Author

Joselyn Chávez

Icahn School of Medicine at Mount SinaiORCID 0000-0002-4974-4591Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3 Genomics· 1

Signature Assays, Organisms & Methods

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Assay:spatial transcriptomics· 3 Research Focus:benchmarking· 2 Research Focus:database / resource· 2 Research Focus:software / tool· 2 Approach:statistical model· 2 Assay:ChIP-seq· 1 Assay:DNA methylation· 1 Organism:E. coli· 1

Frequent Co-Authors

Guo‐Cheng YuaniD· 3 shared Sujung Crystal ShiniD· 2 shared Wen WangiD· 2 shared Adriana SistigiD· 1 shared Alejandro ReyesiD· 1 shared Carmina Barberena-JonasiD· 1 shared Edward C. RuiziD· 1 shared Heladia SalgadoiD· 1 shared

Activity by Year

2020-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersBioinformatics

Guo‐Cheng YuanORCID

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4 papers

Recent·Most cited

sCCIgen: A high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.

Xiaoyu Song, Joselyn Chávez, Weiping Ma, Weijia Fu, Sujung Crystal Shin, Pei Wang, Guo‐Cheng Yuan

sCCIgen generates synthetic spatial transcriptomics data with known cell-cell interaction features to evaluate analytical tools.

Genome biology · Oct 15, 2025Peer-reviewedBioinformatics

Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis

Wen Wang, Shiwei Zheng, Sujung Crystal Shin, Joselyn Chávez, Guo‐Cheng Yuan

ONTraC uses a graph neural network to analyze spatial transcriptomics data, improving trajectory reconstruction and revealing microenvironment-dependent changes in gene regulation and cell interactions during development.

Genome biology · May 8, 2025Peer-reviewedGenomics

Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

Jiaji George Chen, Joselyn Chávez, Matthew O’Brien, Junxiang Xu, Edward C. Ruiz, Wen Wang, Iqra Amin, Irzam Sarfraz, Pratishtha Guckhool, Adriana Sistig, Guo‐Cheng Yuan, Ruben Dries

Giotto Suite provides a modular, open-source framework for analyzing spatial multi-omics data across scales and technologies.

bioRxiv · Nov 26, 2023 · PreprintBioinformatics

Programmatic access to bacterial regulatory networks with regutools

Joselyn Chávez, Carmina Barberena-Jonas, Jesús Emiliano Sotelo-Fonseca, José Alquicira-Hernández, Heladia Salgado, Leonardo Collado‐Torres, Alejandro Reyes

The paper introduces regutools, an R package that enables programmatic access to RegulonDB data for analyzing bacterial regulatory networks within the Bioconductor ecosystem.

Bioinformatics · Jun 15, 2020Peer-reviewedBioinformatics