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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
Posts
publications
Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework
Published in Computational and Structural Biotechnology Journal, 2022
We present ChIPanalyser, a user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of TFs.
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis
Published in Molecular Systems Biology, 2022
Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon.
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data
Published in Molecular Systems Biology, 2022
CellNeighborEX identifies diverse gene sets associated with partnering cell types
ChatGPT and large language models in academia: opportunities and challenges
Published in BioData Mining, 2023
In this editorial, we discuss this technology from the academic’s perspective with regard to its limitations and utility for academic writing, education, and programming
Recommended citation: 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
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Multi-scale and multi-context interpretable mapping of cell states across heterogenous spatial samples.
Published in biorxiv, 2024
There is a growing demand for methods that can effectively align and compare spatial data in the absence of obvious visual correspondence. To address this challenge, we developed an interpretable cell mapping strategy by considering spatial context at various scales.
Recommended citation: 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
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Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference
Published in Advanced Science, 2024
By combining LLMs ability to distillate biological knowledge from text and deep learning methodologies capturing complex patterns in gene expression data, GRNPT overcomes the limitations of traditional GRN inference methods and enables more accurate and comprehensive understanding of gene regulatory dynamics.
Recommended citation: 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
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Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells
Published in Nature Biotechnology, 2024
Here we demonstrate that the expression of Flower Lose and reduced microenvironment fitness is not a pre-existing condition but, rather, a cancer-induced phenomenon
Recommended citation: 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
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software
lighteR
Published:
Analysis of plant photosynthetic efficiency data.
ChIPanalyser
Published:
ChIPanalyser: Predicting Transcription Factor Binding Sites
Kuresi
Published:
Cancer Competition R package and python module.
Vesalius
Published:
Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data
Bombadillo
Published:
Bombadillo
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
writing
What if we contributed to Wikipedia instead of publishing papers?
Published:
Open source publication
The Institute - Chapter I : Reorganize the social network.
Published:
From top down hierarchies to distrubuted social systems.
The Institute - Chapter II : Tipping Points
Published:
A discussion on complex systems and critial tipping points
The Institute - Chapter III : Just 15 minutes away
Published:
A discussion on the concept of chrono-urbanism and 15 minute cities
The Institute - Chapter IV : Rock Vocals
Published:
The link between geology and singing.