Curriculum Vitae

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

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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

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• 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.

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• 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 PRESENTATIONS

International 1. (2019) Construction of cell specific gene co-regulations signatures based on single cell transcriptomics analysis and application in Cancer research. Department of Computer Science, Jilin University. June 17th, 2019. (Invited by Prof. Yan Wang) 2. (2017) Integrated and systematic views of regulatory DNA motif identification and analyses. Department of Computer Science, Jilin University. December 12th, 2017. (Invited by Prof. Yan Wang) 3. (2017) Computational modeling and bioinformatic applications in big biological data. May 23rd. Nankai University, Tianjin, China. (Invited by Dr. Han Zhang and Dr. Quan Zou) 4. (2016) Computational tools for RNA-Seq data analysis in genomes with highly duplicated nature. College of life sciences, Jilin University, July 5th, 2016, Changchun, China. (Invited by Dr. Yan Wang)

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5. (2015) Development and application of bioinformatic tools driven by genomic and transcriptomic data, Institute of Applied Mathematics, Academy of Mathematics & System Science, Chinese Academy of Sciences, May 18th, 2015, Beijing, China 6. (2015) Development and application of bioinformatic tools driven by genomic and transcriptomic data, Institute for Interdisciplinary Information Sciences, Tsinghua University, May 21st, 2015, Beijing, China. 7. (2015) Metabolic and Regulatory Network Analysis in Systems Biology, Dec. 21th, Biological Department, Nanjing Medical University, Nanjing, China. 8. (2015) Computational Methods in Bioinformatics: Omics data mining and modeling, January 6, 2015, Model Animal Research Center of Nanjing University, Nanjing, China.

National 9. (2018) Algorithm design and tool development for gene regulation elucidation from single-cell RNA-Seq data. The 4th International Conference on Mathematical and Computational Medicine in Cancun, Mexico Dec 3-7, 2018. (Invited by Dr. Andrzej Kloczkowski) 10. (2018) Development of computational techniques in elucidating gene regulation. October 1st, 2018. Ohio State University, Columbus, OH 43210. (Invited by Dr. Lang Li) 11. (2018) Development and application of computational methods driven by addressing genomic and transcriptomic questions. September 10th, 2018. Indiana University, Indianapolis, IN 46202. (Invited by Dr. Chi Zhang) 12. (2018) Hypothesis-driven and discovery-driven analysis of Grapevine expression data. January 16th, 2018. Plant & Animal Genome Conference, Jan. 14-18, San Diego, CA, USA. 13. (2017) RNA Sequencing Analyses & Mapping Uncertainty, August 25th, 2017, the University of California, Davis campus in Davis, California. (The Y1 meeting for the NSF Plant Genome Research Program). 14. (2017) Regulatory DNA motif identification by integrating DNA shape in a deep learning framework. Great Lakes Bioinformatics Conference, May 15 – 17. Chicago. 15. (2017) Computational modeling and bioinformatic applications in big biological data, May 11th, Department of Cell Systems and Anatomy, UT Health at San Antonio. 16. (2017) Development and application of computational methods driven by addressing bacterial genomic and transcriptomic questions, Mar. 2nd, University of Nebraska, Lincoln. 17. (2016) DMINDA2 web server: regulatory DNA motif identification and analyses. July 11. Orlando, Florida. Intelligent Systems for Molecular Biology (ISMB). Technology Track Presentation. 18. (2015) Development and application of computational tools driven by addressing bacterial genomic and transcriptomic questions, June 05, 2015, Department of Biostatistics and Bioinformatics, Emory University, GA. 19. (2015) Development and application of bioinformatic tools driven by genomic and transcriptomic data, July 28, 2015, Department of Computer Science, University of Missouri Columbia, MO. (Invited by Dr. Dong Xu) 20. (2015) Omics data mining & modeling and biological systems inference in Bioinformatics, January 22, 2015, MD Anderson Cancer Center, Houston, TX. 21. (2014) Inference of reliable genome-scale bacterial metabolic network based on transcriptomic data in support of genetic engineering, (BioEnergy Science Center) BESC retreat, June 9-11, 2014, Chattanooga, TN.

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22. (2012) Elucidation of the Dynamic Supercoil Structures of folded E. coli Chromosome, Department of Biostatistics and Bioinformatics, Emory University, USA. 23. (2009) QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data, the 8th Annual International Conference on Computational Systems Bioinformatics, Stanford University, USA.

OSU Local 24. (2019) Development and application of computational methods driven by addressing bacterial genomic and transcriptomic questions. May 23rd, Cancer systems biology research group meeting. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210. 25. (2019) Integrated and systematic views of regulatory DNA motif identification and analyses. April 5th, Seminar of the Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210. 26. (2019) Construction of cell specific gene co-regulations signatures based on single cell transcriptomics analysis and application in Cancer research. February 14th, Cancer systems biology research group meeting. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210.

SDSU Local 27. (2017) Development of Bioinformatic Tools in Systems Biology, Mar. 13th, Department of Biology, University of South Dakota, Vermillion. 28. (2017) Computational modeling and bioinformatics applications in big transcriptomic data, Feb. 16th, Department of Pharmaceutical Sciences, South Dakota State University, SD. (Departmental seminar, invited by Dr. Xiangming Guan) 29. (2016) Development & Application of Bioinformatic Tools Driven by Big Genomic & Transcriptomic Data. Nov. 10th, SDSU-Sanford Symposium. (Invited by Dr. Adam Hoppe) 30. (2016) Omic data mining & modeling and biological systems inference in Bioinformatics, Feb. 22nd, Department of Math & Stats, South Dakota State University, SD. (Departmental seminar). 31. (2016) Development of Bioinformatic Tools in Systems Biology, Feb. 12th, Department of Life science, South Dakota State University, SD. (Departmental seminar, invited by Dr. Xiuqing Wang) 32. (2016) Identification and high-throughput modeling of regulatory DNA, Feb. 8th, Department of Plant Science, South Dakota State University, SD. (Departmental seminar) 33. (2015) Systems Biology: Biological Network Analysis, Dec. 3rd, BioSNTR, South Dakota State University, SD. (Departmental seminar) 34. (2015) Network analysis in computational systems biology, Nov. 6th, Lab seminar, Department of Plant Science, South Dakota State University, SD. (Invited by Dr. Senthil Subramanian) 35. (2015) A Computational Pipeline for RNA Read-Mapping and Expression Estimate, Sept. 22nd, 2015, Lab seminar, Department of Plant Science, South Dakota State University, SD. (Invited by Dr. Anne Fennell)

RESEARCH GRANTS

Active Research Grants 1. NIH-NIGMS (R01) PI 09/01/2018-8/30/2022 $1.04 millions 1 Calendar Months

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Title: Construction of cell type specific gene co-regulation signatures based on single cell transcriptomics data. Project website: https://u.osu.edu/bmbl/highlights/r01/. 2. NSF-PGRP Co-PI 09/01/2016-08/31/2021 $4.6 millions 1 Calendar Months Title: RESEARCH-PGR: Adapting perennial crops for climate change: Graft transmissible effects of rootstocks on grapevine shoots. 3. Sanford Health PI 07/01/2017-08/31/2019 $99,084 0.5 Calendar Months Title: Elucidation of gut microbial biomarkers of obesity based on an integrated metagenomic and metatranscriptomic analysis pipeline. 4. USDA Hatch Project PI 08/22/2015-10/12/2019 $200,000 0.5 Calendar Months Title: Development and application of computational tools driven by inferring the genome-scale gene regulatory networks. 5. Xsede Research Program PI 2018-2020 50,000 SUs (Equal to $33,950) Title: A Computational Pipeline for Cell Type Classification and Cell-type-specific Gene Markers Identification based on Single-cell RNA-Sequencing Data. 6. OSU CCTS Teaming up pilot program PI 04/01/2019-03/31/2020 $25,000 A novel computational pipeline for functional profiling of human gut microbial metagenomic and metatranscriptomic data and causal associations with diseases.

Pending Research Grants 1. EPSCoR Track-1 co-PI 09/01/2019-08/31/2024 $3.5 millions Title: Rules of Life in root surface biofilms: Resilience of high efficiency N-fixing bacteria to competitors on artificial and plant root surfaces. 2. NIH/BACPAC co-PI 09/20/2019-09/19/2024 $56 millions BACPAC Data Integration, Algorithm Development and Operations Management Center. 3. NSF/IIBR PI 09/01/2019-08/31/2021 $300,000 EAGER: A Computational Framework for Recovery of scRNA-Seq Expression Estimates using Cell-type Prediction and Deconvolution of Bulk RNA-Seq data.

Completed Research Grants 1. EPSCoR-BioSNTR PI 07/01/2018-06/30/2019 $70,077 Title: SD RIC FY19: The Biochemical Spatiotemporal NeTwork Resource (Bio- SNTR) Center 2. USDA co-PI 11/01/2017-10/31/2019 $116,830 Title: Physiological and Molecular Characterization of Superior Waterlogging (WL) Tolerance Newly Transferred from Sea Wheatgrass (SWG) into Wheat. 3. BioSNTR co-PI 01/01/2016-12/30/2016 $20,000 Title: Identification of Novel Signaling Pathways Controlling Mobile Genetic Elements in Cancer. 4. BioSNTR PI 05/30/2016-08/05/2016 $5,000 Title: Development of a novel gene expression data analysis pipeline. 5. BioSNTR PI 05/30/2017-08/05/2017 $5,000 Title: Computationally assign the orphan enzymes in partially assigned pathways in the KEGG database. 6. BioSNTR co-PI 05/30/2018-08/05/2018 $5,000 Title: Identification of conserved 5’UTR regions among the 90 genes required for heterocyst formation and its oxic N2-fixation in Anabaena sp. PCC7120. 7. BioSNTR PI 05/30/2018-08/05/2018 $5,000

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Qin Ma, Ph.D. May 12, 2019

Title: Identification of cell-type-specific gene markers based on single-cell RNA- Sequencing data 8. South Dakota State University PI 10/01/2015-08/31/2016 $11,500 Title: A Computational Pipeline for High-throughput Gene Expression Data in Plant Genomes. 9. South Dakota State University co-PI 09/01/2016-08/31/2018 $19,920 Title: Using Genomic Technologies to Characterize Sustainability Traits in Prairie Cordgrass. 10. South Dakota State University PI 09/01/2016-08/31/2017 $5,840 Title: Development and application of a novel biclustering pipeline for RNA-seq data analysis in plant genomes. 11. South Dakota State University PI 05/30/2017-08/05/2017 $1,000 Title: Developing a computational pipeline for high-throughput sequencing data in plant genomes 12. South Dakota State University PI 11/01/2017-06/30/2018 $11,806 Title of Project: A Deep Learning Model for Regulatory DNA Motif Prediction Based on Next Generation Sequencing Data. 13. South Dakota State University PI 05/31/2018-10/31/2018 $2,000 Title: Developing a R package for functional metagenome and metatranscriptome data analysis for biofuel. 14. Xsede educational grant PI 2016-2018 3,780+3,000 SUs Title: Next-Generation Sequencing Data Analysis. 15. Xsede startup grant PI 2017-2018 5,000 SUs Title: Regulatory DNA motif identification by integrating DNA shape in a deep learning framework

MENTORING

Post-Docs Gaoyang Li (Bioinformatics at OSU) Mentor 2019-now Adam McDermaid (Statistics at SDSU) Mentor 2018-2019

Research Assistant Cankun Wang (Web server development) Mentor 2019-now Jany Chan (Ph.D. from Cornell University) Mentor 2019-now

Ph.D. Students Anjun Ma (BSGP at OSU) Thesis Committee, Chair 2019-now Juan Xie (Statistics at OSU) Thesis Committee, Chair 2019-now Roberto Villegas-Diaz (Bioinformatics) Thesis Committee 2018-2019 Michael Robben (Plant Science) Thesis Committee 2016-2019 Md. Ehsanul Haque (Plant Science) Thesis Committee 2017-2019 Surendra Neupane (Biology) Thesis Committee 2015-2019 Heather Deter (Computational Biology) Thesis Committee 2017-2019 Trevor Van Den Top (Biology) Thesis Committee 2016-2019 Sadikshya Aryal (Plant Science) Thesis Committee 2018-2019 Adam McDermaid (Statistics) Thesis Committee, Chair 2015-2018 • Thesis: Statistical Algorithms and Bioinformatics Tools Development for Computational Analysis of High-throughput Transcriptomic Data Alexander Harsh (Mathematics) Project Advisor 2017

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Brandon Monier (Biology) Project Advisor 2016-2018 Luai Muhammad (Plant Science) Thesis Committee 2016-2018

Master Students Yuzhou Chang (Biomedical Informatics at OSU) Project Advisor 2019-now Shaopeng Gu (Statistics at SDSU) Thesis Committee, Chair 2018-now Cankun Wang (Software engineering) Thesis Committee, Chair 2018-2019 • Received the best oral presentation of the Research Day 2019 at South Dakota State University. • Thesis: Development of Regulatory DNA Motif Identification Algorithm for ChIP-exo data in prokaryotic genomes Yohannes Tecleab (Statistics) Thesis Committee 2018-2019 Anjun Ma (Bioinformatics) Thesis Committee, Chair 2017-2019 Jinyu Yang (Statistics) Thesis Committee, Chair 2016-2018 • Thesis: Regulatory DNA Motif Identification Based on Big Biological Data and Deep Learning Juan Xie (Statistics) Thesis Committee, Chair 2016-2018 • Thesis: Development of Biclustering Techniques for gene expression Data Modeling and Mining Shihan Wu (Computer Science) Project Advisor 2017-2018 Spencer Schreier (Plant Science) Thesis Committee 2016-2017 Andrew Stocks (Health and Nutrition) Thesis Committee 2015-2016

Undergraduate Students Weiliang Liu Mathematics Department at OSU 2019-now Zichun Zhang Mathematics Department at OSU 2019-now Xubing Hao Software Engineering at Jilin University 2019-now Jennifer Xu Biostatistics at University of North Carolina at Chapel Hill 2019 summer Minxuan Sun Computer Science Department at SDSU 2017-2019 • Agriculture and Biological Sciences (ABS) Undergraduate Engagement Award. Paige Hinton Mathematics and Statistics Department at SDSU 2018-2019 Prajwal Khatiwada Computer Science Department at SDSU 2015-2016 Yiran Zhang Computer Science Department at SDSU 2015-2016 • Received the “Meeting the Grand Challenges Research Award” at SDSU. Xiaozhu Jin Computer Science Department at SDSU 2016-2017 • Received BioSNTR Summer Undergraduate Research Scholarship. Shuai Li Computer Science Department at SDSU 2017 • Received BioSNTR Summer Undergraduate Research Scholarship. Yirong Wang Computer Science Department at SDSU 2018 • Received BioSNTR Summer Undergraduate Research Scholarship. Zoey Glenn REU student from Drake University 2016 • Second-place prize of 2016 Undergraduate Research Symposium (160 posters) Jason Kiehne REU student from Simpson College 2016 • Second-place prize of 2016 Undergraduate Research Symposium (160 posters)

Visiting Scholars Jing Jiang (Ph.D. candidate) Xiamen University 2019-now Zhaoqian Liu (Ph.D. candidate) Shandong University 2019-now Junyi Chen (Ph.D. candidate) City University of Hong Kong 2019-now

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Shuangquan Zhang (Ph.D. candidate) Jilin University 2019-now Jichang Wu (Professor) Shandong University 2016-now Julian Martinez-Henao (Ph.D.) McGill University 05-08/2019 Bingqiang Liu (Professor) School of Mathematics, Shandong University 2016-2017 Shuang Wu (Professor) Fujian Agriculture and Forestry University 2016 Xiaoyu Ji (Ph.D.) Guangzhou University of Chinese Medicine 2016-2017

ACADEMIC SERVICES

International • Research Grants Council of Hong Kong, Peer Reviewer, 2016-now • NSERC, Canada, Peer Reviewer, 2018 Invited by Drs. Laurin and Jamett from Natural Sciences and Engineering Research Council of Canada (NSERC).

National • USDA NIFA FACT program Panel Reviewer, 03/22-25/2019 Invited by Daniel L Schmoldt (https://nifa.usda.gov/program/fact) • NSF ABI review panel, Panel Reviewer, 01/2019 Invited by Dr. Jennifer Weller • NIH NIGMS SEPs, Panel Reviewer, 12/2018 Invited by Dr. Brain Pike • NSF PBI review panel, Panel Reviewer, 09/2016 Reviewed Integrative Organismal Systems (IOS) proposals submitted to the Plant- Biotic Interactions (PBI) Program within the Physiological and Structural Systems Cluster. • Northern Illinois University Peer Reviewer, 01/2015 Summer Research grant program • Research and Scholarship funds Panel Reviewer, 03/2018 of South Dakota State University • Bioinformatics journals Peer Reviewer, 2013-now Reviewed >100 manuscripts from 18 journals, including Genome Research, Nucleic Acid Research, Bioinformatics, mBio, BMC Genomics, Journal of Bioinformatics and Computational Biology, Transactions on Computational Biology and Bioinformatics, Mathematical Biosciences, Journal of Theoretical Biology, Genomics, Proteomics & Bioinformatics, International Journal of Computing Science and Mathematics, International Journal of Genomics, Scientific Reports, Journal Proteome Research, Computational and Structural Biotechnology Journal, Methods, Frontiers in Neuroscience, Frontiers in Microbiology.

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OSU Service • Poster Judge, OSU COM Trainee Research Day, April 11th, 2019. • Organize the service core for Single cell sequencing data analysis and Third- generation sequencing with Department of Neuroscience. • Committee member of the BMI Systems Committee. • Lead the collaboration and service (RNA-Sequencing and scRNA-Sequencing data analysis) with Department of Microbial Infection and Immunity (Dr. Eugene Oltz).

SDSU Service • Poster Judge, Gamma Sigma Delta Second Annual Poster Contest, April 4th, 2016. • Discussion session, Strategic Plan of Plant Science Department, October 30, 2015. • Department Review, 2016. Leading the description and focus on Bioinformatics. • Committee member, Department seminar, 2016-now. • Search committee member, Senior Computer Support Specialist, 11/27/2016-2017. • Search committee member, part-time lecturer position (Crop Production). 05122018 • Judge for the Eastern SD Science and Engineering Fair (ESDSEF), the Computer Sci/Engineering/Math Panel, March 21st, 2017-2018.

JOURNAL PUBLICATIONS ($corresponding author, *co-first author)

2019-now (OSU) 1. Anjun Ma*, Minxuan Sun*, Adam McDermaid, Bingqiang Liu, Qin Ma$, MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. Bioinformatics. Accepted on 05/11/2019. BIOINF-2018-2615.R1. 2. Ren Qi, Anjun Ma, Qin Ma$, Quan Zou$, Clustering and Classification Methods for Single-cell RNA-sequencing Data: A Review. Briefings in Bioinformatics. Accepted on 04/22/2019. BIB-19-0053.R2. 3. Simon Niu, Bingqiang Liu, Qin Ma$, Wen-Chi Chou$, rSeqTU: a machine learning based R package for transcriptional unit prediction in bacterial genomes. Frontiers in Genetics. DOI: 10.3389/fgene.2019.00374. 2019. BIORXIV: https://www.biorxiv.org/content/10.1101/553057v1. 4. Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, and Qin Ma$, IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. PLoS Computational Biology. 15(2): e1006792. 2019. DOI: 10.1371/journal.pcbi.1006792. 5. Xiaoying Wang, Bin Yu, Anjun Ma, Cheng Chen, Bingqiang Liu, Qin Ma$, Protein- protein interaction sites prediction by ensembling random forests with synthetic minority oversampling technique. Bioinformatics. bty995. 2019. doi: 10.1093/bioinformatics/bty995. 6. Yan Wang, Sen Yang, Jing Zhao, Wei Du, Yanchun Liang, Cankun Wang, Fengfeng Zhou, Yuan Tian, and Qin Ma$, Using machine learning to measure relatedness between genes: a multi-feature model. Scientific Reports. Volume 9, Article number: 4192 (2019). 10.1038/s41598-019-40780-7. 7. Ye Xia, Seth Debolt, Adam McDermaid, Qin Ma. Improved Draft Genome Sequence of Pseudomonas poae strain A2-S9 with plant growth promotion activity.

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Genome Announcements. Microbiology Resource Announcements. 2019. MRA00275-19. 8. Jichang Wu, Hajo Broersma, Yaping Mao, Qin Ma$, Removable edges on a Hamilton cycle or outside a cycle in a 4-connected graph. 2018. Discussiones Mathematicae Graph Theory (DMGT). 2019. 10.7151/dmgt.2209. 9. Yan Wang, Shuang-Quan Zhang, Sen Yang, Li-Li Yang, Yuan Tian, Qin Ma, Measurement of Relatedness Between Genes Using Fully Convolutional Neural Network. Frontiers in Genetics. ID: 463811. 04/18/2019. 10. Xing Shi, Zhancheng Gao, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang, Jun Yu. Meta- analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients. Genomics, Proteomics & Bioinformatics. 2019. In press. 11. Ye Xia, Dr. Seth DeBolt, Qin Ma, Adam McDermaid, Cankun Wang, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Improved Draft Genome Sequence of Bacillus sp. YF23 with plant growth promotion activity. Genome Announcements. Microbiology Resource Announcements. 2019. MRA00099-19. 12. Zoë Migicovsky, Zachary N. Harris, Laura L. Klein, Mao Li, Adam McDermaid, Daniel H. Chitwood, Anne Fennell, Laszlo G. Kovacs, Misha Kwasniewski, Jason P. Londo, Qin Ma, and Allison J. Miller. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. Horticulture Research. In press. BioRxiv DOI: https://doi.org/10.1101/484212. 13. Xiaolan Rao, Xin Chen, Hui Shen, Qin Ma, Guifen Li, Yuhong Tang, Maria Pena, William York, Taylor Frazier, Scott Lenaghan, Xirong Xiao, Fang Chen and Richard A. Dixon, Gene Regulatory Networks for Lignin Biosynthesis in Switchgrass (Panicum virgatum). Plant Biotechnology Journal (2019)17, pp. 580–593. DOI: 10.1111/pbi.13000. 14. Vedbar Singh Khadka, Kimberley Vaughn, Padmapriya, Swaminathan, Juan Xie, Qin Ma, Grant R. Cramer, Anne Fennell. Shoot transcriptomic response is more sensitive to water deficit than root transcriptomic response in Vitis riparia (Michx.). BMC Plant Biology, 2019 19:72. https://doi.org/10.1186/s12870-019-1664-7. 15. Suresh Damodaran, Amélie Dubois, Juan Xie, Qin Ma, Valérie Hindié, Senthil Subramanian, GmZPR3d interacts with GmHD-ZIP III proteins and regulates soybean root and nodule vascular development. International Journal of Molecular Sciences. 2019, 20, 827; doi:10.3390/ijms20040827 16. Yan Wang, Keke Liu, Qin Ma, Yongfei Tan, Wei Du, Yidan Lv, Yuan Tian and Hao Wang. Pancreatic Cancer Biomarker Detection by Two Support Vector Strategies for Recursive Feature Elimination. Biomarkers in Medicine. 2019 Feb 15. doi: 10.2217/bmm-2018-0273. 17. Han Shia, Simin Liu, Junqi Chen, Xuan Li, Qin Ma, Bin Yu. Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure. Genomics. 2019. DOI: https://doi.org/10.1016/j.ygeno.2018.12.007. 18. Baoguang Tian, Xue Wu, Cheng Chen, Wenying Qiu, Qin Ma, Bin Yu. Predicting protein-protein interactions by fusing various Chou's pseudo components and using wavelet denoising approach. Journal of Theoretical Biology. S0022-5193(18)30564-2, 2019. DOI: 10.1016/j.jtbi.2018.11.011.

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19. Xiaowen Cui, Zhaomin Yu, Bin Yu, Minghui Wang, Baoguang Tiana, Qin Ma, UbiSitePred: a novel method for improving accuracy of ubiquitination sites prediction by using LASSO to select the optimal Chou's pseudo components. Chemometrics and Intelligent Laboratory Systems. S0169-7439(18)30522-7. 2019. DOI: https://doi.org/10.1016/j.chemolab.2018.11.012. 20. Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao, Chi Zhang. M3S: A comprehensive model selection for multi-modal single-cell RNA sequencing data BMC Bioinformatics. Accepted on 03/25/2019 through International Conference on Intelligent Biology and Medicine (ICIBM 2019).

2015-2018 (SDSU) 21. Adam McDermaid, Xin Chen, Yiran Zhang, Cankun Wang, Juan Xie, Qin Ma$, A new machine learning-based framework for mapping uncertainty analysis in RNA-Seq read alignment and gene expression estimation. Frontiers in Genetics. https://doi.org/10.3389/fgene.2018.00313. 2018. 22. Jinyu Yang, Adam McDermaid, Xin Chen, and Qin Ma$, DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx223. 13 April 2017. 23. Yu Zhang*, Juan Xie*, Jinyu Yang, Anne Fennell and Qin Ma$, QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinformatics. DOI: 10.1093/bioinformatics/btw635. 2017. 24. Bingqiang Liu, Guojun Li, Guanghui Wang, Anne Fennell, Yu Kang, Qi Liu and Qin Ma$, An integrative and applicable phylogenetic footprinting framework for cis- regulatory motifs identification in prokaryotic genomes. BMC Genomics. DOI: 10.1186/s12864-016-2982-x. 2016. 25. Juan Xie, Anjun Ma, Anne Fennell, Jing Zhao, Qin Ma$, A comprehensive review of the biclustering application in addressing biological and biomedical problems. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bby014. 2018. 26. Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Yu Kang, Qin Ma$. Bioinformatics tools for metagenome and metatranscriptome data analysis in microbiome studies. Briefings in Bioinformatics. doi: 10.1093/bib/bbx051. 2017, 1-15. 27. Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma$. An algorithmic perspective of de-novo cis-regulatory motif finding based on ChIP-Seq data. Briefings in Bioinformatics. doi: 10.1093/bib/bbx026. 2017, 1–13. 28. Adam McDermaid, Brandon Monier, Jing Zhao, Bingqiang Liu, and Qin Ma$, Interpretation of differential gene expression results of RNA-Seq data: review and integration. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bby067. 06 August 2018. 29. Sen Liang, Anjun Ma, Yan Wang$, Qin Ma$, Paired Data Feature Selection Methods for Gene Expression Data Analysis: A Comprehensive Review. Computational and Structural Biotechnology Journal, 2018. DOI: https://doi.org/10.1016/j.csbj.2018.02.005. 30. Fang Zhang*, Anjun Ma*, Zhao Wang, Qin Ma, Bingqiang Liu, Lan Huang, Yan Wang, A Central Edge Selection Based Overlapping Community Detection Algorithm for the Detection of Overlapping Structures in Protein-Protein Interaction Networks. Molecules, 23(10), 2633; DOI: 10.3390/molecules23102633. 2018. 31. Siyu Han, Yanchun Liang, Qin Ma, Cankun Wang, Yangyi Xu, Yu Zhang, Wei Du and Ying Li, LncFinder: an integrated package for long non-coding RNA identification

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utilizing sequence intrinsic composition, structural information and physicochemical property. Briefings in Bioinformatics. bby065, https://doi.org/10.1093/bib/bby065. 2018. 32. Yu Zhang, Sha Cao, Jing Zhao, Qin Ma$, and Chi Zhang$, MRHCA: a nonparametric statistics-based method for hub and co-expression module identiﬁcation in large gene co-expression network. Quantitative Biology. DOI: https://doi.org/10.1007/s40484-018-0131-z. 2018. 33. Surendra Neupane, Qin Ma, Madhav P. Nepal, Febina Mathew, Adam Varenhorst, and Ethan J. Andersen, Comparative Analysis of TNL Disease Resistance Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Biochemical Genetics, doi: 10.1007/s10528-018-9851-z. 2018 Mar 2. 34. Bingqiang Liu, Ling Han, Xiangrong Liu, Jichang Wu, Qin Ma$. Computational prediction of sigma-54 promoters in bacterial genomes by integrating motif finding and machine learning strategies. IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2018.2816032. 2018. 35. Guoqing Liu, Qin Ma, Ying Xu, Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome. Mathematical Biosciences. DOI: 10.1016/j.mbs.2018.03.026. 2018. 36. Xin Chen*, Anjun Ma*, Hanyuan Zhang, Chao Liu, Huansheng Cao, Yan Wang, Qin Ma$, RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics analysis. Genes. 2018, 9(6), 278. doi: https://doi.org/10.3390/genes9060278. 37. Huansheng Cao*, Qin Ma*, Xin Chen, Ying Xu$, DOOR: A microbial operon database for gene organization and function discovery. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbx088. 2017. 38. Xin Chen, Wen-Chi Zhou, Qin Ma$ and Ying Xu$, SeqTU: A Web Server for RNA-Seq based Transcription Unit Identification in Bacteria. Scientific Reports. Article number: 43925. doi:10.1038/srep43925. 2017 39. Huansheng Cao, Wei Du, Yuedong Yang, Yu Shang, Gaoyang Li, Yaoqi Zhou, Qin Ma, Ying Xu, Systems-Level Understanding of the Impact of Ethanol-Induced Stresses and Adaptation in E. coli. Scientific Reports. Article number: 44150. doi:10.1038/srep44150. 2017. 40. Quan Zou, Dariusz Mrozek, Qin Ma, Yungang Xu, Special issue: Scalable Data Mining Algorithms in Computational Biology and Biomedicine. BioMed Research International. 2017. 41. Ying Li, Shi Xiaohu, Liang Yanchun, Juan Xie, Yu Zhang, Qin Ma$, RNA-TVcurve: A Web Server for RNA Secondary Structure Comparison based on a Multi-Scale Similarity of its Triple Vector Representation. BMC Bioinformatics 18:51 DOI 10.1186/s12859-017-1481-7. 2017. 42. Lina Yuan, Yang Yu, Yanmin Zhu, Yulai Li, Changqing Li, Rujiao Li, Qin Ma, Gilman Kit-Hang Siu, Jun Yu, Taijiao Jiang, Jingfa Xiao, Yu Kang, GAAP: Genome- Organization-Framework-Assisted Assembly Pipeline for the Prokaryotic Genome. BMC Genomics. 18(Suppl 1):952, DOI: 10.1186/s12864-016-3267-0. 2017. 43. Zhenjia Wang, Chuan Zhou, Bingqiang Liu, Qin Ma, Guojun Li, An Insight into Species from Same Descendent Aspect and the Application into Clostridia. Current Bioinformatics. Volume 12, Issue 2, DOI: 10.2174/1574893611666160616130126. 2017.

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44. Guohui Chuai, Fayu Yang, Yanan Chen, Qin Ma, Chi Zhou, Chenyu Zhu, Feng Gu, and Qi Liu, Deciphering determining factors rather than microhomology on the occurrence of in-frame mutation in human CRISPR-based gene knockout. Molecular Therapy - Nucleic Acids, DOI: 10.1038/mtna.2016.35. 2016. 45. Guishen Wang, Lan Huang, Yan Wang, Wei Pang, and Qin Ma, A link density clustering algorithm based on automatically selecting density peaks for overlapping community detection. International Journal of Modern Physics B. 2016 46. Bingqiang Liu, Chuan Zhou, Guojun Li, Hanyuan Zhang, Erliang Zeng, Qin Ma$, Bacterial regulon modeling and prediction based on systematic cis-regulatory motif analyses. Scientific Reports, doi:10.1038/srep23030. 2016. 47. Yi Sun, Yunqin Chen, Wei Zhang, Qin Ma, Jia Wei, Qi Liu, identifying anti-cancer drug response related genes using integrative analysis of transcriptomic and genomic variations with cell line-based drug perturbations. Oncotarget, DOI: 10.18632/oncotarget.7012. 2016. 48. Zhuoyuan Xin, Qin Ma, Guoqing Wang, Shuangchun Ren, Fan Li, The understanding of circular RNAs as special triggers in carcinogenesis. Briefings in functional genomics, 2016. 49. Jiading Yang, Eric Worley, Qin Ma, Jun Li, Ivone Torres-Jerez, Yi-Ching Lee, Jiyi Zhang, Nick Krom, Fuqi Liao, Yuhong Tang, Patrick X. Zhao, Michael Udvardi, Nitrogen conservation and underlying changes in genome activity associated with annual senescence in perennial Switchgrass, Panicum virgatum. New Phytologist, Jul;211(1):75-89. DOI: 10.1111/nph.13898. 2016. 50. Guishen Wang, Lan Huang, Yan Wang, Qin Ma, Wei Pang, Link community detection based on linear graphs with a novel link similarity measure. International Journal of Modern Physics, https://doi.org/10.1142/S0217979216500235. 2016. 51. Guangyu Xu, Yan Xia, Ying Tang, Huansheng Cao, Qin Ma, Ying Xu, Nan Zhang, Hong Xu, Bibliometric Screening of Helicobacter Pylori Pathogenic Genes Through Pathway Enrichment and Operon Analysis. Clinical laboratory, 62(11):2125-2137. DOI: 10.7754/Clin.Lab.2016.160319. 2016.

2009-2015 (UGA) 52. Wen-Chi Chou*, Qin Ma*, Shihui Yang, Sha Cao, Steven D. Brown, Ying Xu, Analysis of strand-specific RNA-Seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. Nucleic Acids Research (Methods), DOI: 10.1093/nar/gkv177, 2015. 53. Xizeng Mao*, Qin Ma*, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu. DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Research, 42 (Database issue):D654-9. 2014, Jan. 54. Qin Ma, Hanyuan Zhang, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, and Ying Xu, DMINDA: An integrated high-performance web server for DNA Motif analyses. Nucleic Acids Research, 42 (Web Server issue):W12-9. 2014, Jul. 55. Qin Ma, Jaxk Reeves, David A. Liberles, Lili Yu, Zheng Chang, Jing Zhao, Ying Xu, Liang Liu, A phylogenetic model for understanding the effect of gene duplication on cancer progressing. Nucleic Acids Research (Methods), 42(5):2870-8. 2014, Mar.

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56. Qin Ma, Yanbin Yin, Mark A. Shell, Han Zhang, Guojun Li, Ying Xu, Computational Analyses of Transcriptomic Data Reveal the Dynamic Organization of the E. coli Chromosome under Different Conditions. Nucleic Acids Research, 41(11):5594-603. (Regular Article). 2013, Jun. 57. Guojun Li, Bingqiang Liu, Qin Ma, Ying Xu, A new framework for identifying cis- regulatory motifs in prokaryotes. Nucleic Acids Research (Methods), 39(7):e42.39(7):e42. 2011, Apr. 58. Guojun Li*, Qin Ma*, et al., Integration of Sequence-Similarity and Functional Association Information Can Overcome Intrinsic Problems in Orthology Mapping across Bacterial Genomes. Nucleic Acids Research (Methods), 39(22):e150. 2011, Dec. 59. Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, Ying Xu, QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data. Nucleic Acids Research (Methods), 37(15):e101. 2009, Aug. (cited 185 times) 60. Juan Cui, Yanbin Yin, Qin Ma, Guoqing Wang, Victor Olman, Yu Zhang, Wen-Chi Chou, Celine S. Hong, Chi Zhang, Sha Cao, Xizeng Mao, Ying Li, Steve Qin, Shaying Zhao, Jing Jiang, Phil Hastings, Fan Li, Ying Xu, Comprehensive Characterization of the Genomic Alterations in Human Gastric Cancer. International journal of cancer, DOI: 10.1002/ijc.29352. 11/2014. 61. Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu, An integrated toolkit for accurate prediction and analysis of cis regulatory elements at a genome scale. Bioinformatics, 29(18):2261-8. 2013, Sep. 62. Qin Ma, Ying Xu, Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency. Genomics, Proteomics & Bioinformatics, 11: 66-71, 2013. 63. Xin Chen*, Qin Ma*, Xiaolan Rao, Yuhong Tang, Yan Wang, Gaoyang Li, Chi Zhang, Xizeng Mao, Richard A. Dixon and Ying Xu, Genome-scale identification of cell-wall related genes in Switchgrass through comparative genomics and computational analyses of transcriptomic data. BioEnergy Research, DOI: 10.1007/s12155-015-9674-2. 2015. 64. Xizeng Mao*, Qin Ma*, Bingqiang Liu, Xin Chen, Chuan Zhou, Ying Xu. Revisiting Operons: An Analysis of the Landscape of Transcriptional Units in E. coli. BMC Bioinformatics, DOI: 10.1186/s12859-015-0805-8. 2015 65. Chuan Zhou*, Qin Ma*, Xizeng Mao, Yanbin Yin, and Ying Xu, New Insights into Clostridia through Comparative Analyses of Their 40 Genomes. BioEnergy Research, doi: 10.1007/s12155-014-9486-9. 2014. 66. Qin Ma*, Xin Chen*, Fei Ji, Chao Liu, Hanyuan Zhang, Ying Xu, Understanding the commonality and differences in genomic organizations across multiple closely related organisms from an energy perspective. Science China, Vol.57 No.10: 1-10. October 2014, 67. Chuan Zhou*, Qin Ma*, Guojun Li, Elucidation of operon structures across multiple closely related organisms. PLoS ONE, 9(6):e100999. 2014, Jun 24. 68. Charlotte M. Wilson, Shihui Yang, Miguel Rodriguez, Jr., Qin Ma, Courtney M. Johnson, Lezlee Dice, Ying Xu, Steven D. Brown, Clostridium thermocellum transcriptomic profiles after exposure to ethanol, furfural or heat stress. Biotechnology for Biofuels, 2013, 6:131. 69. Lingpeng Meng, Qin Ma, Han Chuanfeng, Qidi Wu, Determining the Number of Facilities for Large-Scale Emergency.

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International Journal of Computing Science and Mathematics, Vol. 4, 242-251. 2013. 70. Shan Wang*, Yanbin Yin*, Qin Ma, Xiaojia Tang, Kan Bao, Dongyun Hao, Ying Xu, Genome-scale identification of cell-wall related genes in Arabidopsis based on co- expression network analysis. BMC Plant Biology, 12:138. 2012, Aug 9. 71. Jing Zhao, Qin Ma, Yuquan Cui, Comparative study on macro-economic regionalization: an application of biclustering algorithm. Journal of Shandong University, 49(7): 71-77. 2012. 72. Sara Blumer-Schuette, Richard Giannone, Jeffrey Zurawski, Inci Ozdemir, Qin Ma, Yanbin Yin, Ying Xu, Irina Kataeva, Farris L. Poole II, Michael W. W. Adams, Scott D. Hamilton-Brehm, James G. Elkins, Frank W. Larimer, Miriam L. Land, Loren Hauser, Robert W. Cottingham, Robert L. Hettich, and Robert M. Kelly, Caldicellulosiruptor core and pan genomes reveal determinants for non-cellulosomal thermophilic deconstruction of plant biomass. Journal of Bacteriology, 194(15):4015-28. 2012. 73. Fengfeng Zhou*, Qin Ma*, Guojun Li, Ying Xu, QServer: a biclustering server for prediction and validation of co-expressed gene clusters. PLoS ONE, 7(3):e32660. 2012. 74. Guojun Li, Qin Ma, Bingqiang Liu, Haibao Tang, Andrew H. Paterson, Ying Xu. A Close-to Optimum Bi-clustering Algorithm for Microarray Gene Expression Data. Computational Systems Bioinformatics, 082Li, 2009.

2007-2009 (SDU) 75. Qin Ma, Jian-Liang Wu, Xiao Yu, Planar graphs without 5-cycles or 6-cycles. Discrete Mathematics, 309: 2998-3005. 2009. 76. Qin Ma, the degree-constrained k-arboricity of outerplanar graphs. Journal of Shandong University, 42 (10): 41-43. 2007.

TEACHING

• Lecture, Analysis and Applications of Genome-Scale Data (BMI 8130), Autumn 2019, TR 9:35-10:55pm. Department of Biomedical Informatics, The Ohio State University. • Guest lecture, Data Mining, Department of Computer Science, OSU, 03/26/2019. Topic: Cluster Analysis in Bioinformatics: Basic Concepts and Algorithms • Lecture, Next Generation Sequencing Data Analysis (PS-735), 2016-2018 Department of Mathematics and Statistics, and Agronomy, Horticulture, and Plant Science Department, SDSU (57 graduate students). • Lecture, SD EPSCoR Bioinformatics workshop. 2017. Integrated and systematic views of regulatory DNA motif identification and analyses. • Guest lecture, Bioinformatics, SDSU, 2015. Topic: Network analysis in computational systems biology, Department of Mathematics and Statistics. • Guest lecture, Graduate seminar class, SDSU, 2015 • Guest Lecturer, Computational Methods in Bioinformatics, 2014-2015, Topic: For microarray analysis and regulatory motif finding, Department of Biochemistry and Molecular Biology, the University of Georgia. • Lecturer, Probability theory, 2008-2009. School of Electrical Engineering, Shandong University • Lecturer, Linear Algebra, 2007-2008, School of Electrical Engineering, Shandong University

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• Lecturer, Operational Research, 2007-2008, School of Information Science and Engineering, Shandong University • Lecturer, Advanced Mathematics, 2006-2007, School of Materials Science and Engineering, Shandong University

DEVELOPED SOFTWARE TOOLS

1. BRIC: A novel biclustering method for the detection of the repertoire of active gene regulatory signals and cell type prediction from single cell RNA-Seq datasets. Link: https://github.com/maqin2001/BRIC. 2. M3S: A user-friendly tool for comprehensive evaluation of multi-modality and statistical model selection for single-cell RNA sequencing data. Link: https://github.com/zy26/M3S. 3. LTMG: An R package for Single Cell RNA-seq data analysis within the Left Truncated Mixture Gaussian scheme. Link: https://github.com/zy26/LTMGSCA. 4. MetaQUBIC: A biclustering-based package for metagenomic and metatranscriptomic data. Link: https://github.com/maqin2001/metaqubic. 5. IRIS3: Integrated Cell-type-specific Regulon Inference from Single-cell RNA-Seq. Link: http://bmbl.sdstate.edu/iris3/. OSU link: https://bmbl.bmi.osumc.edu/iris3/. 6. rSeqTU: A machine learning based R package for identification of bacterial transcriptional units. https://s18692001.github.io/rSeqTU/. 7. EL-SMURF: An Ensemble Learning of SMOTE for Unbalancing samples and RF algorithm in PPI sites prediction. https://github.com/QUST-AIBBDRC/EL-SMURF/. 8. ViDGER: interpretation of differential gene expression results of RNA-seq data. https://github.com/btmonier/vidger. 9. IRIS-EDA: A Shiny package for differentially expressed gene analysis. Link: http://bmbl.sdstate.edu/IRIS/. GitHub: https://github.com/btmonier/iris. 10. DESSO: A web server for DNA and Shape motif identification based on a Deep Learning framework. Link: http://bmbl.sdstate.edu/DESSO/. GitHub source code: https://github.com/viyjy/DESSO. 11. GeneQC: A tool for gene expression level quality control. Link: http://bmbl.sdstate.edu/GeneQC/home.html. The GitHub link: https://github.com/maqin2001/GeneQC. 12. MFR: A machine learning model for measuring relatedness between a pair of genes. Link: http://bmbl.sdstate.edu/MFR/page/home.html. 13. LncFinder: Identifying and discovering new lncRNA transcripts have been the fundamental process in lncRNA-related research. Link: http://bmbl.sdstate.edu/lncfinder/index.php?m=Home&c=Index&a=index. 14. QUBIC2.0: A novel biclustering algorithm for large-scale bulk RNA-sequencing and single-cell RNA-sequencing data analysis. Link: https://github.com/maqin2001/qubic2. 15. DMINDA2.0, DNA motif prediction and analysis web server, Jinyu Yang. Link: http://bmbl.sdstate.edu/DMINDA2/. 16. SeqTU: A Web Server for RNA-seq based Transcription Unit Identification in Bacteria. Link: http://csbl.bmb.uga.edu/SeqTU_dev/index.php. New link at SDSU: http://bmbl.sdstate.edu/SeqTU_dev/. The GitHub R package source code: https://github.com/s18692001/SeqTU/. 17. SPP: A sigma-54 promoter predictor in prokaryotic genomes based on a machine learning method. Link: https://github.com/maqin2001/PromotePredictor.

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18. RAMME: An R package for metagenome and metatranscriptome data modeling and analysis. Link: https://github.com/maqin2001/RAMME. 19. QUBIC R package, Bioconductor, Yu Zhang and Juan Xie. Link: http://bioconductor.org/packages/devel/bioc/html/QUBIC.html 20. DMINDA: An integrated web server for DNA Motif prediction and analyses. Link: http://csbl.bmb.uga.edu/DMINDA/ 21. Cancer-evolution: A phylogenetic model for understanding the effect of gene duplication on cancer progression. Link: http://code.google.com/p/cancer-evolution/ 22. DOOR2: Database of prOkaryotic OpeRons Link: http://csbl.bmb.uga.edu/DOOR/index.php 23. Supercoil: Bacterial chromosome folding structure under different conditions Link: https://code.google.com/p/supercoil/ 24. BoBro: an integrated toolkit for prediction and analysis of cis-regulatory motifs Link: https://code.google.com/p/bobro/ 25. GOST: an orthology mapping tool for prokaryotes. Link: https://code.google.com/p/gost-an-orthology-mapping-tool/ 26. QUBIC: A QUalitative BIClustering tool for analysis of transcriptomic data. Link: https://code.google.com/p/qubic-biclustering/

CONFERENCE POSTERS

1. (2019) Anjun Ma, Qin Ma, IRIS3: Interpretation of cell-type-specific regulons identification from single-cell RNA-Sequencing data. OSU Trainee Research Day. April 1st, 2019. The Ohio State University. 2. (2018) Adam McDermaid, Shaopeng Gu, Qin Ma, Integrated Interpretation for Gene Expression Estimations of RNA-Seq Data. Plant Science Research Day, December 5th, 2018. South Dakota State University. 3. (2018) Anjun Ma, Minxuan Sun, Qin Ma, MetaQUBIC: a biclustering-based package for gene-level functional profiling of metagenome and metatranscriptome. Plant Science Research Day, December 5th , 2018. South Dakota State University. 4. (2019) Zoë Migicovsky, Arianna Bozzolo, Daniel Chitwood, Anne Fennell, Zachary Harris, Laura L. Klein, Laszlo Kovacs, Misha Kwasniewski, Mao Li, Jason Londo, Qin Ma, Adam McDermaid and Allison Miller, Rootstock Effects on Shoot System Phenotypes in Grafted Grapevines. Plant and animal genome conference. Jan 12-16, 2019. San Diego, CA. 5. (2018) Cankun Wang, Qin Ma, Combining computational methods and experimental data for Motif prediction. Plant Science Research Day, April 26th, 2018. South Dakota State University. 6. (2018) Anjun Ma, Qin Ma, Bioinformatics and Mathematical Biosciences Lab, Faculty Excellence Showcase on Celebration of Faculty Excellence. Brookings, SD, February 21, 2018. 7. (2017) Adam McDermaid, Yiran Zhang, Anne Fennell, Qin Ma. RNA Sequencing Analyses, Mapping Uncertainty, & Modeling. NSF Site Visit, Brookings, SD, September 7, 2017. 8. (2017) Shuai Li (presenter), Jinyu Yang, Qin Ma, Development of an integrative pipeline for quantitative and functional metagenome and metatranscriptome data analysis in microbes. BioSNTR undergraduate student research symposium. August 4th, 2017. Pierre.

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9. (2017) Adam McDermaid, Anne Fennell, Qin Ma, RNA Sequencing Analysis, Applications, & Modeling. All investigator meeting in South Dakota. May 22nd. Chamberlain. 10. (2017) Jinyu Yang, Qin Ma, Regulatory DNA motif identification by integrating DNA shape in a deep learning framework. Great Lakes Bioinformatics Conference, May 15 – 17. Chicago. 11. (2017) Xiaolan Rao, Xin Chen, Hui Shen, Qin Ma, Guifen Li, Yuhong Tang and Richard A. Dixon, Transcriptional regulatory network of secondary cell wall formation in switchgrass (Panicum virgatum). BioEnergy Science Center (Annual Retreat), Chattanooga, TN. June. 12. (2017) Shuchi Smita, Jason Kiehne, Qin Ma, Erliang Zeng and Senthil Subramanian, Gene regulatory networks associated with nodule development in soybean. Plant & Animal Genome Conference, Jan. 14-18, San Diego, CA, USA. 13. (2017) Juan Xie, Qin Ma, Biclustering and its applications in the big biological data era. Plant & Animal Genome Conference, Jan. 14-18, San Diego, CA, USA. 14. (2016) Adam McDermaid, Qin Ma, Michael Wisniewski, John Norelli, Timothy Artlip, Wenfeng An, Suman Lee, RNA Sequencing Analysis and Differential Gene Expression Pipelines. Nov. 10th, SDSU Sanford Symposium. Brookings, SD. 15. (2016) Juan Xie, Qin Ma, Biclustering in Big Biological Data Analysis. Oct. 27th, SDSU Avera Symposium, Brookings, SD. 16. (2016) Nepal, M.P., S. Neupane, F. Mathew, Qin Ma, A. Varenhorst, E.J Andersen, R.N. Reese. 2016. Comparative Genomics of Disease Resistance Genes in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Poster presented at the Annual Conference of Botanical Society of America- Botany 2016. July 30 –August 3. Savannah, Georgia, USA. 17. (2016) Jason Kiehne (undergraduate student), Shuchi Smita, Qin Ma, Sen Subramanian, Inference of key gene regulatory network in soybean nodules based on biclustering and modularity algorithms. 2016 Undergraduate Research Symposium, Pierre, SD. 18. (2016) Xiaozhu Jin (undergraduate student), Juan Xie, Qin Ma, A Computational Pipeline for Gene Expression Data Analysis. 2016 Undergraduate Research Symposium, Pierre, SD. 19. (2016) Zoey Glenn (undergraduate student), Qin Ma, Anne Fennell, Modeling Chilling Fulfillment in Grapevine. 2016 Undergraduate Research Symposium, Pierre, SD. (Second-place prize out of 160 posters) 20. (2016) Bingqiang Liu, Jinyu Yang, Guojun Li, Hanyuan Zhang, Ying Xu, Qin Ma, Development of Computational Tools in DNA motif identification and analyses, BioEnergy Science Center, Chattanooga, TN. 21. (2016) Xiaolan Rao, Xin Chen, Hui Shen, Qin Ma, Ying Xu and Richard A. Dixon, Co- expression analysis to identify transcriptional networks that regulate secondary cell wall formation in Switchgrass. BioEnergy Science Center, Chattanooga, TN, 2016. 22. (2016) Yiran Zhang, Swaminathan Padmapriya, Anne Fennell, Qin Ma. Developing A Computational Pipeline for High-throughput Sequencing Data in Plant Genomes. Undergraduate Research, Scholarship and Creative Activity Day. April 18, South Dakota State University, Volstorff Ballroom. Brookings, SD, USA. 23. (2016) Bingqiang Liu and Qin Ma. Development of Computational Tools in DNA motif identification and analyses. RECOME 2016, April 17th-21st, Santa Monica, CA, USA. 24. (2016) Jinyu Yang, Qin Ma, DMINDA2 web server: DNA motif identification and analyses, Gamma Sigma Delta Poster competition, April 4th, Brookings, SD, 2016.

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25. (2016) Xin Chen, Qin Ma, An RNA-seq analysis pipeline for switchgrass integrating co-expression network analysis, Jan. 9-13, San Diego, CA, USA 26. (2015) Bingqiang Liu, Guojun Li, Ying Xu, Qin Ma, Development of Computational Tools in DNA motif identification and analyses, RECOMB/ISCB Conference on Regulatory and Systems Genomics, Nov. 15-18, Philadelphia, 2015. 27. (2015) Qin Ma, Wen-Chi Chou, Shihui Yang, Sha Cao, Dawn M. Klingeman, Steven D. Brown, Ying Xu, Analysis of strand-specific RNA-Seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum, BioEnergy Science Center, Chattanooga, TN, 2015. 28. (2015) Xin Chen, Qin Ma, Xizeng Mao, Yuhong Tang, Xiaolan Rao, Richard A. Dixon and Ying Xu, Genome-scale identification of cell-Wall related genes in Switchgrass through comparative genomics and transcriptomic analyses, BioEnergy Science Center, Chattanooga, TN, 2015. 29. (2015) Xin Chen, Xiaolan Rao, Qin Ma, Hui Shen, Yu Shang, Richard Dixon and Ying Xu, Co-expression analysis of lignin biosynthetic genes for gene regulatory networks in Rice, Switchgrass, and Arabidopsis, BioEnergy Science Center, Chattanooga, TN, 2015. 30. (2015) Xin Chen, Qin Ma, Yuhong Tang, Xizeng Mao, and Ying Xu, A de novo RNA- seq analysis pipeline for Switchgrass integrating the reconstruction of transcriptional regulatory network, BioEnergy Science Center, Chattanooga, TN, 2015. 31. (2015) Gaoyang Li, Qin Ma, Haodi Feng and Ying Xu, A novel framework for identifying all the elementary flux modes in a genome-scale metabolic network, BioEnergy Science Center, Chattanooga, TN, 2015. 32. (2015) Qin Ma, Xin Chen, and Ying Xu. An integrated computational suite of web- servers and tools developed by CSBL, BioEnergy Science Center, Chattanooga, TN, 2015. 33. (2014) Xin Chen, Qin Ma, Yuhong Tang, Ying Xu, Whole genome Computational Analyses of Transcriptomic Data Reveal cell-wall synthesis-related genes in Switchgrass, BioEnergy Science Center, Chattanooga, TN, 2014 34. (2014) Xin Chen, Qin Ma, Yuhong Tang, Xizeng Mao, Ying Xu, Expression level Quality check for RNA-SEQ mapping and multiple hit reads reassignment, BioEnergy Science Center, Chattanooga, TN, 2014 35. (2014) Qin Ma, Hanyuan Zhang, Xizeng Mao, Ying Xu. An integrated web server for DNA motif identification and analysis, BioEnergy Science Center, Chattanooga, TN, 2014 36. (2014) Qin Ma, Xizeng Mao, Xin Chen, Ying Xu, Inference of reliable genome-scale bacterial metabolic network, BioEnergy Science Center, Chattanooga, TN, 2014 37. (2013) Qin Ma, Computational Analyses of Transcriptomic Data Reveal the Dynamic Organization of the E. coli Chromosome under Different Conditions, Genome Biology and Bioinformatics, Atlanta, GA. 38. (2013) Xizeng Mao, Mirko Basen, Xin Chen, Qin Ma, Zheng Ruan, Amanda Rhaesa, Michael Adams and Ying Xu, Reconstruction of a usable whole-genome metabolic network for Caldicellulosiruptor bescii DSM 6725, BioEnergy Science Center, Chattanooga, TN. 39. (2013) Xizeng Mao, Qin Ma, Chuan Zhou, Xin Chen, Hanyuan Zhang, Wei Lai and Ying Xu, DOOR 2.0: An Integrated View of Operons for Prokaryotes, BioEnergy Science Center, Chattanooga, TN. 40. (2013) Qin Ma, Chuan Zhou, Xizeng Mao, Yanbin Yin, Ying Xu, Insights into biofuel production by comparative genomic analysis of Clostridium genomes, BioEnergy Science Center, Chattanooga, TN.

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41. (2013) Xin Chen, Qin Ma, Shan Wang, Xizeng Mao, Rick Dixon and Ying Xu, Biclustering Analyses of Transcriptomic Data Reveal the cell-wall synthesis-related genes in Panicum virgatum, BioEnergy Science Center, Chattanooga, TN. 42. (2013) Chi Zhang, Qin Ma, Xizeng Mao, Xin Chen and Ying Xu, Prediction of transcriptional regulatory logic in Clostridium thermocellum ATCC 27405, BioEnergy Science Center, Chattanooga, TN. 43. (2013) Wen-Chi Chou, Qin Ma, Shihui Yang, Xizeng Mao, Xin Chen, Sha Cao, Steven D. Brown, Ying Xu, SeqTU: Identification of bacterial transcription units using strand- specific RNA-seq data at a genome scale, Institute of Bioinformatics State-of-the-Art Next Generation Sequence Symposium, Athens, GA. (Poster Award) 44. (2012) Qin Ma, Chuan Zhou, Yanbin Yin and Ying Xu, Insights into biofuel production by comparative genomic analysis of Clostridium genomes. BioEnergy Science Center 6rd retreat, Oak Ridge, Tennessee, USA. 45. (2009) Bingqiang Liu, Phuongan Dam, Guojun Li, Qin Ma, Victor Olman, Fenglou Mao, Jacky Chou, Ying Xu, Reconstruction of the transcriptional regulatory network in prokaryotes, BioEnergy Science Center 3rd retreat, Asheville NC, USA

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