Using Recurrence Quantification Analysis Descriptors for Protein Sequence Classification with Support Vector Machines

References and Footnotes

• Eisenberg , D. , Marcotte , E. M. , Xenarios , I. and Yeates , T. O. 2000 . Nature , 405 : 823 – 826 .
   PubMed Web of Science ®Google Scholar
• Kanehisa , M. and Bork , P. 2003 . Nature Genetics , 33 : 305 – 310 .
   PubMed Web of Science ®Google Scholar
• Bystroff , C. , Shao , Y. and Yuan , X. 2004 . Appi Bioinformatics , 3 : 97 – 104 .
   PubMedGoogle Scholar
• Anfinsen , C. B. 1972 . Biochem J , 128 : 737 – 749 .
   PubMed Web of Science ®Google Scholar
• Jones , D. and Thornton , J. 1993 . J Comp Aided Mol Design , 7 : 439 – 456 .
   PubMedGoogle Scholar
• Dunbrack , R. L. 2006 . Curr Op Struct Bio , 16 : 374 – 384 .
   PubMed Web of Science ®Google Scholar
• Gribskov , M. , McLachlan , A. D. and Eisenberg , D. 1987 . PNAS , 84 : 4355 – 4358 .
   PubMed Web of Science ®Google Scholar
• Kyte , J. and Doolittle , R. F. 1982 . J Mol Biol , 157 : 105 – 132 .
   PubMed Web of Science ®Google Scholar
• Callebaut , I. , Labesse , G. , Durand , P. , Poupon , A. , Canard , L. , Chomilier , J. , Henrissat , B. and Mornon , J. P. 1997 . CMLS , 53 : 621 – 645 .
   PubMed Web of Science ®Google Scholar
• Chen , C. P. and Rost , B. 2002 . Appl Bioinformatics , 1 : 21 – 35 .
   PubMedGoogle Scholar
• Phoenix , D. A. and Harris , F. 2002 . Molecular Membrane Biology , 19 : 1 – 10 .
   PubMed Web of Science ®Google Scholar
• Chou , K. C. and Cai , Y. D. 2003 . Journ Cell Biochem , 90 : 1250 – 1260 .
   PubMedGoogle Scholar
• Zbilut , J. P. , Giuliani , A. , Webber , C. L. Jr. and Colosimo , A. 1998 . Protein Engineering , 11 : 87 – 93 .
   PubMedGoogle Scholar
• Webber , C. L. Jr. , Giuliani , A. , Zbilut , J. P. and Colosimo , A. 2001 . Proteins: Structure, Function, and Genetics , 44 : 292 – 303 .
   PubMedGoogle Scholar
• Manetti , C. , Giuliani , A. , Ceruso , M.-A. , Webber , C. L. Jr. and Zbilut , J. P. 2001 . Physics Letters A , 281 : 317 – 323 .
   Google Scholar
• Zbilut , P. , Giuliani , A. , Colosimo , A. , Mitchell , J. C. , Colafranceschi , M. , Marwan , N. , Uversky , V. N. and Webber , C. L. Jr. 2004 . Journal of Proteome Research , 3 : 1243 – 1253 .
   PubMedGoogle Scholar
• Eckmann , J. P. , Kamphorst , S. O. and Ruelle , D. 1987 . Europhysics Letters , 4 : 973
   Google Scholar
• Zbilut , J. P. and Webber , C. L. 1992 . Phys Lett , 171 : 199 – 203 .
   Web of Science ®Google Scholar
• Webber , C. L. and Zbilut , J. P. 1994 . J Appl Physiol , 76 : 965 – 973 .
   PubMed Web of Science ®Google Scholar
• Vapnik , V. 1995 . The Nature of Statistical Learning Theory, 1st Ed. NY : Springer .
   Google Scholar
• Byvatov , E. and Schneider , G. 2003 . Appl Bioinformatics , 2 : 67 – 77 .
   PubMedGoogle Scholar
• Pavlidis , P. , Wapinski , I. and Noble , W. S. 2003 . Bioinformatics , 20 : 586 – 587 .
   Google Scholar
• Mundra , P. , Kumar , M. , Kumar , K. K. , Jayaraman , V. K. and Kulkarni , B. D. 2007 . Pattern Recognition Letters , 28 : 1610 – 1615 .
   Google Scholar
• Ivanciuc , O. 2002 . Internet Electronic Journal of Molecular Design , 1 : 418 – 427 .
   Google Scholar
• Ivanciuc , O. 2002 . Internet Electronic Journal of Molecular Design , 1 : 802 – 821 .
   Google Scholar
• Ivanciuc , O. 2004 . Internet Electronic Journal of Molecular Design , 3 : 802 – 821 .
   Google Scholar
• Markowetz , F. , Edler , L. and Vingron , M. 2003 . Biometrical Journal , 45 : 377 – 389 .
   Google Scholar
• Bhasin , M. , Reinherz , E. L. and Reche , P. A. 2006 . Journ Comp Bio , 13 : 102 – 112 .
   PubMedGoogle Scholar
• Kim , H. and Park , H. 2003 . Protein Engineering , 16 : 553 – 560 .
   PubMedGoogle Scholar
• Bock , J. R. and Gough , D. A. 2001 . Bioinformatics , 17 : 455 – 460 .
   PubMed Web of Science ®Google Scholar
• Ding , C. H. Q. and Dubchak , I. 2001 . Bioinformatics , 17 : 349 – 358 .
   PubMed Web of Science ®Google Scholar
• Cai , Y. D. , Liu , X. J. , Xu , X. B. and Chou , K. C. 2002 . J Peptide Sci , 8 : 297
   PubMed Web of Science ®Google Scholar
• Ward , J. J. , McGuffin , L. J. , Buxton , B. F. and Jones , D. T. 2003 . Bioinformatics , 19 : 1650 – 165 .
   PubMedGoogle Scholar
• Nguyen , M. N. and Rajapakse , J. C. 2003 . Genome Informatics , 14 : 218 – 227 .
   PubMedGoogle Scholar
• Zhang , S. W. , Pan , Q. , Zhang , H. C. , Zhang , Y. L. and Wang , H. Y. 2003 . Bioinformatics , 19 : 2390 – 2396 .
   PubMedGoogle Scholar
• Cai , C. Z. , Han , L. Y. , Ji , Z. L. , Chen , X. and Chen , Y. Z. 2003 . Nucleic Acids Research , 31 : 3692 – 3697 .
   PubMed Web of Science ®Google Scholar
• Raetsch , G. , Sonnenburg , S. and Schafer , C. 2006 . BMC Bioinformatics , 7 : S9
   PubMedGoogle Scholar
• Leslie , C. , Eskin , E. and Noble , W. S. 2002 . Pacific Symposium on Biocomputing , 7 : 566 – 575 .
   Google Scholar
• Weston , J. , Leslie , C. , Ie , E. , Zhou , D. , Elisseeff , A. and Noble , W. S. 2005 . Bioinformatics , 21 : 3241 – 3247 .
   PubMedGoogle Scholar
• Leslie , C. S. , Eskin , E. , Cohen , A. , Weston , J. and Noble , W. S. 2004 . Bioinformatics , 20 : 467 – 476 .
   PubMed Web of Science ®Google Scholar
• Vucetic , S. , Obradovic , Z. , Vacic , V. , Radivojac , P. , Peng , K. , Iakoucheva , L. M. , Cortese , M. S. , Lawson , J. D. , Brown , C. J. , Sikes , J. G. , Newton , C. D. and Dunker , A. K. 2005 . Bioinformatics , 21 : 137 – 140 .
   PubMed Web of Science ®Google Scholar
• Sickmeier , M. , Hamilton , J. A. , LeGall , T. , Vacic , V. , Cortese , M. S. , Tantos , A. , Szabo , B. , Tompa , P. , Chen , J. , Uversky , V. N. , Obradovic , Z. and Dunker , A. K. 2007 . Nucleic Acids Research , 35 ( Da- tabase issue ) : D786 – D793 .
   PubMedGoogle Scholar
• Iakoucheva , L. M. , Brown , C. J. , Lawson , J. D. , Obradovicp , Z. and Dunker , A. K. 2002 . J Mol Biol , 323 : 573 – 584 .
   PubMed Web of Science ®Google Scholar
• Spolar , R. S. , Ha , J. H. and Record , M. T. 1989 . PNAS , 86 : 8382 – 8385 .
   PubMed Web of Science ®Google Scholar
• Kyte , J. and Doolittle , R. F. 1982 . J Mol Biol , 157 : 105 – 132 .
   PubMed Web of Science ®Google Scholar
• Thomas , S. I. , Kulkarni , A. J. , Kulkarni , B. D. , Jayaraman , V. K. and Balaji , R. V. 2006 . Bioinformatics , 22 : 278 – 284 .
   PubMedGoogle Scholar
• Marwan , N. , Thiel , M. and Nowaczyk , N. R. 2002 . Nonlin Proc Geophys , 9 : 325 – 331 .
   Web of Science ®Google Scholar
• Marwan , N. , Wessel , N. , Meyerfeldt , U. , Schirdewan , A. and Kurths , J. 2002 . Phys Rev E , 66 : 026702 – 1026702 . -8
   PubMed Web of Science ®Google Scholar
• Giuliani , A. , Sirabella , R. , Benigni , R. and Colosimo , A. 2000 . Protein Engineering , 13 : 671 – 678 .
   PubMedGoogle Scholar
• Witten , I. H. and Frank , E. 2005 . Data Mining: Practical Machine Learning Tools and Yechniques, 2nd edition. SF Morgan Kaufmann .
   Google Scholar
• Muller , K. R. and et al . 2001 . IEEE Trans Neural Netw , 2 : 181 – 201 .
   Google Scholar
• Gunn , S. 1997 . ISIS technical report
   Google Scholar
• Kulkarni , A. and et al . 2004 . Comput Chem Eng , 28 : 311 – 318 .
   Google Scholar
• Burges , C. J. C. 1998 . Data Min Knowl Disc , 2 : 121 – 167 .
   Web of Science ®Google Scholar
• Chang , C. C. and Lin , C. J. 2001 . LIBSVM: A Library for Support Vector Machines Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm
   Google Scholar
• Oldfield , C. J. , Cheng , Y. , Cortese , M. S. , Brown , C. J. , Uversky , V. N. and Dunker , A. K. 2005 . Biochemistry , 44 : 1989 – 2000 .
   PubMed Web of Science ®Google Scholar
• Lindin , R. , Jense , L. J. , Diella , F. , Bork , P. , Gibson , T. J. and Russell , R. B. 2003 . Structure , 11 : 1453 – 1459 .
   PubMedGoogle Scholar
• Ward , J. J. , Sodhi , J. S. , McGuffin , L. J. , Buxton , B. F. and Jones , D. T. 2004 . J Mol Biol , 337 : 635 – 645 .
   PubMed Web of Science ®Google Scholar
• Romero , P. , Obradovic , Z. , Li , X. , Garner , E. C. , Brown , C. J. and Dunker , A. K. 2001 . Proteins , 42 : 38 – 48 .
   PubMed Web of Science ®Google Scholar
• Haynes , C. and Iakoucheva , L. M. 2006 . Nucleic Acids Research , 34 : 305 – 312 .
   PubMedGoogle Scholar