Qin Ma, Ph.D. May 12, 2019 CURRICULUM VITAE Qin Ma, Ph.D. Associate Professor Bioinformatics and Mathematical Biosciences Lab Department of Biomedical Informatics, College of Medicine The Ohio State University CONTACT INFORMATION Phone: 706-254-4293 (C); 614-688-9857 (O) Email: [email protected]; [email protected] Address: 250 Lincoln Tower, 1800 Cannon Drive, Columbus, OH, 43210 Homepage: https://medicine.osu.edu/bmi/people/faculty/qin_ma/Pages/index.aspx Lab Website: https://u.osu.edu/bmbl/ PROFESSIONAL EXPERIENCE 2019-now Associate Professor Department of Biomedical Informatics, The Ohio State University. 2015-2018 Assistant Professor Department of Mathematics and Statistics Department of Plant Science, South Dakota State University 2014-2015 Research Scientist Department of Biochemistry & Molecular Biology, University of Georgia 2011-2014 Postdoctoral research associate Department of Biochemistry & Molecular Biology, University of Georgia EDUCATION Ph.D. Operations Research, University of Georgia, 2008-2010 (Advisor: Prof. Ying Xu), Training in bioinformatics and computational systems biology. Shandong University, 2005-2008 (Advisor: Prof. Guojun Li), Training in algorithm design and graph theory. Thesis: “Elucidation and identification of regulons for prokaryotic genomes”. B.S. Applied Mathematics, Shandong University, 2001-2005 RESEARCH INTERESTS • Omics data mining & modeling and bioinformatic tools development in gene regulation o Gene regulation from single-cell RNA-Seq data analysis and modeling o Comparative and functional genomics analysis o Biclustering methods for large-scale temporal and spatial transcriptomic data o De-novo cis-regulatory motifs prediction by ChIP-Seq and ATAC-Seq data • Computational systems biology in microbial genomes o Elucidation and application of organizing principles of bacterial genomes o Metagenomics and metatranscriptomics data analysis in microbes o Computational analysis and modeling of human/plant-microbiome interactions o Prediction of metabolic networks and associated regulatory systems CV - Qin Ma – Page 1 of 22 Qin Ma, Ph.D. May 12, 2019 PROFESSIONAL ORGANIZATION MEMBERSHIPS • Member, International Society for Computational Biology (ISCB), 2014-present • Member, Translational Data Analytics Institute of the Ohio State University, 2019-present • Member, The Ohio State University Comprehensive Cancer Center, 2019-present • Member, American Society for Microbiology (ASM), 2013-2015 • Member, Bioenergy Research Center of Department of Energy 2011-2016 • Member, Honor Society of Agriculture (SDSU), 2016-2018 • Associate Editor, Computational Biology and Chemistry 2019-present • Editor board member, Scientific Reports, 2018-present • Editor board member, BMC Genomics, 2015-present • Editor board member, Mathematical Biosciences, 2015-present • Guest Editor, Computational and Structural Biotechnology journal. Topic: Machine learning and pattern recognition techniques in molecular function and structure analysis. 2018 • Guest Editor, International journal of Genomics. Topic: Bioinformatic Tools in Microbial Genomic Data Analysis. 2015 • Guest Editor, Mathematical Biosciences. Topic: State-of-the-art machine learning techniques in biomedical informatics. 2018 • Guest Editor, BioMed Research International. Topic: Scalable Data Mining Algorithms in Computational Biology and Biomedicine. 2015 • Tutorial co-chair, APBC 2020: The 18th Asia Pacific Bioinformatics Conference. Seoul Korea on Feb 12-14 2020 • Program Committee and Award Committee Member, International Conference on Intelligent Biology and Medicine (ICIBM2019), 2019 • Program Committee Member, The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016-2019 • Program Committee Member, International Work-Conference on Bioinformatics and Biomedical Engineering" (IWBBIO), 2017-2019 • Program Committee Member, International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO), 2015-2016 PROFESSIONAL HONORS AND AWARDS • Recognized Reviewer, Computational and Structural Biotechnology journal, 2019 • Significant achievement in research, South Dakota State University, 2018 • Recognized Reviewers, Mathematical Biosciences, 2014-2015 • Excellent Reviewers, Mathematical Biosciences, 2013 LEADERSHIP DEVELOPMENT • Group leader of Cancer systems biology research in the Department of Biomedical Informatics at the Ohio State University (21 faculty members at the Ohio State University, including five new BMI faculty members). 2019-present • Director of the Bioinformatics and Mathematical Biosciences Lab at SDSU: Supervised one postdoc, eight graduate students, and six undergraduate students. 2015-present CV - Qin Ma – Page 2 of 22 Qin Ma, Ph.D. May 12, 2019 • Group Leader of Systems Biology for Biofuel Study in Computational Systems Biology laboratory (CSBL), University of Georgia, (includes two senior scientists, one postdoc, and four graduate students) 2014-2015 • Coordinated/supervised all biofuel and microbial research within the CSBL Lab and established collaborations within and outside university, including universities in China • Regularly organize group meetings and journal clubs within the CSBL lab, University of Georgia. 2013-2015 • Seminar coordinator of the CSBL lab, University of Georgia. 2013-2015 MEDIA APPEARANCES • [November 18, 2018] DD news. It is just an expression. A trio of institutions is looking to explore not just linking genes with diseases, but how they are expressed, in hopes of determining more about how diseases advance. (Link) • [October 10, 2018] SDSU news. Assistant Professor Qin Ma leads a multi-institutional team of researchers who will develop a computational model that tracks how genes are regulated and expressed in specific cell types through a four-year, $1.04 million National Institutes of Health Research Project grant (R01). (Link) • [Jan 24, 2018] Dr. Qin Ma and the BMBL are highlighted on the January edition of the SD EPSCoR Newsletter. The issue looks at Ma lab and profiles a software program (QUBIC-R) that helps model and visualize gene expression networks. (Link) • [Oct 31, 2016] A new grant was received from NSF as a co-PI. Researchers analyze how rootstock affects grapevine characteristics, and Dr. Qin Ma is carrying out mathematical modeling and mining of the large-scale RNA-Sequencing data. (Link) RESEARCH EXPERIENCE Associate Professor 2019-present Department of Biomedical Informatics, Ohio State University • Published 20 papers on reputed bioinformatic journals, such as Nucleotide Acids Research, Bioinformatics, PLoS Computational Biology, and Genomics, Proteomics & Bioinformatics. • Lead the Cancer Systems Biology Research Group in the Department of Biomedical Informatics at the Ohio State University. • Serve the review panel of the FACT program of NIFA. • Serve the journal Computational Biology and Chemistry as a co-editor. Assistant Professor 2015-2018 Department of Mathematics & Statistics, South Dakota State University Department of Agronomy, Horticulture, and Plant Science, South Dakota State University • Published 36 papers on reputed bioinformatic journals, such as Nucleotide Acids Research, Bioinformatics, PLoS Computational Biology, Briefings in Bioinformatics. With 14 papers published as corresponding authors and 4 papers as first authors. • Twenty proposals are funded by NIH, NSF, USDA, Sanford Health, Xsede, BioSNTR, and South Dakota State University. • Serve the review panel of the PBI program of NSF and NIFA. • Supervised one postdoc, eight graduate students and six undergraduate students. • Hosted five visiting scholars from University of Missouri–Columbia, Shandong University, Jilin University, etc. CV - Qin Ma – Page 3 of 22 Qin Ma, Ph.D. May 12, 2019 • Gave 46 oral/poster presentations on international conferences or universities. Assistant Research Scientist (With Dr. Ying Xu) 2014-2015 Department of Biochemistry & Molecular Biology, University of Georgia • Lead the BioEnergy Research group. • Performed flux balance & elementary flux mode analyses for elucidation of the genome-scale bacterial metabolic network in support of genetic engineering • Performed a computational study of plant cell-wall synthesis genes and co-expression modules. Postdoctoral research associate (With Dr. Ying Xu) 2011-2014 Department of Biochemistry & Molecular Biology, University of Georgia • Designed machine-learning and dynamic programming models in understanding the micro- and macro-structures of microbial genomes • Developed an integrated motif prediction and analysis toolkit aiming to elucidation of transcriptional regulatory network • Designed a phylogenetic model for understanding the effect of gene duplication on cancer progressing based on ten sequenced stomach cancer genomes • Collaborated with investigators from areas of biology, microbiology, and plant biology. Visiting Ph.D. student in Bioinformatics (With Dr. Ying Xu) 2008-2010 Department of Biochemistry & Molecular Biology, University of Georgia • Accumulation of substantial biological knowledge for further bioinformatic study • Designed graph-theoretic technique for biclustering of gene expression data • Designed combinatorial algorithms and programs for cis-regulatory motifs • Developed a combinatorial optimization framework for orthology mapping across bacterial genomes Research/Teaching Assistant in Mathematics (With Dr. Guojun Li) 2005-2008 School of Mathematics, Shandong University, Jinan, China • Established firm mathematical foundation for further academic study. INVITED