About Me
More info forI am a professor in the Department of Biomedical Informatics at The Ohio State University and a member of the Molecular Biology and Cancer Genetics Program at the OSUCCC – James, where I study how diverse cells impact cancer development.
One of my current research projects aims to examine the construction of cell type-specific gene co-regulation signatures based on single cell transcriptomics data in order to develop a computational model that tracks how genes are expressed in specific cell types and help scientists unravel how diseases progress and evade treatment.
I have co-authored many articles in well-respected journals, including Nucleic Acids Research, Bioinformatics, PLoS Computational Biology, Oncotarget and International Journal of Cancer. He has also shared his work at events across the world, including the Great Lakes Bioinformatics Conference and the Plant and Animal Genome Conference.
Education & Training
More info forDoctorate Degree - PhD
- University of Georgia
Athens, GA
USA
Doctorate - PhD
- Shandong University
Shandong, China
Undergraduate Degree - BS - Applied Mathematics
- Shandong University
Shandong, China
- University of Georgia
Academic Office & Contact Information
More info forAcademic Office:
Pelotonia Research Center
2255 Kenny Rd
Columbus, Ohio 43210Phone:
706-254-4293Email:
qin.ma@osumc.eduPublications
More info forDecember 1, 2024A contrastive learning approach to integrate spatial transcriptomics and histological images.
Lin Y, Liang Y, Wang D, Chang Y, Ma Q, Wang Y, He F, Xu D
Comput Struct Biotechnol J
October 2, 2024Maternal Blood Cell-Free RNA Signatures in Fetus With Congenital Heart Disease.
Alonzo M, Xu Z, Yu Y, Ye S, Wang C, Wang J, McNutt M, Bering J, Ma Q, Texter K, Garg V, Zhao MT
Circ Res
September 3, 2024An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.
Liu Z, Sun Y, Li Y, Ma A, Willaims NF, Jahanbahkshi S, Hoyd R, Wang X, Zhang S, Zhu J, Xu D, Spakowicz D, Ma Q, Liu B
Adv Sci (Weinh)
September 1, 2024Clinical and translational mode of single-cell measurements: An artificial intelligent single-cell.
Wang X, Powell CA, Ma Q, Fan J
Clin Transl Med
August 29, 2024Graph Fourier transform for spatial omics representation and analyses of complex organs.
Chang Y, Liu J, Jiang Y, Ma A, Yeo YY, Guo Q, McNutt M, Krull JE, Rodig SJ, Barouch DH, Nolan GP, Xu D, Jiang S, Li Z, Liu B, Ma Q
Nat Commun
August 8, 2024Applications of artificial intelligence to myeloproliferative neoplasms: a narrative review.
Srisuwananukorn A, Krull JE, Ma Q, Zhang P, Pearson AT, Hoffman R
Expert Rev Hematol
July 25, 2024Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data.
Li Y, Ma A, Wang Y, Guo Q, Wang C, Fu H, Liu B, Ma Q
Brief Bioinform
July 17, 2024The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors.
Dravillas CE, Coleman SS, Hoyd R, Caryotakis G, Denko L, Chan CHF, Churchman ML, Denko N, Dodd RD, Eljilany I, Hardikar S, Husain M, Ikeguchi AP, Jin N, Ma Q, McCarter MD, Osman AEG, Robinson LA, Singer EA, Tinoco G, Ulrich CM, Zakharia Y, Spakowicz D, Tarhini AA, Tan AC
Cancer Res Commun
June 26, 2024Harnessing the deep learning power of foundation models in single-cell omics.
Ma Q, Jiang Y, Cheng H, Xu D
Nat Rev Mol Cell Biol
June 21, 2024The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer.
Benej M, Hoyd R, Kreamer M, Wheeler CE, Grencewicz DJ, Choueiry F, Chan CHF, Zakharia Y, Ma Q, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Robinson LA, Singer EA, Ikeguchi AP, McCarter MD, Tinoco G, Husain M, Jin N, Tan AC, Osman AEG, Eljilany I, Riedlinger G, Schneider BP, Benejova K, Kery M, Papandreou I, Zhu J, Denko N, Spakowicz D
Cancer Res Commun
June 6, 2024A single-cell and spatial RNA-seq database for Alzheimer's disease (ssREAD).
Wang C, Acosta D, McNutt M, Bian J, Ma A, Fu H, Ma Q
Nat Commun
May 23, 2024Spatial and functional targeting of intratumoral Tregs reverses CD8+ T cell exhaustion and promotes cancer immunotherapy.
Zhou L, Velegraki M, Wang Y, Mandula JK, Chang Y, Liu W, Song NJ, Kwon H, Xiao T, Bolyard C, Hong F, Xin G, Ma Q, Rubinstein MP, Wen H, Li Z
J Clin Invest
March 12, 2024Abnormal Progenitor Cell Differentiation and Cardiomyocyte Proliferation in Hypoplastic Right Heart Syndrome.
Yu Y, Wang C, Ye S, Xu Z, Lin H, Texter K, Shukla V, Ghadiali S, Ma Q, Garg V, Zhao MT
Circulation
March 8, 2024A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.
Li Y, Wang Y, Wang C, Ma A, Ma Q, Liu B
Patterns (N Y)
February 13, 2024Targeting metabolic sensing switch GPR84 on macrophages for cancer immunotherapy.
Li J, Ma A, Zhang R, Chen Y, Bolyard C, Zhao B, Wang C, Pich T, Li W, Sun N, Ma Q, Wen H, Clinton SK, Carson WE, Li Z, Xin G
Cancer Immunol Immunother
January 23, 2024A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset.
Wang C, Ma A, Li Y, McNutt ME, Zhang S, Zhu J, Hoyd R, Wheeler CE, Robinson LA, Chan CHF, Zakharia Y, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Singer EA, Ikeguchi AP, McCarter MD, Denko N, Tinoco G, Husain M, Jin N, Osman AEG, Eljilany I, Tan AC, Coleman SS, Denko L, Riedlinger G, Schneider BP, Spakowicz D, Ma Q
Cancer Res Commun
January 6, 2024Human iPSC-based model of COPD to investigate disease mechanisms, predict SARS-COV-2 outcome and test preventive immunotherapy.
Dagher R, Moldobaeva A, Gubbins E, Clark S, Alfajaro MM, Wilen CB, Hawkins F, Qu X, Chiang CC, Li Y, Clarke L, Ikeda Y, Brown C, Kolbeck R, Ma Q, Rojas M, Koff JL, Ghaedi M
Stem Cells
January 6, 2024MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer.
Wang X, Duan M, Li J, Ma A, Xin G, Xu D, Li Z, Liu B, Ma Q
Nat Commun
January 4, 2024mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T-cell responses in patients with lung cancer.
Song NJ, Chakravarthy KB, Jeon H, Bolyard C, Reynolds K, Weller KP, Reisinger S, Wang Y, Li A, Jiang S, Ma Q, Barouch DH, Rubinstein MP, Shields PG, Oltz EM, Chung D, Li Z
J Immunother Cancer
December 4, 2023Glioblastoma pseudoprogression and true progression reveal spatially variable transcriptional differences.
Wang W, Tugaoen JD, Fadda P, Toland AE, Ma Q, Elder JB, Giglio P, James Cancer Center Integrated Neuro-Oncology Team , Otero JJ
Acta Neuropathol Commun
November 28, 2023DeepProSite: Structure-aware Protein Binding Site Prediction Using ESMFold and Pretrained Language Model.
Fang Y, Jiang Y, Wei L, Ma Q, Ren Z, Yuan Q, Wei DQ
Bioinformatics
November 22, 2023CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.
Wang Y, Li Y, Wang C, Lio CJ, Ma Q, Liu B
Brief Bioinform
November 14, 2023Dimension-agnostic and granularity-based spatially variable gene identification using BSP.
Wang J, Li J, Kramer ST, Su L, Chang Y, Xu C, Eadon MT, Kiryluk K, Ma Q, Xu D
Nat Commun
October 28, 2023VTwins: inferring causative microbial features from metagenomic data of limited samples.
Meng Q, Zhou Q, Shi S, Xiao J, Ma Q, Yu J, Chen J, Kang Y
Sci Bull (Beijing)
August 1, 2023Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis.
Li Y, Wang C, Ma A, Rani AQ, Luo M, Li J, Liu X, Ma Q
J Med Virol
June 16, 2023CD200R signaling contributes to unfavorable tumor microenvironment through regulating production of chemokines by tumor-associated myeloid cells.
Lin CH, Talebian F, Yang L, Zhu J, Liu JQ, Zhao B, Basu S, Pan X, Chen X, Yan P, Carson WE, Xin G, Wen H, Wang R, Li Z, Ma Q, Bai XF
iScience
December 30, 2022Impaired Human Cardiac Cell Development due to NOTCH1 Deficiency.
Ye S, Wang C, Xu Z, Lin H, Wan X, Yu Y, Adhicary S, Zhang JZ, Zhou Y, Liu C, Alonzo M, Bi J, Ramirez-Navarro A, Deschenes I, Ma Q, Garg V, Wu JC, Zhao MT
Circ Res
December 21, 2022Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer's disease.
Chen S, Chang Y, Li L, Acosta D, Li Y, Guo Q, Wang C, Turkes E, Morrison C, Julian D, Hester ME, Scharre DW, Santiskulvong C, Song SX, Plummer JT, Serrano GE, Beach TG, Duff KE, Ma Q, Fu H
Acta Neuropathol Commun
October 30, 2022Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data.
Chen J, Wang X, Ma A, Wang QE, Liu B, Li L, Xu D, Ma Q
Nat Commun
October 21, 2022Molecular Regulation of Heme Oxygenase-1 Expression by E2F Transcription Factor 2 in Lung Fibroblast Cells: Relevance to Idiopathic Pulmonary Fibrosis.
Ye Q, Taleb SJ, Wang H, Parinandi NL, Kass DJ, Rojas M, Wang C, Ma Q, Zhao J, Zhao Y
Biomolecules
September 7, 2022Epigenetic remodeling by vitamin C potentiates plasma cell differentiation.
Chen HY, Almonte-Loya A, Lay FY, Hsu M, Johnson E, González-Avalos E, Yin J, Bruno RS, Ma Q, Ghoneim HE, Wozniak DJ, Harrison FE, Lio CJ
Elife
September 1, 2022Selective targeting of GARP-LTGFβ axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell antitumor immunity.
Li A, Chang Y, Song NJ, Wu X, Chung D, Riesenberg BP, Velegraki M, Giuliani GD, Das K, Okimoto T, Kwon H, Chakravarthy KB, Bolyard C, Wang Y, He K, Gatti-Mays M, Das J, Yang Y, Gewirth DT, Ma Q, Carbone D, Li Z
J Immunother Cancer
August 19, 2022Sex-biased adaptive immune regulation in cancer development and therapy.
Schafer JM, Xiao T, Kwon H, Collier K, Chang Y, Abdel-Hafiz H, Bolyard C, Chung D, Yang Y, Sundi D, Ma Q, Theodorescu D, Li X, Li Z
iScience
July 29, 2022FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling.
Zhou D, Wu Z, Park JG, Fiches GN, Li TW, Ma Q, Huang H, Biswas A, Martinez-Sobrido L, Santoso NG, Zhu J
Nucleic Acids Res
July 27, 2022A bayesian multivariate mixture model for high throughput spatial transcriptomics.
Allen C, Chang Y, Neelon B, Chang W, Kim HJ, Li Z, Ma Q, Chung D
Biometrics
July 1, 2022Deep learning analysis of single-cell data in empowering clinical implementation.
Ma A, Wang J, Xu D, Ma Q
Clin Transl Med
May 4, 2022Author Correction: scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses.
Wang J, Ma A, Chang Y, Gong J, Jiang Y, Qi R, Wang C, Fu H, Ma Q, Xu D
Nat Commun
April 18, 2022AIB1 Is A Novel Target of the High-Risk HPV E6 protein and A Biomarker of Cervical Cancer Progression.
Miller J, Dakic A, Spurgeon M, Saenz F, Kallakury B, Zhao B, Zhang J, Zhu J, Ma Q, Xu Y, Lambert P, Schlegel R, Riegel AT, Liu X
J Med Virol
April 14, 2022Androgen conspires with the CD8+ T cell exhaustion program and contributes to sex bias in cancer.
Kwon H, Schafer JM, Song NJ, Kaneko S, Li A, Xiao T, Ma A, Allen C, Das K, Zhou L, Riesenberg B, Chang Y, Weltge P, Velegraki M, Oh DY, Fong L, Ma Q, Sundi D, Chung D, Li X, Li Z
Sci Immunol
January 10, 2022Treatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology.
Song NJ, Allen C, Vilgelm AE, Riesenberg BP, Weller KP, Reynolds K, Chakravarthy KB, Kumar A, Khatiwada A, Sun Z, Ma A, Chang Y, Yusuf M, Li A, Zeng C, Evans JP, Bucci D, Gunasena M, Xu M, Liyanage NPM, Bolyard C, Velegraki M, Liu SL, Ma Q, Devenport M, Liu Y, Zheng P, Malvestutto CD, Chung D, Li Z
J Hematol Oncol
January 1, 2022Utility of machine learning in developing a predictive model for early-age-onset colorectal neoplasia using electronic health records.
Hussan H, Zhao J, Badu-Tawiah AK, Stanich P, Tabung F, Gray D, Ma Q, Kalady M, Clinton SK
PLoS One
January 1, 2022DESSO-DB: A web database for sequence and shape motif analyses and identification.
Wang X, Wang C, Li L, Ma Q, Ma A, Liu B
Comput Struct Biotechnol J
January 1, 2022Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning.
Chang Y, He F, Wang J, Chen S, Li J, Liu J, Yu Y, Su L, Ma A, Allen C, Lin Y, Sun S, Liu B, Javier Otero J, Chung D, Fu H, Li Z, Xu D, Ma Q
Comput Struct Biotechnol J
October 13, 2021HBFP: a new repository for human body fluid proteome.
Shao D, Huang L, Wang Y, Cui X, Li Y, Wang Y, Ma Q, Du W, Cui J
Database (Oxford)
October 5, 2021Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.
Zhang S, Ma A, Zhao J, Xu D, Ma Q, Wang Y
Brief Bioinform
August 16, 2021DeepSec: a deep learning framework for secreted protein discovery in human body fluids.
Shao D, Huang L, Wang Y, He K, Cui X, Wang Y, Ma Q, Cui J
Bioinformatics
August 4, 2021MiREDiBase, a manually curated database of validated and putative editing events in microRNAs.
Marceca GP, Distefano R, Tomasello L, Lagana A, Russo F, Calore F, Romano G, Bagnoli M, Gasparini P, Ferro A, Acunzo M, Ma Q, Croce CM, Nigita G
Sci Data
July 23, 2021Inhibition of polo-like kinase 1 (PLK1) facilitates reactivation of gamma-herpesviruses and their elimination.
Biswas A, Zhou D, Fiches GN, Wu Z, Liu X, Ma Q, Zhao W, Zhu J, Santoso NG
PLoS Pathog
March 25, 2021scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses.
Wang J, Ma A, Chang Y, Gong J, Jiang Y, Qi R, Wang C, Fu H, Ma Q, Xu D
Nat Commun
February 17, 2021IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis.
Chang Y, Allen C, Wan C, Chung D, Zhang C, Li Z, Ma Q
Bioinformatics
December 1, 2020Single-Cell Techniques and Deep Learning in Predicting Drug Response.
Wu Z, Lawrence PJ, Ma A, Zhu J, Xu D, Ma Q
Trends Pharmacol Sci
September 1, 2020Integrative Methods and Practical Challenges for Single-Cell Multi-omics.
Ma A, McDermaid A, Xu J, Chang Y, Ma Q
Trends Biotechnol
August 29, 2020Elucidation of Biological Networks across Complex Diseases Using Single-Cell Omics.
Li Y, Ma A, Mathé EA, Li L, Liu B, Ma Q
Trends Genet
August 14, 2020The functional determinants in the organization of bacterial genomes.
Liu Z, Feng J, Yu B, Ma Q, Liu B
Brief Bioinform
August 1, 2020Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier.
Chen C, Zhang Q, Yu B, Yu Z, Lawrence PJ, Ma Q, Zhang Y
Comput Biol Med
May 18, 2020IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.
Ma A, Wang C, Chang Y, Brennan FH, McDermaid A, Liu B, Zhang C, Popovich PG, Ma Q
Nucleic Acids Res
May 15, 2020Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources.
Eicher T, Kinnebrew G, Patt A, Spencer K, Ying K, Ma Q, Machiraju R, Mathé AEA
Metabolites