Author

Alan Perez-Rathke

University of Illinois ChicagoORCID 0000-0002-0792-2484Unclaimed 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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Research Focus:gene regulatory network inference· 4 Approach:statistical model· 4 Assay:Hi-C· 3 Organism:human· 3 Approach:deep learning· 1 Organism:Drosophila· 1 Research Focus:drug response / drug discovery· 1 Assay:protein structure· 1

Frequent Co-Authors

Jie LiangiD· 4 shared Boshen WangiD· 2 shared Qiu SuniD· 2 shared Zhifeng ShaoiD· 2 shared Daniel M. Czajkowsky· 1 shared Valentina BoevaiD· 1 shared Wei Tian· 1 shared Xue LeiiD· 1 shared

Activity by Year

2020-2023 · peak 2/yr

Co-Author Collaboration Network

9 top collaborators · 22 mutual co-author links

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4 shared papersBioinformatics

Jie LiangORCID

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4 papers

Recent·Most cited

SPRI: Structure-Based Pathogenicity Relationship Identifier for Predicting Effects of Single Missense Variants and Discovery of Higher-Order Cancer Susceptibility Clusters of Mutations

Boshen Wang, Xue Lei, Wei Tian, Alan Perez-Rathke, Yan Yuan Tseng, Jie Liang

SPRI predicts the pathogenicity of missense variants and identifies spatially organized mutational clusters linked to cancer and Mendelian diseases.

Briefings in Bioinformatics · Jun 8, 2023Peer-reviewedBioinformatics

Minimalistic 3D Chromatin Models: Sparse Interactions in Single Cells Drive the Chromatin Fold and Form Many-Body Units

Jie Liang, Alan Perez-Rathke

This paper introduces a minimalistic 3D chromatin polymer model that uses sparse interactions to generate single-cell chromatin conformations consistent with experimental data and reveals insights into chromatin structure and function.

Current Opinion in Structural Biology · Aug 13, 2021Peer-reviewedBioinformatics

High-Resolution Single-Cell 3D-Models of Chromatin Ensembles during Drosophila Embryogenesis

Qiu Sun, Alan Perez-Rathke, Daniel M. Czajkowsky, Zhifeng Shao, Jie Liang

The paper introduces a computational method to reconstruct high-resolution 3D chromatin conformations from population Hi-C data, revealing chromatin structure dynamics during Drosophila embryogenesis.

Biophysical Journal · Feb 1, 2020Peer-reviewedGenomics

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells

Alan Perez-Rathke, Qiu Sun, Boshen Wang, Valentina Boeva, Zhifeng Shao, Jie Liang

CHROMATIX reconstructs many-body chromatin interactions from Hi-C data and identifies functional features in transcriptionally active loci.

Genome biology · Jan 16, 2020Peer-reviewedBioinformatics