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Qin Ma, Ph.D. November 14, 2019 Qin Ma, Ph.D. November 14, 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: 310G Lincoln Tower 1800 Cannon Drive Columbus, OH, 43210 Lab Website: https://u.osu.edu/bmbl/ PROFESSIONAL EXPERIENCE 2019-now Associate Professor with tenure Department of Biomedical Informatics, College of Medicine, The Ohio State University. 2015-2018 Assistant Professor Department of Mathematics and Statistics and Department of Agronomy, Horticulture & 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 and Bioinformatics, o 2008-2010: University of Georgia, (Advisor: Prof. Ying Xu, with training in Bioinformatics and Computational Systems Biology), Thesis: Elucidation and identification of regulons for prokaryotic genomes. o 2005-2008: Shandong University, (Advisor: Prof. Guojun Li, with training in Algorithm Design and Graph Theory), B.S. (Hons) Applied Mathematics, 2001-2005: Shandong University, Awarded with first-class honors. CV - Qin Ma – Page 1 of 27 Qin Ma, Ph.D. November 14, 2019 PROFESSIONAL ORGANIZATION MEMBERSHIPS Editorship • Associate Editor, Computational Biology and Chemistry 2019-present • Associate Editor, BMC Genomics, 2015-present • Editor board member, Briefings in Bioinformatics 2019-present • Editor board member, BMC Bioinformatics 2019-present • Editor board member, Scientific Reports, 2018-present • Editor board member, Mathematical Biosciences, 2015-present • Guest Editor, IEEE Access. Special issue topic: Feature representation and learning methods with application in large-scale biological sequence analysis (with Dr. Quan Zou). 2019 • Guest Editor, BMC Genomics. International Conference on Intelligent Biology and Medicine (ICIBM 2019) June 9-11, Columbus, OH, USA. 2019 • Guest Editor, Computational and Structural Biotechnology Journal. Topic: Machine learning and pattern recognition techniques in molecular function and structure analysis. 2018 • Guest Editor, Mathematical Biosciences. Topic: State-of-the-art machine learning techniques in biomedical informatics. 2018 • Guest Editor, International Journal of Genomics. Topic: Bioinformatic Tools in Microbial Genomic Data Analysis. 2015 • Guest Editor, BioMed Research International. Topic: Scalable Data Mining Algorithms in Computational Biology and Biomedicine. 2015 Membership • Member, International Society for Computational Biology (ISCB), 2014-present • Member, Translational Data Analytics Institute of the Ohio State University, 2019-present • Member, 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 • Member, International Association for Intelligent Biology and Medicine (IAIBM), 2019 Conference program committee • 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, BIBM'19 The International Workshop on Expository Representation Learning of Biomedical Data (with Juan Cui) 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 CV - Qin Ma – Page 2 of 27 Qin Ma, Ph.D. November 14, 2019 RE SEARCH 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 LEADERSHIP DEVELOPMENT • FAME Faculty Career Acceleration Program at the Ohio State University, 2019-2020 • 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 • 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) CV - Qin Ma – Page 3 of 27 Qin Ma, Ph.D. November 14, 2019 RESEARCH EXPERIENCE Associate Professor with tenure 2019-present Department of Biomedical Informatics, Ohio State University • Faculty member of Biomedical Sciences Graduate Program (P status). • Faculty member of Translational Data Analytics Institute. • https://tdai.osu.edu/faculty/members/qin-ma/) • Faculty member of OSU Comprehensive Cancer Center (OSUCCC). • https://cancer.osu.edu/research-and-education/find-a-researcher/search- researcher-directory/qin-ma • Published 31 papers on reputed journals, such as Nucleotide Acids Research, Bioinformatics, PLoS Computational Biology, and Briefings in Bioinformatics. • Lead the Cancer Systems Biology Research Group in the Department of Biomedical Informatics. • Teach BMI 8130 (Analysis and Applications of Genome•Scale Data) and BSGP 7070 (Fundamentals of grant writing). • Serve the review panel of the FACT program of NIFA. • Serve the journal Computational Biology and Chemistry as a co-editor. • Serve the editorial board of Briefings in Bioinformatics. • Serve the ICIBM 2018 conference as the travel award committee chair. 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. • 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
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