansion of protein interaction capabilities by alternative splicing. Cell. 164(4):805-817.

 

T Rolland, [53 others], Shelly A. Trigg, [14 others], and M Vidal. (2014) A proteome-scale map of the human interactome network. Cell. 159(5):1212-1226.

 

R Corominas, [8 others], Shelly A. Trigg, [18 others], M Vidal, and LM Iakoucheva. (2014) Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nat commun. 5:3650. 

 

O Rozenblatt-Rosen, [36 others], Shelly Wanamaker, [13 others], and M Vidal. (2012) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.  Nature. 487(7408):491-495.

FIRST AUTHOR CONFERENCE PRESENTATIONS

Shelly A. Trigg. (Sept 2019) A protein inventory reveals mechanisms of temperature impact on oyster development. Pacific Coast Shellfish Growers Association 2019 Conference, Portland, OR, talk.

Shelly A. Trigg, P McElhany, M Maher, D Perez, DS Busch, and KM Nichols. (May 2019) What happens to Dungeness crab in high CO2: experiments and questions. 2019 WOAC Ocean Acidification Science Symposium, Seattle, WA, talk and poster.

Shelly A. Trigg, KM Mitchell, R Elliot, B Vadopalas, EB Timmins-Schiffman, SB Roberts. (Apr 2019) Temperature-influenced protein network differences in the Pacific oyster (Crassostrea gigas) during larval development. Bevan Series Symposium and SAFS Centennial, Seattle, WA, poster.

Shelly A. Trigg, P McElhany, M Maher, D Perez, DS Busch, and KM Nichols. (Mar 2019) Effects of ocean acidification on Dungeness crab. NOAA Mukilteo Open House, Mukilteo, WA, poster.

Shelly A. Trigg, KM Mitchell, R Elliot, B Vadopalas, EB Timmins-Schiffman, SB Roberts. (Mar 2019) Temperature-influenced protein network differences in the Pacific oyster (Crassostrea gigas) during larval development. Network Biology Meeting, Cold Spring Harbor Labs, Cold Spring Harbor, NY, poster.

Shelly A. Trigg. (Oct 2018) Be a claw abiding citizen: learn how ocean acidification can affect Dungeness crab. National Marine Sanctuaries Webinar Series, webinar. https://sanctuaries.noaa.gov/education/teachers/be-a-claw-abiding-citizen.html

Shelly A. Trigg, P McElhany, M Maher, D Perez, DS Busch, and KM Nichols. (Mar 2018) Uncovering mechanisms of global ocean change effects on Dungeness crab through metabolomics analysis. NOAA NWFSC 6th Science Symposium, Seattle, WA, talk.

Shelly A. Trigg, P McElhany, M Maher, D Perez, DS Busch, and KM Nichols. (Feb 2018) Uncovering mechanisms of global ocean change effects on Dungeness crab through metabolomics analysis. Ocean Sciences Meeting, Portland, OR, poster.

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, CS Huang, ZZ Zhang, M Galli, and JR Ecker (Sept 2016) ProCREate: A New Assay for Generation of Large-Scale Protein-Protein Interaction Maps, HHMI Scientific Meeting, Janelia Research Campus, Ashburn, VA, poster.

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, CS Huang, ZZ Zhang, M Galli, and JR Ecker (Sept 2016) ProCREate: A New Assay for Generation of Large-Scale Protein-Protein Interaction Maps, UCSD Biology annual retreat, Lake Arrowhead, CA, poster.

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, CS Huang, ZZ Zhang, M Galli, and JR Ecker (Mar 2016) Next-Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstocks Research, USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, Tysons Corner, VA, poster.

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, CS Huang, ZZ Zhang, M Galli, and JR Ecker (October 2015) The ProCREate interactome mapping technique reveals crosstalk and directionality between Arabidopsis regulatory networks, Salk Science at the Seaside, La Jolla, CA, poster and mini presentation. Peoples Choice Award for best mini presentation.

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, CS Huang, ZZ Zhang, M Galli, and JR Ecker (Sept 2015) ProCREate: A New Assay for Generation of Large-Scale Protein-Protein Interaction Maps, UCSD Biology annual retreat, Lake Arrowhead, CA, poster.

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, CS Huang, M Galli, and JR Ecker (Aug 2015) Finding biological relevance in large-scale protein network studies, NSF Data Science Workshop, Seattle, WA, poster.

Shelly A. Trigg, RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, CS Huang, M Galli, and JR Ecker (Feb 2015) Next-Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstocks Research, USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, Tysons Corner, VA, poster.

Shelly A. Trigg, A MacWilliams, JR Nery, A Bartlett, R Castanon, A Goubil, J Feeney, R OMalley, M Galli, and JR Ecker (Feb 2014) Next-Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstocks Research, USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, Arlington, VA, poster.

Shelly A. Trigg, J Feeney, JR Nery, A Bartlett, R Castanon, A Goubil, R OMalley, M Galli, and JR Ecker (Feb 2013) Next-Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstocks Research, USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, Bethesda, MD, poster.

AWARDS

UW Data Science Postdoctoral Fellowship, 2019

NSF GRIP with NOAA Northwest Fisheries Science Center, June 2017- May 2018

Excellence in Teaching Award, UC San Diego Division of Biological Sciences, 2016

Salk Science at the Seaside Annual Retreat Minute-to-win-it poster presentation People’s Choice Award, 2015

NSF Graduate Research Fellowship, 2014-2018

Rookie of the Year Award for being a new Association of Women In Science chapter member who demonstrated a commitment to advancing the goals of the organization by volunteering efforts, providing ideas, and promoting the organization outside of AWIS, 2013

Allen Douglass Bliss Award in Chemistry for academic achievement and promise in the field, 2010

EDUCATION OUTREACH

UW SAFS Open House shellfish and ocean acidification presenter                                              2019

National Marine Sanctuaries ocean acidification multimedia toolkit development                         2017-2018

Salk Institute Education Outreach plant biology video media development                                   2016

Salk Institute AAAS New Frontiers in Science Education curriculum developer                           2014-2017

UC San Diego Undergraduate Biology Showcase poster judge                                                     2015-2016

Reuben H. Fleet Science Center #2Scientists program                                                                 2014-2016

Association for Women in Science (AWIS) San Diego outreach committee member                     2012-2016

Expanding Your Horizons San Diego AWIS presenter                                                                2013-2015

AWIS San Diego undergraduate career panel coordinator                                                            09/2014           

Albert Einstein Academy Family Science Night presenter                                                           04/2014

ACS Chemistry Expo AWIS presenter, San Diego                                                                      10/2013

Greater San Diego Science Festival Expo Day presenter                                                              2013-2014

Greater San Diego Science Festival poster judge                                                                         2013-2014

ACADEMIC SERVICE

Teacher training coursework

Evidence-Based Teaching and Learning in Biological Sciences course, UC San Diego      01/2017-03/2017

Introduction to College Biology Education course, UC San Diego                                    03/2016-06/2016

 

Teaching experience

Head Instructional Assistant, Regulation of Eukaryotic Gene Expression, UC San Diego  01/2017-03/2017

Instructional Assistant, Genomics Research Initiative Lab, UC San Diego                        03/2016-06/2016

Student Instructor, Quantitative Biology graduate seminar, UC San Diego                        09/2015-08/2016

Instructional Assistant, Biochemical Techniques Lab, UC San Diego                               09/2014-12/2014

Teaching Assistant, Biochemistry II, Simmons College                                                   01/2010-05/2010

Teaching Assistant, Organic Chemistry I, Simmons College                                            01/2009-05/2009

Teaching Assistant, Organic Chemistry II, Simmons College                                           09/2008-12/2008

Teaching Assistant, General Chemistry, Simmons College                                              01/2008-04/2010

 

Mentoring Experience

NOAA Hollings Scholar undergraduate student Akofa Kekeh                                          06/2017-08/2017

Biology Department peer mentor committee chair                                                           06/2015-06/2016

Graduate student Eileen Gonzales                                                                                  08/2015-06/2016

Graduate student Natasha Slepak                                                                                   09/2014-06/2015

PROFESSIONAL MEMBERSHIPS

National Shellfish Association

The Ocean Society

American Association for the Advancement of Science

Association of Women in Science

Tri Beta Biological Honors Society

Sigma Xi Biological Honors Society