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 3rd 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 8th
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 8th 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 8th 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
8th 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
8th 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 8th
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. 5th
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. 6th 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 9th 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 9th 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 9th 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. 53rd 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. 15th 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. 7th 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. 19th 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), 19th 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, 19th 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 13th
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. 54th 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 10th 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 10th 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 10th 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 10th 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 10th 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 10th
Critical Assessment of Techniques for Protein Structure Prediction, Gaeta,
Italy, 2012.
56 J.
Eickholt, J. Cheng*. Protein Disorder Prediction by the
MULTICOM Predictors. The 10th 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
10th 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 10th
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. 24th 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 10th 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
10th 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
21st 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 21st
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. ZingÕs
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.