Hector Roux de Bézieux

Ph.D Student in Biostatistics

University of California, Berkeley

Biography

I am a PhD student working on statistical transcriptomics methods in Sandrine Dudoit’s lab. I am collaborating with the He Lab, and with a Berkeley team lead by John Ngai as part of the NIH Brain Inititative, to apply those statistical and computing methods to current biological questions. I am also working on several projects with the microbiome company Pendulum, including a collobaration with Laurent Jacob, developing metagenomics-related methodologies.

Interests

• Transcriptomics
• Metagenomics
• Microbiome-Host interactions
• Triathlon

Education

• Ph.D in Biostatistics, 2021 (expected)

  University of California, Berkeley

• M.S in Biology & Bioengineering, 2017

  UC Berkeley, USA and École polytechnique, France

• B.S in Mathematics & Physics, 2015

  École polytechnique, France

News

• March, 10^th 2021: The condiments workflow has been released in preprint format and as an R package available on Github.
• March, 5^th 2021: My work on remote clinical trials, in collobaration with Pendulum Therapeutics has been published at JMIR Formative research. Check out the full paper or the press release.
• December, 17^th 2020: Conducted a 90mn workshop at European Bioconductor on Trajectory Inference across conditions.
• November, 23^th 2020: Presented a poster on significant subgraph exploration at the Machine Learning in Computational Biology conference.
• July, 31^th 2020: Work by John Ngai on Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia, on which I collaborated, has been published in Science Advances.
• July, 30^th 2020: Conducted a 1h workshop at the Bioconductor Meeting on Trajectory Inference across multiple conditions.
• March, 30^th 2020: Dune, my work on Improving replicability in single-cell RNA-Seq cell type discovery, has been released!!
• March, 5^th 2020: The BICCN integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types, on which I collaborated, has been published in preprint.
• March, 5^th 2020: The tradeSeq paper has been published in Nature Communications.

Projects

.js-id-Research

All Research Classes Tutorials

condiments

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

Cite Preprint Package repo Paper repo Video Workshop

Caldera

Bacterial and metagenome GWAS

PDF Cite Poster

Courses taken at UC Berkeley

List of classes and description of classes taken during the Ph.D years.

CS289 Final Project

Final class project for CS289, in the Spring 2018 - Modelization of single-cell gene expression along a timeline.

Code Report Class website

Dune

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Cite Talk Preprint Package repo Paper repo

ESCAPE

Easy Single-Cell RNA-sequencing Analyis through a Political Example - A short tutorial to help beginners in biostatistics and genomics understand an usual single-cell RNA-sequencing workflow.

Code Tutorial

STAT 215A - Labs

Stat 215 with Bin Yu, lab reports

Class Github repo

tradeSeq

Trajectory-based differential expression analysis for single-cell sequencing data

Cite Paper Short talk Long talk Preprint Package repo Paper repo

Welcome to the RNA-Seq world

Currated list of resources that could be useful to beginners (or not) when learning how dive into RNA-Seq Analysis

Main Publications

Quickly discover relevant content by filtering publications.

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

In single-cell RNA-sequencing (scRNA-seq), gene expression is assessed individually for each cell, allowing the investigation of …

Hector Roux de Bézieux, Koen Van den Berge, Kelly Street, Sandrine Dudoit

Cite Project DOI Preprint Package repo Paper repo Video

Medical Food Assessment Using a Smartphone App With Continuous Glucose Monitoring Sensors: Proof-of-Concept Study

Background: Novel wearable biosensors, ubiquitous smartphone ownership, and telemedicine are converging to enable new paradigms of clinical research. A new generation of continuous glucose monitoring (CGM) devices provides access to clinical-grade measurement of interstitial glucose levels.

Hector Roux de Bézieux, James Bullard, Orville Kolterman, Michael Souza, Fanny Perraudeau

PDF Cite DOI Paper repo

Finding All Significant Closed Connected Subgraphs

In many applications, covariates describing the data are structured according to a known graph $\mathcal{G}$. Subgraphs of …

Hector Roux de Bézieux, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit, Laurent Jacob

PDF Cite Project Poster

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Single-cell transcriptome sequencing (scRNA-Seq) has allowed many new types of investigations at unprecedented and unique levels of …

Hector Roux de Bézieux, Kelly Street, Stephan Fischer, Koen Van den Berge, Rebecca Chance, Davide Risso, Jesse Gillis, John Ngai, Elizabeth Purdom, Sandrine Dudoit

Cite Project DOI Preprint Package repo Paper repo

Trajectory-based differential expression analysis for single-cell sequencing data

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression. …

Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens, Robrecht Cannoodt, Yvan Saeys, Sandrine Dudoit, Lieven Clement

Cite Project DOI Preprint Package repo Paper repo

Collaborations

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Koen Van den Berge, Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street, Davide Risso, John Ngai, Sandrine Dudoit (2021). Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects. bioRxiv.

Cite DOI

Ricky S Adkins, Andrew I Aldridge, Shona Allen, Seth A Ament, Xu An, Ethan Armand, Giorgio A Ascoli, Trygve E Bakken, Anita Bandrowski, Hector Roux de Bézieux, others (2020). A multimodal cell census and atlas of the mammalian primary motor cortex. bioRxiv.

Cite DOI

Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S Adkins, Andrew I Aldrige, Seth A Ament, Ann Bartlett, M Margarita Behrens, Hector Roux de Bézieux, others (2020). An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types. bioRxiv.

Cite DOI

David H Brann, Tatsuya Tsukahara, Caleb Weinreb, Marcela Lipovsek, Koen Van den Berge, Boying Gong, Rebecca Chance, Iain C Macaulay, Hsin-Jung Chou, Hector Roux de Bézieux, others (2020). Non-neuronal expression of SARS-CoV-2 entry genes in the olfaory system suggests mechanisms underlying COVID-19-associated anosmia. Science Advances.

Cite DOI

Gauthier Croizat, Alexandre Kehren, Hector Roux de Bézieux, Abdul Barakat (2018). Influence of pulsatile blood flow on allometry of aortic wall shear stress. arXiv.

Cite DOI

Recent & Upcoming Talks

Trajectory Inference across conditions - differential expression and differential progression

In single-cell RNA-sequencing (scRNA-seq), gene expression is assessed at the level of single cells. In dynamic biological systems, it may not be appropriate to assign cells to discrete groups, but rather a continuum of cell states may be observed, e.

Dec 17, 2020 3:00 PM Europe

Kelly Street, Koen Van den Berge, Hector Roux de Bézieux

Project Workshop Video Image Code

Trajectory inference across multiple conditions: differential expression and differential progression

In single-cell RNA-sequencing (scRNA-seq), gene expression is assessed at the level of single cells. In dynamic biological systems, it may not be appropriate to assign cells to discrete groups, but rather a continuum of cell states may be observed, e.

Jul 30, 2020 3:00 PM USA

Kelly Street, Koen Van den Berge, Hector Roux de Bézieux

Project Workshop Video Code

Bacterial and metagenome GWAS.

Feb 18, 2020 9:00 AM Lawrence Berkeley National Lab, California, USA

Hector Roux de Bézieux

Project Slides

Trajectory inference, Differential Expression and clustering along developmental trajectories in single cell RNA-Sequencing.

Trajectory inference is often used with single-cell RNA-seq data to study dynamic changes in gene expression levels during, e.g., cell cycle, differentiation, or cellular activation. Downstream of trajectory inference, researchers are often interested in discovering genes that are associated with a particular lineage in the trajectory.

Apr 18, 2019 3:00 PM Berkeley, California, USA

Hector Roux de Bézieux

Project Slides

Unlocking the power of continuity in single cell RNA-Seq - Differential gene Expression along developmental trajectories.

Trajectory inference is often used with single-cell RNA-seq data to study dynamic changes in gene expression levels during, e.g., cell cycle, differentiation, or cellular activation. Downstream of trajectory inference, researchers are often interested in discovering genes that are associated with a particular lineage in the trajectory.

Apr 14, 2019 3:00 PM Monterey, California, USA

Hector Roux de Bézieux

Project Slides

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Experience

 

 

 

 

 

Computational Biologist

Pendulum Therapeutics

2018, June – Present California

Responsibilities include:

• Analysis of clinical trial data.
• Helped in designing a future clinical trial.
• Evaluated assembly pipelines for complex metagenomics assembly projects.

 

 

 

 

 

Intern, Strategic Partnership Department

PSA Peugeot Citroën

2015, June – 2015, August Shanghaï

• Independently analyzed financial and auditing reports to give a strategic overview of PSA’s Chinese partners.
• Participated in meetings and interview to conceive the business model for a joint PSA R&D center in China.

 

 

 

 

 

2$^{nd}$ Lieutenant

French Army, Elite Mountain Troop

2013, September – 2014, April France

• Took courses on leadership in the French ground forces.
• Led a group of 8 professional soldiers during a NATO exercise in great Northern Norway.
• Led a group of 30 newly enrolled soldiers through initial military trial.