Internal and External Services

Department Services

Graduate Thesis / Dissertation / Project Committees at MU (+75 students): Jianjiong Gao (graduated), Qi Qi (graduated), Dayang Hao (graduated), Sam Grinter (graduated), Nan Zhao (graduated), Nick Lin (graduated), Yongjian Xi (graduated), Amith R. Gosukonda (graduated), Muneendra Ojha (graduated), Robin Kramer (graduated), Jaturon Harnsomburana (graduated), Jason Green (graduated), Qingguo Wang (graduated), Gyan Srivastava (graduated), Qing He (graduated), Jeff Reneker (graduated), Corey Hudson (graduated), Shi Min Lee (graduated), Yangyang Wu (graduated), Nilesh Mune, Xiaoling Li (graduated), Chao Zhang (graduated), Veerendra Shirole (graduated), Hongfei Cao, Xinyan Kuang (graduated), Mian Pan (graduated), Zhiquan He (graduated), Santosh Patil, Prathyusha Muddasani (graduated), Abhijit Patil (graduated), Allison Tegge (graduated), Garima Kushwaha, Trupti Josh (graduated), Shin Jae Won (graduated), Phaneendra Madala (graduated), Michael Van Devender (graduated), Son Nguyen, Devlina Banerjee (graduated), Kapil Patil (graduated), Madhu Kiran Inala (graduated), Qiuming Yao (graduated), Alexsandre Lobzhanidze (graduated), Zahra Hajihashemi (graduated), Wang Tan (ECE department), Curtis Kelsey (graduated), Anuradha Jagtap (graduated), Xiaolin Xie (graduated), Xiange Li (graduated in 2013), Tuo Zhao, Lingyan Jiang (plant science), Sandeep Ravi, Di Wu (graduated), Caiwei Wang (graduated), Minxin Cheng (graduated), Rahul Singh, Yang Liu (graduated), Shravya Ramisetty (graduated), Rui Wu (graduated), Brittany Morago, Ning Zhang, Michael Phinney, Robert Wallace (graduated), Yifeng Zeng, Sean Lander (graduated), Xu Wang, Giang Bui, Yuan Lu (graduated, biochemistry), Yue Zhang (ECE, graduated), Sachin Meena, Adam Johnson (biological science), Xiaobo Jiang, Torre Fernando, Matthew England (graduated), Chanmann Lim (graduated), Qiyuan Gao (graduated), Xinwei Du (graduated), Samuel Harris (graduated), Sachin Meena (PhD student), Rui Huang (Master student), Shirish Gajul (Master student)

Research and Education Collaboration Services in the CS Department: Collaborating with many faculty in the computer science department on various education and research projects.

Other Department Committee Services

2016 - Present, Chair of faculty search committee of machine learning and data mining

2016, PhD qualifying exam committee of Rina Bao

2016, PhD qualifying exam committee of Suliang Bu

2016, PhD qualifying exam committee of Guang Chen

2016, PhD qualifying exam committee of Cao Fang

2016, PhD qualifying exam of Minguang Song

2016, PhD qualifying exam committee of Minguang Song

2016, member of qualifying exam committee of Feng Cao

2016 – Present, CS graduate committee

2016, IT faculty search committee

2015, Chair of qualifying exam committee of Avimanyou Vasta

2007 – Present (except a sabbatical semester), Participating in almost all Computer Science (CS) faculty meetings

2007 - 2016, IT committee, Department of Computer Science, University of Missouri, Columbia

2014, Committee member, PhD qualifying exam of Michael Phinney, Computer Science Department, University of Missouri, Columbia

2014, Chair of system administrator search committee, Computer Science Department, University of Missouri, Columbia

2013, Judge of CS poster competition, Computer Science Department, University of Missouri, Columbia

2013, Qualifying exam committee of Pelapur Rengarajan, Computer Science Department, University of Missouri

2013, System administrator search committee, University of Missouri, Columbia

2013, Teaching instructor search committee, University of Missouri, Columbia

2012 – Present, Computer science tenure and promotion committee, University of Missouri, Columbia

2010 - 2013, Computer science GAANN fellowship committee, University of Missouri, Columbia

2012, System administrator search committee, University of Missouri, Columbia

2009 - 2012, Contributions to the ABET accreditation of undergraduate curriculum in computer science, University of Missouri, Columbia

2007 – 2011, Computer science PhD qualifying exam committee, University of Missouri, Columbia

2011, System administrator search committee, University of Missouri, Columbia

2008 - 2009, Curriculum committee, Informatics Institute, University of Missouri, Columbia

2007 - 2009, Informatics admission committee, Informatics Institute, University of Missouri, Columbia

2008, Machine learning curriculum committee, Department of Computer Science, University of Missouri, Columbia

2009, 2010, Assessor of the OPT English test for teaching assistants in computer science, University of Missouri, Columbia

2007 - 2009, Invited and hosted four external bioinformatics speakers, Computer Science Department and Informatics Institute, University of Missouri, Columbia

2007, Bioinformatics faculty search committee, School of Electrical Engineering and Computer Science, University of Central Florida

2007, Bioinformatics curriculum committee, School of Electrical Engineering and Computer Science, University of Central Florida

2006, Undergraduate foundation exam committee, School of Electrical Engineering and Computer Science, University of Central Florida

College Services

2016, Committee of merger of CS and ECE departments

2015, Participating in the search of new dean of the College of Engineering

2007 - Present, Library committee, College of Engineering, University of Missouri, Columbia

2007 - Present, Participating in faculty meetings and activities, College of Engineering, University of Missouri, Columbia

2010, 2013 - 2015 Participating in undergraduate student research honor program, College of Engineering, University of Missouri, Columbia

2009 - 2013, Graduate committee, Informatics Institute, University of Missouri, Columbia

2007 Participating in organizing and teaching undergraduate introduction courses, College of Engineering, University of Missouri, Columbia

Campus Services

Affiliation Services (4 organizations)

Affiliated with MU Informatics Institute (since 2007), Life Science Center (2008 - 2014), National Center for Soybean Biotechnology (since 2007), and Interdisciplinary Plant Group (since 2008). Participating in meetings, symposiums, planning, and external / internal seminars organized by these four organizations.

Research and Education Collaboration and Consulting Services at University of Missouri (+40 groups / PIs)

• Collaboration with Drs. Kristen Bilyeu, Henry Nguyen, Gary Stacey, Jay Thelen, Dong Xu to develop bioinformatics methods and databases for soybean research
• Collaboration with Drs. James Birchler, Brian Mooney, Kathy Newton to develop bioinformatics methods for drosophila and maize research
• Collaboration with Drs. Charles Caldwell and Kristen Taylor to develop bioinformatics, genomics, epigenomics methods for cancer research
• Collaboration with Drs. Dennis Lubahn, Mark Hannink, William Folk, Kevin Fritsche, Michael Greenlief, Frank Schmidt, Grace Sun, Zezong Gu, Alan Parrish to develop computational systems biology methods for the MU botanical center
• Collaboration with Drs. Scott Peck and John Walker to develop bioinformatics methods for Arabidopsis research
• Collaboration with John Tanner on Protein Structure Prediction and Validation
• Collaboration with Xiaoqin Zou on Protein Interaction and Docking Prediction
• Collaboration with Drs. Alan Parrish, Bill Harrison, Bruce McClure, Cheryl Rosenfeld, Chi-Ren Shyu, Chris Pires, David Emerich, David Geary, Dmitry Korkin, Dong Xu, Elizabeth Bryda, Frank Schmidt, Gavin Conant, Heidi Appel, Hongyuan Cao, Ioan Kotzin, Jack Schultz, Judith Miles, Karen Bennett, Michela Becchi, Wenjun Zeng, Tieming Ji, Xinhua Zhuang, Yi Shang, Ye Duan, and Yunxin Zhao on a variety of research and education topics

Other Campus Services

2016, Participated in NIH T15 training grant, MU Informatics Institute (MUII)

2016, Participated in NIH T32 training grant, Biochemistry department

2015, Participated in NIH T32 training grant, MU Informatics Institute (MUII)

2013 - 2015, Systems Biology Faculty Search Committee, Division of Biological Science, MU

2015, Reviewer, Research Board Grants, University of Missouri, Columbia

2014, Reviewer, Research Board Grants, University of Missouri, Columbia

2013, Reviewer, Research Board Grants, University of Missouri, Columbia

2013, Reviewer of Missouri Letters of Intent for NSF proposals

2013, The 30^th Annual Research and Creative Activities Forum, University of Missouri, Columbia

2011 – 2013, Network Modeling Group, University of Missouri, Columbia

2011 - present, Participated in NIH Molecular Biology Training Grant, Life Science Center, MU

2010 - 2013, Seminar in the course Research Methods in Health and Biomedical Informatics, Department of Health Informatics, University of Missouri, Columbia

2008 - 2011, Interview with college and university media six times to advocate for the importance of scientific research for the society

2010, Reviewer of student NIH grant proposals, Department of Biochemistry and Department of Animal Science, University of Missouri, Columbia

2010, Participated in CTSA center proposal (bioinformatics component), School of Medicine, University of Missouri, Columbia

2010, Poster judge, Life Science Week, University of Missouri, Columbia

2009 – 2010, Co-organizer, Interdisciplinary Plant Group (IPG) symposium, University of Missouri, Columbia

2008, 2009, Reviewer for University of Missouri research board grant

2009, Participated in two IGERT grant applications, the Life Science Center, University of Missouri, Columbia

2007, Bioinformatics faculty search, Animal Science, University of Missouri, Columbia

2007, Poster judge, Department of Computer Science, University of Missouri, Columbia

2007, Adobe Journalism competition judge, School of Journalism, University of Missouri, Columbia

Regional, National and International Services

Membership

AAAS (since 2012), ACM (since 2012), IEEE (since 2012), ACM SIGBio (since 2012), ISCB (since 2005), MCBIOS (since 2013)

Journal / Conference Paper Reviewing (33 International Journals, 4 International Conferences)

P.N.A.S., Proteins, Nucleic Acids Research, Bioinformatics, BMC Bioinformatics, BMC Genomics, BMC Structural Biology, Journal of Machine Learning Research, Journal of Bioinformatics and Computational Biology, Data Mining and Knowledge Discovery, FEBS letter, Journal of Theoretical Biology, Journal of Structure Biology, International Journal of Data Mining and Bioinformatics, Advances in Neural Information Processing Systems (NIPS), Molecular Simulation, International Conference on Intelligent Systems for Molecular Biology (ISMB), Current Protein and Peptide Science, Computational Systems Biology Conference (CSB), Computers in Biology and Medicine, IEEE Transaction on Bioinformatics and Computational Biology, IEEE Transaction on Neural Networks and Learning Systems, PLoS ONE, Nature Protocols, Advances in Bioinformatics, Journal of Respiratory Research, Journal of Computational Chemistry, Knowledge and Information Systems, Proteins and Proteomics, PLoS Computational Biology, Nature Methods, Frontier in Bioinformatics, Genome Biology, Plant Cells, Great Lake Bioinformatics Conference (GLBIO), Scientific Report, EURASIP journal on Bioinformatics and Systems Biology, International Journal of Molecular Sci

Vice Conference Chair, Session Chair, Committee Member, Editorial Board, Grant Review, Membership, and Other Services

2016, NIH SBBR study section

2016, NIH BDMA study section

2016, PhD dissertation committee of a student at University of Alberta, Canada

2016, External reviewer of the joint bioinformatics program at UALR and UAMS

2016, NIH R15 study section

2016, NIH SBBR study section

2016, NIH SCORE study section

2016, Session Chair, 18^th International Conference on Bioinformatics and Biochemical Engineering, Tokyo, Japan

2016, Area Co-Chair of Protein Structure and Function of ISMB conference

2016, Program committee, ACM Bioinformatics and Computational Biology (BCB) conference, Seattle, WA

2016, Program committee, IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Shenzhen, China.

2016, NSF IIS panelist

2016, NSF Graduate Training Program panelist

2016, NIH Study Section (I)

2016, NSF GRFP panelist

2015, NSF DBI Panelist

2015, NIH R15 Study Section (II)

2015, NIH SBTR/SBBR Study Section

2015, NIH Special Center Funding Study Section

2015, NSF Graduate Training Program Panelist

2015, NIH Special Funding Study Section (online)

2015, NIH R15 Study Section (I)

2015, NIH SBIR/SBTR Study Section

2015, Program Committee, International Conference on Intelligent Biology and Medicine

2015, Program Committee, Great Lake Bioinformatics Conference (GLBIO)

2015, Program Committee, Computational Structural Bioinformatics Workshop

2015, NSF Graduate Fellowship Panelist

2015, Publicity Co-Chair, IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2015, Review tenure/promotion/reappointment of two assistant professors at two US universities

2015, Program Committee, 2014 ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)

2015, Session chair, MCBIOS Conference, Little Rock, Arkansas

2014 – Present, Editorial Board, Scientific Report, Nature Publishing Group

2013 – Present, Board of Directors, Mid-South Computational Biology and Bioinformatics Society

2014, NIH R15 Study Section

2014, NIH SCORE Study Section (Oct.)

2014, NSF Graduate Training Program Panelist (Sept.)

2014, NSF Graduate Training Program Panelist (August)

2014, Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2014, Program Committee, Computational Structural Bioinformatics Workshop

2014, Program Committee, Critical Assessment of Protein Function Annotation (CAFA), a Special Interest Group of 2014 ISMB

2014, Publicity Chair and Program Committee, 2014 ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)

2014, Co-Chair, Workshop on Robotics Methods for Structural and Dynamic Modeling of Molecular Systems

2014, Co-Chair, KDD Workshop on Big Data Analytic Technology for Bioinformatics and Health Informatics

2014, NIH Big Data Study Section

2014, NIH SCORE Study Section (Feb.)

2014, External Reviewer of a PhD Thesis, University of Queensland, New Zealand

2013, NSF Panelist

2013, Review the Tenure and Promotion Dossier for a Faculty at an External US Research University

2013, Program Committee, Computational Structural Bioinformatics Workshop.

2013, Program Committee, Critical Assessment of Protein Function Annotation (CAFA), a Special Interest Group of 2013 ISMB / ECCB conference.

2013, Program Committee & Local Co-Organizer, The Mid-South Computational Biology and Bioinformatics Conference

2013 – present, Editorial Board, Current Synthetic and Systems Biology

2013, Program Committee, The International Conference on Intelligent Systems for Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB)

2013, NIH Grant Reviewer

2013, Publicity Chair, ACM Bioinformatics and Computational Biology conference, DC

2013, Co-Chair, AAAI Workshop on Artificial Intelligence and Robotics Methods in Computational Biology

2012 – present, Editorial Board Member, International Journal of Computational Intelligence in Bioinformatics and Systems Biology

2012, NSF DBI Panelist

2012, Participating in National Science Foundation (NSF) Plant Genome Meeting, Arlington, VA

2012, Program Committee, Computational Structural Bioinformatics Workshop (CSBW), Philadelphia, PA

2012, Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2011 – Present, Editorial Board, ISRN Artificial Intelligence

2011 – Present, Review Editor, Journal Frontiers in Bioinformatics and Computational Biology

2011, Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Atlanta, Georgia

2011, Grant Review, National Science Foundation (NSF)

2011, Grant Review, Kentucky Science and Technology Corporation

2011 - 2012, Co-Organizing the Intrinsically Disordered Protein Session at 2012 Pacific Symposium on Biocomputing (PSB) - one of the top conferences in bioinformatics and computational biology

2004 – 2014, Actively making contributions (e.g., writing blogs) at the discussion forum of Critical Assessment of Techniques for Protein Structure Prediction (CASP)

2010, Grant Review, National Science Foundation (NSF)

2010, Program Committee, International Workshop on Graph Theoretic Approaches for Biological Network Analysis, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Hongkong, China

2010, Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Hongkong, China

2010, Program Committee, 20^th International Conference on Pattern Recognition (ICPR), Istanbul, Turkey

2010, Program Committee, 7^th International Symposium on Neural Networks (ISNN), Shanghai, China

2010, Program Committee, Special Track on Artificial Intelligence and Bioinformatics, 24^th Conference on Artificial Intelligence (AAAI), Atlanta, Georgia, USA

2010, Program Committee, International Workshop on Graph Theoretic Approaches for Biological Network Analysis, ACM International Conference on Bioinformatics and Computational Biology

2009, External Referee of a Project Scientist Position, University of California San Diego

2009, Grant Review, National Institute of Health (NIH)

2009, Panelist, National Science Foundation (NSF)

2009, External Reviewer of a MS Thesis, University of Queensland, New Zealand

2009, Participation in Bioinformatics Education Panel, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington DC

2009, Vice Conference Chair, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington DC

2009, Track Chair, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington DC

2009, Participation in the NIH Southeast Grant Seminar and Workshop, Atlanta, Georgia

2009, Program Committee, International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS)

2007 – 2009, Editorial Board Member, Journal of Computational Intelligence in Bioinformatics and Systems Biology

2007 – 2009, Editorial Board Member, International Journal of Computational Biology and Drug Design

2008, Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008)

2008, Grant Review, Canadian Research Council

2008, Grant Review, National Science Foundation (NSF)

2008, Program Committee, International Joint Conference on Neural Networks (IJCNN)

2008, Program Committee, International Conference on Biomedical Engineering and Informatics

2008, Invited Participant, iPlant Grand Challenge Team, Computational Morphodynamics of Plants

2007, 2008, Grant Review, Leonard Wood Institute (LWI)

2007, Panelist, National Science Foundation (NSF)

2007, Program Committee & Session Chair, IEEE 7^th Symposium on Bioinformatics and Bioengineering

2007, Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2007, Chair of the Genomics Session, International Conference on Bioinformatics and Computational Biology (BIOCOMP)

Bioinformatics Software and Web Services

Developed / co-developed / maintained the following software tools and web services free for scientific and academic use (some are widely used by the community):

1. MULTICOM: protein tertiary structure prediction (ranked among best methods CASP8 – CASP11)
2. SeqRate: sequence-based prediction of protein folding rates
3. SoyDB: a knowledge database of soybean transcription factors
4. PreDisorder: prediction of protein disorder regions (ranked among best in CASP8 and CASP9)
5. FOLDpro and 3Dpro: protein homology modeling and fold recognition (ranked among best in high-accuracy protein structure prediction in CASP7)
6. DOMpro: protein domain boundary prediction (ranked among best in CASP7)
7. BETApro: protein beta-sheet topology prediction (ranked among best in protein contact map prediction in CASP7)
8. SSpro 4: protein secondary structure prediction
9. ACCpro 4: protein solvent accessibility prediction
10. DISpro: protein disorder region prediction (ranked among best in CASP7)
11. DIpro: protein disulfide bond prediction
12. CMAPpro2, BMAPpro, CMAPCon: protein contact map prediction
13. MUpro: protein mutation stability prediction
14. NNCon: contact map prediction using support vector machines (ranked among best in CASP8)
15. SVMCon: contact map prediction using support vector machines (ranked among best in protein contact map prediction in CASP8 and CASP9)
16. DOMAC: hybrid protein domain prediction using homology modeling and neural networks (ranked among top in domain prediction in CASP8)
17. DoBo: protein domain boundary prediction
18. SIGMOID 1.0: a biological network database and simulation system (chief designer/developer)
19. NNRank 1.0: neural network software for ordinal regression and classification
20. ModelEvaluator 1.0: protein model evaluation using support vector machine (ranked among best methods in protein model quality assessment in CASP8)
21. HMMEditor: a visual editing tool for profile hidden Markov model
22. MUPrimer: primer design for homologous genes
23. ModelEvaluatorLocal: evaluating the local quality of a single protein model
24. APOLLO: protein model quality assessment (ranked among best in CASP9)
25. SCRATCH: protein structure prediction suite
26. MSACompro: improved multiple sequence alignment using protein structural features
27. MULTICOM-PDCN: protein function prediction (ranked among best in CAFA 2011)
28. MTMG: template-based protein model generation
29. GNET: gene regulatory network construction
30. MNET: metabolic network construction
31. REFINEpro: protein model refinement using conformation ensembles
32. 3DRefine: protein model refinement
33. DNcon: protein contact prediction using deep network (ranked no. 1 in CASP10)
34. DNdisorder: protein disorder prediction using deep network
35. RNAMiner: RNAseq data analysis pipeline
36. i3DRefine: protein model refinement
37. GMOL: visualization of 3D genome structure
38. FUSION: ab initio prediction, evaluation and refinement of protein structure
39. SMOQ: evaluation of quality of a single protein model
40. Gen3D: reconstruction of 3D structure of chromosome
41. DNSS: deep learning for protein secondary structure prediction
42. MOGEN: modeling of 3D structure of genome
43. CONFOLD: contact-based ab initio protein structure modeling
44. RFFold: random forest method for protein fold recognition
45. HMMSato: protein profile alignment based on Hidden Markov Models.
46. DNFold: deep learning for protein fold recognition
47. Chromosome3D: reconstruction of 3D structures of chromosomes from Hi-C data
48. UniCon3D: a unified tool for ab initio protein structure modeling
49. LorDG: a distance-based tool for genome structure modeling
50. FRAGSION: a tool for generating protein structural fragments
51. Qprob: protein model quality assessment
52. QAcon: protein model quality assessment using neural networks
53. ConEVA: assessment of protein residue-residue contact predictions
54. DNpro: deep learning based prediction of protein stability change induced by mutations
55. DeepQA: deep learning for protein model quality assessment
56. DNTor: deep learning for protein torsion angle prediction

Selected Talks

1. 2016, Deep learning methods for bioinformatics, University of North Carolina, Charlotte.
2. 2016, Deep learning for predicting the stability change of protein mutations, 18^th International Conference on Bioinformatics and Biochemical Engineering, Tokyo, Japan. (Best presentation award)
3. 2016, Computational Modeling of 3D Human Genome and its Applications, Virginia Commonwealth University, Richmond VA.
4. 2016, De novo protein conformation sampling using a probabilistic graphical model. The Mid-South Computational Biology and Bioinformatics Conference (MCBIOS), Memphis, TN.
5. 2015, De novo protein conformation sampling using a fragment-free probabilistic graphical model. The 3^rd Conference on Protein and RNA Structure Prediction, Punta Cana, Dominican Republic.
6. 2015, Talk on protein and genome structures, Missouri State University, Springfield, MO.
7. 2015, Modeling 3D Structure of Human Genome, The Jackson Laboratory, CT, USA.
8. 2015, Large-Scale Sampling and Evaluation of Protein Structural Models. 23^rd Conference on Intelligent Systems for Molecular Biology (ISMB), Dublin, Ireland, 2015.
9. 2015, CONFOLD: Contact-driven Ab Initio Folding of Proteins. 3DSig Meeting, 23^rd Conference on Intelligent Systems for Molecular Biology (ISMB), Dublin, Ireland, 2015.
10. 2015, Contact-driven Ab Initio Folding of Proteins. The Great Lake Bioinformatics Conference (GLBIO), Purdue University, Indiana.
11. 2015, Reconstruction of 3D Models of Human Genome. The 12^th Mid-South Bioinformatics Conference (MCBIOS), Little Rock, Arkansas. (featured talk)
12. 2014, MULTICOM – Large-Scale Sampling and Mining of Template-Based Protein Models. 11^th Critical Assessment of Techniques for Protein Structure Prediction (CASP11), Cancun, Mexico. (invited talk)
13. 2014, Deep Learning and its Application to Protein Structure Prediction. Computer Science Department, University of Missouri, Columbia.
14. 2014, Predicting Gene Regulatory Networks of Soybean Nodulation from RNA-Seq Transcriptome Data. ACM Bioinformatics and Computational Biology (ACM-BCB) Conference, Newport Beach, CA, USA. (highlight talk)
15. 2014, Deep Learning and its Application to Protein Structure Prediction, Deep Learning in Health and Bio-Informatics workshop, ACM-BCB, Newport Beach, CA, USA.
16. 2014, Template-Based Protein Structure Modeling, Computational Structural Bioinformtics Workshop, ACM-BCB, Newport Beach, CA, USA.
17. 2014, Deep Learning and its Application to Protein Structure Prediction, Tokyo Institute Technology – Purdue Summer School, Purdue University, USA.
18. 2014, Modeling 3D Human Genome Structure, Intelligent Systems for Molecular Biology (ISMB), Boston, MA, USA. (highlight talk)
19. 2014, Reconstruction of 3D Human Genome Structure. The Great Lake Bioinformatics Conference (GLBIO), Cincinnati, OH, USA. (highlight talk)
20. 2013, Ab Initio Prediction of Protein Structure. Zing’s Conference on Protein and RNA Structures, Cancun, Mexico.
21. 2013, The Properties of 3D Conformation of the Human Genome. ACM Bioinformatics and Computational Biology (ACM-BCB) Conference, Washington DC, USA.
22. 2013, Associations between Gene Function and Spatial Gene-Gene Interaction in 3D Genome. The Automated Function Annotation of Protein (AFP) SIG meeting of the ISMB conference, Berlin, Germany.
23. 2013, Computational Modeling of 2D and 3D Genome Structure, MU-Korean Plant Science Symposium, Columbia, MO.
24. 2013, Deep Network Learning for Protein Residue-Residue Contact Prediction, the Great Lake Bioinformatics Conference (GLBIO), Pittsburgh, PA.
25. 2013, Computational Modeling of Protein Structure, University of Missouri - Kansas City
26. 2013, Machine Learning Methods for Protein Tertiary Structure Prediction, Purdue University
27. 2013, Computational Modeling of 2D and 3D Genome Structure, Purdue University
28. 2012, Protein Model Quality Assessment, 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy
29. 2012, Protein Model Refinement, 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy
30. 2012, Template-Based Protein Modeling, 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy
31. 2012, Computational Construction, Analysis and Application of Biological Networks, Computer Science Department, University of Missouri, Columbia
32. 2012, Computational Construction, Analysis and Application of Biological Networks, Computer Science Department, Wayne State University, Michigan
33. 2012, RNA-Seq Data Analysis of Mouse Transcriptomes, MU Botanical Center, University of Missouri, Columbia
34. 2012, Modeling Protein Structure and Gene Regulatory Networks, Department of Statistics, University of Missouri, Columbia
35. 2012, Tutorial Presentation of Disordered Proteins, Pacific Symposium on BioComputing, Hawaii
36. 2011, Presentation of Recursive Protein Modeling, in the Computational Structural Bioinformatics Workshop (CSBW), Atlanta, USA
37. 2011, Presentation of RNA-Seq Data Analysis at MU Botanical Center Meeting, University of Missouri, Columbia
38. 2011, Protein Structure Prediction, Department of Biochemistry, Kansas State University, Manhattan, Kansas
39. 2011, Presentation in the Critical Assessment of Protein Function Annotation (CAFA), Vienna, Austria
40. 2010, Panelist in Protein Model Quality Assessment, the 9^th Critical Assessment of Techniques for Protein Structure Prediction (CASP9), Asilomar, California
41. 2010, Panelist and Presentation in Template-Free Protein Structure Prediction, the 9^th Critical Assessment of Techniques for Protein Structure Prediction (CASP9), Asilomar, California
42. 2010, Challenges and Solutions to Protein Structure Prediction, Institute for Genomics and Bioinformatics, University of California, Irvine
43. 2010, Protein Structure and Function Prediction, Life Science Center, University of Missouri - Columbia
44. 2010, Protein Structure Prediction, Informatics Institute, University of Missouri, Columbia
45. 2009, Protein Structure Prediction (MULTICOM), Department of Computer Science, University of Missouri, Columbia
46. 2009, Bioinformatics Seminar, Department of Computer Science and Computer Engineering, University of Missouri, Kansas City
47. 2008, Protein Disorder Region Prediction, the 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy
48. 2008, Protein Model Quality Assessment, the 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy
49. 2008, Template-Free Protein Modeling, the 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy
50. 2008, Template-Based Protein Modeling, the 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy
51. 2008, Systems Biology for Cancer, Ellis Fischel Cancer Center, University of Missouri - Columbia
52. 2008, A Systems Biology Approach to Plant Science Research, Interdisciplinary Plant Group (IPG) Retreat, University of Missouri
53. 2008, iPlant Presentation, Life Science Center, University of Missouri, Columbia
54. 2007, Life Science Center, University of Missouri, Columbia
55. 2007, National Center for Soybean Technology, Division of Plant Sciences, University of Missouri
56. 2007, Department of Computer Science, University of Missouri Columbia
57. 2007, Department of Computer Science, University of California Irvine
58. 2006, Protein Domain Boundary Prediction, the 7^th Critical Assessment of Techniques for Protein Structure Prediction (CASP7), Asilomar, Monterey, California
59. 2006, Department of Chemistry, University of Central Florida, Orlando
60. 2005, Department of Computer Science, University of Central Florida, Orlando
61. 2005, Presentation at the 13^th International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, Michigan