Author

Daniel Neri-Rosario

National Institute of Genomic MedicineORCID 0000-0002-3899-5133Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:diffusion model· 2 Research Focus:imputation· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:dimensionality reduction· 1 Assay:metagenomics· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Aarón Vázquez-JiméneziD· 2 shared Cristian Padrón-ManriqueiD· 2 shared David Giron-VillalobosiD· 2 shared Diego Armando Esquivel-HernandeziD· 2 shared Osbaldo Reséndis-AntonioiD· 2 shared Yoscelina Estrella Martínez-LópeziD· 2 shared Jean Paul Sánchez-Castañeda· 1 shared Sánchez-Castañeda Jean PauliD· 1 shared

Activity by Year

2022-2023 · peak 1/yr

Co-Author Collaboration Network

8 top collaborators · 27 mutual co-author links

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2 shared papersBioinformatics

Aarón Vázquez-JiménezORCID

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2 papers

Recent·Most cited

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data

Cristian Padrón-Manrique, Aarón Vázquez-Jiménez, Diego Armando Esquivel-Hernandez, Yoscelina Estrella Martínez-López, Daniel Neri-Rosario, Jean Paul Sánchez-Castañeda, David Giron-Villalobos, Osbaldo Reséndis-Antonio

mb-PHENIX denoises microbiota data by combining diffusion and supervised UMAP, improving differential abundance analysis in sparse and noisy count matrices.

Bioinformatics · Nov 28, 2023Peer-reviewedBioinformatics

Diffusion on PCA-UMAP manifold captures a well-balance of local, global, and continuum structures to denoise single-cell RNA sequencing data

Cristian Padrón-Manrique, Aarón Vázquez-Jiménez, Diego Armando Esquivel-Hernandez, Yoscelina Estrella Martínez-López, Daniel Neri-Rosario, Sánchez-Castañeda Jean Paul, David Giron-Villalobos, Osbaldo Reséndis-Antonio

The paper introduces sc-PHENIX, an imputation method for scRNA-seq data that addresses over-smoothing issues in diffusion-based approaches by using PCA-UMAP initialization.

bioRxiv · Jun 9, 2022 · PreprintBioinformatics