Conference Abstracts / Posters (Bold - Cheng and his students, * - Cheng as corresponding author)

1 P. Baldi, J. Cheng, A. Randall, and M. Sweredoski. Prediction of Protein Structural Features and Tertiary Structures from SCRATCH Using Recursive Neural Networks, Evolutionary Information, Fragment Libraries, and Energy Functions. The Sixth Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP6), Italy, 2004.

2 C.R. Yang, J. Cheng, T. Su, B. Compani-Tabrizi, K. Petrov, L. Scharenbroich, B.E. Shapiro, A. Levchenko, L. Bardwell, P. Baldi, G.W. Hatfield, and E. Mjolsness. kMech/Cellerator/SIGMOID: A Web Service Oriented Software Infrastructure for Systems Biology. Third International Symposium on Computational Cell Biology, Lenox, MA, 2005.

3 M. Sweredoski and J. Cheng. Prediction of Protein Disordered Regions Using Machine Learning Techniques. The 3^rd Annual Institute for Genomics and Bioinformatics Biomedical Informatics Training Program Symposium, Irvine, California, 2005.

4 J. Cheng, A. Randall, M. Sweredoski, and P. Baldi. 3D structure Prediction Using FOLDpro, 3Dpro, and ABIpro. The Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), Asilomar, California, 2006.

5 J. Cheng and P. Baldi. Contact Map Prediction Using BETApro and SVMcon. The Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), Asilomar, California, 2006.

6 J. Cheng, M. Sweredoski, and P. Baldi. Protein Disordered Region Prediction Using DISpro. The Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), Asilomar, California, 2006.

7 J. Cheng, M. Sweredoski, and P. Baldi. Domain Prediction Using FOLDpro and DOMpro. The Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), Asilomar, California, 2006.

8 M. Ahmad, R. Skrabis, M. Smehilova, D. Xu, J. Cheng, K. Bilyeu. MUPrimer: Finding Allele-Specific Primers for Homologous Genes. Interdisciplinary Plant Group (IPG) Symposium, Ozarks, Missouri, 2008.

9 Z. Wang, T. Joshi, M. Libault, B. Valliyodan, G. Stacey, H. Nguyen, D. Xu, J. Cheng*. YouSoybean: A Knowledge Database of Soybean Transcription Factors. Interdisciplinary Plant Group (IPG) Symposium, Ozarks, Missouri, 2008.

10 Z. Wang, T. Langewisch, K. Newton, J. Cheng*. Large-Scale Scanning of PPR Proteins in the Maize Genome. Interdisciplinary Plant Group (IPG) Symposium, Ozarks, Missouri, 2008.

11 J. Cheng*, A. N. Tegge, Z. Wang. Model Combination, Refinement, and Assessment by MULTICOM-REFINE. The 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy, 2008.

12 J. Cheng*, Z. Wang, A. N. Tegge, X. Deng, M. Dickinson. Model Ranking, Combination, Refinement and Assessment by MULTICOM Human Predictor. The 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy, 2008.

13 J. Cheng*, Z. Wang, A. N. Tegge. Multi-Template Model Generation and Hybrid Model Quality Assessment by MULTICOM-CLUSTER. The 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy, 2008.

14 J. Cheng*, Z. Wang, A. N. Tegge. Prediction of Tertiary Structure, Model Quality, Domain Boundary, Contact Map and Disorder Regions by MULTICOM-CMFR. The 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy, 2008.

15 J. Cheng*, A. N. Tegge, Z. Wang. Multi-Template Combination, Alternative Alignments, Model Evaluation and Contact Predictions by MULTICOM-RANK. The 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy, 2008.

16 J. Cheng*, Z. Wang, A. N. Tegge. Model Ranking, Model Combination and Refinement by MUProt. The 8^th Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Italy, 2008.

17 A. Tegge, Z. Wang, X. Deng, B. Compani, T. Su, I. Chang, M. Vaughn, B. Shapiro, J. Cheng*, E. Mjolsness. Pacific Symposium on Biocomputing (PSB), Hawaii, 2009.

18 Z. Wang, T. Joshi, M. Libault, G. Stacey, H. Nguyen, D. Xu, J. Cheng*. YouSoybean: A Knowledge Database of Soybean Transcription Factors. Interdisciplinary Plant Group (IPG) Symposium, Life Science Center, University of Missouri, Columbia, MO, 2009.

19 Z. Wang, M. Libault, T. Joshi, G. Stacey, H. Nguyen, D. Xu, J. Cheng*. YouSoybean: A Knowledge Database of Soybean Transcription Factors. 5^th National Center for Soybean Biotechnology (NCSB) Symposium, Life Science Center, University of Missouri, Columbia, MO, 2009.

20 A. Tegge, Z. Wang, X. Deng*, B. Compani, T. Su, I. Chang, B. Shapiro, E. Mjolsness, J. Cheng*. Interdisciplinary Plant Group(IPG) Symposium, Life Science Center, University of Missouri, MO, 2009.

21 J. Eickholt, Tatiana Danilova, Jim Birchler, J. Cheng*. ChromoProbe: A Pipeline to Automatically Identify Unique Segments for Chromosome Probe Development. Interdisciplinary Plant Group(IPG) Symposium, Missouri Life Science Week, University of Missouri, Columbia, MO, 2009.

22 A. Tegge and J. Cheng*. MULTICOM Protein Structure Prediction in CASP8. Symposium of National Library of Medicine Bioinformatics Training Program, Oregon, 2009.

23 X. Deng, C. Niederhuth, A. Tegge, J. C. Walker, and J. Cheng*. A Computational Study of the Function and Regulations of Genes Involved in Abscission in Arabidopsis. Missouri Life Science Week, University of Missouri, Columbia, MO, 2010.

24 A. Tegge, G. Arthur, L. Bennett, C. Caldwell, D. Xu, and J. Cheng*. A Pathway Based Correlation Method for Identifying Perturbation in Follicular Lymphoma from Gene Expression Microarray Data. Missouri Life Science Week, University of Missouri, Columbia, MO, 2010.

25 Z. Wang, M. Libault, T. Joshi, G. Stacey, H. Nguyen, D. Xu, J. Cheng*. SoyDB: A Knowledge Database of Soybean Transcription Factors. 6^th National Center for Soybean Biotechnology Symposium, Life Science Center, University of Missouri, Columbia, MO, 2010.

26 A. Tegge, G. Arthur, L. Bennett, C. Caldwell, D. Xu, and J. Cheng*. A Pathway Based Correlation Method for Identifying Perturbation in Follicular Lymphoma from Gene Expression Microarray Data. Symposium of National Library of Medicine Bioinformatics Training Program, 2010.

27 A. Tegge, G. Arthur, L. Bennett, C. Caldwell, D. Xu, and J. Cheng*. A Pathway Based Correlation Method for Identifying Perturbation in Follicular Lymphoma from Gene Expression Microarray Data. International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA, 2010.

28 T. Joshi, Q. Yao, L.D. Franklin, Z. Wang, J. Cheng, G. Stacey, H. Nguyen, D. Xu. Soybean Knowledge Base (SoyKB): a Web Resource for Soybean Translational Genomics. International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA, 2010.

29 Z. Wang, J. Eickholt, J. Cheng*. Evaluating the Quality of Single and Multiple Protein Models by MULTICOM Quality Assessment Predictors. The 9^th Critical Assessment of Techniques for Protein Structure Prediction (CASP9), Asilomar, California, 2010.

30 J. Eickholt, Z. Wang, J. Cheng*. A Conformation Ensemble Approach to Protein Residue-Residue Contact Prediction. The 9^th Critical Assessment of Techniques for Protein Structure Prediction (CASP9), Asilomar, California, 2010.

31 J. Cheng*, Z. Wang, J. Eickholt. Integrated Prediction of Protein Tertiary Structure by MULTICOM Predictors. The 9^th Critical Assessment of Techniques for Protein Structure Prediction (CASP9), Asilomar, California, 2010.

32 T. Langewisch, Z. Wang, J. Cheng, K. Newton. Identifying Candidates for the Restorer-of-Fertility Gene Rf3 in Maize CMS-S. 53^rd Annual Maize Genetics Conference, St. Charles, Illinois, USA, 2011.

33 J. Cheng*, Z. Wang, and J. Eickholt. Designing and Benchmarking the MULTICOM Protein Structure Prediction System. 15^th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, Canada, 2011.

34 T. Joshi, K. Patil, L.D. Franklin, M. Titzpatrick, Q. Yao, Z. Wang, M. Libault, L. Brechenmacher, B. Valliyodan, X. Wu, J. Cheng, G. Stacey, H. Nguyen, D. Xu. Soybean Knowledge Base (SoyKB): A Web Resource for Soybean Translational Genomics. 7^th Annual National Center for Soybean Biotechnology (NCSB) Symposium, University of Missouri, Columbia, MO, 2011.

35 J. Cheng*, J. Li, Z. Wang, J. Eickholt, X. Deng, J. He. The MULTICOM Toolbox for Protein Structure Prediction. 19^th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria, 2011.

36 X. Deng, J. Cheng*. MSACompro: Improved Protein Multiple Sequence Alignment Method Using Predicted Secondary Structure, Solvent Accessibility, and Residue-Residue Contacts. The Great Lakes Bioinformatics Conference, Athens, Ohio, 2011.

37 Z. Wang, X. Zhang, M.H. Le, D. Xu, G. Stacey, J. Cheng*. A Protein Domain Co-Occurrence Network Approach for Predicting Protein Function and Inferring Species Phylogeny. Graduate Student Poster Symposium, Department of Computer Science, University of Missouri, Columbia, MO, 2011.

38 Z. Wang, J. Cheng*. Protein Function Prediction Using Homology Search and Domain Co-Occurrence Networks. Special Interest Group in Critical Assessment of Protein Function Prediction (CAFA), 19^th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria, 2011.

39 J. Eickholt, X. Deng, J. Cheng*. DoBo: Domain Boundary Prediction by Integrating Evolutionary Signals and Machine Learning. Special Interest Group in Structural Bioinformatics and Computational Biophysics, 19^th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria, 2011.

40 T. Langewisch, Z. Wang, J. Cheng, K. Newton. Identifying Candidates for the Restorer-of-Fertility Gene Rf3 in Maize CMS-S. Plant Genomes to Phenomes at 13^th Annual Fall Symposium, Donald Danforth Plant Science Center, St. Louis, Missouri, 2011.

41 J. Li, J. Wilkins, M. Zhu, K. Fritsche, M. Greenlief, W. Folk, D. Lubahn, M. Hannink, J. Cheng*. MULTICOM – RNA-Seq Data Analysis of Mouse Transcriptomes Perturbed by Botanicals. The annual NIH Botanical Research Center meeting, North Carolina, 2011.

42 T. Langewisch, Z. Wang, J. Cheng, K. Newton. Identifying candidates for the restorer-of-fertility gene Rf3 in maize CMS-S. 54^th annual genetics conference, Portland, Oregon, 2012.

43 T. Langewisch, Z. Wang, J. Cheng, K. Newton. Identifying candidates for the restorer-of-fertility gene Rf3 in maize CMS-S, Interdisciplinary Plant Group (IPG) Symposium, Columbia, MO, 2012.

44 Z. Qu, F. Meng, R.D. Bomgarden, J.C. Rogers, R.I. Viner, J. Li, J. Cheng, J. Cui, G.Y. Sun, Z. Gu. Quantitative proteomics analysis of protein s-nitrosylation using sixplex iodoTMT. The ASMS conference, 2012.

45 J. Eickholt, J. Cheng*. Residue-Residue Contact and Disorder Prediction with Deep Networks & Gene-Gene Proximity Study. The annual conference of bioinformatics training program, National Library of Medicine, 2012.

46 J. Eickholt, J. Cheng*. Residue-Residue Contact and Disorder Prediction with Deep Networks. 3Dsig: Structural Bioinformatics and Computational Biophysics, the International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, California, 2012.

47 G. Stacey, D. Xu, J. Cheng, D. Koppenaal, L. Pasa-Tolic, L. Brechenmacher, T. Joshi, L. Blockus, A. Waldron. Soybean Root Hairs: A Model for Single-Cell Plant Biology. NSF Plant Genome Program Awardee Meeting, Arlington, VA, 2012.

48 G. A. Khoury, F. Khatib, H. Zhou, G. Chopra, Jilong Li, S. Cooper, J. Flatten, T. Hussain, K. Xu, J. Smadbeck, X. Deng, Z. Popovic, J. Cheng, M. Levitt, J. Skolnick, D. Baker, C. A. Floudas, S. N. Crivelli, and Foldit Players. wfFUIK Branch: Hybrid Human Protein Structure Prediction via the Online Multiplayer Game Foldit Coupled with an Iterative Clustering Approach for Selection of Near-Native Structures, Knowledge-Based Refinement, and State-of-the-Art Scoring Functions. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

49 H. Zhou, J. Li, J. Cheng, J. Skolnick, S. N. Crivelli. Protein Structure Prediction via Model Selection by APOLLO and Refinement by TASSER. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

50 D. Bhattacharya, J. Cheng*. REFINEpro: A Novel Conformation Ensemble Approach to Protein Structure Refinement. Missouri Informatics Symposium, Columbia, MO, 2012.

51 R. Cao, Z. Wang, J. Li, C. Shang, J. Cheng*. Protein Model Quality Prediction by MULTICOM server predictors. Missouri Informatics Symposium, Columbia, MO, 2012.

52 X. Deng, J. Li, B. Adhikari, J. Cheng*. The MULTICOM Conformation Ensemble Approach to Protein Tertiary Structure Prediction. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

53 R. Cao, Z. Wang, J. Li, C. Shang, J. Cheng*. Protein Model Quality Prediction by MULTICOM Server Predictors. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

54 J. Eickholt, J. Cheng*. Protein Residue-Residue Contact Prediction by the MULTICOM Predictors. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

55 D. Bhattacharya, J. Cheng*. A Conformation Ensemble Approach to Protein Structure Refinement. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

56 J. Eickholt, J. Cheng*. Protein Disorder Prediction by the MULTICOM Predictors. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

57 B. Adhikari, X. Deng, J. Li, D. Bhattacharya, J. Cheng*. Contact Assisted Protein Structure Prediction by MULTICOM-CONSTRUCT. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

58 D. Bhattacharya, J. Cheng*. Protein Structure Refinement by Two-Step Atomic-Level Energy Minimization. The 10^th Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, 2012.

59 H. Zhou, Z. Qu, J. Cui, A. Simonyi, V.A. Engel, S. Chen, J. Li, J. Cheng, M. Greenlief, S. Li, A.L. Thomas, K.L. Fritsche, W.R. Folk, D.B. Lubahn, G.Y. Sun, Z. Gu. Quantitative Proteomic Analysis of Anti-oxidant Signaling of Elderberry and Sutherlandia in Diet against Mouse Focal Cerebral Ischemia by Isobaric Labeling with DiART. 24^th Biennial Meeting ISN-ASN, Cacun, Mexico, 2013.

60 M. Zhu, J.L. Dahmen, G. Stacey, J. Cheng*. Predicting Regulatory Module Networks of Soybean Nodulation Based on RNA-Seq Data. Interdisciplinary Plant Group meeting, Ozark Lake, Missouri, 2012.

61 Q. Qi, J. Cheng*. Probabilistic and Knowledge-based Methods for Automatic Construction of Metabolic Pathways. Interdisciplinary Plant Group meeting, Ozark Lake, Missouri, 2012.

62 Z. Qu, F. Meng, J. Purdy, J. Li, W. Sheng, F. Wei, Q. Wang, S Liu, J. Cheng, M.C. Greenlief, D.B. Lubahn, G.Y. Sun, Z. Gu. Quantitative Proteomic Analysis of S-nitrosylated Proteins: Effect of Botanicals under Neuroinflammation in Microglial Cells. NIH annual botanical center meeting, 2012.

63 H. Zhou, J. Li, X. Deng, J. Cheng, J. Skolnick, S. N. Crivelli. Protein Structure Prediction via Model Selection by APOLLO and Refinement by TASSER. The 10^th Critical Assessment of Techniques for Protein Structure Prediction (CASP10), Gaeta, Italy, 2012.

64 G. A. Khoury, F. Khatib, H. Zhou, G. Chopra, J. Li, S. Cooper, J. Flatten, T. Husain, K. Xu, J. Sadbeck, X. Deng, Z. Popovic, J. Cheng, M. Levitt, J. Skolnick, D. Baker, C. A. Floudas, S. N. Crivelli, Foldit players. Hybrid Human Protein Structure Prediction via the Online Multiplayer Game Foldit Coupled with an Iterative Clustering Approach for Selection of Near-Native Structures, Knowledge-based Refinement, and State-of-the-Art Scoring Functions. The 10^th Critical Assessment of Techniques for Protein Structure Prediction (CASP10), Gaeta, Italy, 2012.

65 H. Zhou, Z. Qu, D. L. Nkholise, J. Li, J. Cheng, M. Greenlief, V. V. Mossine, T. Mawhinney, P. Brown, K. L. Fritsche, D. B. Lubahn, G. Y. Sun, Z. Gu. Quantitative Proteomics Analysis for the Effects of Garlic Extracts on Neuroinflammation. American Society for Mass Spectrometry (ASMS) conference, 2013.

66 X. Deng, J. Cheng*. Prediction of Protein Model Quality from Sequence Alignment by Support Vector Machines. Pacific Symposium on Biocomputing, Hawaii, 2013

67 D. Bhattacharya, J. Cheng*. REFINEpro: a Novel Conformation Ensemble Approach to Protein Structure Refinement. Pacific Symposium on Biocomputing, Hawaii, 2013

68 Z. Wang, R. Cao, K. Taylor, A. Briley, C. Caldwell, J. Cheng*. The Properties of Human Genome Conformation and Spatial Gene Interaction and Regulation Networks. Pacific Symposium on Biocomputing, Hawaii, 2013.

69 R. Cao, Z. Wang, J. Li, J. Cheng*. Protein Model Quality Prediction by MULTICOM Servers. Pacific Symposium on Biocomputing, Hawaii, 2013.

70 B. Adhikari, X. Deng, J. Li, D. Bhattacharya, J. Cheng*. Contact-Assisted Protein Structure Prediction. Pacific Symposium on Biocomputing, Hawaii, 2013.

71 J. Li et al. MULTICOM-RNA – A Bioinformatics Pipeline for RNA-Seq Transcription Data Analysis. The Great Lake Bioinformatics Conference, Pittsburgh, PA, 2013.

72 C. He, J. Cheng*. GMOL: A Tool for 3D Genome Structure Visualization. The Great Lake Bioinformatics Conference, Pittsburgh, PA, 2013.

73 Q Qi, J. Cheng*. Automatic Reconstruction of Cellular Metabolic Networks by Combination of Probabilistic Graphical Models and Knowledge-based Methods. The Great Lake Bioinformatics Conference, Pittsburgh, PA, 2013.

74 Q Qi, J. Cheng*. Combining Probabilistic Graphical Model-Based and Knowledge-Based Methods for Automatic Construction of Metabolic Pathways. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

75 B. Adhikari, X. Deng, J. Li, D. Bhattacharya, J. Cheng*. Contact-Assisted Protein Structure Prediction. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

76 Z. Wang, R. Cao, K. Taylor, A. Briley, C. Caldwell, J. Cheng*. The Properties of Human Genome Conformation and Spatial Gene Interaction and Regulation Networks. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

77 J. Eickholt, J. Cheng*. A Study and Extension of DNcon: a Method for Protein Residue-Residue Contact Prediction Using Deep Networks. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

78 J. Li, J. Wilkins, M. Zhu, K. Fritsche, M. Greenlief, W. Folk, D. Lubhan, M. Hannink, J. Cheng*. MULTICOM – RNA-Seq Data Analysis of Mouse Transcriptomes Perturbed by Botanicals. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

79 R. Cao, J. Cheng*. Local and Global Quality Assessment by MULTICOM during CASP10. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

80 C. He, A. Wells, J. Cheng*. GMOL: A Tool for 3D Genome Structure Visualization. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

81 T. Trieu, J. Cheng*. Constructing Three-Dimensional Structures of Human Chromosomes from Chromosome Contact Data. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

82 S. Ahmed, J. Cheng*. Iterative Reconstruction of Three-Dimensional Model of Human Genome from Chromosomal Contact Data. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

83 T. Joshi et al. Bridging the Gap between Soybean Translational Genomics and Breeding with Soybean Knowledge Base (SoyKB). The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

84 X. Deng, J. Cheng*. Predicting Protein Model Quality from Sequence Alignment by Support Vector Machines. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

85 D. Bhattacharya, J. Cheng*. Improving Structural Accuracy of Protein Models by a Decoy-Based Iterative Fragment Exchange Greedy Sampling and Selection Strategy. The Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013.

86 R. Cao, J. Cheng*. Deciphering the Association between Gene Function and Spatial Gene-Gene Interactions in 3D Genome Conformation. The 21^st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB). Berlin, Germany, 2013.

87 R. Cao, J. Cheng*. Deciphering the Association between Gene Function and Spatial Gene-Gene Interactions in 3D Genome Conformation. The Automated Protein Function Annotation (AFA) SIG meeting of the 21^st Annual International Conference on Intelligent Systems for Molecular Biology. Berlin, Germany, 2013.

88 D. Bhattacharya, J. Cheng*. Automated Protein Structure Refinement Using i3DRefine Software and its Assessment in CASP10. The ACM Bioinformatics and Computational Biology (ACM-BCB) Conference, Washington DC, USA, 2013.

89 J. Eickholt, Taeho Jo, M. Spencer, J. Cheng*. Predicting Aspects of Protein Structure with Deep Network. The Annual NLM Bioinformatics Conference, University of Utah, Salt Lake City, USA, 2013.

90 T. Trieu, J. Cheng*. Constructing Three-Dimensional Structures of Human Chromosomes from Chromosome Contact Data. Life Science Week, University of Missouri, Columbia, MO, 2013.

91 S. Ahmed, J. Cheng*. Iterative Reconstruction of Three-Dimensional Structures of Human Genome from Chromosomal Contact Data. Life Science Week, University of Missouri, Columbia, MO, 2013.

92 D. Bhattacharya, J. Cheng*. Automated protein structure refinement using i3Drefine software and its assessment in CASP10. Missouri Informatics Day, Columbia, USA, 2013.

93 H. Zhou, Z. Qu, D.L. Nkholise, J. Li, J. Cheng, C.M. Greenlief, V.V. Mossine, t. Mawhinney, P.N. Brown, K.L. Fritsche, D.B. Lubahn, G.Y. Sun, Z. Gu. Quantitative Proteomics, Analysis for the Effects of Garlic Extracts on Neuroinflammation. ASMS 2013.

94 Z. Qu, H. Zhou, D.L. Nkholise, V.V. Mossine, J. Cui, J. Li, J. Cheng, C.M. Greenlief, T. Mawhinney, P.N. Brown, K.L. Fritsche, D.B. Lubahn, G.Y. Sun, Z. Gu. Effects of Aged Garlic Extracts in Lipopolysaccharide-induced Nitrosative Stress and Microglial Activation Using Quantitative Proteomic Analysis. Annual Society for Neuroscience Meeting, 2013.

95 J. Cheng. Ab Initio Prediction and Refinement of Protein Structure. Zing’s conference on Protein and RNA Structures, 2013.

96 J. Li, J. Cheng, MULTICOM-RNA: a Bioinformatics Pipeline for RNA-Seq data Analysis. The Annual Botanical Center Meeting, University of Missouri, Columbia, 2013.