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  • Qin Ma, Ph.D. September 2, 2013

    1

    Qin Ma, Ph.D.

    Postdoctoral Research Associate

    Department of Biochemistry & Molecular Biology, Institute of Bioinformatics,

    University of Georgia

    CONTACT INFORMATION

    Work Mailing: A108B Life Science Building, 120 Green Street, Athens, GA 30602

    Home Mailing: Apt. U22, Milledge Ave Ext., Athens, GA, 30605

    Office Phone: 706-583-5543

    Cell Phone: 706-254-4293

    Email: maqin@uga.edu; maqin2001@gmail.com

    Homepage: http://csbl.bmb.uga.edu/~maqin/

    EDUCATION AND TRAINING

    2011.01-now : Postdoc in Bioinformatics,

    Computational Systems Biology laboratory (CSBL), University of Georgia

    2008.10-2010.09: Visiting Scholar in Bioinformatics,

    Computational Systems Biology laboratory (CSBL), University of Georgia

    2005.09-2010.11: Ph.D. in Operations Research,

    School of Mathematics, Shandong University,

    2001.09-2005.07: B.S. in Applied Mathematics,

    School of Mathematics, Shandong University

    GRANTS AND AWARDS

    Co-Principal Investigator, National Natural Science Foundation of China

    #61303084, 2014-1016

    mailto:maqin@uga.eduhttp://csbl.bmb.uga.edu/~maqin/

  • Qin Ma, Ph.D. September 2, 2013

    2

    Member, Shandong University Global Partnership Program (SDU GPP): between

    Shandong University and University of Georgia

    Poster Awards (2013) 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.

    RESEARCH INTERESTS

    Comparative genomics analyses and functional elements elucidation in prokaryotic

    genomes.

    Prediction and modeling of biological pathways for microbial organisms.

    Folded bacterial chromosome and relationship to transcriptional regulation.

    Biclustering analyses of gene expression data.

    Computational study of plant cell-wall synthesis genes and co-expression modules.

    MENTORING EXPERIENCE

    Ph.D. students from Department of Biochemistry and Molecular Biology/Institute of Bioinformatics, University of Georgia, GA Chi Zhang

    (2013present): elucidation of transcriptional regulatory logic in bacterial genomes

    Fei Ji

    (2013present): Chip-seq based cis regulatory motifs prediction

    Ph.D. students from Department of Computer Science, Jilin University, China

    Yu Shang

    (2013-present): the Biclustering algorithm for large-scale microarray data and

    RNA-seq data; plant cell-wall synthesis genes evolution analysis

    Gaoyang Li

    (2013-present): the dynamic folding structures of bacterial chromosome and the

    properties of supercoil boundaries.

    Visiting scholars from School of Mathematics, Shandong University:

    Bing Xue

  • Qin Ma, Ph.D. September 2, 2013

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    (2012-2013): Global regulon prediction in E. coli genome

    Shan Li

    (2012-2013): Transcription units identification based on RNA-seq data in bacterial

    genomes.

    Chuan Zhou

    (20112012): A novel motif analysis toolkit development and comparative genomics

    analysis study for Clostridium; (2012-present): A Novel Paradigm for Elucidating Regulons of Prokaryote Based Solely on Genome Sequences Zheng Chang

    (20112012): The relationship between Exon-intron structure and alternative splicing;

    cancer evolution model based on the gastric sequencing data. Xiaoran Zhu

    (20102011): Orthology relationship identification among prokaryotic genomes.

    Visiting scholars from Department of Computer Science, Jilin University, China

    Xin Chen

    (2013-present): the genome efficiency model of bacterial genomes and the

    co-expression modules in plant cell-wall synthesis genes.

    (2013-present): A co-expression analysis of Recalcitrance genes and lignin genes

    Hanyuan Zhang

    (2013-present): A DNA motif analysis webserver.

    (2013-present): A RNA-seq data analysis pipeline for switchgrass

    Visiting scholar from Jinan University

    Haiqing Hu

    (2011-2012): New orthologous genes identification method.

    Undergraduates from University of Georgia

    Stephen Lago

    (2013present): Metabolic pathway holes assignment in microbial genomes.

    Wei Lai

    (2013-present): DOOR2 database and SeqTU webserver

    (2013-present): A RNA-Seq based Transcription Unit Finder for Prokaryotes

    Undergraduates from Department of Computer Science, Jilin University, China

    Tu Ba

  • Qin Ma, Ph.D. September 2, 2013

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    (2012-2013): Research and prediction of E. coil transcription units based on

    next-generation sequencing

    PUBLICATIONS (including submitted) (*equal contribution)

    1. 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. Ready for submission

    2. Qin Ma*, Chuan Zhou*, Xizeng Mao, Yanbin Yin, Ying Xu, New Insights Revealed

    through Comparative Genomic Analysis of 40 Clostridium Genomes. Under review of

    Bioenergy Research

    3. 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. In revision of Nucleic Acids Research

    4. Juan Cui, Yanbin Yin, Qin Ma, Guoqing Wang, Victor Olman, Yu Zhang, Wen-Chi

    Chou, Celine S. Hong, Chi Zhang, Sha Cao, Xizheng Mao, Ying Li, Steve Qin,

    Shaying Zhao, Jing Jiang, Phil Hastings, Fan Li, Ying Xu, Towards Understanding the

    Genomic Alterations in Human Gastric Cancer. Under review of PLoS Genetics

    5. 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. Under review of Nucleic Acids Research

    (Database Issue).

    6. 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, doi:10.1186/1754-6834-6-131, 2013

    7. 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, 10.1093/bioinformatics/btt397, 2013, July 10

    8. Lingpeng Meng, Qin Ma, Han Chuanfeng, Qidi Wu, Determining the Number of

    Facilities for Large-Scale Emergency, International Journal of Computing Science

    and Mathematics (EI), 2013

  • Qin Ma, Ph.D. September 2, 2013

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    9. 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, 2013, 1-10,

    doi:10.1093/nar/gkt261

    10. Qin Ma, Ying Xu (2013) Global genomic arrangement of bacterial genes is closely

    tied with the total transcriptional efficiency. Genomics, Proteomics &

    Bioinformatics, 2013, 11: 66-71

    11. Shan Wang*, Yanbin Yin*, Qin Ma, Xiaojia Tang, Kan Bao, Dongyun Hao, Ying Xu

    (2012) Genome-scale identification of cell-wall related genes in Arabidopsis based on

    co-expression network analysis, BMC Plant Biology, 12:138

    12. Jing Zhao, Qin Ma, Yuquan Cui (2012) Comparative study on macro-economic

    regionalization: an application of biclustering algorithm, Journal of Shandong

    University, 49(7): 71-77.

    13. Sara Blumer-Schuette, Richard Giannone, Jeffrey Zurawski, Inci Ozdemir, Qin Ma, et

    al. (2012) Caldicellulosiruptor core and pan genomes reveal determinants for

    non-cellulosomal thermophilic deconstruction of plant biomass, Journal of

    Bacteriology, 194(15):4015-28

    14. Fengfeng Zhou*, Qin Ma*, Guojun Li, Ying Xu (2012) QServer: a biclustering server

    for prediction and validation of co-expressed gene clusters, PLoS ONE 7(3): e32660.

    doi:10.1371/journal.pone.0032660

    15. Guojun Li*, Qin Ma*, Xizeng Mao, Yanbin Yin, Xiaoran Zhu, Ying Xu

    (2011) Integration of Sequence-Similarity and Functional Association Information Can

    Overcome Intrinsic Problems in Orthology Mapping across Bacterial

    Genomes, Nucleic Acids Research, 1-9, doi:10.1093/nar/gkr766

    16. Guojun Li*, Bingqiang Liu*, Qin Ma, Ying Xu (2011) A new framework for identifying

    cis-regulatory motifs in prokaryotes, Nucleic Acids Research, 39(7):e42.

    17. Guojun Li, Qin Ma, Bingqiang Liu, Haibao Tang, Andrew H. Paterson, Ying Xu

    (2009) A Close-to Optimum Bi-clustering Algorithm for Microarray Gene Expression

    Data, Computational Systems Bioinformatics, 082Li

    18. Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, Ying Xu (2009) QUBIC: A

    Qualitative Biclustering Algorithm for Analyses of Gene Expression Data, Nucleic

    Acids Research, 37(15): e101-

    19. Qin Ma, Jian-liang Wu, Xiao Yu (2009) Planar graphs without 5-cycles or

    6-cycles, Discrete Mathematics, 309: 2998-3005.

  • Qin Ma, Ph.D. September 2, 2013

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    20. Qin Ma (2007) The degree-constrained k-arboricity of outerplanar graphs, Journal of

    Shandong university, 42 (10): 41-43.

    MANUSCRIPTS IN PREPARATION

    1. Bingqiang Liu*, Qin Ma*, Chuan Zhou, Guojun Li and Ying Xu, Regulatory Region

    Preselecting can Benefits Motif Finding with Phylogenetic Footprinting.

    2. Qin Ma, Xizeng Mao, Fengfeng Zhou, Ying Xu, Genomic Location is Information:

    Towards Effectively Assignment of Metabolic Pathway by Bacterial Genes.

    3. Xizeng Mao*, Victor Olman*, Chi Zhang*, Qin Ma, Tian Yuan, Zheng Chang, Henry

    Schwartz, Ying Xu. Elucidation of sub-operonic transcription units in E. coli based on

    gene-expression data.

    4. Xizeng Mao*, Qin Ma*, Bingqiang Liu, Zheng Chang, Chuan Zhou, Henry Schwartz,

    Ying Xu. Revisiting Operons: An Analysis of the Landscape of Transcriptional Units

    in E. coli.

    5. Qin Ma*, Zheng Chang*, Bingqiang Liu, Chuan Zhou, Fei Ji, Ying Xu, The

    Exon-Intron Structures of Human Genes Are Solely to Facilitate Alternative Splicing.

    6. Qin Ma, Chuan Zhou, Guojun Li, Ying Xu, A Novel Paradigm for Elucidating

    Regulons of Prokaryote Based Solely on Genome Sequences.

    7. Qin Ma*, Chi Zhang*, Yu Shang, Victor Olman, Ying Xu, From Co-expression to

    Co-regulation: A Novel Biclustering algorithm for analyses of Transcriptomic Data.

    PROFESSIONAL ACTIVETIES

    1. Invited talk (2013) Computational Analyses of Transcriptomic Data Reveal the

    Dynamic Organization of the E. coli Chromosome under Different Conditions,

    International Conference on Integrative Biology, August 5-7, 2013, Embassy Suites

    Las Vegas, USA.

    2. Invited talk (2012) Elucidation of the Dynamic Supercoil Structures of folded E. coli

    Chromosome, Department of Biostatistics and Bioinformatics, Emory University,

    USA.

    http://www.omicsgroup.com/conferences/integrative-biology-summit-2013/scientific-programme.php?day=2&sid=80&date=2013-08-06http://www.omicsgroup.com/conferences/integrative-biology-summit-2013/scientific-programme.php?day=2&sid=80&date=2013-08-06

  • Qin Ma, Ph.D. September 2, 2013

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    3. Invited talk (2010) Elucidation and identification of Regulons for Prokaryotic

    Genomes, College of computer science and Technology, Jilin University, Changchun,

    China

    4. Invited talk (2010) An introduction of Biclustering algorithm in gene microarray

    analysis. School of Mathematics, Shandong University, Jinan, China.

    5. Invited talk, (2009) QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene

    Expression Data, the 8th Annual International Conference on Computational Systems

    Bioinformatics, Stanford University, USA.

    6. Ph.D. thesis (2010) Elucidation and identification of Regulons for Prokaryotic

    Genomes, Shandong University.

    7. Mentoring Bachelor thesis (2013) Tu Ba, Research and prediction of E.

    coil transcription units based on next-generation sequencing, Jilin University

    8. Program Committee Member, BICLUS Workshop, 2013

    9. Membership of American Society for Microbiology, 2013

    10. Reviewer for Journals

    Nucleic Acid Research

    PLoSONE

    Mathematical Biosciences

    Journal of Bioinformatics and Computational Biology

    Bioinformatics

    BMC Bioinformatics

    BMC Research Notes

    Journal of Theoretical Biology

    11. Reviewer for Conferences

    Bioinformatics 2010-2011

    BIBM 2010-2011

    ACM-BCB 2010-2011

    ICIC 2011

    ISBRA 2010-2012

    12. Poster (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.

    http://csbl.bmb.uga.edu/~maqin/http://www.asm.org/

  • Qin Ma, Ph.D. September 2, 2013

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    13. Poster (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.

    14. Poster (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.

    15. Poster (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.

    16. Poster (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.

    17. Poster (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.

    18. Poster (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.

    19. Poster (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.

    20. Member of Conferences

    the 5th International Bioinformatics Workshop (IBW 2007)

    IBW 2008

    Georgia Tech-ORNL International Conference on Bioinformatics, 2009

    Georgia Tech-ORNL International Conference on Bioinformatics, 2011

    TEACHING 1. 2008-2009, Probability theory, School of Electrical Engineering, Shandong

    University

    2. 2007-2008, Linear Algebra, School of Electrical Engineering, Shandong Univer...