Gervaise Henry

Dallas, TX
gervaise.henry@gmail.com
1-202-417-1088

LinkedIn: https://www.linkedin.com/in/gervaise-henry-7790679a/
GitLab: https://git.biohpc.swmed.edu/ghenry/
GitHub: https://github.com/GHAStVHenry/
ORCiD: https://orcid.org/0000-0001-7772-9578

Skills

Certification
- AWS Certified Solutions Architect - Associate
- AWS Certified Cloud Practitioner
- Scrum Alliance Certified Scrum Product Owner

Languages, Operating Systems & Tools
- R
- Python
- Nextflow
- WDL
- git
- linux
- bash

Website Development
- Static Site Generators
- Serverless Deployment
- GitLab Pages
- html5
- css3
- javascript

Cloud Platforms
- AWS
- Azure
- GCP

AWS Tools
- S3
- EC2
- Batch
- Lambda
- DynamoDB
- API Gateway
- Certificate Manager
- Route53
- CloudFront
- CloudTrail
- Athena

Container Environments
- Docker
- Singularity

Biological Analytic Modalities
- bulkRNA-Seq
- Gene Expression Microarray
- scRNA-Seq
- scTCR-seq
- Variant Calling
- Proteomics (Mass Spec)
- Varied Molecular Biology Techniques

Experience

Manager, Solutions and Services Engineering

Solutions and Services: DNAnexus, Mountain View CA (remote)
March 2024 - Present

Manage 13 people (across the US and Europe) including:
- 2 group managers.
- 2 solutions architects.
- 3 solutions engineers.
- 9 services engineers.
Responsible for all tool and workflow development, in both pre-sales and professional services settings.
Responsible for all ingenstion for translational datasets, in both pre-sales and professional services settings.
Responsible for staffing projects, including the use of a large contigent of off-shore contractors.
Work with other stakeholders in developing process to ensure profitable services.
Work closely with Product Engineering and Product Management teams to assist in scoping and prioritizing new features and functionality.
Build proof-of-concept assets to assist in architecting new features and functionality.
Assist in technical evaluation of potential partners, as well as building proof-of-concept integrations when necessary.
Act as a liaison between the sales team, the customer, and internal product, professional services, and support teams.

Manager, Solutions Engineer

Solutions Sales: DNAnexus, Mountain View CA (remote)
February 2023 - July 2023

Manager of presales engineering group:
- Manage a team if 5-6 Solutions Engineers.
- Build proof-of-concept assets to prove the customer’s need are possible on the platform, both scientifically and technically.
- Assist in scoping a customer’s scientific and technical needs.
- Perform platform demos to customer.
- Provide technical customer training in a presales setting.
- Provide technical support in a presales setting.
Work closely with Product Engineering and Product Management teams to assist in scoping and prioritizing new features and functionality.
Build proof-of-concept assets to assist in architecting new features and functionality.
Act as a liaison between the sales team, the customer, and internal product, professional services, and support teams.

Senior Solutions Engineer

Solutions Science: DNAnexus, Mountain View CA (remote)
August 2021 - February 2023

Presales engineer:
- Assist with customer discovery.
- Scope and scale customer needs and wants to adiquately demmonstrate platform functionality.
- Build demo, proof-of-concept, and pilot assets.
- Perform demontrations of the platform to customers.
- Provide customer training.
- Provide white-glove technical support experience for potential strategic accounts.
Act as liaison between sales team, customer, and external partners with internal product and services teams.

Computational Biologist

Strand Lab: UT Southwestern Medical Center, Dallas TX
September 2019 - July 2021

Big-Data Analysis: Responsible for producing high quality statistical analysis for a wide range of data types, in particular, genomics-based modalities. This is dominated by the analysis of large amounts of singe-cell RNA-sequencing data.
Tool Development: Created tools (including shiny-apps) for data exploration by the lab.
Website Development: Create and manage the lab website using static site generators. The website includes custom tools for exploring the lab’s biorepository and scRNA-seq data, and serverless deployment on AWS, as well as gitlab pages.
Pipeline Development: In collaboration with the Bioinformatics Core Facility (BICF), I help to create and manage automated pipelines to ensure reproducibility, transparent analysis, and to increase analytical throughput.
Collaboration Management: Manage a funded collaboration to create pipelines for standardizing data analysis for the intent of integration of data from disparate studies on a consortium level. This includes designing the pipelines, contributing to the development, and managing a team of developers.
Cloud Architect: Migrated a variety of BICF pipelines to function seamlessly in the cloud (including AWS and Azure).
Instructor: Contributed regularly in the instruction of the Department of Bioinformatics computational nano-courses across multiple topics including programing languages and analytic techniques.
RESULTS: Published three pipelines, with an additional four in active development. Secured consortium level funding for pipeline development. Successfully migrated 2 pipelines and the Strand Lab website to AWS, and actively migrating remaining pipelines.

Research Associate

Strand Lab: UT Southwestern Medical Center, Dallas TX
April 2015 - September 2019

Research: Designed, conducted, and analyzed cellular and molecular experiments, leveraging best practices, statistical techniques, and available resources to maximize outcomes and publish impactfully.
Author: I presented annually at conferences, both in poster and oral formats. I was a named author in nine journal publications, three of which I was the primary researcher and the first author.
RESULTS: Authored (first, and co-authored) 8 journal papers, including a very successful first-author Cell Reports (2018) paper.

Research Associate

Guzman Lab: Harbor Branch Oceanographic Institute at Florida Atlantic University, Ft. Pierce FL
November 2014 - March 2015

Assay Development: Develop high-content image-based assays for high throughput drug discovery.
RESULTS: Optimized high throughput assays for early-stage drug discovery on marine natural products.

Teaching Assistant/Research Assistant

DeCicco-Skinner Lab: American University, Washington DC
August 2012 - May 2014

Research: Utilized cellular and molecular techniques to further projects.
Supervision: Supervised several of undergraduate researchers to sustain collaborations.
Instructor: Independently taught freshman and senior level lab courses. Responsible for assisting with design of laboratory content including assessments, independently teaching lab content, grading, and counseling students.
RESULTS: Successfully defended master’s thesis linking obesity and BMI to the progression of multiple myeloma. Contributed to the success of three lab projects not associated with master’s work.

Research Technician

Malter Lab: UT Southwestern Medical Center, Dallas TX
September 2011 - May 2012

Research: Conducted research to support several projects.
Vendor Management: Managed the lab budget, oversaw ordering, and developed vendor relationships.
RESULTS: Successfully allowed for the seamless transition of the new Pathology Department chairman’s lab to UT Southwestern.

Screening Scientist

HTS/RNAi Core: UT Southwestern Medical Center, Dallas TX
February 2010 - September 2011

High-Throughput Screening: Conducted high throughput compound and whole genome RNAi screens for client labs.
Assay Development: Involved in all aspects of projects including assay choice and development, optimization, implementation, and data analysis.
RESULTS: Contributed to successful screens, which led to significant lead-generation and fueled many research projects.

Publications

Cell Reports (2022): Adipocyte mesenchymal transition contributes to mammary tumor progression https://doi.org/10.1016/j.celrep.2022.111362
Bioinformatics (2022): SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers https://doi.org/10.1093/bioinformatics/btac050
The Journal of Pathology (2021): 5-alpha reductase inhibitors induce a prostate luminal to club cell transition in human benign prostatic hyperplasia https://doi.org/10.1002/path.5857
The Journal of Pathology (2021): Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions https://doi.org/10.1002/path.5751
Physiological Reports (2021): A NEW Approach for Characterizing Mouse Urinary Pathophysiologies https://doi.org/10.14814/phy2.14964
Cell Stem Cell (2021): Pathologic HIF1α signaling drives adipose progenitor dysfunction in obesity https://doi.org/10.1016/j.stem.2020.12.008
The Prostate (2020): Urethral luminal epithelia are castration-insensitive cells of the proximal prostate https://doi.org/10.1002/pros.24020
Cell Reports (2019): Expansion of Luminal Progenitor Cells in the Aging Mouse and Human Prostate https://doi.org/10.1016/j.celrep.2019.07.007
Cell Reports (2018): A cellular anatomy of the normal human prostate https://doi.org/10.1016/j.celrep.2018.11.086
Cancer Cell (2018): Molecular evolution of early-onset prostate cancer identifies molecular risk markers and clinical trajectories https://doi.org/10.1016/j.ccell.2018.10.016
eLife (2018): Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice https://doi.org/10.7554/eLife.39636.001
Cytometry Part A (2017): OMIP-040: Optimized gating of human prostate cellular subpopulations https://doi.org/10.1002/cyto.a.23187
The Prostate (2017): Molecular pathogenesis of human prostate basal cell hyperplasia https://doi.org/10.1002/pros.23394
Molecular Cell (2016): Non-cell-autonomous regulation of prostate epithelial homeostasis by androgen receptor https://doi.org/10.1016/j.molcel.2016.07.025
Differentiation (2016): Isolation and analysis of discrete human prostate cellular populations https://doi.org/10.1016/j.diff.2015.10.013
JoVE (2014): Endothelial cell tube formation assay for the in vitro study of angiogenesis http://dx.doi.org/10.3791/51312

Presentations

ACMG (2024): Automated Genome Interpretation Solution to Accelerate Diagnostic Decisions via Intelliseq GeneSpect™ Reporter (ORAL PRESENTATION)
BioTechX Europe (2023): Bridging the Gap: Solutions for Data Integration, Security, and Collaborative Exploration in Precision Medicine (ORAL PRESENTATION)
Precision Medicine Leaders Summit: Advances in Single Cell & Spatial Biology (2023): Democratizing Access to Single-Cell RNA Sequencing with the Parse Biosciences Evercode Platform (ORAL PRESENTATION)
Precision Medicine Leaders Summit: Advances in Single Cell & Spatial Biology (2023): Innovation Panel: Building the Spatial Biology Ecosystem (PANELIST)
BioIT World (2023): Towards Precision Medicine: Datasets, Computation, and Data Integration for Patient Subsetting Research - Part I (PANELIST)
BioIT World (2023): Achieving FAIRness with Multimodal Data (PANELIST)
Collaborating for the Advancement of Interdisciplinary Research in Benign Urology: Meeting (2021): Spatial transcriptomics reveals a transition from a prostate luminal to club-like cell state in 5-alpha reductase inhibitor treated BPH patients (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2021): Spatial transcriptomics reveals a transition from a prostate luminal to club-like cell state in 5-alpha reductase inhibitor treated BPH patients (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2021): Immune cell Single cell RNA sequencing and interaction analyses suggest a prominent role for T cells and T cell-macrophage interactions in Benign Prostatic Hyperplasia (POSTER PRESENTATION)
American Urological Association: Annual Meeting (2021): Understanding Prune Belly Syndrome at Single Cell Resolution (POSTER PRESENTATION)
American Urological Association: Annual Meeting (2021): Characterization of 5ARI treatment response at the single cell level (POSTER PRESENTATION)
Collaborating for the Advancement of Interdisciplinary Research in Benign Urology: Meeting (2020): Decoding Stromal Heterogeneity Across BPH Phenotypes (POSTER PRESENTATION)
Collaborating for the Advancement of Interdisciplinary Research in Benign Urology: Meeting (2020): A Phenome-Based Approach for Characterizing Mouse Urinary Pathophysiologies (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2020): Decoding Stromal Heterogeneity across BPH Phenotypes (POSTER PRESENTATION)
Collaborating for the Advancement of Interdisciplinary Research in Benign Urology: Meeting (2019): Immune Cell Interactions in Benign Prostatic Hyperplasia (POSTER PRESENTATION)
Collaborating for the Advancement of Interdisciplinary Research in Benign Urology: Meeting (2019): Identification of Cognate Proximal Cell Types of the Mouse and Human Prostate and Their Enrichment in Human Benign Prostatic Hyperplasia (POSTER PRESENTATION)
Cold Spring Harbor: Single Cell Analysis (2019): A Cellular Atlas of Human Prostate Disease (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2019): Identification of cognate proximal cell types of the mouse and human prostate and their enrichment in human Benign Prostatic Hyperplasia (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2019): Immune Cell Interactions in Benign Prostatic Hyperplasia (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2019): Expansion of Luminal Progenitor Cells in the Aging Mouse and Human Prostate (POSTER PRESENTATION)
Prostate Cancer Foundation: Annual Scientific Retreat (2019): Urethral Hillock Epithelia Extend into the Proximal Prostate Stem Cell Niche (POSTER PRESENTATION)
International Society for Advancement of Cytometry: CYTO (2019): Cloud-based cytometry workflow for big data analysis (POSTER PRESENTATION)
American Urological Association: Annual Meeting (2019): Cellular pathogenesis of human BPH (POSTER PRESENTATION)
Collaborating for the Advancement of Interdisciplinary Research in Benign Urology: Meeting (2018): Building a comprehensive cellular anatomy of the normal and diseased human prostateia (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2018): Global Transcriptional Dynamics Identify Key Functional Pathways Involved in the Pathogenesis of Prune Belly Syndrome (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2018): Characterizing the metabolic effect of enzalutamide on prostate cancer (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2018): A Cellular Anatomy of the Normal Human Prostate and BPH (POSTER PRESENTATION)
10x Genomics User Group Meeting: Houston (2018): Determining Cellular Heterogeneity in Human Prostate using the Chromium™ Single Cell 3’ Solution (ORAL PRESENTATION)
FlowTex Conference (2018): Determining cellular heterogeneity in human prostate with flow cytometry and single-cell RNA-sequencing (ORAL PRESENTATION)
North Texas Flow Cytometry Conference (2017): Determining cellular heterogeneity in human prostate with flow cytometry and single-cell RNA-sequencing (ORAL PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2017): Pathogenesis of Inflammation in Human BPH (POSTER PRESENTATION)
North Texas Flow Cytometry Conference (2016): Deconstructing BPH Phenotypes: Molecular Pathogenesis of Basal Hyperplasia (ORAL PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2016): Deconstructing BPH phenotypes (POSTER PRESENTATION)
Society for Basic Urologic Research: Annual Meeting (2015): Cell-specific responses to inflammation in BPH (POSTER PRESENTATION)
American Association of Cancer Research: Annual Meeting (2014): Adipocytes, Obesity and the Multiple Myeloma Microenvironment (POSTER PRESENTATION)

Contributions

Projects
- 2021: GUDMAP/RBK Analytics
  Design and manage the Agile group responsible for creating analytics for data stored on the NIH consortiums GUDMAP and RBK. This analytics are not only best-practices pipelines written in Nextflow, but also integrates seamlessly with the consortiums' data-hub, in terms of initiation, and data ingress/egress. It is built with the flexibility to utilize on premises HPC, or a custom built AWS architecture (including many serverless resources) for low-cost, highly-available queueing, compute, and reporting. It can also be easily adapted to almost any running environment using custom configs. The entire pipeline utilizes dockerized micro-services which is orchestrated by Nextflow.
- 2020: Nextflow in the Cloud
  Manage a small agile team to create a proof of concept AWS architecture to run Nextflow pipelines in the cloud. It utilizes low-cost, highly-availability queueing, compute, and storage resources. (NOTE: project decomissioned and the git repository is no longer public, for more information feel free to reach out to [Gervaise Henry](ghenry@gmail.com))
- 2019: Pipeline Run Tracking
  Creating a pipeline run tracking tool for the Bioinformatics Core Facility at UT Southwestern Medical Center. This tool utilizes AWS serverless offerings, including REST-API and a website for run tracking. (NOTE: project decomissioned and the git repository is no longer public, for more information feel free to reach out to [Gervaise Henry](ghenry@gmail.com))
- 2019: Strand Lab Internal Data Website
  Developed the internal Strand Lab website and manage the server used explore and share pre-publication single-cell RNA-sequencing data. (NOTE: project is private, for more information feel free to reach out to [Gervaise Henry](ghenry@gmail.com))
- 2019: Strand Lab External Website
  The Strand Lab website was designed to not only provide a location to share information about the lab, but also provide a means to showcase the lab's data and biorepository. The single-cell data is displayed using CZI's cellxgene visualization tool as well as pre-generated genome-wide visualization of the expression data. The lab has an extensive biorepository of human lower urinary tract biosamples and de-identified clinical data as well as H&E images are available for viewing and filtering on the website. The site is hosted serverlessly on AWS.
- 2018: BICF Pipelining
  Creating analytics for the Bioinformatics Core Facility at UT Southwestern Medical Center, using the pipelining language Nextflow.
Open Source Vizualizations
- 2021: cellxgene: Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions
  https://cellxgene.cziscience.com/collections/4b54248f-2165-477c-a027-dd55082e8818
- 2020: cellxgene: Urethral luminal epithelia are castration-insensitive cells of the proximal prostate
  https://cellxgene.cziscience.com/collections/fbc5881f-1ee3-4ffe-8095-35e15e1a08fc
- 2018: cellxgene: A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra
  https://cellxgene.cziscience.com/collections/e2a4a67f-6a18-431a-ab9c-6e77dd31cc80
Open Source Data
- 2021: GEO: Single cell RNA-sequencing of verumontanum region and peripheral zone of normal human prostate
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179312
- 2021: GEO: Human prostate luminal epithelia adopt a club-like state in response to low androgen levels
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178934
- 2021: GUDMAP: Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions
  https://doi.org/10.25548/17-DRBC
- 2021: GEO: Single-cell RNA-sequencing of adult mouse lower urinary tracts v2
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE173096
- 2021: GEO: Single-cell RNA-sequencing of adult human normal and BPH (glandular and stroma) prostates and urethra
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172357
- 2021: GEO: Bulk RNA-sequencing of fibroblasts isolated by FACS from normal human prostate
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172347
- 2020: GUDMAP: Urethral luminal epithelia are castration-insensitive cells of the proximal prostate
  https://doi.org/10.25548/16-WM8C
- 2020: GEO: Single-cell RNA-sequencing of adult mouse lower urinary tracts
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145929
- 2020: GEO: Single-cell RNA-sequencing of adult human prostates and urethra (normal and diseased)
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145928
- 2018: GEO: Single Cell RNA-sequencing of cell types isolated by FACS from normal human prostates
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403
- 2018: GEO: Bulk RNA-sequencing of cell types isolated by FACS from normal human prostates
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117271
- 2018: FLOWRepository: OMIP-040: Optimized gating of human prostate cellular subpopulations
  https://flowrepository.org/id/FR-FCM-ZY6D
- 2018: GUDMAP: Determining cellular heterogeneity in the human prostate with single-cell RNA sequencing
  https://doi.org/10.25548/w-r8cm
Open Source Code
- 2021: RNA-seq Analytic Pipeline for GUDMAP/RBK
  https://doi.org/10.5281/zenodo.4429315
- 2020: Strand Lab analysis of single-cell RNA sequencing
  https://doi.org/10.5281/zenodo.3687064
- 2019: Single-Cell RNA-Seq Image Generation Pipeline for GUDMAP/RBK
  https://doi.org/10.5281/zenodo.2652611
- 2019: BICF Cellranger mkfastq Analysis Workflow
  https://doi.org/10.5281/zenodo.2652611
- 2019: BICF Cellranger count Analysis Workflow
  https://doi.org/10.5281/zenodo.2652611
- 2018: Determining cellular heterogeneity in the human prostate with single-cell RNA sequencing
  https://doi.org/10.5281/zenodo.2652611

Education

American University
Masters of Science: Biology
Graduated 2014
Thesis: Adipocytes, obesity and multiple myeloma

Eckerd College
Bachelors of Science: Biomedical Molecular Biology
Graduated 2009
Thesis: The Search for Novel NF-kB Inhibitors from Compounds Derived from Marine Invertebrates as Potential Anti-tumor Therapies