Publications
Found 5 results
Filters: Author is C. Lin [Clear All Filters]
“Acute toxic effects of sonodynamic therapy on hypertrophic scar fibroblasts of rabbit ears”, vol. 14, pp. 4203-4214, 2015.
, “Effect of RAGE polymorphisms on susceptibility to and severity of osteoarthritis in a Han Chinese population: a case-control study”, vol. 14, pp. 11362-11370, 2015.
, “A meta-analysis to evaluate the effectiveness of real-time PCR for diagnosing novel coronavirus infections”, vol. 14, pp. 15634-15641, 2015.
, “Improved method for predicting protein fold patterns with ensemble classifiers”, vol. 11, pp. 174-181, 2012.
, Boisvert S, Marchand M, Laviolette F and Corbeil J (2008). HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology 5: 110.
http://dx.doi.org/10.1186/1742-4690-5-110
PMid:19055831 PMCid:2637298
Breimin L (2001). Random forests. Machine Learn. 45: 5-32.
http://dx.doi.org/10.1023/A:1010933404324
Cai CZ, Han LY, Ji ZL, Chen X, et al. (2003). SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res. 31: 3692-3697.
http://dx.doi.org/10.1093/nar/gkg600
PMid:12824396 PMCid:169006
Call ME, Schnell JR, Xu C, Lutz RA, et al. (2006). The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 127: 355-368.
http://dx.doi.org/10.1016/j.cell.2006.08.044
PMid:17055436
Chen K and Kurgan L (2007). PFRES: protein fold classification by using evolutionary information and predicted secondary structure. Bioinformatics 23: 2843-2850.
http://dx.doi.org/10.1093/bioinformatics/btm475
PMid:17942446
Chou KC (2004). Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 11: 2105-2134.
PMid:15279552
Ding CHQ and Dubchak I (2001). Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 17: 349-358.
http://dx.doi.org/10.1093/bioinformatics/17.4.349
PMid:11301304
Douglas SM, Chou JJ and Shih WM (2007). DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl. Acad. Sci. U. S. A. 104: 6644-6648.
http://dx.doi.org/10.1073/pnas.0700930104
PMid:17404217 PMCid:1871839
Gao WN, Wei DQ, Li Y, Gao H, et al. (2007). Agaritine and its derivatives are potential inhibitors against HIV proteases. Med. Chem. 3: 221-226.
http://dx.doi.org/10.2174/157340607780620644
PMid:17504192
Honda M, Kawai H, Shirota Y, Yamashita T, et al. (2005). cDNA microarray analysis of autoimmune hepatitis, primary biliary cirrhosis and consecutive disease manifestation. J. Autoimmun. 25: 133-140.
http://dx.doi.org/10.1016/j.jaut.2005.03.009
PMid:16150573
Li Y, Wei DQ, Gao WN, Gao H, et al. (2007). Computational approach to drug design for oxazolidinones as antibacterial agents. Med. Chem. 3: 576-582.
http://dx.doi.org/10.2174/157340607782360362
PMid:18045208
Murzin AG, Brenner SE, Hubbard T and Chothia C (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
http://dx.doi.org/10.1016/S0022-2836(05)80134-2
Nanni L (2006). A novel ensemble of classifiers for protein fold recognition. Neurocomputing 69: 2434-2437.
http://dx.doi.org/10.1016/j.neucom.2006.01.026
Niels L, Mark H and Eibe F (2005). Logistic model trees. Machine Learn 95: 161-205.
Pu X, Guo J, Leung H and Lin Y (2007). Prediction of membrane protein types from sequences and position-specific scoring matrices. J. Theor. Biol. 247: 259-265.
http://dx.doi.org/10.1016/j.jtbi.2007.01.016
PMid:17433369
Schaffer AA, Aravind L, Madden TL, Shavirin S, et al. (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29: 2994-3005.
http://dx.doi.org/10.1093/nar/29.14.2994
PMid:11452024 PMCid:55814
Schnell JR and Chou JJ (2008). Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451: 591-595.
http://dx.doi.org/10.1038/nature06531
PMid:18235503 PMCid:3108054
Shen HB and Chou KC (2006). Ensemble classifier for protein fold pattern recognition. Bioinformatics 22: 1717-1722.
http://dx.doi.org/10.1093/bioinformatics/btl170
PMid:16672258
Shen HB and Chou KC (2009). Predicting protein fold pattern with functional domain and sequential evolution information. J. Theor. Biol. 256: 441-446.
http://dx.doi.org/10.1016/j.jtbi.2008.10.007
PMid:18996396
Sumner M, Frank E and Hall MA (2005). Speeding up Logistic Model Tree Induction. In: Proceedings of 9th European Conference on Principles and Practice of Knowledge Discovery in Databases, Porto, Portugal (Jorge A, ed.). Springer, Germany, 675-683.
Vendruscolo M and Dobson CM (2005). A glimpse at the organization of the protein universe. PNAS 102: 5641-5642.
http://dx.doi.org/10.1073/pnas.0500274102
PMid:15827120 PMCid:556289
“Novel representation of RNA secondary structure used to improve prediction algorithms”, vol. 10, pp. 1986-1998, 2011.
, Brown JW (1999). The ribonuclease P database. Nucleic Acids Res. 27: 314.
http://dx.doi.org/10.1093/nar/27.1.314
PMid:9847214 PMCid:148169
Byun Y and Han K (2006). PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. Nucleic Acids Res. 34: W416-W422.
http://dx.doi.org/10.1093/nar/gkl210
PMid:16845039 PMCid:1538805
Chan PP and Lowe TM (2009). GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37: D93-D97.
http://dx.doi.org/10.1093/nar/gkn787
PMid:18984615 PMCid:2686519
Ding Y, Chan CY and Lawrence CE (2004). Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32: W135-W141.
http://dx.doi.org/10.1093/nar/gkh449
PMid:15215366 PMCid:441587
Gardner PP and Giegerich R (2004). A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140.
http://dx.doi.org/10.1186/1471-2105-5-140
PMid:15458580 PMCid:526219
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, et al. (2005). Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33: D121-D124.
http://dx.doi.org/10.1093/nar/gki081
PMid:15608160 PMCid:540035
Hertel J, Hofacker IL and Stadler PF (2008). SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24: 158-164.
http://dx.doi.org/10.1093/bioinformatics/btm464
PMid:17895272
Hofacker IL (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429-3431.
http://dx.doi.org/10.1093/nar/gkg599
PMid:12824340 PMCid:169005
Knudsen B and Hein J (1999). RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15: 446-454.
http://dx.doi.org/10.1093/bioinformatics/15.6.446
PMid:10383470
Lambert A, Fontaine JF, Legendre M, Leclerc F, et al. (2004). The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res. 32: W160-W165.
http://dx.doi.org/10.1093/nar/gkh418
PMid:15215371 PMCid:441556
Larkin MA, Blackshields G, Brown NP, Chenna R, et al. (2007). Clustal W and clustal X version 2.0. Bioinformatics 23: 2947-2948.
http://dx.doi.org/10.1093/bioinformatics/btm404
PMid:17846036
Leland W (1999). Dot Plots. Am. Statistician 53: 276-281.
http://dx.doi.org/10.2307/2686111
Lowe TM and Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
http://dx.doi.org/10.1093/nar/25.5.955
PMid:9023104 PMCid:146525
Rounsevell R, Forman JR and Clarke J (2004). Atomic force microscopy: mechanical unfolding of proteins. Methods 34: 100-111.
http://dx.doi.org/10.1016/j.ymeth.2004.03.007
PMid:15283919
Siebert S and Backofen R (2005). Marna: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 21: 3352-3359.
http://dx.doi.org/10.1093/bioinformatics/bti550
PMid:15972285
Touzet H and Perriquet O (2004). Carnac: folding families of related RNAs. Nucleic Acids Res. 32: W142-W145.
http://dx.doi.org/10.1093/nar/gkh415
PMid:15215367 PMCid:441553
Witwer C, Hofacker IL and Stadler PF (2004). Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans. Comput. Biol. Bioinform. 1: 66-77.
http://dx.doi.org/10.1109/TCBB.2004.22
PMid:17048382
Zhang TT, Guo M and Zou Q (2007). RNA Secondary Structure Prediction Based on Forest Representation and Genetic Algorithm. Proceedings of the Third International Conference on Natural Computation, IEE Computer Society, Washington, 370-374.
Zou Q, Guo MZ, Liu Y and Xing ZA (2008). A Novel Comparative Sequence Analysis Method for ncRNA Secondary Structure Prediction Without Multiple Sequence Alignment. Proceedings of the Fourth International Conference on Natural Computation. IEE Computer Society, Washington, 29-33.
Zou Q, Guo MZ, Wang CY and Han YP (2009a). Novel H/ACA Box snoRNA Mining and Secondary Structure Prediction Algorithms. Proceedings of the Rough Sets and Knowledge Technology, Gold Coast, 538-546.
Zou Q, Zhao T, Liu Y and Guo M (2009b). Predicting RNA secondary structure based on the class information and hopfield network. Comput. Biol. Med. 39: 206-214.
http://dx.doi.org/10.1016/j.compbiomed.2008.12.010
PMid:19215914
Zou Q, Guo M, Liu Y and Xuan P (2010). DuplexFinder: predicting the miRNA-miRNA* duplex from the animal precursors. Int. J. Bioinform. Res. Appl. 6: 69-81.
http://dx.doi.org/10.1504/IJBRA.2010.031293
PMid:20110210
Zuker M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.
http://dx.doi.org/10.1093/nar/gkg595
PMid:12824337 PMCid:169194