Invited presentations


2021

Invited presentations

[09/22/2021] Keynote speaker for a webcast of Single cell multi-omics methods. Nature Reviews Molecular Cell Biology and Nature Communications and sponsored by Illumina.

[07/25/2021] scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses. Intelligent Systems for Molecular Biology and European Conference on Computational Biology 2021 Abstracts. Track: General Computational Biology. 2021. (Presenter: Juexin Wang)

[06/07/2021] Deep learning methods for cis-regulatory motif identification and gene regulatory mechanism elucidation. AI in Digital Health Conference 2021.

[05/28/2021] DeepMAPS: Deep learning based Multi-omics Analysis Portal for Single cells. Research seminar of Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210.

[03/31/2021] CTSA Community Reviewer Training Program: Increasing Diverse Perspectives in Pilot Grant Reviews by Integrating Community Input. Washington Marriott Wardman Park. Faculty representative at OSU.

[03/17/2021] Identify cellular heterogeneity and elucidate underlying mechanisms using single-cell multi-omics data. Research seminar of Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210.

2020

Invited presentations

[10/09/2020] Cell-type-specific gene regulatory network inference based on single-cell multi-omics data. Research seminar of Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210.

[06/25/2020] Cell-type-specific gene regulation inference using single-cell RNA-seq data. PIIO at OSU. June 25th, 2020. (Presenter: Anjun Ma. Invited by Dr. Zihai Li)

[06/19/2020] Cell-type-specific gene regulation inference using single-cell RNA-seq data. Emory University. June 19th, 2020. (Presenter: Anjun Ma. Invited by Dr. Steve Qin)

[06/08/2020] Development and application of computational tools driven by addressing bacterial genomic and transcriptomic questions. 5th International Conference on Mathematical and Computational Medicine. Telluride Science Research Center (TSRC), CO. June 8-12, 2020.

[05/17/2020] Construction of cell-specific gene co-regulations signatures based on single-cell multi-omics data analysis, May 17-20, 2020, ICSA (International Chinese statistical association) Applied Statistics Symposium Huston.

[03/13/2020] Development of Enabling Computational Techniques for Single-cell Multi-Omics Data. March 13th. Nationwide Children’s Hospital. (Invited by Dr. Kloczkowski).

[02/21/2020] Development and application of computational methods driven by addressing bacterial genomic and transcriptomic questions. Seminar of Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210. February 21st.

Poster Presentations

[06/22/2020] Anjun Ma, Cankun Wang, Yuzhou Chang, Adam McDermaid, Bingqiang Liu, Chi Zhang, and Qin Ma. Towards cell-type-specific gene regulation in heterogeneous cancer cells. #4409. American Association for Cancer Research. June 2020. Online.

2019

Invited presentations

[11/21/2019] Towards heterogeneous regulatory landscapes across complex diseases based on single-cell multi-omics data. Keynote Speaker for International Conference on Mathematics and Bioinformatics Interdisciplinary Research”, Qingdao, China.

[10/22/2019] Co-regulation Gene Signatures from Single-cell RNA-Sequencing Data Analysis, International Conference on Mathematical Multiscale Modeling in Biology – Guanacaste, Costa Rica.

[06/17/2019] 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. (Invited by Prof. Yan Wang)

[08/15/2019] Construction of cell-specific gene co-regulations signatures based on single-cell multi-omics data analysis, Department of Computer Science, University of Missouri Columbia, MO. (Invited by Dr. Dong Xu)

[08/12/2019] Develop computational methods driven by addressing fundamental microbial genomic and transcriptomic questions. Indiana University, Indianapolis, IN 46202. (Invited by Dr. Chi Zhang)

[11/01/2019] Development of Enabling Computational Techniques for Single-cell Multi-Omics Data, Special research seminar of Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210.

[08/01/2019] Machine learning and artificial intelligence applications in translational science: Un-Meeting update. CCTS Program Directors meeting, The Ohio State University, Columbus, OH, 43210.

[06/06/2019] Computational modeling and bioinformatic applications in big biological data. Summer intern program. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210.

[05/23/2019] Development and application of computational methods driven by addressing bacterial genomic and transcriptomic questions. Cancer systems biology research group meeting. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210.

[04/05/2019] Integrated and systematic views of regulatory DNA motif identification and analyses. Seminar of the Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210.

[02/14/2019] Construction of cell-specific gene co-regulations signatures based on single-cell transcriptomics analysis and application in Cancer research. Cancer systems biology research group meeting. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210.

Poster Presentations

[11/04/2019] Anjun Ma, Cankun Wang, Yuzhou Chang, Qin Ma, CeRIS: Cell-type-specific Regulon Inference from Single-cell RNA-Seq. The Program in Quantitative Genomics will host its 12th annual conference: Quantitative Challenges in Cancer Immunology and Immunotherapy. Joseph B. Martin Conference Center at Harvard Medical School in Boston, MA.

[07/25/2019] Jennifer Xu, Zichun Zhang, Qin Ma, Integrative Methods for Single-Cell Multi-Omics Data: A review and practical recommendations for integrative methods. Summer internship of the department of Biomedical Informatics, The Ohio State University.

[07/25/2019] Cankun Wang, Qin Ma, Development of DNA Motifs Identification Program Using ChIP-exo Data. Summer internship of the department of Biomedical Informatics, The Ohio State University.

[04/01/2019] Anjun Ma, Qin Ma, IRIS3: Interpretation of cell-type-specific regulons identification from single-cell RNA-Sequencing data. OSU Trainee Research Day. The Ohio State University.

2016 – 2018

Invited presentations

[01/14/2018] Juan Xie, Hypothesis-driven and discovery-driven analysis of Grapevine expression data. Plant and Animal Genome Conference, San Diego, CA.

[09/10/2018] Qin Ma, Development of computational techniques in elucidating gene regulation. Indiana University, Indianapolis, IN 46202. (Invited by Dr. Chi Zhang)

[08/25/2017] Adam McDermaid, RNA Sequencing Analyses & Mapping Uncertainty, The Y1 meeting for the NSF Plant Genome Research Program, the University of California, Davis campus in Davis, California.

[05/13/2017] Dr. Qin Ma, Development of Bioinformatic Tools in Systems Biology, Department of Biology, University of South Dakota, Vermillion. (Invited by Dr. Erliang Zeng)

[02/16/2017] Dr. Qin Ma, Computational modeling and bioinformatics applications in big transcriptomic data, Department of Pharmaceutical Sciences, South Dakota State University, SD. (Departmental seminar, invited by Dr. Xiangming Guan)

[02/13/2017] Dr. Jixiang Wu, Symplastic communication and plant root development, SDSU Department of Agronomy, Horticulture and Plant Science USDA-ARS North Central Agricultural Research Laboratory, Brookings, SD. (Departmental seminar)

[01/30/2017] Adam McDermaid, Computational Techniques & Algorithm Design in RNA Sequencing Analyses, SDSU Department of Agronomy, Horticulture and Plant Science USDA-ARS North Central Agricultural Research Laboratory, Brookings, SD. (Departmental seminar)

[11/10/2016] Dr. Qin Ma, Development & Application of Bioinformatic Tools Driven by Big Genomic & Transcriptomic Data. Brookings, SD.

[7/11/2016] DMINDA2 web server: regulatory DNA motif identification and analyses. Intelligent Systems for Molecular Biology (ISMB). Technology Track Presentation. Orlando, Florida.

[07/05/2016] Dr. Qin Ma, Computational tools for RNA-Seq data analysis in genomes with highly duplicated nature. College of life sciences, Jilin University, Changchun, China. (Invited by Dr. Yan Wang)

[05/22/2016] BMBL: New investigator representative presentation. Cedar Shore Resort. Oacoma, SD.

[02/22/2016] Dr. Qin Ma, Omic data mining & modeling and biological systems inference in Bioinformatics, Department of Maths & Stats, South Dakota State University, SD. (Departmental seminar).

[02/12/2016] Dr. Qin Ma, Development of Bioinformatic Tools in Systems Biology, Department of Biology and Microbiology, South Dakota State University, SD. (Departmental seminar, invited by Dr. Xiuqing Wang)

[02/08/2018] Dr. Qin Ma, Identification and high-throughput modeling of regulatory DNA, Department of Plant Science, South Dakota State University, SD. (Departmental seminar)

Poster Presentations

[07/26/2018] Yirong Wang, Juan Xie, Anjun Ma, Qin Ma, Elucidation and Evaluation of Module Detection Methods for Single-cell RNA-Sequencing Data. 2018 Undergraduate Research Symposium, Pier, SD.

[04/26/2018] Cankun Wang, Qin Ma, Combining Computational Methods and Experimental Data for Motif Prediction, BioSNTR Plant Science Research Day. Brookings, SD.

[02/21/2018] Anjun Ma, Qin Ma, Bioinformatics and Mathematical Biosciences Lab, Faculty Excellence Showcase on Celebration of Faculty Excellence. Brookings, SD.

[09/07/2017] Adam McDermaid, Yiran Zhang, Anne Fennell, Qin Ma. RNA Sequencing Analyses, Mapping Uncertainty, & Modeling, NSF Site Visit, Brookings, SD.

[05/23/2017] Adam McDermaid, Anne Fennell, Qin Ma, RNA Sequencing Analysis, Applications and Modeling, 2017 EPSCoR All Investigator Meeting (AIM), Oacoma, SD.

[05/15/2017] Jinyu Yang, Qin Ma, Regulatory DNA motif identification by integrating DNA shape in a deep learning framework, 2017 Great Lakes Bioinformatics Conference (GLBIO), Chicago, IL.

[10/26/2016] Juan Xie, Qin Ma, Biclustering in Big Biological Data Analysis, 8th Annual Avera SDSU Research Symposium, Brookings, SD.

[07/30/2016] Neupane, Surendra, Ma, Qin, etc., Comparative Genomics of Disease Resistance Genes in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Botany 2016, Savannah, Georgia.

[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.

[2016] Zoey Glenn (undergraduate student), Qin Ma, Anne Fennell, Modeling Chilling Fulfillment in Grapevine. 2016 Undergraduate Research Symposium, Pierre, SD.

[2016] Xiaozhu Jin (undergraduate student), Juan Xie, Qin Ma, A Computational Pipeline for Gene Expression Data Analysis. 2016 Undergraduate Research Symposium, Pierre, SD.

[2016] Gaoyang li, Huansheng Cao, Qin Ma and Ying Xu, A New Computational Framework of Metabolic Network Analysis, BioEnergy Science Center, Chattanooga, TN.

[2016] Bingqiang Liu, Jinyu Yang, Guojun Li, Hanyuan Zhang, Qin Ma, Ying Xu, Development of Computational Tools in DNA motif identification and analyses, BioEnergy Science Center, Chattanooga, TN.

[2016] Xin Chen, Wen-Chi Chou, Qin Ma, Ying Xu, SeqTU: A Web Server for Identification of Bacterial Transcription Units, BioEnergy Science Center, Chattanooga, TN.

[2016] Xin Chen, Huansheng Cao, Gaoyang Li, Chunman Zuo, Qin Ma, Ying Xu, An integrated computational suite of web-servers and tools developed by CSBL, BioEnergy Science Center, Chattanooga, TN.

[04/18/2016] 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. South Dakota State University, Volstorff Ballroom. Brookings, SD, USA.

[04/08/2016] Juan Xie, Qin Ma, QUBIC: an R package of qualitative biclustering for gene co-expression analysis, the 101st Annual Meeting of the South Dakota Academy of Science, Sioux Falls, SD.

[04/04/2016] Jinyu Yang, Qin Ma, DMINDA2 web server: DNA motif identification and analyses, Gamma Sigma Delta Poster competition, Brookings, SD.

[01/09/2016] Qin Ma, Xin Chen, An RNA-seq analysis pipeline for switchgrass integrating co-expression network analysis, Plant & Animal Genome Conference, San Diego, CA, USA.


2015 and before (presented by Dr. Ma)

Invited presentations

[12/21/2015] Metabolic and Regulatory Network Analysis in Systems Biology, Biological Department, Nanjing Medical University, Nanjing, China.

[12/21/2015] Development and application of computational tools driven by addressing bacterial genomic and transcriptomic questions, Nanjing Agriculture University, Nanjing, China.  (Invited by Dr. Huochun Yao)

[12/19/2015] Metabolic and Regulatory Network Analysis in Systems Biology,  School of Science and Technology, Tongji University, Shanghai, China.  (Invited by Dr. Qi Liu)

[12/03/2015] Systems Biology: Biological Network Analysis, BioSNTR, South Dakota State University, SD. (Departmental seminar)

[07/28/2015] Development and application of bioinformatic tools driven by genomic and transcriptomic data,  Department of Computer Science, University of Missouri Columbia, MO.  (Invited by Dr. Dong Xu)

[06/05/2015] Development and application of computational tools driven by addressing bacterial genomic and transcriptomic questions, Department of Biostatistics and Bioinformatics, Emory University, GA.

[05/22/2015] Development of computational tools driven by understanding micro- and macro-structures of bacterial genomes, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

[5/21/2015] Development and application of bioinformatic tools driven by genomic and transcriptomic data, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.

[5/20/2015] Development and application of bioinformatic tools driven by genomic and transcriptomic data, Institute of Computing Technology, Chinese Academy of Sciences,  Beijing, China.

[5/19/2015] Development of computational tools driven by understanding micro- and macro-structures of bacterial genomes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

[05/18/2015] 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, Beijing, China.

[05/11/2015] An introduction to Bioinformatics. School of Mathematics (for undergraduate students), Shandong University,  Jinan, China.

[04/29/2015] Development of computational tools driven by understanding micro- and macro-structures of bacterial genomes, College of basic medical sciences, Jilin University, Changchun, China.

[04/28/2015] Computational Methods in Bacterial Bioinformatics: omic data mining and modeling, College of life sciences, Jilin University, Changchun, China.

[04/27/2015] Development and application of bioinformatic tools driven by genomic and transcriptomic data, College of Computer Science and Technology, Jilin University, Changchun, China.

[03/30/2015] Development and application of bioinformatic tools driven by genomic and transcriptomic data,  The School of Electrical Engineering and Computer Science, Washington State University, WA.

[02/17/2015] Development and application of computational tools driven by addressing bacterial genomic and transcriptomic questions, Department of Microbiology and Plant Biology, University of Oklahoma, Oklahoma.

[02/11/2015] Omic data mining & modeling and biological systems inference in Bioinformatics, Department of Mathematical Sciences, University of Texas at El Paso, TX.

[01/22/2015] Omic data mining & modeling and biological systems inference in Bioinformatics,  MD Anderson Cancer Center, Houston, TX.

[01/07/2015] Omic data mining & modeling and biological systems inference in Bioinformatics, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

[01/06/2015] Computational Methods in Bioinformatics: omic data mining and modeling, Model Animal Research Center of Nanjing University, Nanjing, China.

[12/24/2015] Omic Data Mining and Biological Systems Modelling in BioEnergy Related Organisms,  Department of Plant Science, South Dakota State University, SD.

[06/09/2015] Inference of reliable genome-scale bacterial metabolic network based on transcriptomic data in support of genetic engineering, BESC retreat, Chattanooga, TN.

[01/06/2014] An RNA-seq dataset analysis pipeline for plants, BESC characterization workshop,  Riverside, CA.

[08/05/2013] Computational Analyses of Transcriptomic Data Reveal the Dynamic Organization of the E. coli Chromosome under Different Conditions, International Conference on Integrative Biology, Embassy Suites Las Vegas, USA.

[09/28/2012] Elucidation of the Dynamic Supercoil Structures of folded E. coli Chromosome, Department of Biostatistics and Bioinformatics, Emory University,  USA.

[2010] Elucidation and identification of Regulons for Prokaryotic Genomes, College of computer science and Technology, Jilin University, Changchun, China.

[09/2010] An introduction of Biclustering algorithm in gene microarray analysis. School of Mathematics, Shandong University, Jinan, China.

[2009] QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data, The 8th Annual International Conference on Computational Systems Bioinformatics, Stanford University, USA.

Poster Presentations

[11/15/2015] 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, Philadelphia.

[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] 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] 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] 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] 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] Qin Ma, Xin Chen, and Ying Xu, An integrated computational suite of web-servers and tools developed by CSBL, BioEnergy Science Center, Chattanooga, TN.

[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] Xin Chen, Qin Ma, Yuhong Tang, Xizeng Mao, Ying Xu, Expression level Quality check for RNA-SEQ mapping and multiple hit-reads reassignments, BioEnergy Science Center, Chattanooga, TN.

[2014] Qin Ma, Hanyuan Zhang, Xizeng Mao, Ying Xu, A integrated web server for DNA motif identification and analysis, BioEnergy Science Center, Chattanooga, TN.

[2014] Qin Ma, Xizeng Mao, Xin Chen, Ying Xu, Inference of reliable genome-scale bacterial metabolic network, BioEnergy Science Center, Chattanooga, TN.

[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.

[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.

[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.

[2013] Qin Ma, Chuan Zhou, Xizeng Mao, Yanbin Yin, Ying Xu, Insights into biofuel production by comparative genomic analysis ofClostridium genomes, BioEnergy Science Center, Chattanooga, TN.

[2013] Xin Chen, Qin Ma, Shan Wang, Xizeng Mao, Rick Dixon and Ying Xu, Biclustering Analyses of Transcriptomic Data Reveal the cell-wall synthesis-relatedgenes in Panicum virgatum, BioEnergy Science Center, Chattanooga, TN.

[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.

[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, 2013 (award).

[2012] Qin Ma, Yanbin Yin, Chuan Zhou, Ying Xu, Insights into biofuel production by comparative genomic analysis of Clostridium genomes, BioEnergy Science Center, Chattanooga, TN.

[2010] 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 retreat, Asheville, NC, USA.