Author

Hamid Mattoo

Ragon Institute of MGH, MIT and HarvardORCID 0000-0002-5415-9661Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 3 Organism:human· 3 Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Approach:deep learning· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Alexander KaganiD· 1 shared Alisa A. OmelchenkoiD· 1 shared Alyson WangiD· 1 shared Amanda C. PoholekiD· 1 shared Chinmay V. Gadiraju· 1 shared Dafne Díaz-RiveraiD· 1 shared Emanuele de RinaldisiD· 1 shared Euxhen HasanajiD· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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1 shared paperBioinformatics

Alexander KaganORCID

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3 papers

Recent·Most cited

BioinformaticsBioinformaticsPeer-reviewedAug 27, 2026

Finetuning Foundation Models for Temporal Clinical Transcriptomics Data

Sachin Mathur, Alexander Kagan, Peyman Passban…·Ziv Bar‐Joseph

The paper finetunes gene embeddings from foundation models for temporal clinical transcriptomics data, improving gene network analysis and detection of disease progression and drug response mechanisms.

DOI 10.1093/bioinformatics/btag640

humanbulk RNA-seq

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ImmunologyNature CommunicationsPeer-reviewedJul 22, 2026

A unified network systems approach uncovers a core novel program underlying T follicular helper cell differentiation

Alisa A. Omelchenko, Syed Ashiqur Rahman, Alyson Wang…·Jishnu Das

This study identifies a core gene program underlying Tfh cell differentiation using a multi-scale network systems approach, revealing a novel role for IL-12 in regulating Tfh precursor differentiation.

DOI 10.1038/s41467-026-75559-8

humanmouse

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BioinformaticsbioRxivPreprintSep 11, 2023

Comparative Analysis of Association Networks Using Single-Cell RNA Sequencing Data Reveals Perturbation-Relevant Gene Signatures

Nima Nouri, Giorgio Gaglia, Hamid Mattoo…·Virginia Savova

The paper introduces GENIX, a platform for identifying perturbation-relevant genes using gene association networks, applied to influenza vaccine responses in COVID-19 recovered patients.

1 citation

humanscRNA-seq

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