Gervaise Henry

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Proven Computational Biologist, capable of leveraging considerable “bench” cellular and molecular biology experience, as well as DevOps knowledge to develop and manage large scale distributed platforms both on premises and in public cloud.

CSPO

Skills

Certification
  • Certified Scrum Product Owner
Languages, Operating Systems & Tools
  • R
  • Python
  • Nextflow
  • git
  • linux
  • bash
Website Development
  • Static Site Generators
  • Serverless Deployment
  • GitLab Pages
  • html5
  • css3
  • javascript
Cloud Platforms
  • AWS
  • Azure
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
  • Proteomics (Mass Spec)
  • Varied Molecular Biology Techniques

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.

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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.

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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.

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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.

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Experience

Senior Solutions Engineer

DNAnexus, Mountain View CA (remote)

August 2021 - Present

Computational Biologist

Strand Lab: UT Southwestern Medical Center, Dallas TX

  • 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.

September 2019 - July 2021

Research Associate

Strand Lab: UT Southwestern Medical Center, Dallas TX

  • 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.

April 2015 - September 2019

Research Associate

Guzman Lab: Harbor Branch Oceanographic Institute at Florida Atlantic University, Ft. Pierce FL

  • 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.

November 2014 - March 2015

Teaching Assistant/Research Assistant

DeCicco-Skinner Lab: American University, Washington DC

  • 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.

August 2012 - May 2014

Research Technician

Malter Lab: UT Southwestern Medical Center, Dallas TX

  • 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.

September 2011 - May 2012

Screening Scientist

HTS/RNAi Core: UT Southwestern Medical Center, Dallas TX

  • 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.

February 2010 - September 2011

cellxgene: Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions

Single-cell RNA-sequencing of adult human prostates and urethras from organ donors, and BPH (glandular and stromal) patients as well as adult mouse lower urinary tracts.

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RNA-seq Analytic Pipeline for GUDMAP/RBK

This pipeline conducts end-to-end RNA-seq analysis on replicates stored in the GenitoUrinary Development Molecular Anatomy Project and ReBuilding the Kidney consortium. This pipeline was created in a collaboration between the Strand Lab and Bioinformatics Core Facility (BICF) at UT Southwestern Medical Center.This pipeline conducts end-to-end RNA-seq analysis on replicates stored in the GenitoUrinary Development Molecular Anatomy Project and ReBuilding the Kidney consortium. This pipeline was created in a collaboration between the Strand Lab and Bioinformatics Core Facility (BICF) at UT Southwestern Medical Center.

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Strand Lab analysis of single-cell RNA sequencing

This code was used for the single-cell RNA-sequencing analysis in the Strand Lab at UT Southwestern Medical Center

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BICF Cellranger count Analysis Workflow

BICF Cellranger count Analysis Workflow is a wrapper for the cellranger count tool from 10x Genomics. This pipeline, used by the Bioinformatics Core Facility at UT Southwestern, takes fastq files from 10x Genomics single-cell gene expression libraries and passes them to cellranger count, managing parallelization of multiple runs, as well as, aggregation as appropriate. This pipeline is primarily used with a SLURM cluster on BioHPC, but it should be able to run on any system that Nextflow supports. Additionally, this pipeline is designed to work using a simple web interface.

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GEO: Single-cell RNA-sequencing of adult human normal and BPH (glandular and stroma) prostates and urethra

Single-cell RNA-sequencing of adult human prostates and urethras from organ donors, and BPH (glandular and stromal) patients.

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GEO: Single-cell RNA-sequencing of adult mouse lower urinary tracts v2

Single-cell RNA-sequencing of adult mouse prostates and urethras.

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GUDMAP: Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions

Sequencing data relating to the in preparation publication: 'Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions'

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The Journal of Pathology - Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions

Joseph DB, Henry GH, Malewska A, Reese JC, Mauck RJ, Gahan JC, Hutchinson RC, Malladi VS, Roehrborn CG, Vezina CM, Strand DW
Stromal-epithelial interactions are critical to the morphogenesis, differentiation and homeostasis of the prostate, but the molecular identity and anatomy of discrete stromal cell types is poorly understood. Using single cell RNA-sequencing, we identified and validated the in situ localization of three smooth muscle subtypes (prostate smooth muscle, pericytes and vascular smooth muscle) and two novel fibroblast subtypes in human prostate. Peri-epithelial fibroblasts (APOD+) wrap around epithelial structures while interstitial fibroblasts (C7+) are interspersed in extracellular matrix. In contrast, the mouse displayed three fibroblast subtypes with distinct proximal-distal and lobe specific distribution patterns. Statistical analysis of mouse and human fibroblasts showed transcriptional correlation between mouse prostate (C3+) and urethral (Lgr5+) fibroblasts and the human interstitial fibroblast subtype. Both urethral fibroblasts (Lgr5+) and ductal fibroblasts (Wnt2+) in the mouse contribute to a proximal Wnt/Tgfb signaling niche that is absent in human prostate. Instead, human peri-epithelial fibroblasts express secreted WNT inhibitors SFRPs and DKK1, which could serve as a buffer against stromal WNT ligands by creating a localized signaling niche around individual prostate glands. We also identified proximal-distal fibroblast density differences in human prostate that could amplify stromal signaling around proximal prostate ducts. In human Benign Prostatic Hyperplasia, fibroblast subtypes upregulate critical immunoregulatory pathways and show distinct distributions in stromal and glandular phenotypes. A detailed taxonomy of leukocytes in BPH reveals an influx of myeloid dendritic cells, T cells and B cells, resembling a mucosal inflammatory disorder. A receptor-ligand interaction analysis of all cell types revealed a central role for fibroblasts in growth factor, morphogen and chemokine signaling to endothelia, epithelia and leukocytes. These data are foundational to the development of new therapeutic targets in benign prostatic hyperplasia.
June 2021

The Prostate - Urethral luminal epithelia are castration‐insensitive cells of the proximal prostate

Joseph DB, Henry GH, Malewska A, Iqbal NS, Ruetten HM, Turco AE, Abler LL, Sandhu SK, Cadena MK, Malladi VS, Reese JC, Mauck RJ, Gahan JC, Hutchinson RC, Roehrborn CG, Baker LA, Vezina CM, Strand DW
Castration‐insensitive epithelial progenitors capable of regenerating the prostate have been proposed to be concentrated in the proximal region based on facultative assays. Functional characterization of prostate epithelial populations isolated with individual cell surface markers has failed to provide a consensus on the anatomical and transcriptional identity of proximal prostate progenitors. Here, we use single‐cell RNA sequencing to obtain a complete transcriptomic profile of all epithelial cells in the mouse prostate and urethra to objectively identify cellular subtypes. Pan‐transcriptomic comparison to human prostate cell types identified a mouse equivalent of human urethral luminal cells, which highly expressed putative prostate progenitor markers. Validation of the urethral luminal cell cluster was performed using immunostaining and flow cytometry. Our data reveal that previously identified facultative progenitors marked by Trop2, Sca‐1, KRT4, and PSCA are actually luminal epithelial cells of the urethra that extend into the proximal region of the prostate, and are resistant to castration‐induced androgen deprivation. Mouse urethral luminal cells were identified to be the equivalent of previously identified human club and hillock cells that similarly extend into proximal prostate ducts. Benign prostatic hyperplasia (BPH) has long been considered an “embryonic reawakening,” but the cellular origin of the hyperplastic growth concentrated in the periurethral region is unclear. We demonstrate an increase in urethral luminal cells within glandular nodules from BPH patients. Urethral luminal cells are further increased in patients treated with a 5‐α reductase inhibitor. Our data demonstrate that cells of the proximal prostate that express putative progenitor markers, and are enriched by castration in the proximal prostate, are urethral luminal cells and that these cells may play an important role in the etiology of human BPH.
June 2020

Cell Reports - A cellular anatomy of the normal human prostate

Henry GH, Malewska A, Joseph DB, Malladi VS, Lee J, Torrealba J, Mauck RJ, Gahan JC, Raj GV, Roehrborn CG, Hon GC, MacConmara MP, Reese JC, Hutchinson RC, Vezina CM, Strand DW
A comprehensive cellular anatomy of normal human prostate is essential for solving the cellular origins of benign prostatic hyperplasia and prostate cancer. The tools used to analyze the contribution of individual cell types are not robust. We provide a cellular atlas of the young adult human prostate and prostatic urethra using an iterative process of single-cell RNA sequencing (scRNA-seq) and flow cytometry on ∼98,000 cells taken from different anatomical regions. Immunohistochemistry with newly derived cell type-specific markers revealed the distribution of each epithelial and stromal cell type on whole mounts, revising our understanding of zonal anatomy. Based on discovered cell surface markers, flow cytometry antibody panels were designed to improve the purification of each cell type, with each gate confirmed by scRNA-seq. The molecular classification, anatomical distribution, and purification tools for each cell type in the human prostate create a powerful resource for experimental design in human prostate disease.
December 2018

Cytometry Part A - OMIP‐040: Optimized gating of human prostate cellular subpopulations

Henry GH, Loof N, Strand DW
This panel was optimized to quantify the relative frequency of the major cell types present in the human prostate in addition to their sorting for downstream applications. Tissue resident white blood cells (referred to here as leukocytes) are identified by CD45, epithelia are identified by CD326, and stroma are double negative with those markers. Epithelia can be further segregated into basal, luminal, and “other” populations using CD26 and CD271. Fibromuscular stroma can be identified by removing CD31‐positive endothelia from the stroma. This panel can also serve as a backbone for the addition of markers to interrogate subpopulations within these major cell types. The panel has been validated on freshly digested and cryopreserved human prostate cells collected from young organ donors, BPH patients, and prostate cancer patients. Other tissue types have not been tested. Other basal cell markers including CD49f, podoplanin, and CD104 are tested and compared with CD271.
August 2017

The Prostate - Molecular pathogenesis of human prostate basal cell hyperplasia

Henry GH, Malewska A, Hutchinson R, Gahan J, Mauck R, Francis F, Torrealba J, Roehrborn C, Strand DW
Background: Understanding the molecular pathogenesis of distinct phenotypes in human benign prostatic hyperplasia (BPH) is essential to improving therapeutic intervention. Current therapies target smooth muscle and luminal epithelia for relief of lower urinary tract symptoms (LUTS) due to BPH, but basal cell hyperplasia (BCH) remains untargeted. The incidence of has been reported at 8‐10%, but a molecular and cellular characterization has not been performed on this phenotype. Methods: Using freshly digested tissue from surgical specimens, we performed RNA‐seq analysis of flow cytometry‐purified basal epithelia from 3 patients with and 4 patients without a majority BCH phenotype. qPCR was performed on 28 genes identified as significant from 13 non‐BCH and 7 BCH specimens to confirm transcriptomic analysis. IHC was performed on several non‐BCH and BCH specimens for 3 proteins identified as significant by transcriptomic analysis. Results: A total of 141 human BPH specimens were analyzed for the presence of BCH. Clinical characteristics of non‐BCH and BCH cohorts revealed no significant differences in age, PSA, prostate volume, medical treatment, or comorbidities. Quantitation of cellular subsets by flow cytometry in 11 BCH patients vs. 11 non‐BCH patients demonstrated a significant increase in the ratio of basal to luminal epithelia in patients with BCH (P <0.05), but no significant differences in the total number of leukocytes. RNA‐seq data from flow cytometry isolated basal epithelia from patients with and without BCH were subjected to gene set enrichment analysis of differentially expressed genes, which revealed increased expression of members of the epidermal differentiation complex. Transcriptomic data were complemented by immunohistochemistry for members of the epidermal differentiation complex, revealing a morphological similarity to other stratified squamous epithelial layers. Conclusions: Increased expression of epidermal differentiation complex members and altered epithelial stratification resembles the progression of other metaplastic diseases. These data provide insight into the plasticity of the human prostate epithelium and suggest a classification of basal cell hyperplasia as a metaplasia.
June 2017


Differentiation - Isolation and analysis of discrete human prostate cellular populations

Strand D W, Aaron L, Henry G, Franco O E, Hayward SW
The use of lineage tracing in transgenic mouse models has revealed an abundance of subcellular phenotypes responsible for maintaining prostate homeostasis. The ability to use fresh human tissues to examine the hypotheses generated by these mouse experiments has been greatly enhanced by technical advances in tissue processing, flow cytometry and cell culture. We describe in detail the optimization of protocols for each of these areas to facilitate research on solving human prostate diseases through the analysis of human tissue.
April 2016


JoVE - Endothelial cell tube formation assay for the in vitro study of angiogenesis

DeCicco-Skinner KL, Henry GH, Cataisson C, Tabib T, Gwilliam JC, Watson NJ, Bullwinkle EM, Falkenburg L, O’Neill RC, Morin A, Wiest JS
The tube formation assay is a fast, quantifiable method for measuring in vitro angiogenesis. Endothelial cells are combined with conditioned media and plated on basement membrane extract. Tube formation occurs within hours and newly formed tubules easily quantified.
September 2014


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Cold Spring Harbor: Single Cell Analysis - November 2019

A Cellular Atlas of Human Prostate Disease

Henry GH, Malewska A, Malladi VS, Lee J, Gahan JC, Reese J, Strand DW
POSTER


American Urological Association: Annual Meeting - May 2019

Cellular pathogenesis of human BPH

Henry G, Malewska A, Binoy Joseph D, Roehrborn C, Hutchinson R, Vezina C, Strand D
POSTER


Collaborating for the Advancement of Interdisciplinary Research in Benign Urology: Meeting - December 2018

Building a comprehensive cellular anatomy of the normal and diseased human prostateia

Henry GH, Malewska A, Joseph DB, Malladi VS, Lee J, Torrealba J, Mauck RJ, Gahan JC, Raj JV, Roehrborn CG, Hon GC, MacConmara MP, Reese JC, Hutchinson RC, Vezina CM, Strand DW
POSTER


Society for Basic Urologic Research: Annual Meeting - November 2018

A Cellular Anatomy of the Normal Human Prostate and BPH

Henry G, Malewska A, Binoy Joseph D, Malladi V, Lee J, Gahan J, Mauck R, Raj G, Roehrborn C, Hon G, Reese J, Hutchinson R, Vezina C, Strand D
POSTER


10x Genomics User Group Meeting: Houston - May 2018

Determining Cellular Heterogeneity in Human Prostate using the Chromium™ Single Cell 3’ Solution

Henry GH
ORAL PRESENTATION


FlowTex Conference - February 2018

Determining cellular heterogeneity in human prostate with flow cytometry and single-cell RNA-sequencing

Henry GH
ORAL PRESENTATION


North Texas Flow Cytometry Conference - December 2017

Determining cellular heterogeneity in human prostate with flow cytometry and single-cell RNA-sequencing

Henry GH
ORAL PRESENTATION


Society for Basic Urologic Research: Annual Meeting - November 2017

Pathogenesis of Inflammation in Human BPH

Henry G, Malewska A, Hutchinson R, Gahan J, Mauck R, Torrealba J, Francis F, Roehrborn C, Strand D
POSTER


North Texas Flow Cytometry Conference - December 2016

Deconstructing BPH Phenotypes: Molecular Pathogenesis of Basal Hyperplasia

Henry GH
ORAL PRESENTATION


Society for Basic Urologic Research: Annual Meeting - November 2016

Deconstructing BPH phenotypes

Henry G, Malewska A, Mauck R, Torrealba J, Roehrborn C, Strand D
POSTER


Society for Basic Urologic Research: Annual Meeting - November 2015

Cell-specific responses to inflammation in BPH

Henry G, Malewska A, Mauck R, Roerborn C, Strand D
POSTER


American Association of Cancer Research: Annual Meeting - April 2014

Adipocytes, Obesity and the Multiple Myeloma Microenvironment

Henry GH, Watson NJ, O’Neill R, Tabib T, Bullwinkle EM, DeCicco-Skinner KL
POSTER


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Education

American University

Masters of Science
Biology

Graduated 2014

Eckerd College

Bachelors of Science
Biomedical Molecular Biology

Graduated 2009