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

[Jul 14, 2024] The paper titled “Clinical and translational mode of single-cell measurements: An artificial intelligent single-cell” has been accepted for publication in Clinical and Translational Medicine!

[Jul 11, 2024] The paper titled “Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data” has been accepted for publication in Briefings in Bioinformatics!

[Jul 11, 2024] We are happy to announce that our Postdoc, Dr. Yang Li, has been offered a position as an Assistant Professor at the Beijing University of Technology in China.

[Jul 5, 2024] Our collaborative paper titled “Analysis of community connectivity in spatial transcriptomics data” has been officially published in the Journal of Frontiers in Applied Mathematics and Statistics!

[Jun 26, 2024] Our collaborative paper titled “The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer” has been officially published in the Journal of Cancer Research Communications!

[Jun 23, 2024] We are thrilled to share the exciting news about Dr. Zhaoqian Liu, an alumnus of our visiting scholar. Dr. Liu has been offered a position as an Assistant Professor at the Xi’an University of Science and Technology in China.

[Jun 11, 2024] The paper titled “Harnessing the deep learning power of foundation models in single-cell omics” has been accepted for publication in Nature Reviews Molecular Cell Biology.

[Jun 7, 2024] We are excited to share this news about our recent published paper “A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease (ssREAD)”!

[May 31, 2024] We are thrilled to share this news about our co-I research R21 grant (PI: Giovanni Nigita)!

[May 21, 2024] Led by Cankun Wang, the paper titled “A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease (ssREAD)” has been officially accepted for publication in Nature Communications!

[May 17, 2024] Our collaborative paper titled “Spatial and functional targeting of intratumoral Tregs reverses CD8+ T cell exhaustion and promotes cancer immunotherapy” has been officially accepted for publication in the Journal of Clinical Investigation!

[May 14, 2024] We are happy to announce that our current OSU undergraduate volunteer, Pavan Thota has been accepted to Georgia Institute of Technology, starting Fall 2024, M.S. in Computer Science and Bioinformatics.

[May 13, 2024] Yi Jiang is set to present an intriguing poster titled “HyperGRN: Elucidate High-order-relation Gene Regulatory Networks in the Spatial Context ” at the 2024 International Conference on Intelligent Systems for Molecular Biology (ISMB).

[May 7, 2024] We are overjoyed to share some delightful personal news from our graduate student, Michael Hsu. He and his wife, Vicky, have welcomed a beautiful baby girl into their family. Both mother and baby are doing well, and the family is taking some time to enjoy these precious early days together.

[May 3, 2024] We are happy to announce that Hangxiao Zhu, one of our OSU undergraduate volunteer, has been accepted into the Computer Science PhD program at Texas A&M University.

[May 3, 2024] Our graduate research assistant, Qi Guo, successfully presented his poster titled “An Integrated Mouse Spinal Cord Atlas Revealing Microglia Phenotypes in Health and Injury Conditions” for the 4th Annual Department of Neuroscience Research Day. Check out a live photo from the event.

[May 2, 2024] We are thrilled to share the wonderful news that Jack Wu, an alumnus of our high school trainee, has been accepted into the Computer Science major at the University of Minnesota this fall.

[May 1, 2024] We are delighted to announce that Dr. Anjun Ma has joined the editorial team of Heliyon Genetics (Impact Factor: 4). Dr. Ma brings with him a wealth of expertise in Single-cell and spatial omics, Deep Learning, and Bioinformatics.

[April 25, 2024] We are thrilled to share the exciting news about Dr. Ren Qi, an alumnus of our visiting scholar. Dr. Qi has been offered a position as an Assistant Professor in the Department of Computer Science at the Beijing Institute of Technology in China.

[April 23, 2024] Ana Xiong, an alumnus of our OSU undergraduate volunteer, has been admitted into the PhD program at the University of North Carolina at Chapel Hill. She will begin her studies this fall, focusing on machine learning and medical imaging under the guidance of Dr. Martin Styner. We look forward to witnessing her future academic achievements (Group Photo).

[April 19, 2024] We are excited to highlight the presentation by Dr. Jordan Krull at 2024 Pelotonia Scholars Symposium on how Deep Learning is revolutionizing digital pathology. His insights on extracting crucial numerical features from pathology slides are reshaping medical diagnostics.

[March 28, 2024] We are thrilled to extend our congratulations to our lab research technician Ms. Megan McNutt, who has been admitted to The Ohio State University Medical School!

[March 24, 2024] Dr. Qin Ma presented “Graph Representation Learning of Single-Cell and Spatial Transcriptomics Data,” at the 20th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS) held at the Rollins School of Public Health, Emory University.

[March 12, 2024] The paper titled “Abnormal progenitor cell differentiation and cardiomyocyte proliferation in hypoplastic right heart syndrome” has been officially published in Circulation (IF=39.9).

[March 6, 2024] We are thrilled to welcome a new cohort of students to our lab. Joining us as Graduate Research Assistants are Xiaojie Jin and Weidong Wu (co-mentored by Dr. Anjun Ma). Additionally, Zhantao Du will be joining as a rotation PhD student.

[February 22, 2024] We are delighted to announce Mr. Hu Chen will be joining our lab as a Graduate Research Assistant in the summer of 2024. Welcome aboard!

[February 21, 2024] Congratulations on Dr. Anjun Ma, who has been awarded the PKD RRC Pilot and Feasibility Award, securing a grant of $63,500 for his project titled “Constructing a Cross-Species Single-cell Database in Polycystic Kidney Disease”.

[February 20, 2024] We are delighted to announce that Dr. Ahmed Hamdy Ghobashi will be joining our lab as a postdoc fellow. His start date will be on June 17, 2024. Welcome aboard!

[Feb-14-2024] Led by Jianying Li, the manuscript “Targeting metabolic sensing switch GPR84 on macrophages for cancer immunotherapy” has been officially published in Cancer Immunology, Immunotherapy.

[Feb-7-2024] Dr. Qin Ma has been featured in interview by the “The Multi-Omics Playbook”. This playbook is a comprehensive guide that delves into the integrated application of multi-omics approaches in our research. It covers essential methodologies, best practices, and insightful case studies that can enhance our understanding and application of multi-omics data.

[Jan-24-2024] The manuscript “MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer” was recently recognized among the top 50 Biotechnology and methods papers by Nature Communications.

 

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