CV

Education

Ph.D in Biology - Bioinformatics - Biophysics

Title: Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. University of Essex
Colchester, UK
Oct 2016 - Jun 2020

MSc in Molecular Biology, Genetics and Plant Science
Uppsala University
Uppsala, Sweden
Sep 2013 - Oct 2015

BSc in Biochemistry, Cellular and Molecular Biology
University of Liege
Liege, Belgium
Oct 2008 - Oct 2013

Leadership Course - HFP Consulting BRIC - University of Copenhagen
Copenhagen, DK
March 2022

• 3-day workshop on leadership and supervision in scientific research led by HFP Consulting

Work experience

Bioinformatics Data Engineer & Research Infrastructure Specialist

Karolinska Institute & SciLifeLab Stockholm, Sweden April 2026 - Present

Project Data Manager

Cedars-Sinai Medical Center
Los Angeles, USA
July 2024 - March 2026

• Project Data Manager - CIRM DISC0 – Responsible for FAIR data sharing compliance.
• Bioinformatician – Responsible for building reproducible analysis pipelines (Nextflow, Docker/Apptainer, uv)

Research Data Scientist

Cedars-Sinai Medical Center
Los Angeles, USA
Sep 2022 - March 2026

• Lead Developer - Mapping Spatial omics across samples and Multi-Modal spatial omics. Improved the accuracy of spatial context mapping by 20% compared to state-of-the art methods. Publication in Nature Communications (IF: 16.6)
• Analysis Pipeline development for Visium/STOmics/VisiumHD/Curio-seeker/Xenium
• Lead Researcher (Supervision, Research Lead, Pipeline developer) to understand multi-scale genes expression programs using super-pixels.
• Lead Bioinformatician (Bioinformatics Research Lead, Lead Developer and Analyst) for Cancer competitivity projects.

Post Doctoral Researcher

BRIC - University of Copenhagen
Copenhagen, DK
Feb 2020 - Jul 2022

• Lead Researcher - Analysis of Spatial transcriptomics through image processing and computer vision. Improved detection of territories in spatial data compared to state-of-the-art methods across various spatial contexts. Publication in Molecular Systems Biology (IF: 8.5)
• Analyst on various single cell projects
• Graduate student supervision

Senior Research Officer

University of Essex
Colchester, UK
Sep 2019 - Dec 2019

• Developer of the lighteR R package dedicated to the analysis and modelling of Photosynthetic efficiency data. Available on GitHub.
• Analysis of hundreds of plant photosynthetic data samples and modelled plant response behavior.

Research Assistant

University of Essex
Colchester, UK
Jul 2016 - Oct 2016

• R package development (ChIPanalyser) – Published in Bioconductor.
• NGS data analysis

Skills

Computational Skills

• High proficiency with R. Developer and maintainer of the Vesalius R package (GitHub-Molecular Systems Biology and Nature Communications publication), the ChIPanalyser package (Computational and Structural Biotechnology Journal - Bioconductor – over 3500 downloads in 2025), the lightR (GitHub), and the Kuresi package (GitHub)

• Proficient with python and Julia (Bombadillo – GitHub)

• Experience with containerization and reproducible environments (Docker, Apptainer, Nix, uv, conda)

• Experience with bash, shell-scripting, UNIX and HPC environments

• Experience with version control (git, CI/CD GitHub actions)

• Experience with parallel and distributed computing (Future, Dask, DaskML)

• Experience with out-of-core chunked formats (h5, zarr)

• Experience with LaTex, markdown, and automated report building (pandoc)

• Basic experience with C++ (Vesalius backend) and Rust

Bioinformatics and Data science Skills

• Extensive experience with bulk NGS analysis (ChIP-seq, HiC, RNA-seq, ATAC-seq, DNAse-seq)

• Extensive experience with single cell and spatial analysis (10X chromium, 10X Visium, 10X VisiumHD, 10X Xenium, Slide-seq, Stereo-seq, Vizgen MERFISH, ICM Proteomics, Spatial-CITE-seq, Spatial-ATAC-seq, Seurat, Scanpy, Vesalius)

• Experience with pipeline orchestration (Nextflow, grid engines)

• Experience with Genetic Algorithms, Biophysical Modelling, Computer Vision, Clustering, Dimensionality Reduction, ML/DL/AI Frameworks (PyTorch, TensorFlow, scikit-learn), Regression, Statistical Analysis, Synthetic data, Data integration

Soft Skills

• Extensive teaching and supervision of undergraduate and post-graduate students at the University of Essex, University of Copenhagen, and Cedars-Sinai Medical Center. Certification in scientific leadership (HFP Consulting BRIC - University of Copenhagen)

• Extensive experience and proficiency in scientific communication and out-reach through scientific conferences (15 invited-talks and poster including at the ISMB conference), podcast invited guest (The Genomics Lab), and scientific writing (https://pcnmartin.substack.com/).

• Experience in leading and developing interdisciplinary scientific research from conceptualization to final publication.

• Strong ability to bridge wet-lab and dry-lab research with research experience in both areas.

• Languages: English and French

Publications

A Generalizable Transformer Framework for Gene Regulatory Network Inference from Single-Cell Transcriptomes

GuangzhengWeng, HyobinKim, PatrickMartin, JunilKim, Tae-HyungKim, Gi-HoonNam, DonghaKim, Kyoung JaeWon. Adv. Intell. Syst.. 2025; 000, e202500781. https://doi.org/10.1002/aisy.202500781

Multi-scale and multi-context interpretable mapping of cell states across heterogenous spatial samples.

Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells

Madan, E., Palma, A.M., Vudatha, V. et al. Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02453-3

Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference

G. Weng, P. Martin, H. Kim, K. J. Won, Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference. Adv. Sci. 2024, 2409990. https://doi.org/10.1002/advs.202409990

Data enhancement in the age of spatial biology

Identification of mammalian transcription factors that bind to inaccessible chromatin

ChatGPT and large language models in academia: opportunities and challenges

Meyer, J.G., Urbanowicz, R.J., Martin, P.C.N. et al. ChatGPT and large language models in academia: opportunities and challenges. BioData Mining 16, 20 (2023). https://doi.org/10.1186/s13040-023-00339-9

CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data

Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis

Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework

Talks

Presentations

Invited Speaker: Mapping spatial omics when tissue architecture doesn’t match
Event: ISMB24
Location: Montreal, Canada
Date: July 2024

• Highlighted Advances in the development of Vesalius, including multi-modal embedding and cell mapping

Invited Speaker: Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis
Event: Single Cell Network Copenhagen
Location: Copenhagen, Denmark
Date: December 2021

• Showcased the Vesalius package - a novel tool to decipher tissue anatomy from Spatial transcriptomics using image analysis

Invited Speaker: Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis
Event: HeaDS Copenhagen
Location: Copenhagen, Denmark
Date: November 2021

• Showcased the Vesalius package - a novel tool to decipher tissue anatomy from Spatial transcriptomics using image analysis

Presenter: Vesalius: Image-free extraction and analysis of tissue anatomy by using image processing applied to sequencing-based Spatial Transcriptomics
Event: ISMBECCB21
Location: Online
Date: July 2021

• Showcased the Vesalius package - a novel tool to decipher tissue anatomy from Spatial transcriptomics using image analysis

Presenter: Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework
Event: Chromatin Workshop
Location: Colchester, UK
Date: July 2019

• Presented the latest results obtained using ChIPanalyser in understanding transcription factor binding mechanisms

Presenter: Estimating Transcription Factor binding in *Drosophila with ChIPanalyser*
Event: Quantitative Methods in Gene Regulation
Location: Cambridge, UK
Date: December 2017

• Introduced analysis carried out using ChIPanalyser

Presenter: It from bit, bit from it
Event: DIANA Science Conference
Location: Uppsala, Sweden
Date: October 2013

• Introduced the issue of information VS reality in science

Posters

Poster: Exploring tissue structure across spatial omic modalities with Vesalius
Event: Single Cell Symposium
Location: San Diego, USA
Date: August 2023

• Highlighted Advances in the development of Vesalius, including multi-modal embedding and cell mapping

Poster: Exploring tissue structure across spatial omic modalities with Vesalius
Event: ISMB23
Location: Lyon, France
Date: July 2023

• Highlighted Advances in the development of Vesalius, including multi-modal embedding

Poster: Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis
Event: Welcome Trust Single Cell Biology Conference
Location: Cambridge, UK
Date: June 2022

• Showcased the Vesalius package - a novel tool to decipher tissue anatomy from Spatial transcriptomics using image analysis

Poster: Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis
Event: Swedish Bioinformatics Workshop
Location: Lund, Sweden
Date: October 2021

• Showcased the Vesalius package - a novel tool to decipher tissue anatomy from Spatial transcriptomics using image analysis

Poster: Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis
Event: OzSingleCell
Location: Online
Date: October 2021

• Showcased the Vesalius package - a novel tool to decipher tissue anatomy from Spatial transcriptomics using image analysis

Poster: ChIPanalyser: a versatile R/Bioconductor package to model and predict binding of transcription factors to DNA
Event: ISCB/RECOMB
Location: New York, USA
Date: December 2018

• Showcased advances in analysis done using ChIPanalyser

Poster: Estimating Transcription Factor binding in *Drosophila with ChIPanalyser*
Event: EMBO Nuclear Dynamics
Location: Isle-sur-la-Sorgue, France
Date: October 2017

• Introduced analysis carried out using ChIPanalyser

Poster: ChIPanalyser – Transcription Factor binding prediction in R
Event: GATE Symposium
Location: University of Essex, UK
Date: September 2017

• Introduced ChIPanalyser - an R package implementing a statistical thermodynamic framework for transcription factor binding

Outreach

Invited Guest
Event: The Genomics Lab podcast hosted by Dr. Olivia Grant
Date: December 2021

• Introduced Spatial Transcriptomics and the development of analysis methods

Invited Guest
Event: The Genomics Lab podcast hosted by Dr. Olivia Grant
Date: August 2021

• Introduced analysis of transcription factor binding to DNA using ChIPanalyser

Teaching

Teaching

Spatial Transcriptomic - Applied Computational Genomics - Graduate Course

Cedars-Sinai Medical Center
Los Angeles, USA
2024 - Current

• Spatial Transcriptomic Analysis with Vesalius

Spatial Transcriptomic Workshop

Cedars-Sinai Medical Center - Spatial Biology Symposium
Los Angeles, USA
May 2023

• Workshop on workflows and considerations for Spatial Transcriptomic analysis

Graduate Laboratory Assistant (GLA)

University of Essex
Colchester, UK
February 2017 - April 2020

• Computational Data Analysis: R for Life Sciences
• Genome Bioinformatics - GLA
• Genomics - GLA

Lecturer

University of Essex
Colchester, UK
February 2017 - April 2019

• Essex Big Data and Analytics Summer School - Lecturer

Student Supervision

Master’s Student Supervision

Cedars-Sinai Medical Center - Soongsil University
Los Angeles, USA - Seoul, Korea
July 2024 - Current

• Supervision of project students working on the development of Multi-scale spatial methods

Master’s Student Supervision

BRIC - University of Copenhagen
Copenhagen, DK
February 2021 - April 2022

• Supervision of project students working on the development of Vesalius

Master’s Student Supervision

University of Essex
Colchester, UK
February 2018 - April 2019

• Supervision of project students working with ChIPanalyser

Undergraduate Student Supervision

University of Essex
Colchester, UK
February 2017 - April 2020

• Supervision of project students working with ChIPanalyser

Honors & Awards

Grant: CIRM DISC0 Grant
Contribution: Data Manager Salary Contribution
Location: Los Angeles, USA
Date: 2024

Grant: Travel Grant
Event: Genetic Society - Junior Scientist Conference Travel Grants
Location: London, UK
Date: 2017

Grant: Travel Grant
Event: University of Essex School Travel Grants
Location: Colchester, UK
Date: 2017

Award: Award for Best Student Presentation
Event: DIANA Science Conference
Location: Uppsala, Sweden
Date: 2013

Reviews

Reviewer: PeerJ
Organization: PeerJ
Location: Los Angeles
Date: 2025- Current

• Reviewed papers for PeerJ

Reviewer: BMC Genomics
Organization: BMC Genomics - Springer Nature Publications
Location: Colchester
Date: 2017 - Current

• Reviewed papers for BMC Genomics academic journal

Grant Reviewer: Massey Innovation Award Application
Organization: Virginia Commonwealth University School of Medicine
Location: Richmond
Date: 2024

• Reviewed bioinformatics grant proposal

Conference Organization

Co-organizer: Spatial Biology Seminar Series
Organization: Cedars-Sinai Medical Center Location: Los Angeles
Date: Jan 2025

Organizer: The Graduate Forum
Organization: University of Essex
Location: Colchester
Date: Aug 2019 - Sep 2019

• Organized and coordinated the Graduate Forum, an annual postgraduate student conference

Assistant: GATE Symposium
Organization: University of Essex
Location: Colchester
Date: Sep 2019

• Assisted in the organization of the GATE Symposium at the University of Essex

Writing

Role Playing: Tabletop Role Playing Games and Storytelling
Organization: Role Playing Games and Storytelling
Date: 2016 - Present

• Tabletop role-playing games like Dungeons & Dragons are not only incredibly fun but also teach teamwork, people management, and storytelling

Writer: The Institute
Organization: Writing - Real Science in a fictional setting. Location: pcnmartin.substack.com
Date: 05/2024 - Present

• Explores recent advances in research that could lead to a Solar Punk future, alongside philosophical opinion pieces

Writer: Fantasy/Sci-Fi Book Series
Organization: Writing - Fiction
Date: 2020 - Present

• Writing a fantasy and science fiction book series and short stories (Published in Nature Futures)

Writer: Popular Science Books
Organization: Writing - Non-Fiction
Date: 2023 - Present

• Writing popular science books on the subject of Intelligence, Modeling, and the scientific method