TY - JOUR AU - Ofran, Y. AU - Punta, M. AU - Schneider, R. AU - Rost, B. PY - 2005 DA - 2005// TI - Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery JO - Drug Discov Today VL - 10 UR - https://doi.org/10.1016/S1359-6446(05)03621-4 DO - 10.1016/S1359-6446(05)03621-4 ID - Ofran2005 ER - TY - JOUR AU - Bastien, O. AU - Ortet, P. AU - Roy, S. AU - Marechal, E. PY - 2007 DA - 2007// TI - The configuration space of homologous proteins: A theoretical and practical framework to reduce the diversity of the protein sequence space after massive all-by-all sequence comparisons JO - Fut Gen Comput Syst VL - 23 UR - https://doi.org/10.1016/j.future.2006.07.016 DO - 10.1016/j.future.2006.07.016 ID - Bastien2007 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Smith, T. F. AU - Waterman, M. S. PY - 1981 DA - 1981// TI - Identification of common molecular subsequences JO - J Mol Biol VL - 147 UR - https://doi.org/10.1016/0022-2836(81)90087-5 DO - 10.1016/0022-2836(81)90087-5 ID - Smith1981 ER - TY - BOOK AU - Setubal, J. AU - Meidanis, J. PY - 1997 DA - 1997// TI - Introduction to Computational Molecular Biology PB - Pws Publishing Company CY - Boston ID - Setubal1997 ER - TY - JOUR AU - Dayhoff, M. O. AU - Schwartz, R. M. AU - Orcutt, B. C. PY - 1978 DA - 1978// TI - A Model of Evolutionary Change in Proteins JO - Atlas Prot Seq Struct VL - 5 ID - Dayhoff1978 ER - TY - JOUR AU - Henikoff, S. AU - Henikoff, J. G. PY - 1992 DA - 1992// TI - Amino acid substitution matrices from protein blocks JO - Proc Natl Acad Sci USA VL - 89 UR - https://doi.org/10.1073/pnas.89.22.10915 DO - 10.1073/pnas.89.22.10915 ID - Henikoff1992 ER - TY - JOUR AU - Bastien, O. AU - Roy, S. AU - Marechal, E. PY - 2005 DA - 2005// TI - Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions JO - C R Biol VL - 328 UR - https://doi.org/10.1016/j.crvi.2005.02.002 DO - 10.1016/j.crvi.2005.02.002 ID - Bastien2005 ER - TY - JOUR AU - Ouzonis, C. A. AU - Valencia, A. PY - 2003 DA - 2003// TI - Early bioinformatics: the birth of a discipline – a personal view JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg309 DO - 10.1093/bioinformatics/btg309 ID - Ouzonis2003 ER - TY - JOUR AU - Lipman, D. J. AU - Pearson, W. R. PY - 1985 DA - 1985// TI - Rapid and sensitive protein similarity searches JO - Science VL - 227 UR - https://doi.org/10.1126/science.2983426 DO - 10.1126/science.2983426 ID - Lipman1985 ER - TY - JOUR AU - Comet, J. P. AU - Aude, J. C. AU - Glemet, E. AU - Risler, J. L. AU - Henaut, A. AU - Slonimski, P. P. AU - Codani, J. J. PY - 1999 DA - 1999// TI - Significance of Z-value statistics of Smith-Waterman scores for protein alignments JO - Comput Chem VL - 23 UR - https://doi.org/10.1016/S0097-8485(99)00008-X DO - 10.1016/S0097-8485(99)00008-X ID - Comet1999 ER - TY - JOUR AU - Bacro, J. N. AU - Comet, J. P. PY - 2001 DA - 2001// TI - Sequence alignment: an approximation law for the Z-value with applications to databank scanning JO - Comput Chem VL - 25 UR - https://doi.org/10.1016/S0097-8485(01)00074-2 DO - 10.1016/S0097-8485(01)00074-2 ID - Bacro2001 ER - TY - JOUR AU - Bastien, O. AU - Aude, J. C. AU - Roy, S. AU - Marechal, E. PY - 2004 DA - 2004// TI - Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg440 DO - 10.1093/bioinformatics/btg440 ID - Bastien2004 ER - TY - JOUR AU - Bastien, O. AU - Ortet, P. AU - Roy, S. AU - Marechal, E. PY - 2005 DA - 2005// TI - A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-49 DO - 10.1186/1471-2105-6-49 ID - Bastien2005 ER - TY - JOUR AU - Fitch, W. M. PY - 1983 DA - 1983// TI - Random sequences JO - J Mol Biol VL - 163 UR - https://doi.org/10.1016/0022-2836(83)90002-5 DO - 10.1016/0022-2836(83)90002-5 ID - Fitch1983 ER - TY - JOUR AU - Aude, J. C. AU - Louis, A. PY - 2002 DA - 2002// TI - An incremental algorithm for Z-value computations JO - Comput Chem VL - 26 UR - https://doi.org/10.1016/S0097-8485(02)00003-7 DO - 10.1016/S0097-8485(02)00003-7 ID - Aude2002 ER - TY - JOUR AU - Petryszak, R. AU - Kretschmann, E. AU - Wieser, D. AU - Apweiler, R. PY - 2005 DA - 2005// TI - The predictive power of the CluSTr database JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti542 DO - 10.1093/bioinformatics/bti542 ID - Petryszak2005 ER - TY - JOUR AU - Pearson, W. R. PY - 1998 DA - 1998// TI - Empirical statistical estimates for sequence similarity searches JO - J Mol Biol VL - 276 UR - https://doi.org/10.1006/jmbi.1997.1525 DO - 10.1006/jmbi.1997.1525 ID - Pearson1998 ER - TY - BOOK AU - Coles, S. PY - 2001 DA - 2001// TI - An introduction to Statistical Modeling of Extreme Values PB - Springer-Verlag CY - New York UR - https://doi.org/10.1007/978-1-4471-3675-0 DO - 10.1007/978-1-4471-3675-0 ID - Coles2001 ER - TY - JOUR AU - Karlin, S. AU - Altschul, S. F. PY - 1990 DA - 1990// TI - Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes JO - Proc Natl Acad Sci USA VL - 87 UR - https://doi.org/10.1073/pnas.87.6.2264 DO - 10.1073/pnas.87.6.2264 ID - Karlin1990 ER - TY - JOUR AU - Vingron, M. AU - Waterman, M. S. PY - 1994 DA - 1994// TI - Sequence alignment and penalty choice. Review of concepts, case studies and implications JO - J Mol Biol VL - 235 UR - https://doi.org/10.1016/S0022-2836(05)80006-3 DO - 10.1016/S0022-2836(05)80006-3 ID - Vingron1994 ER - TY - JOUR AU - Altschul, S. F. AU - Bundschuh, R. AU - Olsen, R. AU - Hwa, T. PY - 2001 DA - 2001// TI - The estimation of statistical parameters for local alignment score distributions JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.2.351 DO - 10.1093/nar/29.2.351 ID - Altschul2001 ER - TY - JOUR AU - Webber, C. AU - Barton, G. J. PY - 2001 DA - 2001// TI - Estimation of P-values for global alignments of protein sequences JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.12.1158 DO - 10.1093/bioinformatics/17.12.1158 ID - Webber2001 ER - TY - JOUR AU - Gavrilov, L. A. AU - Gavrilova, N. S. PY - 2001 DA - 2001// TI - The reliability theory of aging and longevity JO - J Theor Biol VL - 213 UR - https://doi.org/10.1006/jtbi.2001.2430 DO - 10.1006/jtbi.2001.2430 ID - Gavrilov2001 ER - TY - CHAP AU - Lespinats, S. PY - 2006 DA - 2006// TI - Style du genome explore par analyse textuelle de l'ADN BT - PhD thesis PB - Paris VI University CY - Department of Epidemiology and Health Informatics ID - Lespinats2006 ER - TY - JOUR AU - Müller, T. AU - Vingron, M. PY - 2000 DA - 2000// TI - Modeling Amino Acid Replacement JO - J Comput Biol VL - 7 UR - https://doi.org/10.1089/10665270050514918 DO - 10.1089/10665270050514918 ID - Müller2000 ER - TY - JOUR AU - Müller, T. AU - Spang, R. AU - Vingron, M. PY - 2002 DA - 2002// TI - Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likehood method JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003985 DO - 10.1093/oxfordjournals.molbev.a003985 ID - Müller2002 ER - TY - JOUR AU - Altschul, S. F. PY - 1991 DA - 1991// TI - Amino acid substitution matrices from an information theoretic perspective JO - J Mol Biol VL - 219 UR - https://doi.org/10.1016/0022-2836(91)90193-A DO - 10.1016/0022-2836(91)90193-A ID - Altschul1991 ER - TY - BOOK AU - Crowder, M. J. AU - Kimber, A. C. AU - Smith, R. L. AU - Sweeting, T. J. PY - 1991 DA - 1991// TI - Statistical analysis of reliability data PB - Chapman and Hall CY - London UR - https://doi.org/10.1007/978-1-4899-2953-2 DO - 10.1007/978-1-4899-2953-2 ID - Crowder1991 ER - TY - BOOK AU - Rigdon, S. E. AU - Basu, A. P. PY - 2000 DA - 2000// TI - Statistical methods for the reliability of repairable systems PB - Wiley and Son CY - New-York ID - Rigdon2000 ER - TY - BOOK AU - Valleron, A. J. PY - 1998 DA - 1998// TI - Introduction à la Biostatistique PB - Masson CY - Paris ID - Valleron1998 ER - TY - JOUR AU - Shkovskii, B. I. PY - 2005 DA - 2005// TI - A simple derivation of the Gompertz law for human mortality JO - Theory in Biosciences VL - 123 UR - https://doi.org/10.1016/j.thbio.2005.01.001 DO - 10.1016/j.thbio.2005.01.001 ID - Shkovskii2005 ER - TY - BOOK AU - Dobzhansky, T. PY - 1974 DA - 1974// TI - Studies in the Philosophy of Biology: Reduction and Related Problems PB - University of California Press CY - Los Angeles ID - Dobzhansky1974 ER - TY - JOUR AU - Wu, T. T. AU - Fitch, W. M. AU - Margoliash, E. PY - 1974 DA - 1974// TI - The information content of protein amino acid sequences JO - Annu Rev Biochem VL - 43 UR - https://doi.org/10.1146/annurev.bi.43.070174.002543 DO - 10.1146/annurev.bi.43.070174.002543 ID - Wu1974 ER - TY - JOUR AU - Risler, J. L. AU - Delorme, M. O. AU - Delacroix, H. AU - Henaut, A. PY - 1988 DA - 1988// TI - Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix JO - J Mol Biol VL - 204 UR - https://doi.org/10.1016/0022-2836(88)90058-7 DO - 10.1016/0022-2836(88)90058-7 ID - Risler1988 ER - TY - JOUR AU - Hartley, R. V. L. PY - 1928 DA - 1928// TI - Transmission of Information JO - Bell System Technical Journal VL - 3 UR - https://doi.org/10.1002/j.1538-7305.1928.tb01236.x DO - 10.1002/j.1538-7305.1928.tb01236.x ID - Hartley1928 ER - TY - JOUR AU - Shannon, C. E. PY - 1948 DA - 1948// TI - A Mathematical Theory of Communication JO - Bell System Technical Journal VL - 27 UR - https://doi.org/10.1002/j.1538-7305.1948.tb01338.x DO - 10.1002/j.1538-7305.1948.tb01338.x ID - Shannon1948 ER - TY - BOOK AU - Cover, T. M. AU - Thomas, J. A. PY - 1991 DA - 1991// TI - Elements of Information Theory PB - Wiley and Son CY - New-York UR - https://doi.org/10.1002/0471200611 DO - 10.1002/0471200611 ID - Cover1991 ER - TY - JOUR AU - Aynechi, T. AU - Kuntz, I. D. PY - 2005 DA - 2005// TI - An information theoretic approach to macromolecular modeling: I. Sequence alignments JO - Biophys J VL - 289 UR - https://doi.org/10.1529/biophysj.104.054072 DO - 10.1529/biophysj.104.054072 ID - Aynechi2005 ER - TY - JOUR AU - Aynechi, T. AU - Kuntz, I. D. PY - 2005 DA - 2005// TI - An information theoretic approach to macromolecular modeling: II. Force fields JO - Biophys J VL - 289 UR - https://doi.org/10.1529/biophysj.105.059618 DO - 10.1529/biophysj.105.059618 ID - Aynechi2005 ER - TY - BOOK AU - Waterman, M. S. PY - 1995 DA - 1995// TI - Introduction to computational biology PB - Chapman and Hall CY - London UR - https://doi.org/10.1007/978-1-4899-6846-3 DO - 10.1007/978-1-4899-6846-3 ID - Waterman1995 ER - TY - JOUR AU - Bastien, O. AU - Lespinats, S. AU - Roy, S. AU - Metayer, K. AU - Fertil, B. AU - Codani, J. J. AU - Marechal, E. PY - 2004 DA - 2004// TI - Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference JO - Gene VL - 336 UR - https://doi.org/10.1016/j.gene.2004.04.029 DO - 10.1016/j.gene.2004.04.029 ID - Bastien2004 ER - TY - JOUR AU - Callebaut, I. AU - Prat, K. AU - Meurice, E. AU - Mornon, J. P. AU - Tomavo, S. PY - 2005 DA - 2005// TI - Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes JO - BMC Genomics VL - 6 UR - https://doi.org/10.1186/1471-2164-6-100 DO - 10.1186/1471-2164-6-100 ID - Callebaut2005 ER - TY - JOUR AU - Hulsen, T. AU - De Vlieg, J. AU - Leunissen, J. A. M. AU - Groenen, P. A. M. PY - 2006 DA - 2006// TI - Testing statistical significance scores of sequence comparison methods with structure similarity JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-444 DO - 10.1186/1471-2105-7-444 ID - Hulsen2006 ER -