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Basta, H.A., Cleveland, S.B., Clinton, R.A, Dimitrov, A.J., and McClure, M.A. (2009) “Evolution of Teleost Fish Retroviruses: Characterization of New Retroviruses With Cellular Genes,” Journal of Virology, 83:10152-10162. [pdf copy]

Novick, P.A., Basta, H.A., Floumanhaft, M., McClure, M.A. and Boissinot, S., (2009) The Evolutionary Dynamics Of Non-LTR Retrotransposons In The Lizard Anolis Carolinensis Shows More Similarity To Fish Than Mammals, Molecular Biology and Evolution, 18:1849-1863. [pdf copy

Holly A. Basta, Alex J. Buzak and Marcella A. McClure, (2007) "Identifcation of Novel Retroid Agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis" Evolutionary Bioinformatics Online. 3: 179-195[pdf copy]

McClure, M.A., Richardson, H.S., Clinton, R.A., Hepp,C.M., Crowther, B.A.,Donaldson, E.F.,(2005) "Automated characterization of potentially active retroid agents in the human genome".Genomics 85(2005) 512-523[pdf copy]

Franklin, M.J., Stephanie , D.A., McClure, M.A.,(2004) "Evidence that the algI/algJ Gene Cassette, Required for O Acetylation of P.aeruginosa Alginet, Evolved by Lateral Gene Transfer", Journal Of Bacteriology, July 2004 p.4759-4773[pdf copy]

McClure, M.A., Donaldson, E., Corro, S., (2002) "Potential Multiple Endonuclease Functions and a Ribonuclease H Encoded in Retroposon Genomes," Virology, 296,147-158. [  PDF copy]

McClure, M.A., (2001) "Evolution of the DUT Gene: Horizontal Transfer between Host and Pathogen in all Three Domains of Life," Current Protein and Peptide Science, 2,313-324. [  PDF copy] 

McClure, M.A., (2000) "The Complexities of Genome Analysis, the Retroid Agent Perspective," Bioinformatics, 16(2):79-95.  [ Zipped PDF copy] 

Jordan, I.K., Sutter, B. and McClure, M.A., (2000) "Molecular Evolution of Paramyxoviridae and Rhabdoviridae Multiple Protein Encoding Gene," Molecular Biology and Evolution, 17:75-86. [ Zipped PDF copy] 

Baldo, A.M. and McClure, M.A., (1999) "Evolutionary History of the dUTPase Enzyme: Horizontal Exchange between Viral Pathogens and Their Hosts," Journal of Virology, 73: 7710-7721. [ Zipped PDF copy] 

McClure, M.A. (1999) "The Retroid Agents: Disease, Function, and Evolution" in Origin and Evolution of Viruses, Eds. Domingo, E., Webster, R. and Holland J., (Academic Press, London) pp163-195. [ Zipped PDF copy] 

Hudak, J. and McClure, M.A., (1999) "A Comparative Analysis of Computational Motif-detection Methods," in Proceedings of the Pacific Symposium on Biocomputing, '99, Eds. Altman, R.B., Dunker, A.K., Hunter, L., Klein, T.E. & Lauderdale, K. (World Scientific. New Jersey) pp 138-149. [  Zipped PDF copy] 

McClure, M.A., and Kowlask J., (1999) The Effects of Ordered-series-of-motifs Anchoring and Sub-class Modeling on the Generation of HMMs Representing Highly Divergent Protein Sequences" in Proceedings of the Pacific Symposium on Biocomputing, '99, Eds. Altman, R.B., Dunker, A.K., Hunter, L., Klein, T.E. & Lauderdale, K. (World Scientific. New Jersey) pp 162-170. [ Zipped PDF copy] 

McClure, M.A., Hudak, J. and Kowalski, J. (1998) "Low Identity, Low Similarity Protein Sequences: Independent Modeling of the Ordered-series-of-motifs and Motif-intervening-regions, in Genome Informatics 1998, Eds. Miyano, S. & Takagi, T. (Universal Academy Press, Inc., Tokyo, Japan) pp 183-192. 

McClure, M.A. (1996) "The Complexities of Viral Genome Analysis: the Primate Lentiviruses" Current Opinion in Genetics and Development, 6:749-756. 

McClure, M.A., Smith, C. & Elton, P. (1996) "Parameterization Studies for the SAM and HMMER Methods of Hidden Markov Model Generation" Proceedings, Fourth International Conference on Intelligent Systems for Molecular Biology, Eds. D.J. States, P. Agarwal, T. Gaasterland, L. Hunter & R. F. Smith (AAAI Press, Menlo Park, CA) pp 155-164. 

McClure, M.A. (1995) "Multiple Protein-Sequence Alignment Methods: How Well Do They Perform," In: Bioinformatics and Genome Research, Eds. H.A. Lim & C. Cantor, (World Scientific Publishing Co., Ltd.) pp 365-378. 

Weiller, G. F., McClure, M.A. & Gibbs, A. (1995) "Molecular Phylogenetic Analysis," In: Molecular Basis of Virus Evolution Eds. A. Gibbs, C. H. Calisher & F. Garcia-Arenal, (Cambridge University Press) pp: 553-585. 

McClure, M.A. (1995) "The Molecular Evolution of the Retroid Family," In: Molecular Basis of Virus Evolution Eds. A. Gibbs, C. H. Calisher &F. Garcia-Arenal, (Cambridge University Press) pp:404-415. 

McClure, M.A. and Raman, R. (1995) "Parameterization Studies of Hidden Markov Models Representing Highly Divergent Protein Sequences," Proceedings of the 28th Hawaii International Conference on System Sciences, Eds. L. Hunter & B.D. Shriver, (IEEE Computer Society Press) V: 184-193. 

McClure, M.A., Vasi, T.K. and Fitch, W.M. (1994) "Comparative Analysis of Multiple Protein-Sequence Alignment Methods," Molecular Biology and Evolution, 11:571-592. 

Baldi, P., Chauvin, Y., Hunkapiller, T., and McClure, M.A. (1994) "Hidden Markov Models of Biological Primary Sequence Information," Proceedings of the National Academy of Science, USA 91: 1059-1063. 

Baldi, P., Chauvin, Y., Hunkapiller, T. and McClure, M.A. (1993) "Hidden Markov Models in Molecular Biology: New Algorithms and Applications," In Advances in Neural Information Processing Systems 5, Eds. S.J. Hanson, J.D. Cowan and C. Lee Giles, (Morgan Kaufmann) pp 747-754. 

McClure, M.A. (1993) "Evolutionary History of the Reverse Transcriptase," In: Cold Spring Harbor Symposia (Cold Spring Harbor Laboratory, Cold Harbor, NY) pp. 425- 444. 

McClure, M.A., Thibault, K.J., Hatalski, C. G. and Lipkin, I. W. (1992) "Sequence Similarity between Borna Disease Virus p40 and a Duplicated Domain within the Paramyxo- and Rhabdovirus Polymerase Proteins," Journal of Virology 66:6572- 6577. 

Baldi, P., Chauvin, Y., Hunkapiller, T. and McClure, M.A. (1992) "Adaptive Algorithms for Modeling and Analysis of Biological Primary Sequence Information," Technical Report, Cal Tech. 

McClure, M.A. (1992) "Sequence Analysis of Eukaryotic Retroid Proteins," Mathematical and Computer Modeling, An International Journal 16:121-136. 

McClure, M.A. (1991) "Evolution of Retroposons by Acquisition or Deletion of Retrovirus-like Genes," Molecular Biology and Evolution 8:835-856. 

Doolittle, R.F., Feng, D.-F., McClure, M.A. & Johnson, M.S. (1990) "Retrovirus Phylogeny and Evolution," In: Current Topics in Microbiology and Immunology Eds. Swanstrom, R. and Vogt, P.K. (Springer-Verlag, Berlin-Heidlberg) 157:1-18. 

McClure, M.A. & Perrault, J. (1989) "Two Domains Distantly Related to Tyrosine Protein Kinases in the Vesicular Stomatitis Virus Polymerase," Virology 172:391-397. 

Doolittle, R.F., Feng, D.-F., Johnson, M.S., & McClure, M.A. (1989) "Origins and Evolutionary Relationships of Retroviral Proteins," Quarterly Review of Biology 64:1- 30. 

Perrault, J., Beckes, J.D., Helfman, W.B., Childers, L.C., Singer, P.A., Chuang, J. C. & McClure, M.A. (1989) "On the Role of ATP and Protein Kinases in VSV RNA Synthesis," In: Genetics & Pathogenicity of Negative Strand Viruses Elsevier Biomedical Press pp.138-145. 

McClure, M.A., Johnson, M.S., Feng, D.-F., & Doolittle, R. F. (1988) "Sequence Comparisons of Retroviral Proteins: Relative Rates of Change and General Phylogeny," Proceedings of the National Academy of Science, U.S.A. 85:2469- 2473. 

McClure, M.A., Johnson, M.S., & Doolittle, R.F. (1987) "Relocation of a Protease-Like Gene Segment Between Two Retroviruses," Proceedings of the National Academy of Science, U.S.A. 84:2693-2697. 

Johnson, M.S., McClure, M.A., Feng, D.-F., Gray, J. & Doolittle, R.F. (1986) "Computer Analysis of Retroviral pol Genes: Assignment of Enzymatic Functions to Specific Sequences and Homologies with Non-Viral Enzymes," Proceedings of the National Academy of Science, U.S.A. 83:7648-7652. 

McClure, M.A. & Perrault, J. (1986) "RNA Virus Genomes Hybridize to Cellular rRNAs and to Each Other," Virology 57:917-921. 

Doolittle, R.F., Feng, D.-F. Johnson, M.S. & McClure, M.A. (1986) "Relationships of Human Protein Sequences to Those of Other Organisms," In: Cold Spring Harbor Symposia (Cold Spring Harbor Laboratory, Cold Harbor, NY) pp. 447-455. 

McClure, M.A. & Perrault, J. (1985) "Poliovirus Genome RNA Hybridizes Specifically to Higher Eukaryotic Ribosomal RNAs," Nucleic Acid Research 13:6797- 6816. 

Perrault, J., McClear, P.W., Clinton, G.M., & McClure, M.A. (1984) "Does Modification of the Template N Protein Play a Role in Regulation of VSV RNA Synthesis?," In: Nonsegmented Negative Strand Viruses Eds. Bishop, D.H.L. and Compans, R.W.(Academic Press, New York) pp. 71-77. 

Perrault, J., Clinton, G.M., & McClure, M.A. (1983) "RNP Template of Vesicular Stomatitis Virus Regulates Transcription and Replication Functions," Cell 35:175-185. 

Perrault, J., Lane, J.L., & McClure, M.A. (1981) "In Vitro Transcription Alterations in a Vesicular Stomatitis Virus Variant," In: Replication of Negative Strand Viruses Eds. Bishop, D.H.L. and Compans, R.W. (Elsevier: North Holland) pp. 829-836. 

Perrault, J., Lane, J.L., & McClure, M.A. (1980) "A Variant VSV Generates Defective Interfering Particles with Replicase- like Activity In Vitro," In: Animal Virus Genetics, ICN- UCLA Symposia on Molecular and Cellular Biology (Academic Press, New York) XVIII:370-390. 

McClure, M..A., Holland, J.J., & Perrault, J. (1980) "Generation of Defective Interfering Particles in Picornaviruses," Virology 100:408-418. 

Note: In Bioinformatics peer-reviewed technical papers are published as meeting Proceedings that are listed in Science Citation Index.