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.
1. Ma, Q., Xu, D. Deep learning shapes single-cell data analysis. Nat Rev Mol Cell Biol (2022)
2. Ma, Q., Jiang, Y., Cheng, H., Xu, D. Harnessing the deep learning power of foundation models in single-cell omics. Nat Rev Mol Cell Biol (2024)
Recent news
[May 7, 2025] We are delighted to share that our collaborate paper titled “Relation Equivariant Graph Neural Networks to Explore the Mosaic-like Tissue Architecture of Kidney Diseases on Spatially Resolved Transcriptomics” has been accepted for publication in Bioinformatics!
[Apr 30, 2025] We are happy to share that our collaborate paper titled “Sex Differences in Bladder Cancer: Understanding Biological and Clinical Implications” has been accepted for publication in Biology of Sex Differences!
[Apr 15, 2025] We are delighted to share that our paper titled “A visual–omics foundation model to bridge histopathology image with transcriptomics” has been accepted for publication in Nature Methods!
[Apr 15, 2025] We are happy to share that our undergraduate research intern, Chayse Arnhold, has successfully completed her undergraduate honors research thesis defense. Congratulations!
[Apr 10, 2025] We are excited to announce that Dr. Qin Ma is appointed as the Vice Chair of Research in the Department of Biomedical Informatics (DBMI). Congratulations to Dr. Ma’s new leadership!
[Apr 9, 2025] We are delighted to share that the BMBL and McPop (Dr. McTigue and Dr. Popovich) Labs the first Joint Journal Club, titled “Single-Cell Analysis in Neuroscience”, was successfully held in EAIC 130. This is a great start to strengthen cooperation between two labs!
[Apr 9, 2025] We are happy to share that our GRA, Jia Qu, has successfully completed her Master’s Degree Graduation Defense. Congratulations!
[Apr 8, 2025] We are happy to share that our GRA, Yi Jiang, has successfully completed his Master’s Degree Graduation Defense. Congratulations!
[Apr 2, 2025] Dr. Qin Ma was invited to give a talk titled “Single-cell and Spatial Omics Data Analyses for Alzheimer’s Disease” at the April 2025 Monthly ARCOE Meeting.
[Mar 30, 2025] We are happy to share that our PostDoc, Yuzhou Chang, has won the Young Scientist Excellence Award for Post Doctoral in 2025 MCBIOS Annual Meeting. Congratulations!
[Mar 23, 2025] We are excited to announce that our high school intern, Grace Xu, has been accepted into Johns Hopkins University. This outstanding accomplishment is a clear reflection of Grace’s hard work and unwavering dedication. We extend our heartfelt congratulations to Grace on this impressive accomplishment. Congratulations!
[Mar 17, 2025] We are excited to share that our paper titled “Perspectives on Integrating Artificial Intelligence and single-cell Omics for Cellular Plasticity Research” has been accepted for publication in Quantitative Biology. Congrats to our Postdoc, Dr. Ahmed Ghobashi!
[Mar 6, 2025] We are delighted to share that our paper titled “Common and divergent cellular aetiologies underlying hypoplastic left heart syndrome and hypoplastic right heart syndrome” has been published in European Heart Journal!
[Mar 4, 2025] Our undergraduate research intern, Chayse Arnhold, presented her insightful study, “Assessing the Impact of COVID-19 Infection on the Choroid Plexus and Prefrontal Cortex at the Single-Nucleus Level,” at the Denman Undergraduate Research Forum Spring 2025, OSU. Congratulations!
[Feb 28, 2025] Dr. Qin Ma presented his cutting-edge research titled “Graph Representation AI in Sex Bias Research” at the Third Annual Symposium on the Biological Basis of Sex Differences in Cancer, held at The Ohio State University.
[Feb 11, 2025] We are happy to share that our collaborate paper titled “Regulation of lung progenitor plasticity and repair by fatty acid oxidation” has been officially published in JCI Insight (Link)!
[Jan 22, 2025] We are excited to share that our collaborate paper titled “A platform for the biomedical application of large language models” has been officially published in Nature Biotechnology (Link)!
[Jan 8, 2025] We are delighted to share that our collaborate paper titled “Brain-Derived Tau Oligomer Polymorphs: Distinct Aggregations, Stability Profiles, and Biological Activities” has been accepted for publication in Communications Biology!
[Jan 5, 2025] Our paper titled “Graph Fourier transform for spatial omics representation and analyses of complex organs” has been highlighted by Nature Portfolio. Cheers!
[Jan 3, 2025] We are excited to share that our paper titled “The NAE1-mediated Neddylation operates as an essential post-translational modification checkpoint for effector CD8+ T cells” has been accepted for publication in PNAS!
[Dec 30, 2024] Congratulations to Dr. Qin Ma (MPI) and Dr. Jordan Krull (co-I) for winning OSU CCC Transitional Therapeutics FY25 seed award (grant), titled “AI-Driven Predictive Biomarkers for Immune Checkpoint Inhibitor Therapy in Clear Cell Renal Cell Carcinoma”!
[Dec 6, 2024] Congratulations to Dr. Qin Ma for winning the 2024 BSGP Faculty Peer Mentor Award!
[Dec 6, 2024] We are happy to share that our PostDoc, Xiaoying Wang, has been selected for the 2024 BMI Award Winner for Postdoctoral Researcher. Congratulation!