Research Interests
Deep learning and single-cell studies have been making waves in the science and technology communities. Deep learning offers a broad range of methods that can be used to investigate diverse data- and hypothesis-driven questions in single-cell biology. The highly heterogeneous nature of single-cell and spatial omics data can be analyzed across a wide range of research topics by deep-learning modeling and optimization in a hypothesis-free manner. Recently, the applications of foundation models showcased significant promise for new insights discovery in single-cell biology. Our lab focuses on developing cutting-edge deep-learning methods for single-cell and spatial omics data, aiming to discover underlying mechanisms (e.g., gene regulation, cell-cell interactions, and cellular senescence) in diverse biological systems and complex diseases. Ma et al. Deep learning shapes single-cell data analysis. Nat Rev Mol Cell Biol (2022). Harnessing the deep learning power of foundation models in single-cell omics. Nat Rev Mol Cell Biol (2024)
Qin Ma, PhD
Professor & Vice Chair for Research
Division Chief, Bioinformatics & Computational Biology
Dept. of Biomedical Informatics, College of Medicine
Director, Center for AI & Bioinformatics Immuno-Oncology (CATION)
Pelotonia Institute for Immuno-Oncology | OSUCCC
Editor-in-Chief, Computational Biology and Chemistry (CBAC)
Contact Information
Pelotonia Research Center, Rm 3049
2255 Kenny Rd
Columbus, Ohio 43210
The Ohio State University
qin.ma@osumc.edu
About Me
I am Vice Chair for Research and Division Chief of Computational Biology and Bioinformatics in the Department of Biomedical Informatics at The Ohio State University (OSU), and Director of the Center for AI & Bioinformatics in Immuno-Oncology (CATION) with the Pelotonia Institute for Immuno-Oncology (PIIO) at The OSU Comprehensive Cancer Center (OSUCCC). I hold a Ph.D. in Computational Biology and have over 17 years of research experience.
My research career has been driven by a relentless pursuit of innovation, particularly in decoding the functional machinery embedded within genomes and unraveling the regulatory mechanisms underpinning complex diseases. Central to my approach has been the development of advanced computational methods that leverage high-throughput Omics data, particularly in single-cell and spatial sequencing analyses. These efforts have culminated in multiple NIH and NSF-funded projects as an independent investigator (PI/MPI), leading to over 190 publications in top-tier journals such as Nature Reviews Molecular Cell Biology, Nature Neuroscience, Nature Immunology, Nature Communications, New England Journal of Medicine, Nucleic Acids Research, and Genome Research, with ~8,800 citations to date. My work exemplifies the intersection of methodological innovation and biological discovery, particularly by integrating machine learning and graph representation AI into bioinformatics. For example, I have pioneered methods that utilize graph neural network, graph transformer, and graph Fourier transform to enlighten unique analyses of single-cell and spatial omics data, a breakthrough that has significantly advanced our understanding of cellular heterogeneity in health and disease. Meanwhile, I am also actively involved in professional activities, including (1) serving as the editor-in-chief of the journal Computational Biology and Chemistry; (2) serving as an invited (keynote) speaker in seminars and international conferences (>40 times); and (3) serving as a regular reviewer for various funding agencies (e.g., NSF and NIH) and peer-reviewed journals (e.g., Nature, Nature Biotechnology, and Nature Methods) (> 100 times).
Recent news
[Oct 1, 2025] We are excited to share that our collaborative paper titled “Activation of USP30 disrupts endothelial cell function and aggravates acute lung injury through regulating S-adenosylmethionine cycle” has been accepted for publication in Advanced Science! Congratulations to all authors on this impactful study.
[Sep 26, 2025] We are pleased to share that our collaborative paper titled “Epigenetic Modulation, Intra-tumoral Microbiome and Immunity in Early Onset Colorectal Cancer” has been accepted for publication in Cancer Research Communications! Congratulations to all authors!
[Sep 23, 2025] We are pleased to share that our collaborative paper titled “DAP12 deletion reduces neuronal SLIT2 and demyelination and enhances brain resilience in female tauopathy mice” has been accepted for publication at Molecular Neurodegeneration Journal. Congratulations to all authors, on this important contribution to neurodegenerative disease research!
[Sep 12, 2025] We are delighted to share that our lab lead paper titled “scBSP: A fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data” has been accepted for publication at Bioinformatics. Congratulations to all authors on this exciting achievement!
[Sep 4, 2025] We are thrilled to share that our lab lead paper titled “Ad-hoc, post-hoc, and intrinsic-hoc in bioinformatics” has been accepted for publication in Nature Biotechnology! Congratulations to Dr. Qin Ma and other co-authors on this milestone achievement!
[Aug 31, 2025] We are excited to share that our collaborative paper titled “Targeting TGFβ docking receptor Glycoprotein A Repetitions Predominant (GARP) via novel chimeric antigen receptor (CAR)-T cell platform to treat glioblastoma” has been accepted for publication. Congratulations to all authors on this important contribution to cancer immunotherapy!
[Aug 28, 2025] We are pleased to share that our collaborative paper titled “Evaluation of statistical differential analysis methods in the Seurat package for identification of senescent cells using single-cell transcriptomics” has been published in Cell Reports Methods! Congratulations to all authors!
[Aug 26, 2025] We are delighted to welcome two new interns to our lab! Prateek Bhandari, an undergraduate student pursuing a B.S. in Computer Science Engineering with a Minor in Statistics, and Jason Li, a research intern with an M.S. in Computer Science from OSU, have joined us this month. Welcome aboard, Prateek and Jason!
[Aug 26, 2025] We are excited to welcome Matt Gust and George Roy from the MCDB Graduate Program at Ohio State University as rotation students in our lab. They will be with us through mid-October 2025. Welcome, Matt and George!
[Aug 25, 2025] We are excited to welcome our Fall 2025 new lab members! Julia Grace will join us as a Graduate Research Associate (GRA) through the T32 Program from the College of Dentistry, and Donte Johnson will join as a post-baccalaureate student through the CAMELOT/ACS Program. Welcome aboard, Julia and Donte!
[Aug 12, 2025] We are pleased to share that our collaborative paper titled “Multi-scaled Transcriptomics of Chronically Inflamed Nasal Epithelium Reveals Immune-Epithelial Dynamics and Tissue Remodeling in Nasal Polyp Formation” has been accepted for publication in Immunity! Congratulations to the team that contributed to the success!
[Aug 8, 2025] We are happy to share that our collaborative paper titled “O-GlcNAc transferase plays dual antiviral roles by integrating innate immunity and lipid metabolism” has been accepted for publication in Nature Communications! Congratulations!
[Aug 6, 2025] We are pleased to share that our collaborative paper titled “Analysis of Head and Neck Cancer scRNA-seq Data Identified PRDM6 Promotes Tumor Progression by Modulating Immune Gene Expression” has been accepted for publication in Frontiers in Immunology! Congratulations to all authors!
[Aug 2, 2025] We are delighted to share that our collaborative grant application to the American Brain Tumor Association (ABTA) Discovery Grant program has been accepted! Congratulations to Dr. Nandini Acharya (PI) and Dr. Qin Ma (co-I), along with all collaborators, on this exciting achievement!
[Jul 31, 2025] We are excited to share that Dr. Qin Ma, along with collaborators Dr. Phillip Popovich, Dr. Lang Li, and Dr. Andrew Fischer, has received the 2025 CBI Resource Award for the project “Neuroinformatics Collaborative Initiative with AI.” This $100,000 award will support the development of a new resource to benefit the CBI research community at OSU. Congratulations to the team!
[Jul 30, 2025] We are pleased to share that Dr. Qin Ma will present at the PIIO Research in Progress seminar on August 8. His talk, titled “CATION – AI and Foundation Models for Cancer Research”, will highlight advances in AI-driven cancer research.
[Jul 28, 2025] We are excited to share that Shaopeng Gu, our Senior Bioinformatics Specialist, has been selected to present at ICIBM 2025. His talk is titled “BioGuider: Standardize and Optimize Documentation of Bioinformatics Tools Using AI Multi-Agents.” Congratulations!
[Jul 28, 2025] We are excited to share that Jordan Krull has been selected to present at the Future Scientist Session at ICIBM 2025. His talk is titled “Large Scale, AI-Enabled, Spatial Signal Processing of Breast Cancer Pathology Identifies Consensus Tissue Structures Related to Biology and Outcomes.” Congratulations!
[Jul 25, 2025] We are happy to share that our lead Perspective article titled “The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes” has been accepted for publication in Nature Methods! Congratulations to everyone who contributed to this success!
[Jul 23, 2025] We are thrilled to share that our collaborative review article, titled “Advancing biological understanding of cellular senescence with multi-omics”, has been accepted for publication in Nature Genetics! Congratulations to all collaborators on this exciting achievement!
[Jul 14, 2025] We are delighted to share that Charlotte Hawley have joined our lab as a rotating post-baccalaureate student. Welcome aboard!
[Jul 14, 2025] We are delighted to share that Donte Johnson have joined our lab as a rotating post-baccalaureate student. Welcome aboard!
[Jul 2, 2025] We are happy to share that our collaborate paper titled titled “TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues” has been accepted for publication in Nature Communications!