Research Interests

Artificial intelligence (AI) and single-cell studies have been making waves in the science and technology communities. AI 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 data can be analyzed across a wide range of research topics by generalizing deep-learning model design and optimization in a hypothesis-free manner. Our lab focuses on the research of single-cell multi-omics data, aiming to develop cutting-edge computational tools to discover underlying mechanisms in diverse biological systems.
Ma, Q., Xu, D. Deep learning shapes single-cell data analysis. Nat Rev Mol Cell Biol (2022)


Recent news

[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.

[Jan-23-2024] Led by Cankun Wang, the paper titled “A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset” has been officially published in Cancer Research Communications.

[Jan-20-2024] Congratulations on Yingjie Li’s abstract “Identification of HPV oncogene and host cell differentiation associated heterogeneity in cervical cancer via single‐cell transcriptomics” has been selected for an oral presentation at Translational Research Cancer Centers Consortium (TRCCC) 2024!

[Jan-19-2024] We warmly welcome Michael Parthun, a graduate student from OSU, has joined the lab as a rotating student.

[Jan-6-2024] The paper titled “CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq” has been officially published in Briefings in Bioinformatics.

[Jan-6-2024] Our collaborative paper titled “Human iPSC-based model of COPD to investigate disease mechanisms, predict SARS-COV-2 outcome, and test preventive immunotherapy,” has been officially published in Stem Cells!

[Jan-6-2024] Led by Dr. Xiaoying Wang, the paper titled “MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer” has been officially published in Nature Communications.

[Jan-4-2024] Our collaborative paper titled “mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T-cell responses in patients with lung cancer,” has been officially published in Journal for Immunotherapy of Cancer!

[Dec-14-2023] Congratulations to Dr. Jordan Krull for securing 2nd place in the Postdoc/Resident/Fellows category at the PIIO Symposium Poster Session!

[Dec-12-2023] Our collaborative paper titled “Targeting Metabolic Sensing Switch GPR84 on Macrophages for Cancer Immunotherapy,” is accepted to be published in Cancer Immunology, Immunotherapy!

[Dec-12-2023] Congratulations to Yuzhou Chang on a successful defense and a smooth Ph.D. graduation journey!

[Dec-12-2023] Dr. Qin Ma was awarded Excellence in Faculty Teaching in the Department of Biomedical Informatics for the year 2023. Congratulations!

[Dec-12-2023] Dr. Jordan Krull was awarded Excellence in Postdoc Research in the Department of Biomedical Informatics for the year 2023. Congratulations!

[Dec-3-2023] The paper titled “CEMIG: Prediction of the cis-regulatory motif using the De Bruijn graph from ATAC-seq,” is accepted to be published in Briefings in Bioinformatics.

[Nov-29-2023] Lead by Xiaoying Wang, the paper titled “MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer” has been officially accepted for publication in Nature Communications.

[Nov-29-2023] Our manuscript “Dimension-agnostic and granularity-based spatially variable gene identification using BSP”, has been featured in Nature Communications Editors’ Highlights page among the top 50 papers in Biotechnology and methods.

[Nov-23-2023] The paper titled “mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T cell responses in lung cancer patients,” is accepted to be published in Journal for ImmunoTherapy of Cancer.

[Nov-15-2023] Our collaborative paper titled “Abnormal progenitor cell differentiation and cardiomyocyte proliferation in hypoplastic right heart syndrome,” is accepted to be published in Circulation (IF=40)!.

[Nov-13-2023] A new paper titled “DeepProSite: Structure-aware Protein Binding Sites Prediction Using ESMFold and Pre-trained Language Model,” is accepted to be published in Bioinformatics.

[Nov-3-2023] The paper titled “Dimension-agnostic and granularity-based spatially variable gene identification using BSP” has been officially accepted for publication in Nature Communications.

[Oct-20-2023] The paper titled “A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset” lead by Cankun Wang has been accepted for publication in Cancer Research Communications.

[Oct-13-2023] Dr. Qin Ma has offered his expert opinion for the Research Briefing accompanying the paper titled “STAligner: Enabling the Integration and Alignment of Multiple Spatial Transcriptomics Datasets” on Nature Computational Science.

[Sep-17-2023] We are delighted to welcome Pavan Thotas, currently pursuing a Bachelor of Science with a major in Health Sciences and a minor in Biology at OSU, to the BMBL team as an undergraduate intern volunteer.

[Sep-6-2023] Dr. Qin Ma has been invited to deliver a talk at the NIH/NIEHS Biostatistics and Computational Biology Branch DIR Seminar. The seminar, titled “Graph Representation Learning of Single-cell Omics Data,” will take place on Wednesday, September 20, 2023, at 11 AM (EST). To join the seminar remotely, use this Zoom link.

[Sep-4-2023] The paper titled “Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data” lead by Dr. Zhaoqian Liu has been accepted for publication in Computers in Biology and Medicine.

[Aug-25-2023] The New York Times featured the news titled “Researchers Dispute High-Profile Discoveries of Cancer Microbes,” reported on the recent scientific discourse surrounding the presence of microorganisms within tumors. Dr. Ma has been interviewed to provide his insights on this matter.

[Aug-16-2023] We are thrilled to share that Yingjie Li, in her first year of PhD studies, has achieved a remarkable milestone with her first author paper. The manuscript, titled “Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis,” has been accepted for publication in the Journal of Medical Virology.

[Aug-14-2023] We’re pleased to welcome Dr. Qianjiang Hu to our lab as a PostDoc Fellow. Collaboratively mentored by Dr. Melanie Königshoff from the University of Pittsburgh.

[Aug-14-2023] We’re delighted to have Qufei Wu join us as a High School Intern from the Class of 2024 at Culver Military Academy.

[Aug-10-2023] Dr. Qin Ma recently delivered a presentation at the 2023 Joint Statistical Meetings (JSM).

[Aug-4-2023] Kevin Liu, a BMI summer intern under the primary mentorship of Dr. Lang Li and secondary mentorship of Dr. Qin Ma, has been awarded Graduate Honorable Mention for his poster on “Data Curation of Hydroxyurea for Pediatric and Maternal Populations.”

[Jul-24-2023] We are delighted to share that Mirage Modi, previously a rotating student from the Medical Scientist Training Program (MSTP) MD-PhD program, has made the decision to join our BMBL team!

[Jul-20-2023] Cindy Tong, an alumnus of our high school trainee, has been admitted into Princeton University with a Computer Science major. We look forward to witnessing her future academic achievements.

[Jul-18-2023] Exciting development as our P01 program “Sex, Chromosomes, and Immunity in Bladder Cancer” (1P01CA278732) is officially launched! Visit our website at https://www.bcgsp.org/ to learn more about our latest research endeavors.

[Jul-6-2023] Yuzhou Chang has been honored with the Student & Trainee Travel Award at the International Conference on Intelligent Biology and Medicine (ICIBM 2023).

[Jul-6-2023] Our collaborative work with Dr. Dongjun Chung, titled “LRT: Integrative Analysis of scRNA-seq and scTCR-seq Data to Investigate Clonal Differentiation Heterogeneity,” has been formally accepted for publication in PLOS Computational Biology.

[Jun-20-2023] Dr. Anjun Ma’s abstract, “Deep Transfer Learning of Cancer Drug Responses by Integrating Bulk and Single-cell RNA-seq data”, has been selected for a 10-minute flash talk at the International Conference on Intelligent Biology and Medicine (ICIBM 2023) on July 18th, 2023.

[Jun-15-2023] We warmly welcome Anjali Byappanahalli, a dedicated PhD student from the Biomedical Sciences Graduate Program at OSU, who has joined our lab as a rotating student!

[Jun-15-2023] A hearty welcome to Mirage Modi, an ambitious MD & PhD student from the Biomedical Sciences Graduate Program at OSU, who has now joined our lab as a rotating student!

[Jun-10-2023] Congratulations to Megan McNutt and her team from The Ohio State University, who were among the top three finalists in the American Society for Artificial Internal Organs: For Young Innovators (ASAIOfyi) Student Design Competition. They presented their groundbreaking project, “A Removal Device for Tunneled Intravascular Catheters,” at the American Society for Artificial Internal Organs Conference in San Francisco.

[Jun-6-2023] The International Conference on Intelligent Biology and Medicine (ICIBM 2023) accepts four of BMBL’s work for presentations:

 

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