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. Most of my projects are large-scale, often meta-analyses, across bulk, single-cell and spatial transcriptomics, LC-MS metabolomics and genetic variant datasets. I build end-to-end pipelines and lead analyses through to biological interpretation. I am exploring integrating large language models and AI agents into these workflows. 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. 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.

Beyond research, I am an avid reader and keen photographer, and I am happiest outdoors. I am also all in on Formula 1, drawn to engineering, teamwork and the precision required in the sport, and I love how much of it comes down to data and strategy.

Data I work with

Click a data type to see related papers and resources.

Research

Immunology

An expanded atlas of human vaccine responses

Blood transcriptional responses in the first week after vaccination across 46 studies in healthy adults, extended to newer platforms and adjuvants, including SARS-CoV-2 mRNA and viral-vectored, dengue, malaria, typhoid and pertussis vaccines, and how they relate to antibody responses.

Not yet published · Project page
Transcriptomic signatures of SARS-CoV-2 infection and vaccination

A comparison of the gene expression signatures induced by SARS-CoV-2 infection, COVID-19 vaccination and other established vaccines, including early innate signatures that predict binding antibody titers.

Not yet published · Project page
Broad and disease-specific signatures of respiratory infections

A meta-analysis of 53 published studies and 11,199 blood transcriptomes, profiled by microarray and RNA-seq, developing diagnostic gene signatures that separate respiratory from non-respiratory and viral from bacterial infections, and identify tuberculosis and influenza.

Not yet published · Project page
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.

npj Vaccines, 2023 · Paper
Tryptophan catabolism in human tuberculosis

Transcriptomic and plasma-biomarker analysis showing that tryptophan catabolism reflects disease activity in active tuberculosis, with classifiers for diagnosis.

JCI Insight, 2020 · Paper

Software & databases

The Immune Signatures Data Resource 2.0

An expanded compendium of systems vaccinology datasets.

The Journal of Immunology, 2026, conference abstract · Abstract · Resource page
asari

Trackable and scalable processing of LC-MS metabolomics data. Open-source Python tool.

Nature Communications, 2023 · Paper · Code
BTM: Blood Transcription Modules

Updated blood transcription modules for interpreting blood transcriptomics data. Python package (pip install BTM).

Code
ANGPTL8 pathway, WikiPathways WP3915

A curated pathway of ANGPTL8 in glucose and lipid metabolism, in the open WikiPathways database.

Pathway

Selected publications

All publications: Google Scholar · ORCID

2023

A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination

Siddiqa A, Wang Y, Thapa M, Martin DE, Cadar AN, Bartley JM, Li S

npj Vaccines 8:92 · DOI
2023

Trackable and scalable LC-MS metabolomics data processing using asari

Li S, Siddiqa A, Thapa M, Chi Y, Zheng S

Nature Communications 14:4113 · DOI
2020

Tryptophan catabolism reflects disease activity in human tuberculosis

Collins JM, Siddiqa A, Jones DP, et al.

JCI Insight 5(10) · DOI
2019

Deciphering the expression dynamics of ANGPTL8 associated regulatory network in insulin resistance using formal modeling approaches

Siddiqa A, Ahmad J, Ali A, Khan S

IET Systems Biology · DOI
2018

Biological pathways leading from ANGPTL8 to diabetes mellitus: a co-expression network based analysis

Siddiqa A, Cirillo E, Tareen SHK, et al.

Frontiers in Physiology · DOI
2017

Visualizing the regulatory role of ANGPTL8 in glucose and lipid metabolic pathways

Siddiqa A, Cirillo E, Tareen SHK, et al.

Genomics 109(5–6):408–418 · DOI

Experience

Positions

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

Hobby projects

Imaging-based spatial transcriptomics

I am going through the tools at each step of the imaging-based spatial transcriptomics workflow, from panel design and segmentation to downstream analysis, and keeping a curated list as I go. I will share my insights in blog posts.

Tool list on GitHub · Blog posts coming soon