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The citations to these papers in Google Scholar and the papers listed in PubMed

Journal Articles

    51. L. Sun, A.F. Johnson, R.C. Donohue, J. Li, J. Cheng, J.A. Birchler. Dosage Compensation and Inverse Effects in Triple X Metafemales of Drosophila. Proceedings of the National Academy of Sciences (PNAS). Accepted.

    50. K.H. Taylor, A. Briley, Z. Wang, J. Cheng, H. Shi, C.W. Caldwell. Aberrant Epigenetic Gene Regulation in Lymphoid Malignancies. Seminars in Hematology. 50(1):38-47, 2013. [at Elsevier's web site].

    49. J. Eickholt, J. Cheng. DNdisorder: Predicting Protein Disorder Using Boosting and Deep Networks. BMC Bioinformatics. 14:88, 2013. [at BMC Structural Biology's website]

    48. J. Li, X. Deng, J. Eickholt, J. Cheng. Designing and Benchmarking the MULTICOM Protein Structure Prediction System. BMC Structural Biology. 13:2, 2013. [at BMC Structural Biology Website] .

    47. Z. Wang, R. Cao, K. Taylor, A. Briley, C. Caldwell, J. Cheng. The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types. PLoS ONE. 8(3):e58793, 2013 [at PLoS ONE's web site].

    46. L. Sun, H.R. Fernandez, R.C. Donohue, J. Li, J. Cheng, J.A. Birchler. Male-Specific Lethal Complex in Drosophila Counteracts the Effect of Histone Acetylation and Does Not Mediate Dosage Compensation. Proceedings of National Academy of Sciences (P.N.A.S.), USA, in press. [at PNAS' website].

    45. P. Radivojac, W. Clark, T.B. Oron, A.M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, G. Pandey, J.M. Yunes, A.S. Talwakar, S. Repo, M.L. Souza, D. Piovesan, R. Casadio, Z. Wang, J. Cheng, H. Fang, J. Gough, P. Koskinen, P. Toronen, J. Nokso-Koivisto, L. Holm, D. Cozzetto, D.W. Buchan, K. Bryson, D.T. Jones, B. Limaye, H. Inamdar, A. Datta, S.K. Manjari, R. Joshi, M. Chitale, D. Kihara, A.M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, H. Yang, A.E. Romero, P. Bhat, A. Paccanaro, T. Hamp, R. Kassner, S. Seemayer, E. Vicedo, C. Schaefer, D. Achten, F. Auer, A. Bohm, T. Braun, M. Hecht, M. Heron, P. Honigschmid, T. Hopf, S. Kaufmann, M. Kiening, D. Krompass, C. Landerer, Y. Mahlich, M. Roos, J. Bjorne, T. Salakoski, A. Wong, H. Shatkay, M.N. Wass, M.J.E. Sternberg, N. Skunca, F. Supek, M. Bosnjak, P. Panov, S. Dzeroski, T. Smuc, Y.A.I. Kourmpetis, A.D.J. van Dijk, C.J.F. ter Braak, Y. Zhou, Q. Gong, X. Dong, W. Tian, M. Falda, P. Fontana, E. Lavezzo, B.D. Camillo, S. Toppo, L. Lan, N. Djuric, Y. Guo, S. Vucetic, A. Bairoch, M. Linial, P.C. Babbitt, S.E. Brenner, C. Orengo, B. Rost, S.D. Mooney, I. Friedberg. A Large-Scale Evaluation of Computational Protein Function Prediction. Nature Methods, 2013. [at Nature Methods' website].

    44. Z. Wang, R. Cao, J. Cheng. Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-occurrence Networks. BMC Bioinformatics. 14(Suppl 3):S3, 2013. [at BMC Bioinformatics' website].

    43. D. Bhattacharya, J. Cheng. 3DRefine: Consistent Protein Structure Refinement by Optimizing Hydrogen Bonding Network and Atomic Level Energy Minimization. Proteins, 81(1):119-31, 2013. [at PubMed].

    42. J. Eickholt, J. Cheng. Predicting Protein Residue-Residue Contacts Using Deep Networks and Boosting. Bioinformatics. 28(23):3066-3072, 2012. [at Bioinformatics web site].

    41. M. Zhu, X. Deng, T. Joshi, D. Xu, G. Stacey, J. Cheng. Reconstructing Differentially Co-expressed Gene Modules and Regulatory Networks of Soybean Cells. BMC Genomics, 13:434, 2012. [at BMC Genomics web site].

    40. J. Cheng, J. Li, Z. Wang, J. Eickholt, X. Deng. The MULTICOM Toolbox for Protein Structure Prediction. BMC Bioinformatics, 13:65, 2012. [at BMC Bioinformatics web site]

    39. J. Cheng, J. Eickholt, Z. Wang, and X. Deng. Recursive Protein Modeling: a Divide and Conquer Strategy for Protein Structure Prediction and its Case Study in CASP9. Journal of Bioinformatics and Computational Biology, vol. 10, no. 3, 2012. [at JBCB journal]. DOI: 10.1142/S0219720012420036. [PDF]

    38. X. Zhang, Z. Wang, X. Zhang, M. Le, J. Sun, D. Xu, J. Cheng, and G. Stacey. Evolutionary Dynamics of Protein Domain Architecture in Plants. BMC Evolutionary Biology, 12:6, 2012. [at BMC Evolutionary Biology web site]

    37. T. Joshi, K. Patil, M.R. Fitzpatrick, L.D. Franklin, Q. Yao, Z. Wang, M. Libault, L. Brechenmacher, B. Valiyodan, X. Wu, J. Cheng, G. Stacey, H. Nguyen, and D. Xu. Soybean Knowledge Base (SoyKB): A Web Resource for Soybean Translational Genomics. BMC Genomics, 13(Suppl 1):S15, 2012. [at BMC Genomics web site]

    36. Z. Wang and J. Cheng. An Iterative Self-Refining and Self-Evaluating Approach for Protein Model Quality Estimation. Protein Science, 21(1):142-151, 2012. [at Protein Science's web site] [PDF]

    35. X. Deng, J. Eickholt, J. Cheng. A Comprehensive Overview of Computational Protein Disorder Prediction Methods. Molecular BioSystems, 8(1):114-121, 2012. [at Molecular BioSystems web site]

    34. J. Eickholt, Z. Wang, J. Cheng. A Conformation Ensemble Approach to Protein Contact Prediction. BMC Structural Biology, 11:38, 2011. [at BMC Structural Biology web site]

    33. X. Deng and J. Cheng. MSACompro: Protein Multiple Sequence Alignment Using Predicted Secondary Structure, Solvent Accessibility, and Residue-Residue Contacts. BMC Bioinformatics. 12:472, 2011. [Open access at BMC Bioinformatics] .

    32. Z. Wang, J. Eickholt, J. Cheng. APOLLO: A Quality Assessment Service for Single and Multiple Protein Models. Bioinformatics. 27(12):1715-1716, 2011. [Open Access at Bioinformatics Website]

    31. K. Tanaka, C. Nguyen, M. Libault, J. Cheng, Gary Stacey. Enzymatic Activity of the Soybean Ecto-Apyrase GS52 is Essential for Stimulation of Nodulation. Plant Physiology. 155(4):1988-98, 2011. [at Plant Physiology's web site].

    30. Z. Wang, X. Zhang, M. Le, D. Xu, G. Stacey, and J. Cheng. A Protein Domain Co-Occurrence Network Approach for Predicting Protein Function and Inferring Species Phylogeny. PLoS ONE. 6(3): e17906, 2011. [at PLoS ONE web site].

    29. J. Eickholt, X. Deng, and J. Cheng. DoBo: Protein Domain Boundary Prediction by Integrating Evolutionary Signals and Machine Learning. BMC Bioinformatics. 12:43, 2011. [at BMC Bioinformatics] .

    28. M. Libault, L. Brechenmacher, J. Cheng, D. Xu, G. Stacey. Root Hair Systems Biology. Trends in Plant Science. 15(11):641-650, 2010. [at Trends' web site].

    27. Z. Wang, J. Eickholt, and J. Cheng. MULTICOM: A Multi-Level Combination Approach to Protein Structure Prediction and its Assessment in CASP8. Bioinformatics. 26(7):882-888, 2010. [at Bioinformatics web site]. The MULTICOM system was ranked among the best methods in template-based modeling, template-free modeling, protein model quality assessment, protein contact map prediction, and protein disorder prediction during CASP9, 2010.

    26. J. Schmutz, S. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D. Hyten, Q. Song, J. Thelen, J. Cheng, D. Xu, U. Hellsten, G. May, Y. Yu, T. Sakurai, T. Umezawa, M. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X. Zhang, S. Shinozaki, H. Nguyen, R. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R. Shoemaker and S. Jackson. Genome Sequence of the Palaeopolyploid Soybean. Nature. 463:178-83, 2010. [at Nature website].

    25. Z. Wang, M. Libault, T. Joshi, B. Valliyodan, H. Nguyen, D. Xu, G. Stacey, and J. Cheng. SoyDB: A Knowledge Database of Soybean Transcription Factors. BMC Plant Biology. 10:14, 2010 [SoyDB database] [open access at BMC Plant Biology] .

    24. G. Lin, Z. Wang, D. Xu, and J. Cheng. Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. BMC Bioinformatics, 11(Suppl 3):S1, 2010. [at BMC Bioinformatics website]

    23. X. Deng, J. Eickholt, and J. Cheng. PreDisorder: Ab Initio Sequence-Based Prediction of Protein Disordered Regions. BMC Bioinformatics, 10:436, 2009. [at BMC Bioinformatics website]. Predisorder was ranked among the best protein disorder prediction methods in CASP9, 2010.

    22. J. Cheng, Z. Wang, A.N. Tegge and J. Eickholt. Prediction of Global and Local Quality of CASP8 Models by MULTICOM series. Proteins, vol. 77, pp. 181-184, 2009. [at Proteins web site] CASP8 invited contribution

    21. A.N. Tegge, Z. Wang, J. Eickholt, and J. Cheng. NNcon: Improved Protein Contact Map Prediction Using 2D-Recursive Neural Networks. Nucleic Acids Research , vol. 37, pp. w515-w518, 2009. [at NAR web site]. NNcon was ranked among the best contact map prediction methods in CASP8.

    20. E.E. Stagner, D.J. Bouvrette, J. Cheng, and E.C. Bryda. The Polycystic Kidney Disease-related Proteins Bicc1 and SamCystin Interact. Biochemical and Biophysical Researh Communications. 383(1):16-21, 2009. [PDF]

    19. Z. Wang, A. N. Tegge, and J. Cheng. Evaluating the Absolute Quality of a Single Protein Model Using Support Vector Machines and Structural Features. Proteins, vol. 75, no. 3, 638-647, 2009. [at Proteins website] ModelEvaluator was ranked among the best model evaluation methods in CASP8. [CASP8 model quality assessment talk]

    18. J. Cheng. A Multi-Template Combination Algorithm for Protein Comparative Modeling. BMC Structural Biology.8:18, 2008. [Open Access at BMC website] MULTICOM was ranked among the best template-based and template-free structure prediction methods in CASP8. [CASP8 template-based modeling talk]; [CASP8 template_free modeling talk]

    17. J. Dai and J. Cheng. HMMEditor: A Visual Editing Tool for Profile Hidden Markov Model. BMC Genomics. 9(S1):S8, 2008. [Open Access at BMC website]

    16. J. Hecker, J. Yang, and J. Cheng. Protein Disorder Prediction at Multiple Levels of Sensitivity and Specificity. BMC Genomics. 9(S1):S9, 2008. [Open Access at BMC website] PreDisorder was ranked among the best disorder predictors in CASP8. [CASP8 disorder prediction talk]

    15. J. Cheng, A. N. Tegge, and P. Baldi. Machine Learning Methods for Protein Structure Prediction. IEEE Reviews in Biomedical Engineering. 1:41-49, 2008. [PDF]

    14. A. Randall, J. Cheng, M. Sweredoski, and P. Baldi. TMBpro: Secondary Structure, Beta-Contact, and Tertiary Structure Prediction of Transmembrane Beta-Barrel Proteins. Bioinformatics, vol. 24, pp. 513-520, 2008. [Bioinformatics website] [PDF]

    13. J. Cheng. DOMAC: An Accurate, Hybrid Protein Domain Prediction Server. Nucleic Acids Research, vol. 35, pp. w354-w356, 2007. [PDF] [Open Access at NAR website] DOMAC was ranked among the best domain predictors in CASP8

    12. J. Cheng and P. Baldi. Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set. BMC Bioinformatics. 8:113, 2007. [PDF][Free access at BMC Bioinformatics website] SVMcon is one of the best contact map predictors in CASP7, CASP8 and CASP9.

    11. M. Tress, J. Cheng, P. Baldi, K. Joo, J. Lee, J.H. Seo, J. Lee, D. Baker, D. Chivian, D. Kim, A. Valencia, and I. Ezkurdia. Assessment of Predictions Submitted for the CASP7 Domain Prediction Category. Proteins: Structure, Function and Bioinformatics, vol. 68 (S8):137-151, 2007. [CASP7 Invited Contribution] [PDF] [Paper at Proteins Website]

    10. L. Larson, M. Zhang, N. Beliakova-Bethell, V. Bilanchone, A. Lamsa, K. Nagashima, R. Najdi, K. Kosaka, V. Kovacevic, A. Lamsa, J. Cheng, P. Baldi, G.W. Hatfield, and S. Sandmeyer. Ty3 Capsid Scanning Mutations Reveal Early and Late Functions of the Amino-Terminal Domain. Journal of Virology, vol. 81, pp. 6957-6972, 2007. [PDF] [Free Access at Journal of Virology website]

    9. J. Cheng and P. Baldi. A Machine Learning Information Retrieval Approach to Protein Fold Recognition. Bioinformatics, vol. 22, no. 12, pp. 1456-1463, 2006. [PDF][Free Access at Bioinformatics website] . FOLDpro and 3Dpro are the No. 2 and No. 3 Servers for High-Accuracy Protein Structure Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7). Recommended by Faculty of 1000 Biology.

    8. J. Cheng, M. Sweredoski, and P. Baldi. DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. Data Mining and Knowledge Discovery, vol. 13, no. 1, pp. 1-10, 2006. [PDF] [DAMI advance online] . FOLDpro-DOMpro is the No. 1 Server for Automated Protein Domain Prediction in CASP7.

    7. S. A. Danziger, S. J. Swamidass, J. Zeng, L. R. Dearth, Q. Lu, J. H. Chen, J. Cheng, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, R. K. Brachmann, and R. H. Lathrop. Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants. IEEE Transactions on Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 114-125, 2006. [PDF]

    6. J. Cheng, A. Randall, and P. Baldi. Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines. Proteins: Structure, Function, Bioinformatics, vol. 62, no. 4, pp. 1125-1132, 2006. [PDF][PDF at Proteins website]

    5. J. Cheng, H. Saigo, and P. Baldi. Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.Proteins: Structure, Function, Bioinformatics, vol 62, no. 3, pp. 617-629, 2006. [PDF][PDF at Proteins website]

    4. J. Cheng, M. Sweredoski, and P. Baldi. Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data, Data Mining and Knowledge Discovery, vol. 11, no. 3, pp. 213-222, 2005. [PDF] [PDF at DAMI website] DISpro is No. 2 server in disorder prediction in CASP7 (No. 5 in both human and server predictors).

    3. J. Cheng, A. Randall, M. Sweredoski, and P. Baldi, SCRATCH: a Protein Structure and Structural Feature Prediction Server. Nucleic Acids Research, vol. 33 (web server issue), w72-76, 2005. [PDF][PDF at NAR website]

    2. J. Cheng, L. Scharenbroich, P. Baldi, and E. Mjolsness. Sigmoid: Towards a Generative, Scalable, Software Infrastructure for Pathway Bioinformatics and Systems Biology. IEEE Intelligent Systems, vol. 20, no. 3, pp. 68-75, 2005.[PDF][PDF at IEEE website]

    1. J. Cheng and P. Baldi. Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms. Bioinformatics, vol. 21(Suppl 1), pp. i75-84, 2005. (This is the journal version of Conference paper 2) [PDF][Free Access at Bioinformatics website][ISMB Talk]. BETApro is one of the Best Residue Contact Predictors in CASP7 and CASP8.

Conference Papers and Tutorials

    8. J. Chen, J. Cheng, A.K. Dunker. Intrinsically Disordered Proteins - A Tutorial. Pacific Symposium on Biocomputing (PSB), Hawaii, 2012. [PDF] [Tutorial Slides].

    7. J. Chen, J. Cheng, A.K. Dunker. Intrinsically Disordered Proteins: Analysis, Prediction, Simulation, and Biology. Pacific Symposium on Biocomputing (PSB), Hawaii, 2012. [at PSB web site].

    6. T. Joshi, K. Patil, M.R. Fitzpatrick, L.D. Franklin, Q. Yao, Z. Wang, M. Libault, L. Brechenmacher, B. Valiyodan, X. Wu, J. Cheng, G. Stacey, H. Nguyen, and D. Xu. Soybean Knowledge Base (SoyKB): A Web Resource for Soybean Translational Genomics. The 10th Asia Pacific Bioinformatics Conference (APBC), Melbourne, Australia, 2012. [PDF] (same as Journal article 36).

    5. J. Cheng, J. Eickholt, Z. Wang, and X. Deng. Recursive Protein Modeling: a Divide and Conquer Strategy for Protein Structure Prediction and its Case Study in CASP9. Computational Structural Bioinformatics Workshop, Atlanta, Georgia, 2011. [PDF], [Presentation Slides].

    4. G. Lin, Z. Wang, D. Xu, and J. Cheng. Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington D.C., 2009. [PDF]

    3. J. Cheng, Z. Wang, and G. Pollastri. A Neural Network Approach to Ordinal Regression. International Joint Conference on Neural Networks (IJCNN), Hongkong, 2008. [PDF]

    2. J. Cheng and P. Baldi. Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms. Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 2005). Bioinformatics, vol. 21(Suppl 1), pp. i75-84, 2005. [PDF][Free Access at Bioinformatics website][ISMB Talk].

    1. P. Baldi, J. Cheng, and A. Vullo. Large-Scale Prediction of Disulphide Bond Connectivity . Advances in Neural Information Processing Systems 17 (NIPS 2004), L. Saul,Y. Weiss, and L. Bottou editors, MIT press, pp.97-104, Cambridge, MA, 2004. [PDF][Free Access at NIPS website]

Book Chapters

    4. J. Li, D. Bhattacharya, R. Cao, B. Adhikari, X. Deng, J. Eickholt, J. Cheng. The MULTICOM Protein Tertiary Structure Prediction System. in press.

    3. X. Deng, J. Cheng. MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features. in press.

    2. B. Compani, T. Su, I. Chang, J. Cheng, K. Shah, T. Whisenant, Y. Dou, A. Bergmann, R. Cheong, L. Bardwell, A. Levchenko, P. Baldi, and E. Mjolsness. A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology. Adv Exp Med Biol. 680:523-534, 2010. [at PubMed].

    1. A. N. Tegge, Z. Wang, and J. Cheng. Integrative Protein Fold Recognition by Alignments and Machine Learning. in Protein Structure Prediction: Method and Algorithms (editors: H. Rangwala and G. Karypis), Wiley, 2009.

Theses

    4. Z. Wang. Revealing the Conformation and Properties of Human Genome, Protein Molecules, and Protein Domain Co-Occurrence Network. PhD Dissertation. University of Missouri, Columbia, 2012.

    3. M. Ahmad. MUPRIMER: A Tool for Finding Allele Specific PCR-Primers for Homologous Gene Sequences . Master Thesis. University of Missouri, Columbia, 2009.

    2. J. Cheng. Machine Learning Algorithms for Protein Structure Prediction. PhD Dissertation. University of California Irvine, Irvine, CA, 2006. [PDF]

    1. J. Cheng. A Comparative Study of the Similarity Measures of Text Categorization. Master Thesis. Utah State University, Logan, UT, 2001.