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Publications and submitted manuscripts- John Logsdon & the Logsdon lab
Refereed articles:
Malik S.-B., Pightling A.W., Stefaniak L.M., Schurko A.M., Logsdon J.M. Jr. An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. accepted pending revisions, Public Library of Science,One 6/9/08.
Schurko A.M. and J. M. Logsdon, Jr. 2008. Using a meiosis detection toolkit to investigate ancient asexual scandals and the evolution of sex. BioEssays, 30:6:579 - 589. [article]
McQuiston, J.R., P.I. Fields, R.V. Tauxe and J. M. Logsdon, Jr. 2008. Do Salmonella carry spare tyres?Trends Microbiol. 16:4:142-148. [article]
Moore, R.B., Oborník, M., Janouskovec, J., Chrudimsk, T., Vancová, M., Green, D.H., Wright, S.W., Davies, N.W., Bolch, C.J., Heimann, K., Slapeta, J., Hoegh-Guldberg, O., Logsdon, J.M. Jr. and D.A. Carter. 2008. A photosynthetic alveolate closely related to apicomplexan parasites. Nature, 451:7181:959-63.[article] [supplemental material]
Yoon, H.S., Grant, J., Tekle, Y.I., Wu, M., Chaon, B.C., Cole, J.C., Logsdon, J.M. Jr., Patterson, D.J., Bhattacharya, D. and L.A. Katz. 2008. Broadly sampled multigene trees of eukaryotes. BMC Evolutionary Biology, 8:14.[article]
Malik*, S.-B., M.A. Ramesh*, A.M. Hulstrand and J. M. Logsdon, Jr. 2007. Protist homologs of the meiotic Spo11 gene and topoisomerase VI reveal an evolutionary history of gene duplication and lineage-specific loss. Molecular Biology and Evolution, 24:12:2827-2841.[article] [supplemental material] *equal contributions.
Vanderford, T.H., L.J. Demma, M.B. Feinberg, S.I. Staprans and J. M. Logsdon, Jr. 2007. Adaptation of a diverse simian immunodeficiency virus population to a new host is revealed through a systematic approach to identify amino acid sites under selection. Molecular Biology and Evolution, 24:3:660-669. [article]
Andersson,J.O., Å.M. Sjögren, D.S. Horner, C.A. Murphy, P.L. Dyal, S.G. Svard, J.M. Logsdon, Jr., M.A. Ragan, R.P. Hirt and A.J. Roger. 2007. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BioMednetCentral Genomics 8:51. [article]
Carlton J.M., Hirt R.P., Silva J.C., Delcher A.L., Schatz M., Zhao Q., Wortman J.R., Bidwell S.L., Alsmark U.C.M., Besteiro S., Sicheritz-Ponten T., Noel C.J., Dacks J.B., Foster P.G., Simillion C., van der Peer Y., Miranda-Saavedra D., Barton G.J., Westrop G.D., Muller S., Dessi D., Fiori P.L., Ren Q., Paulsen I., Zhang H., Bastida-Corcuera F.D., Simoes-Barbosa A., Brown M.T., Hayes R.D., Mukherjee M., Okumura C.Y., Schneider R., Smith A.J., Vanacova S., Villalvazo M., Haas B.J., Pertea M., Feldblyum T., Utterback T.R., Shu C.-L., Osoegawa K., de Jong P.J., Hrdl I., Horvathova L., Zubacova Z., Dolezal P., Malik S.-B., Logsdon J.M. Jr., Henze K., Gupta A., Wang C.C., Dunne R.L., Upcroft J.A., Upcroft P., White O., Salzberg S.L., Tang P., Chiu C.-H., Lee Y.-S., Embley T.M., Coombs G.H., Mottram J.C., Tachezy J., Fraser-Liggett C.M., Johnson P.J. 2007. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315:5807:207-212. [article] [supporting online material]
Demma, L.J., T.H. Vanderford, J. M. Logsdon, Jr., M.B. Feinberg and S.I. Staprans. 2006. Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host. Retrovirology 3:19. [PDF]
Thomas, S.E., M. Soltani-Bejnood, P. Roth, R. Dorn, J. M. Logsdon, Jr. and B.D. McKee. 2005. Identification of two proteins required for conjunction and regular segregation of achiasmate homologs in Drosophila male meiosis. Cell, 123:555-568. [PDF]
Demma, L.J., J. M. Logsdon, Jr., T.H. Vanderford, M.B. Feinberg and S.I. Staprans. 2005. SIVsm quasispecies adaptation to a new simian host. Public Library of Science, Pathogens 1(1): e3. [PDF]
Stewart, A.D., J. M. Logsdon, Jr. and S.E. Kelley. 2005. An empirical study of the evolution of virulence under both horizontal and vertical transmission. Evolution, 59:730-739. [PDF]
Nicholson*, A.C., S.-B. Malik*, J. M. Logsdon, Jr. and E.G. van Meir. 2005. Functional evolution of ADAMTS genes: Evidence from analyses of phylogeny and gene organization. BioMednetCentral Evolutionary Biology. 5:11. [PDF, additional files 1 and 2] *equal contributions.
Ramesh*, M.A., S.-B. Malik* and J. M. Logsdon, Jr. 2005. A phylogenomic inventory of meiotic genes: Evidence for sex in Giardia and an early eukaryotic origin of meiosis. Current Biology, 15:2:185-191. [PDF and supplemental material] *equal contributions. (related articles in: Current Biology, The Scientist, NPR, ScienceNews)
Li, Y., W. G. Kelly, J. M. Logsdon, Jr., A. M. Schurko, B. D. Harfe, K. L. Hill-Harfe, and R. A. Kahn. 2004. Functional genomic analysis of the ADP-ribosylation factor family of GTPases: phylogeny among diverse eukaryotes and function in C. elegans. FASEB Journal, 18:1834-1850. [PDF]
Solomon, K.S., J. M. Logsdon, Jr. and A. Fritz. 2003. Expression and phylogenetic analysis of three zebrafish FoxI class genes. Developmental Dynamics 228:301 - 307. [PDF]
Genereux, D. P., and J. M. Logsdon, Jr. 2003. Much ado about Bacteria-to-vertebrate lateral gene transfer. Trends in Genetics, 19:191-195. [PDF]
Dacks, J. B., A. Marinets, W. F. Doolittle, T. Cavalier-Smith, and J. M. Logsdon, Jr. 2002. Analyses of RNA polymerase II genes from free-living protists: phylogeny, long branch attraction and the eukaryotic big bang. Molecular Biology and Evolution, 19:830 - 840. [PDF]
Striepen, B., M. W. White, C. Li, M. N. Guerini, S.-B. Malik, J. M. Logsdon, Jr., C. Liu, and M. S. Abrahamsen. 2002. Genetic complementation in Apicomplexan parasites. Proceedings of the National Academy of Sciences USA, 99:6304-6309. [PDF]
Orelli, B. J., J. M. Logsdon, Jr. and D. K. Bishop. 2001. Nine novel conserved motifs in BRCA1 identified by the chicken orthologue. Oncogene 20:4433-4438. [PDF]
Borodovsky, M., E. Koonin, C. Burge, J. Fickett, J. M. Logsdon, Jr. A. Sali, G. Stormo, and I. Zhulin. 2001. The third Georgia Tech-Emory International Conference on Bioinformatics: in silico Biology; Bioinformatics after the Human Genome (November 15-18, 2001, Atlanta, GA, USA). Bioinformatics 17:859-61. [PDF]
Archibald, J. M., J. M. Logsdon, Jr. and W. F. Doolittle. 2000. Origin and evolution of eukaryotic chaperonins: Phylogenetic evidence for ancient duplications in CCT genes. Molecular Biology and Evolution 17:1456-1466. [PDF]
Leong, W. L., M. J. Dobson, J. M. Logsdon, Jr., R. M. Abdel-Majid, L. C. Schalkwyk, D. L. Guernsey, and P. E. Neumann. 2000. ETn insertion in the mouse Adcy1 gene: transcriptional and phylogenetic analyses. Mammalian Genome 11:97-103. [PDF]
Archibald, J. M., J. M. Logsdon, Jr. and W. F. Doolittle. 1999. Recurrent paralogy in the evolution of archaeal chaperonins. Current Biology 9:1053-6. [PDF]
Fast*, N. M., J. M. Logsdon*, Jr., and W. F. Doolittle. 1999. Phylogenetic analysis of the TATA box binding protein (TBP) gene from Nosema locustae: evidence for a microsporidia-fungi relationship and spliceosomal intron loss. Molecular Biology and Evolution 16:1415-9. [PDF] *equal contributions
Funke, R. P., J. L. Kovar, J. M. Logsdon, Jr., J. C. Corrette-Bennett, D. R. Straus, and D. P. Weeks. 1999. Nucleus-encoded, plastid-targeted acetolactate synthase genes in two closely related chlorophytes, Chlamydomonas reinhardtii and Volvox carteri: phylogenetic origins and recent insertion of introns. Molecular and General Genetics 262:12-21. [PDF]
Hirt*, R. P., J. M. Logsdon*, Jr., B. Healy, M. W. Dorey, W. F. Doolittle, and T. M. Embley. 1999. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proceedings of the National Academy of Sciences USA 96:580-5. [PDF] *equal contributions
Stassen, N. Y., J. M. Logsdon, Jr., G. J. Vora, H. H. Offenberg, J. D. Palmer, and M. E. Zolan. 1997. Isolation and characterization of rad51 orthologs from Coprinus cinereus and Lycopersicon esculentum, and phylogenetic analysis of eukaryotic recA homologs. Current Genetics 31:144-57. [PDF]
Stoltzfus, A., J. M. Logsdon, Jr., J. D. Palmer, and W. F. Doolittle. 1997. Intron "sliding" and the diversity of intron positions. Proceedings of the National Academy of Sciences USA 94:10739-44. [PDF]
Unkles, S. E., J. M. Logsdon, Jr., K. Robison, J. R. Kinghorn, and J. M. Duncan. 1997. The tigA gene is a transcriptional fusion of glycolytic genes encoding triose-phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase in oomycota. Journal of Bacteriology 179:6816-23. [PDF]
Keeling, P. J., and J. M. Logsdon, Jr. 1996. Highly divergent Caenorhabditis and Saccharomyces tubulins evolved recently from genes encoding gamma-tubulin. Trends in Cell Biology 6:375-375. [PDF]
Ragan, M. A., J. M. Logsdon, Jr., C. W. Sensen, R. L. Charlebois, and W. F. Doolittle. 1996. An archaebacterial homolog of pelota, a meiotic cell division protein in eukaryotes. FEMS Microbiology Letters 144:151-5. [PDF]
Logsdon, J. M., Jr., M. G. Tyshenko, C. Dixon, J. D.-Jafari, V. K. Walker, and J. D. Palmer. 1995. Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory. Proceedings of the National Academy of Sciences USA 92:8507-11. [PDF]
Stoltzfus, A., D. F. Spencer, M. Zuker, J. M. Logsdon, Jr., and W. F. Doolittle. 1995. Introns and the origin of protein-coding genes (Response). Science 268:1367-1369. [PDF]
Logsdon, J. M., Jr., and J. D. Palmer. 1994. Origin of introns--early or late? Nature 369:526; discussion 527-8.
Stoltzfus, A., D. F. Spencer, M. Zuker, J. M. Logsdon, Jr., and W. F. Doolittle. 1994. Testing the exon theory of genes: the evidence from protein structure. Science 265:202-7. [PDF]
Pichersky, E., J. M. Logsdon, Jr., J. M. McGrath, and R. A. Stasys. 1991. Fragments of plastid DNA in the nuclear genome of tomato: prevalence, chromosomal location, and possible mechanism of integration. Molecular and General Genetics 225:453-8.
Invited articles:
Logsdon, J.M. Jr. 2008. Evolutionary genetics: Sex happens in Giardia. Current Biology, 18:2:R66-8.[article]
Logsdon, J.M. Jr. 2004. Worm genomes hold the smoking guns of intron gain. Proceedings of the National Academy of Sciences USA, 101:11195-11196. [PDF]
Logsdon, J.M. Jr. and D. M. Faguy. 1999. Evolutionary genomics:Thermotoga heats up lateral gene transfer. Current Biology 9:R747-51. [PDF]
Logsdon, J. M., Jr. 1998. The recent origins of spliceosomal introns revisited. Current Opinion in Genetics and Development 8:637-48. [PDF]
Doolittle, W. F., and J. M. Logsdon, Jr. 1998. Archaeal genomics: do Archaea have a mixed heritage? Current Biology 8:R209-11. [PDF]
Logsdon, J. M., Jr., A. Stoltzfus, and W. F. Doolittle. 1998. Molecular evolution: recent cases of spliceosomal intron gain? Current Biology 8:R560-3. [PDF]
Logsdon, J. M., Jr., and W. F. Doolittle. 1997. Origin of antifreeze protein genes: a cool tale in molecular evolution. Proceedings of the National Academy of Sciences USA 94:3485-7. [PDF]
Palmer, J. D., and J. M. Logsdon, Jr. 1991. The recent origins of introns. Current Opinion in Genetics and Development 1:470-7.
Invited book chapters:
Logsdon, J.M. Jr. and R.A. Kahn. 2003. The Arf family tree. Chapter 1, In Small GTPases: ARF Family, R.A. Kahn, ed. Kluwer, Netherlands.
R.A. Price, P.J. Calie, S.R. Downie, J.M. Logsdon Jr. and J.D. Palmer. 1990. Chloroplast DNA variation in the Geraniaceae-A preliminary report. In: Proc Int. Geraniaceae Symp., ed. P. Vorster, pp. 235-242.
J.D. Palmer, P.J. Calie, C.W. dePamphilis, J.M. Logsdon Jr., D. S. Katz-Downie and S. R. Downie. 1990. An evolutionary genetic approach to understanding plastid gene function: Lessons from photosynthetic & nonphotosynthetic plants. In: Current Research in Photosynthesis, v. III, ed. Baltscheffsky, Kluwer, pp. 475-482.
Copyright © 2008 John M. Logsdon Jr.
Last modified 19th June 2008.