Amnah Siddiqa, PhD
Associate Research Scientist · Cincinnati Children's Hospital Medical Center
I'm a computational biologist with more than seven years of post-PhD experience analyzing multi-omics data from human studies, much of it in immunology. My focus has recently shifted toward single-cell and spatial transcriptomics. I currently work in the Hagan Lab at Cincinnati Children's Hospital Medical Center.
I work across multiple programming languages and computing environments, from workstation to HPC and cloud, and lead analyses end to end, from raw data through statistical modeling to biological interpretation. A long-standing advocate for reproducible science, I design analyses to be transparent, version-controlled and portable, so that results can be independently verified and built upon.
Data I work with
Research
Immunology
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Metabolomics of the influenza vaccine response
A pilot metabolomic study of how commonly used drugs interact with the immune response to seasonal influenza vaccination, using time-series statistical modeling and pathway analysis.
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Tryptophan catabolism in human tuberculosis
Transcriptomic and plasma-biomarker analysis showing that tryptophan catabolism reflects disease activity in active tuberculosis, with classifiers for diagnosis.
Software & databases
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The Immune Signatures Data Resource 2.0
An expanded compendium of systems vaccinology datasets.
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asari
Trackable and scalable processing of LC-MS metabolomics data. Open-source Python tool.
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BTM: Blood Transcription Modules
Updated blood transcription modules for interpreting blood transcriptomics data. Python package (
pip install BTM). -
ANGPTL8 pathway, WikiPathways WP3915
A curated pathway of ANGPTL8 in glucose and lipid metabolism, in the open WikiPathways database.
Selected publications
- A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination. npj Vaccines 8:92, 2023. doi:10.1038/s41541-023-00682-2
- Trackable and scalable LC-MS metabolomics data processing using asari. Nature Communications 14:4113, 2023. doi:10.1038/s41467-023-39889-1
- Tryptophan catabolism reflects disease activity in human tuberculosis. JCI Insight 5(10), 2020. doi:10.1172/jci.insight.137131
- Deciphering the expression dynamics of ANGPTL8 associated regulatory network in insulin resistance using formal modeling approaches. IET Systems Biology, 2019. doi:10.1049/iet-syb.2019.0032
- Biological pathways leading from ANGPTL8 to diabetes mellitus: a co-expression network based analysis. Frontiers in Physiology, 2018. doi:10.3389/fphys.2018.01841
- Visualizing the regulatory role of ANGPTL8 in glucose and lipid metabolic pathways. Genomics 109(5–6):408–418, 2017. doi:10.1016/j.ygeno.2017.06.006
Full list on Google Scholar.
Experience
- 2023 – present Associate Research Scientist, Hagan Lab, Cincinnati Children's Hospital Medical Center
- 2020 – 2023 Postdoctoral Associate, Li Lab, The Jackson Laboratory for Genomic Medicine
- 2019 – 2020 Postdoctoral Fellow, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University
- 2016 – 2017 Graduate Research Fellow, Integrative Systems Biology, Maastricht University
Teaching & service
Associate Editor, Vaccine Safety and Regulation section, Frontiers in Drug Safety and Regulation (since 2026). Served as a Nextflow Ambassador, contributing to community training and outreach on reproducible workflows. Certified Software Carpentry instructor since 2020. Member of the American Association of Immunologists and ISCB. Ad hoc reviewer for IET Systems Biology, IEEE Access and Complex Adaptive Systems Modeling.
Snapshots
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Ballgame · 2023
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Farewell dinner · 2025
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Thomas's birthday · 2026
Contact
- Personal
- amnahsiddiqa@gmail.com
Hagan Lab, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio