Adelaide Rhodes has over 15 years of experience in bioinformatics and analyzing large datasets for environmental, metagenomic, and human health applications. She has strong skills in programming languages like R, Python, and UNIX/Linux and has experience building workflows for analyzing NGS data using tools like Nextflow, Snakemake, and Kubernetes on cloud platforms. She currently works as a Senior Bioinformatics Scientist at Tufts University, where she provides strategic consulting and trains researchers on analytical methods and cloud resources.

1. Adelaide Rhodes, Ph.D.
Bioinformatic Scientist and Strategic Cloud Consultant
Salem, MA
I have more than 15 years of experience in analyzing "big data” at the molecular,
organismal, and ecological scales for environmental, metagenomic and human health
data. I have experience with experimental design and advanced analytical software
programs such as IPA as well as the ability to build bespoke scripts in R, Python, MATLAB,
UNIX, and SAS to clean, interrogate and visualize data sets for multidisciplinary teams
from the wet lab to the software engineers who maintain the pipelines. I enjoy speeding
up and innovating data discovery using the FAIR best practices in test driven
development of bioinformatics workflows on HPC and commercial cloud computing
resources using advanced workflow tools such as Nextflow, Snakemake, Kubernetes,
Cromwell and common workflow languages such as WDL and CWL.
● Effective and confident science communicator and collaborator with a strong
customer service ethic, resulting in dozens of successfully executed research
projects, publications, and grant proposals at all levels of collaboration with bench
scientists who do not program to high level cancer researchers with multi-level
complex ‘omic, biochemical and patient data sets.
● Adaptable implementer of new technologies used to facilitate reproducibility and
transport of scalable analyses of public and patient-protected data on cloud
platforms such as Broad’s app.Terra.bio and the National Center for Biotechnology
Information. Efficient networker and collaborator with more advanced research labs
and with the developers of science platforms on the cloud.
● Creative and friendly co-worker with wet lab experience who enjoys working in a
multi-disciplinary and collaborative environment that has the ability to troubleshoot
both individually and as part of a team. I thrive in environments with unique
challenges in bioinformatics that have a big impact on human health or improving
our understanding of the planet and how we can protect it for future generations.
EDUCATION
M.S. Biotechnology/Bioinformatics 2012 Johns Hopkins University
Ph.D. Zoology/Nutrition 2004 North Carolina State University
M.S. Oceanography 1992 Florida Institute of Technology
B.A. Physics 1990 University of Virginia

2. PROGRAMMING, PLATFORM AND LABORATORY SKILLS
● In-depth understanding of computational methods for NGS analysis: RNASeq (Bulk
and Single Cell), ATAC-Seq, ChIP-Seq, GSEA, WCGNA, genome assembly and
polishing of novel organisms, Metagenomics (16S QIIME2 and mothur as well as
WGS binning and assembly of microbiomes), restriction enzyme digest methods
(GBS, RAD-Seq, 2BRad), advanced transcriptomic analyses (Transfusion,
Transcription Factor and long non-coding RNA discovery),as well as variant-finding
for cancer and disease genomics (GATK, HAIL and GWAS), amplicon-based
sequencing and WGS analysis for synthetic biology and CRSPR-based and other
gene editing projects.
● Familiarity with processing and troubleshooting sequencing data from Sanger,
Illumina Nextseq, NovaSeq, MiSeq, PacBio SMRT and Oxford Nanopore MinION and
PromethION platforms.
● Strong hands-on skills in relevant programming languages (e.g., R, Python, Shiny,
UNIX/Linux, SQL, Matlab), statistical software, cloud computing, visualization tools,
and relevant R/Bioconductor packages and Python/BioPython/Bioconda modules
including writing algorithms and scaling implementation using parallel computing.
● Knowledge of how to build, test, scale and deploy bioinformatics pipelines using
biocontainers (Docker, Singularity, Podman) and virtual Conda environments for
next-generation sequencing (NGS), functional genomics, statistics for big data
analysis, or multi-omics data integration using cloud platforms (AWS,GCP) and
workflow languages and tools (WDL, CWL, Nextflow, Snakemake, Kubernetes, ,
Lambda deployments).
● Knowledge of existing bioinformatics databases and file formats on the cloud (e.g.
NCBI SRA on AWS and GCP, GTex, ENCODE, dbGAP, UKBioBank, DNANexus, Seven
Bridges, NHGRI Terra, etc.) and ability to build custom databases in AWS Athena,
GCP BigQuery, SQLite, NoSQL as well as build and extract data from Data Lakes
and Data Warehouses using ETL mapping.
● Builder of dashboard tools to enable data discovery by non-coders: RShiny, Jupyter
Notebooks, JBrowse, Dash, Nextflow Tower and Flask.
● Demonstrated ability to produce well-designed and documented code using
Bitbucket and Github (e.g. https://github.com/RareSeas/test-scanpy-workflow).
● Planning and project management experience on Confluence and Jira.
● LIMS construction in collaboration with bench scientists to manage and integrate
experimental metadata with bioinformatics pipelines.
● Software Applications: ArcGIS, Microsoft Office, Adobe Illustrator, R, SAS, S-PLUS,
MATLAB, Statistica, Sigmastat, Sigmaplot, Systat, Tableau, IPA and Geneious.
● Hands-on wet lab experience with advanced analytical techniques: Scanning
electron microscopy, HPLC, GC-MS, DNA/RNA extraction, Amplicon-based
sequencing, NGS Sequencing on short read (Illumina) and long-read (PacBio,
Oxford Nanopore) platforms, DNA barcoding, PCR, RTqPCR, cDNA library and
plasmid vector development, RADSeq, GBS and 2B-Rad restriction enzyme digests.

3. CURRENT ACADEMIC APPOINTMENTS
Affiliate Research Faculty, Halmos College of Natural Sciences and
Oceanography, Nova Southeastern University July 2021 to
present. MS level class on Bioinformatics Project Management
RECENT WORK EXPERIENCE
Senior Bioinformatics Scientist, Tufts University Research
Technology
Tufts University, Medford, MA
June 2022 to present
● Strategic consulting with researchers in medical, environmental, and engineering
data for constructing bioinformatic and data science pipelines and visualizations
for ATAC-Seq, ChIP-Seq, scRNASeq, bulk RNASeq and metagenomics pipelines
(e.g. MetaPhlAn and other Huttenhower lab tools).
● Train university researchers on introductory and advanced methods that utilize
HPC and cloud-based resources - budgeting, permission setting and
implementation (mainly metagenomics and RNA-Seq and pre-processing).
● Writing and reviewing documentation for internal and external stakeholders at all
levels in the university (from undergraduate students to the provost).
● Consulting in experimental design and data analysis for metagenomic, cancer
genomics and other disease-based data sets.
● Construction of bioinformatics pipelines in Nextflow for metagenomics and
RNA-Seq
Principal Computational Biologist, Cutivarium FRO
Convergent Research, LLC, Jamaica Plains, MA
January 2022 to June 2022
● Developed a business plan to manage human resources and budget for data
ingest, analysis, automation and innovation
● Managed cloud resources - budgeting, permission setting and implementation.
• Designed and built custom scripts to bring in large data sets from a diverse set
of public databases and web scraping projects.
● Built a cloud database in BigQuery of relevant biological factors for bacteria
web-scraped from open resources and augmented with laboratory-generated
data as well as a custom searchable web portal in Google Data Studio for the
bench scientists.
● Developed a framework for deriving insights from large data sets, including
custom dashboards in Dash, Google Cloud Data Studio and RShiny.
● Met regularly with research scientists to assess upcoming data needs and act on
feature requests for dashboards and consult on experimental design including
the selection of relevant organisms from collaborative biorepositories such as
ATCC and UTEX.

4. Cloud Strategic Consultant and Bioinformatics Specialist, IEB, NCBI, NIH
National Center for Biotechnology Information, NLM, NIH, Bethesda,
MD Dec 2020 to Dec 2021
● Managed GCP and AWS cloud resources - budgeting, permission setting and
implementation of best practices for special projects in COVID-19 publicly
curated variant databases used for petabyte scale demo projects. This resulted
in a 95% reduction of monthly cloud costs as compared to the previous two
years.
● Designed and built cloud infrastructure on AWS using Terraform, Cloudwatch
and Cognito permission setting for interactive development and workshop tools
as well as designed an internal process to request and deploy these resources.
● Developed and delivered custom bioinformatics webinars, workshops and
conference presentations highlighting new services and cloud data options for
NCBI databases and command line tools.
● Trained colleagues on reproducible workflows on the cloud and cloud best
management practices for benchmarking, testing and optimization.
● Pioneered the transition of the NCBI workshop materials to an open source and
FAIR format by training colleagues on Git best practices and Jupyter notebook
and Binder development and deployment.
Senior Bioinformatics Scientist
LifeMine Therapeutics, Cambridge, MA
June 2020 to Nov 2020
● Consulted on experimental designs with bench scientists and the sequencing
team for targeted exploration of interesting biosynthetic gene clusters.
● Performed large-scale integrated analyses of proprietary fungal genomics
datasets for novel drug target identification and validation, specifically in
biosynthetic gene clusters.
● Developed cloud and on-prem workflows for bioinformatics pipelines for
RNASeq and Oxford Nanopore MinION workflows to speed up discovery and
analysis of target genomes.
● Integrated output from the bioinformatics and genomics pipelines with
metadata hosted on a custom LIMS using the RShiny visualization tool to help
bench scientists visualize and derive insights from their results.
● Built an inhouse browser-based genomics viewer (JBrowse2) to allow for manual
verification of annotations and outputs from the RNASeq analysis.
● Reduced turnaround time for RNASeq workflows on multiplexed NovaSeq
sequences from 2 weeks to less than 24 hours using GCP cloud tools.
● Optimized bioinformatics quality control and analysis parameters for fungal
species and integrated bioinformatics QC findings into the bespoke LIMS system.
● Wrote custom multi-omics tools to synthesize datasets from proteomics,
transcriptomics and metabolomics in R and Python.
● Wrote custom scripts to identify interesting biosynthetic gene clusters with
potential drug therapy applications.

5. Cloud Strategic Consultant
Onix Networking Inc, Cleveland, OH
Aug 2019 to April 2020
● Conducted pre sales discovery for targeted cloud infrastructure development as
a consultant for a third-party cloud provider.
● Developed and optimized best practices for diagnostic, precision medicine and
genomic health science research across cloud-based platforms (AWS and GCP).
● Participated in cloud security and budget assessments to design the best
available solutions for biomedical and health science research clients.
● Oversaw technical development of customer dashboards linked to FHIR
databases built by offshore software developers.
● Handled business development and strategic consulting to grow business
opportunities in the Boston area.
● Optimized complex bioinformatics workflow issues for cloud customers
wanting to integrate machine learning and AI with internal relational
databases.
● Provided training on cloud research analytic methods for novice and
advanced researchers.
Senior Research Associate, Terra Cloud Platform
Broad Institute of MIT and Harvard, Cambridge, MA
Nov 2018 to Aug 2019
● Developed WDL and documentation for existing (Hail and PyGMQL) and new
(XTEA, ENCODE, Cumulus) workflows to be loaded into the Terra cloud platform.
● Provided input to software developers to optimize the user experience on the
Terra cloud platform. Acted as the research user’s in-house representation to
drive innovation.
● Answered customer questions on bioinformatics (GATK) and usage of the Terra
cloud platform.
● Taught workshops on cloud computing (GCP) and GATK (Cambridge,
England).
● Presented at international conferences on open-source workflows in Terra.
● Facilitated hackathon teams on synthetic bam generation and single cell
analysis.
LINKS
● Twitter: @RareSeas
● LinkedIn: https://www.linkedin.com/in/adelaide-rhodes-ph-d-376b9133
● Github: https://github.com/RareSeas
● Recent Publications: https://nova.academia.edu/AdelaideRhodes

6. RECENT GENOMICS AND BIOINFORMATICS PUBLICATIONS
Naz et al. Isolation and Identification of a Novel Extremely Salt Tolerant
Cyanobacterium from the Hyperarid Yungay Region of the Atacama Desert.
(2023) Submitted to Astrobiology.
Tully et al. The Bioinformatics Virtual Coordination Network: an open-source and
interactive learning environment. Frontiers in Education.
doi:10.3389/feduc.2021.711618
Al Khleifat, Ahmad, Jenny L. Smith, Brandon Blobner, Sierra Miller, Kymberleigh
Pagel, Annie Nadkarni, Melanie Gainey, et al. 2021. “Snpreportr: A Tool for
Clinical Reporting of RNASeq Expression and Variants.” BioHackrXiv. June 29.
doi:10.37044/osf.io/5j7cm
Auld, H.L., Jacobson, D.P., Rhodes, A.C. and Banks, M.A. Auld, H. L., Jacobson, D.
P., Rhodes, A. C., & Banks, M. A. (2021). Differences in mate pairings of
hatchery and natural origin coho salmon inferred from offspring genotypes.
Integrative Organismal Biology.
Rayko, M., Komissarov, A., Kwan, J.C. et al. Draft genome of Bugula neritina, a
colonial animal packing powerful symbionts and potential medicines. Sci
Data 7, 356 (2020). https://doi.org/10.1038/s41597-020-00684-y
Sparks, M.E., Bansal, R., Benoit, J.B. et al. Brown marmorated stink bug,
Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy,
insecticide resistance potential and biology of a top worldwide pest. BMC
Genomics 21, 227 (2020). https://doi.org/10.1186/s12864-020-6510-7
Sparks, Michael, Rhodes, Adelaide et al. (2020). Halyomorpha halys Official Gene
Set v1.2. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1518751.
Kashyap, A., Rhodes, A., Kronmiller, B. et al. Pan-tissue transcriptome analysis of
long noncoding RNAs in the American beaver Castor canadensis. BMC
Genomics 21, 153 (2020). https://doi.org/10.1186/s12864-019-6432-4
Dombrowski, J.E., Kronmiller, B.A., Hollenbeck, V.G. et al. Transcriptome analysis
of the model grass Lolium temulentum exposed to green leaf volatiles. BMC
Plant Biol 19, 222 (2019). https://doi.org/10.1186/s12870-019-1799-6
Rhodes A, Blanco Y, Miossec MJ et al. Fake it 'til You Make It (Reproducible):
Open Source Tools for Synthetic Data Generation [version 1; not peer
reviewed]. F1000Research 2019, 8(ISCB Comm J):1380 (poster)
(https://doi.org/10.7490/f1000research.1117300.1)
Ramsey, S.A., Xu, T., Goodall, C. Rhodes, A.C., Kashyap, A., He, J., and S. Bracha.
Cross-species analysis of the canine and human bladder cancer
transcriptome and exome. Genes, Chromosomes and Cancer 2017;00:000–
000. doi:10.1002/gcc.22441.
Robertson, H. E., Lapraz, F., Rhodes, A. C. and Telford, M. J. 2015. The complete
mitochondrial genome of the geophilomorph centipede Strigamia maritima.
PloS one, 10(3), e0121369.
Chipman, A. D. (+50 authors). 2014. Prototypical arthropod gene content and
genome organisation in the centipede Strigamia maritima. PloS Biology 12

7. (11) p. e1002005.
Lopez et al. (+50 authors). 2014. Global Invertebrate Genomics Alliance (GIGA):
Developing Community Resources to Study Diverse Invertebrate Genomes.
Journal of Heredity 105 (1): 1-18 doi:10.1093/jhered/est084.
ACADEMIC WORK EXPERIENCE
Academic Specialties: Metagenomics, transcriptomics, pan-transcriptomics,
transcription regulation, multi-omics, genome assembly of non-model organisms, Iso-seq
epigenetics, cross species analysis, population genetics, GBS, RadSeq, Chip Seq, ATAC
Seq, metagenomics, metabarcoding, microbiome and epigenetics. Deep sea
biogeography and crustacean taxonomy (copepods and peracarid crustaceans);
bioinformatics and gene expression analysis of marine organisms stressed by pollution,
ocean acidification and other environmental impacts; cultivation of marine
zooplankton for ecotoxicology, demographic, environmental and aquaculture
research; Community ecological data analysis for Deepwater Horizon oil spill impacts.
Bioinformatics Resource Manager and Research Faculty
Department of Microbiology and Molecular Genetics
University of Vermont, Burlington VT - October 2017 to August 2018
Center for Genomic Research and Biocomputing Research Faculty
Oregon State University, Corvallis, OR – July 2014 to September 2017
Ecological, Organismal and Genomic Researcher
Fish Genetics and Copepod Ecology, OSU Newport Marine Lab, 2014-2017
Benthic Ecology, Harte Research Institute, Corpus Christi, TX 2011-2014 Benthic
Ecology, Smithsonian Institution Marine Station, Fort Pierce, FL 2010-2011
Fisheries Ecology, University of Florida, Fort Pierce, FL 2009
Aquatic & Fisheries Science, University of Washington & NOAA, 2005-2008
Aquaculture, North Carolina State University, 2000-2004
University Teaching for Credit
Methods in Bioinformatics (undergraduate, University of Vermont)
Advanced Bioinformatics Course Series (graduate students, Oregon State Univ.)
Metagenomics I & II
Genotyping by Sequencing & Conservation Genomics
Intro to Command Line and Advanced Data Analysis
RNA Seq I & II
Marine Benthic Ecology (graduate, Texas A&M Corpus Christi)
Marine Plankton (undergraduate, University of Washington Tacoma) Global
Climate Change Seminar (undergraduate, University of Washington)
Animal Diversity and Intro to Molecular Biology (TA, undergraduate, NCSU)
Intro to Biology for Non-Majors (TA, undergraduate, NCSU)