Gervaise Henry

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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

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Experience

Head, Professional Services Engineering

Professional Services: DNAnexus, Mountain View CA (remote)
June 2024 - Present

• Manage a large organization of diverse technical global staff:
  • Across the US, Europe, and Asia.
  • Solutions Architects.
  • Services Bioinformatics Engineers.
  • Services Contractors.
• Team responsible for all tool and workflow development as a service for customers.
• Team responsible for ingenstion for translational datasets as a service for customers.
• Team responsible for building external integrations, including customer cloud integrations, and software development, to automate and layer novel funtionality to the DNAnexus platofrm.
• Responsible for staffing projects, including the use of a large contigent of off-shore contractors (not limited to those directly reporting to the PS Engineering Organization).
• 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, and support teams.

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Manager, Solutions and Services Engineering

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

• 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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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

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• EU Biobank Week 2024 (2024): Efficiently Analyzing Population-Scale Genomics Data (ORAL PRESENTATION)
• 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

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• 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

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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