SHELLY A. TRIGG, Ph.D.
(339) 368-0029 ·
shellywanamaker@gmail.com · ORCID ID: 0000-0001-6904-4149 ·
https://gihub.com/shellywanamaker
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 O’Malley,
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 O’Malley,
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 O’Malley,
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, Tyson’s Corner, VA,
poster.
Shelly A. Trigg,
RM Garza, A MacWilliams, JR Nery, J Reyna, A Bartlett, R Castanon, A Goubil, J
Feeney, R O’Malley,
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. People’s
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 O’Malley,
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 O’Malley,
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 O’Malley,
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, Tyson’s Corner, VA,
poster.
Shelly A. Trigg,
A MacWilliams, JR Nery, A Bartlett, R Castanon, A Goubil, J Feeney, R O’Malley, 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 O’Malley, 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