Author

Nilesh Kumar

University of Alabama at BirminghamORCID 0000-0001-6095-7902Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Neuroscience· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Research Focus:batch correction / integration· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1 Research Focus:dimensionality reduction· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1

Frequent Co-Authors

M. Shahid MukhtariD· 2 shared Adeel MehmoodiD· 1 shared Adriana V. F. MassicanoiD· 1 shared Alan UmfressiD· 1 shared Amarnath NatarajaniD· 1 shared Anna G. SoraceiD· 1 shared Austyn TrulliD· 1 shared Ayanabha ChakrabortiiD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersNeuroscience

M. Shahid MukhtarORCID

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Author profile →

3 papers

Recent·Most cited

nf_xpatial: A Reproducible Framework for Standardized Preprocessing and Clustering of Xenium Data

Luke Potter, Austyn Trull, Nilesh Kumar, Olivia R. Drake, Margareth Nogueira, Jamie Peters, Jasper A. Heinsbroek, Jeremy J. Day, Elizabeth A. Worthey, Lara Ianov

nf_xpatial provides a standardized Nextflow pipeline for preprocessing and clustering Xenium spatial transcriptomics data, enabling reproducible analysis and parameter comparison.

bioRxiv · Aug 29, 2026 · PreprintBioinformatics

Characterization and Preclinical Treatment of Rotational Force-Induced Brain Injury

Alan Umfress, Ayanabha Chakraborti, Suma Priya Sudarsana Devi, Raegan Adams, Daniel Epstein, Adriana V. F. Massicano, Anna G. Sorace, Sarbjit Singh, M. Iqbal Hossian, Shaida A. Andrabi, David K. Crossman, Nilesh Kumar, M. Shahid Mukhtar, Claire M. Simpson, Kathryn Abell, , James A. Bibb

This study develops a rodent model of rotational head trauma, identifies Cdk5 as a key mediator, and shows its inhibition reduces cognitive and pathological effects.

bioRxiv · Jul 20, 2022 · PreprintNeuroscience

Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis

Nilesh Kumar, Bharat Mishra, Adeel Mehmood, Mohammad Athar, M. Shahid Mukhtar

The paper constructs a human-SARS-CoV-2 interactome using network biology and multiomics data to identify key targets and regulatory circuits involved in SARS-CoV-2 pathogenesis.

iScience · Jan 1, 2020Peer-reviewedSystems Biology