Author

Matias Alejandro Paz

Boston University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 1 Microbiology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 3 Research Focus:differential expression· 2 Organism:human· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Assay:ChIP-seq· 1 Approach:deep learning· 1 Assay:DNA methylation· 1

Frequent Co-Authors

Juan I. Fuxman BassiD· 3 shared Luis F. Soto-Ugaldi· 3 shared Benedetta D’Elia· 2 shared Elvis Morara· 2 shared George D. Muñoz-EsquiveliD· 2 shared Harshpreet ChandokiD· 2 shared Jacob Purinton· 2 shared Joseph Alexander Finkelberg· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersSystems Biology

Juan I. Fuxman BassORCID

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Author profile →

3 papers

Recent·Most cited

Multilayered specificity of transcription factor binding at cytokine promoters

Anna Berenson, Ryan Lane, Yunwei Lu, Sakshi Shah, Zhaorong Li, Luis F. Soto-Ugaldi, Mahir Patel, Cosmin Ciausu, Matias Alejandro Paz, Juan I. Fuxman Bass

The paper identifies TF-DNA binding interactions at cytokine promoters, showing that TF cooperativity and antagonism significantly influence DNA-binding specificity.

bioRxiv · Jul 8, 2026 · PreprintSystems Biology

Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

Berkay ENGİN, Mohamed Yousry ElSadec, Joseph Alexander Finkelberg, Tommy Henry Taslim, Daniel L. Bryant, Luis F. Soto-Ugaldi, Susan Kales, Ching‐Huang Ho, Maryam Dashtiahangar, George D. Muñoz-Esquivel, Elvis Morara, Jacob Purinton, Benedetta D’Elia, Rodrigo I. Castro, Harshpreet Chandok, , Juan I. Fuxman Bass

The paper creates a regulatory atlas of HIV-1 and HIV-2 by analyzing transcriptional variation across clades, isolates, and individuals using MPRAs and predictive models.

bioRxiv · Apr 6, 2026 · PreprintMicrobiology

Global cis-regulatory landscape of double-stranded DNA viruses

Tommy Henry Taslim, Joseph Alexander Finkelberg, Susan Kales, Luis F. Soto-Ugaldi, Benedetta D’Elia, Berkay Engin, George D. Muñoz-Esquivel, Elvis Morara, Jacob Purinton, Harshpreet Chandok, Jaice T. Rottenberg, Rodrigo I. Castro, Lucía Martínez Cuesta, Matias Alejandro Paz, Ryan Tewhey, Juan I. Fuxman Bass

The paper identifies ~2,000 cis-regulatory elements (CREs) across 27 dsDNA viruses using reporter assays and machine learning, revealing their regulatory features and associated transcription factors.

bioRxiv · Jul 20, 2025 · PreprintGenomics