CV

Education

Ph.D in Biology - Bioinformatics - Biophysics
University of Essex
Colchester, UK
Oct 2016 - Jun 2020

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

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

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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

Project Data Manager

Cedars-Sinai Medical Center
Los Angeles, USA
July 2024 - Present

• Project Data Manager - CIRM DISC0

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Research Data Scientist

Cedars-Sinai Medical Center
Los Angeles, USA
Sep 2022 - Present

• Lead Developer - Mapping Spatial omics across samples and Multi-Modal spatial omics
• Analyst for a wide variety of biomedical spatial omics data sets - Visium/STOmics/VisiumHD/Curio-seeker/Xenium
• Review and Perspective papers
• Lead Researcher to understand multi-scale gene expression programs using super-pixels
• Lead Bioinformatician for Cancer competitivity projects

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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
• Analyst on various single-cell projects

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Senior Research Officer

University of Essex
Colchester, UK
Sep 2019 - Dec 2019

• Developer of lighteR - an R package dedicated to the analysis and modelling of Photosynthetic efficiency data - Lawson Lab

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Research Assistant

University of Essex
Colchester, UK
Jul 2016 - Oct 2016

• R package development (ChIPanalyser) - Zabet Lab

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Publications

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

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

Multi-scale and multi-context interpretable mapping of cell states across heterogenous spatial samples Patrick C.N. Martin, Wenqi Wang, Hyobin Kim, Henrietta Holze, Kyoung Jae Won bioRxiv 2024.08.31.610638; doi: https://doi.org/10.1101/2024.08.31.61063

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Spatial Transcriptomic Workshop

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

• Workshop on workflows and considerations for Spatial Transcriptomic analysis

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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

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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

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Master’s Student Supervision

University of Essex
Colchester, UK
February 2018 - April 2019

• Supervision of project students working with ChIPanalyser

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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

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

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

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

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Reviews

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

• Reviewed papers for PeerJ

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

• Reviewed papers for BMC Genomics academic journal

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

• Reviewed bioinformatics grant proposal

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Conference Organization

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

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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

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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

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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

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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

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

• Writing a fantasy and science fiction book series

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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

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