Uri Gophna - Publications

Affiliations: 
Tel Aviv University, Tel Aviv-Yafo, Tel Aviv District, Israel 
Area:
Evolutionary Biology, Microbiology

70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Lavy O, Gophna U, Gefen E, Ayali A. Dynamics of bacterial composition in the locust reproductive tract are affected by the density-dependent phase. Fems Microbiology Ecology. 96. PMID 32175575 DOI: 10.1093/Femsec/Fiaa044  0.32
2019 Turgeman-Grott I, Joseph S, Marton S, Eizenshtein K, Naor A, Soucy SM, Stachler AE, Shalev Y, Zarkor M, Reshef L, Altman-Price N, Marchfelder A, Gophna U. Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nature Microbiology. 4: 177-186. PMID 30478289 DOI: 10.1038/S41564-018-0302-8  0.354
2018 Yair Y, Gophna U. Pandemic Bacteremic Escherichia Coli Strains: Evolution and Emergence of Drug-Resistant Pathogens. Current Topics in Microbiology and Immunology. 416: 163-180. PMID 30046983 DOI: 10.1007/82_2018_109  0.303
2018 Shulman A, Yair Y, Biran D, Sura T, Otto A, Gophna U, Becher D, Hecker M, Ron EZ. The Escherichia coli Type III Secretion System 2 Has a Global Effect on Cell Surface. Mbio. 9. PMID 29970469 DOI: 10.1128/Mbio.01070-18  0.364
2018 Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U. Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax. Genes. 9. PMID 29558455 DOI: 10.3390/Genes9030172  0.327
2018 Yitzhaki S, Reshef L, Gophna U, Rosenberg M, Sterer N. Microbiome associated with denture malodour. Journal of Breath Research. 12: 027103. PMID 29341956 DOI: 10.1088/1752-7163/Aa95E0  0.326
2017 Shalev Y, Turgeman-Grott I, Tamir A, Eichler J, Gophna U. Cell Surface Glycosylation Is Required for Efficient Mating of . Frontiers in Microbiology. 8: 1253. PMID 28725221 DOI: 10.3389/Fmicb.2017.01253  0.302
2017 Artieri CG, Naor A, Turgeman-Grott I, Zhou Y, York R, Gophna U, Fraser HB. Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids. Scientific Reports. 7: 3986. PMID 28638059 DOI: 10.1038/S41598-017-04278-4  0.323
2017 Gophna U, Allers T, Marchfelder A. Finally, Archaea Get Their CRISPR-Cas Toolbox. Trends in Microbiology. 25: 430-432. PMID 28391963 DOI: 10.1016/J.Tim.2017.03.009  0.304
2017 Gophna U, Konikoff T, Nielsen HB. Oscillospira and related bacteria - From metagenomic species to metabolic features. Environmental Microbiology. 19: 835-841. PMID 28028921 DOI: 10.1111/1462-2920.13658  0.394
2016 Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U, Ruppin E. Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. Plos Computational Biology. 12: e1004705. PMID 26821166 DOI: 10.1371/Journal.Pcbi.1004705  0.333
2015 Adato O, Ninyo N, Gophna U, Snir S. Detecting Horizontal Gene Transfer between Closely Related Taxa. Plos Computational Biology. 11: e1004408. PMID 26439115 DOI: 10.1371/Journal.Pcbi.1004408  0.384
2015 Keren N, Konikoff FM, Paitan Y, Gabay G, Reshef L, Naftali T, Gophna U. Interactions between the intestinal microbiota and bile acids in gallstones patients. Environmental Microbiology Reports. PMID 26149537 DOI: 10.1111/1758-2229.12319  0.321
2015 Roterman YR, Benayahu Y, Reshef L, Gophna U. The gill microbiota of invasive and indigenous Spondylus oysters from the Mediterranean Sea and northern Red Sea. Environmental Microbiology Reports. 7: 860-7. PMID 26111733 DOI: 10.1111/1758-2229.12315  0.312
2015 Lurie-Weinberger MN, Gophna U. Archaea in and on the Human Body: Health Implications and Future Directions. Plos Pathogens. 11: e1004833. PMID 26066650 DOI: 10.1371/Journal.Ppat.1004833  0.326
2015 Reshef L, Kovacs A, Ofer A, Yahav L, Maharshak N, Keren N, Konikoff FM, Tulchinsky H, Gophna U, Dotan I. Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa. Gastroenterology. 149: 718-27. PMID 26026389 DOI: 10.1053/J.Gastro.2015.05.041  0.307
2015 Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV. No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. The Isme Journal. 9: 2021-7. PMID 25710183 DOI: 10.1038/Ismej.2015.20  0.321
2014 Eilam O, Zarecki R, Oberhardt M, Ursell LK, Kupiec M, Knight R, Gophna U, Ruppin E. Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. Mbio. 5. PMID 25118239 DOI: 10.1128/Mbio.01526-14  0.343
2014 Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E. A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness. Plos Computational Biology. 10: e1003726. PMID 25033033 DOI: 10.1371/Journal.Pcbi.1003726  0.345
2014 Pelchovich G, Nadejda S, Dana A, Tuller T, Bravo IG, Gophna U. Ribosomal mutations affecting the translation of genes that use non-optimal codons. The Febs Journal. 281: 3701-18. PMID 24966114 DOI: 10.1111/Febs.12892  0.345
2014 Amir I, Bouvet P, Legeay C, Gophna U, Weinberger A. Eisenbergiella tayi gen. nov., sp. nov., isolated from human blood International Journal of Systematic and Evolutionary Microbiology. 64: 907-914. PMID 24282142 DOI: 10.1099/Ijs.0.057331-0  0.305
2014 Shifman A, Ninyo N, Gophna U, Snir S. Phylo SI: a new genome-wide approach for prokaryotic phylogeny. Nucleic Acids Research. 42: 2391-404. PMID 24243847 DOI: 10.1093/Nar/Gkt1138  0.348
2014 Pasternak Z, Njagi M, Shani Y, Chanyi R, Rotem O, Lurie-Weinberger MN, Koval S, Pietrokovski S, Gophna U, Jurkevitch E. In and out: an analysis of epibiotic vs periplasmic bacterial predators. The Isme Journal. 8: 625-635. PMID 24088628 DOI: 10.1038/Ismej.2013.164  0.367
2013 Wagner A, Zarecki R, Reshef L, Gochev C, Sorek R, Gophna U, Ruppin E. Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious. Proceedings of the National Academy of Sciences of the United States of America. 110: 19166-71. PMID 24198337 DOI: 10.1073/Pnas.1312361110  0.351
2013 Kaminski L, Lurie-Weinberger MN, Allers T, Gophna U, Eichler J. Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea. Molecular Phylogenetics and Evolution. 68: 327-39. PMID 23567024 DOI: 10.1016/J.Ympev.2013.03.024  0.365
2013 Pasternak Z, Pietrokovski S, Rotem O, Gophna U, Lurie-Weinberger MN, Jurkevitch E. By their genes ye shall know them: genomic signatures of predatory bacteria. The Isme Journal. 7: 756-69. PMID 23190728 DOI: 10.1038/Ismej.2012.149  0.388
2013 Naor A, Gophna U. Cell fusion and hybrids in Archaea: prospects for genome shuffling and accelerated strain development for biotechnology Bioengineered. 4: 126-129. PMID 23111319 DOI: 10.4161/Bioe.22649  0.375
2012 Lurie-Weinberger MN, Peeri M, Tuller T, Gophna U. Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae. Frontiers in Genetics. 3: 182. PMID 23049536 DOI: 10.3389/Fgene.2012.00182  0.382
2012 Naor A, Thiaville PC, Altman-Price N, Cohen-Or I, Allers T, de Crécy-Lagard V, Gophna U. A genetic investigation of the KEOPS complex in Halophilic Archaea Plos One. 7. PMID 22927945 DOI: 10.1371/Journal.Pone.0043013  0.326
2012 Gophna U, Brodt A. CRISPR/Cas systems in archaea: What array spacers can teach us about parasitism and gene exchange in the 3rd domain of life. Mobile Genetic Elements. 2: 63-64. PMID 22754756 DOI: 10.4161/Mge.19907  0.339
2012 Naor A, Lapierre P, Mevarech M, Papke RT, Gophna U. Low species barriers in halophilic archaea and the formation of recombinant hybrids. Current Biology : Cb. 22: 1444-8. PMID 22748314 DOI: 10.1016/J.Cub.2012.05.056  0.368
2012 Lurie-Weinberger MN, Peeri M, Gophna U. Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen. Genomics. 99: 52-8. PMID 22056789 DOI: 10.1016/J.Ygeno.2011.10.005  0.405
2011 Brodt A, Lurie-Weinberger MN, Gophna U. CRISPR loci reveal networks of gene exchange in archaea. Biology Direct. 6: 65. PMID 22188759 DOI: 10.1186/1745-6150-6-65  0.31
2011 Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, Kupiec M, Gophna U, Sharan R, Ruppin E. Competitive and cooperative metabolic interactions in bacterial communities. Nature Communications. 2: 589. PMID 22158444 DOI: 10.1038/Ncomms1597  0.324
2011 Gophna U. Microbiology. The guts of dietary habits. Science (New York, N.Y.). 334: 45-6. PMID 21980098 DOI: 10.1126/Science.1213799  0.314
2011 Zurel D, Benayahu Y, Or A, Kovacs A, Gophna U. Composition and dynamics of the gill microbiota of an invasive Indo-Pacific oyster in the eastern Mediterranean Sea. Environmental Microbiology. 13: 1467-76. PMID 21635673 DOI: 10.1111/J.1462-2920.2011.02448.X  0.317
2011 Zhang X, Kupiec M, Gophna U, Tuller T. Analysis of coevolving gene families using mutually exclusive orthologous modules. Genome Biology and Evolution. 3: 413-23. PMID 21498882 DOI: 10.1093/Gbe/Evr030  0.349
2011 Tuller T, Girshovich Y, Sella Y, Kreimer A, Freilich S, Kupiec M, Gophna U, Ruppin E. Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Research. 39: 4743-55. PMID 21343180 DOI: 10.1093/Nar/Gkr054  0.401
2011 Naor A, Lazary R, Barzel A, Papke RT, Gophna U. In Vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii Plos One. 6. PMID 21283796 DOI: 10.1371/Journal.Pone.0015833  0.38
2011 Kovacs A, Ben-Jacob N, Tayem H, Halperin E, Iraqi FA, Gophna U. Genotype is a stronger determinant than sex of the mouse gut microbiota. Microbial Ecology. 61: 423-8. PMID 21181142 DOI: 10.1007/S00248-010-9787-2  0.309
2011 Gophna U, Ofran Y. Lateral acquisition of genes is affected by the friendliness of their products. Proceedings of the National Academy of Sciences of the United States of America. 108: 343-8. PMID 21149709 DOI: 10.1073/Pnas.1009775108  0.347
2011 Cohen O, Gophna U, Pupko T. The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Molecular Biology and Evolution. 28: 1481-9. PMID 21149642 DOI: 10.1093/Molbev/Msq333  0.373
2010 Katz C, Cohen-Or I, Gophna U, Ron EZ. The ubiquitous conserved glycopeptidase Gcp prevents accumulation of toxic glycated proteins. Mbio. 1. PMID 20824107 DOI: 10.1128/Mbio.00195-10  0.311
2010 Omer S, Kovacs A, Mazor Y, Gophna U. Integration of a foreign gene into a native complex does not impair fitness in an experimental model of lateral gene transfer. Molecular Biology and Evolution. 27: 2441-5. PMID 20554693 DOI: 10.1093/Molbev/Msq145  0.347
2010 Lurie-Weinberger MN, Gomez-Valero L, Merault N, Glöckner G, Buchrieser C, Gophna U. The origins of eukaryotic-like proteins in Legionella pneumophila. International Journal of Medical Microbiology : Ijmm. 300: 470-81. PMID 20537944 DOI: 10.1016/J.Ijmm.2010.04.016  0.418
2010 Stern A, Mayrose I, Penn O, Shaul S, Gophna U, Pupko T. An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Systematic Biology. 59: 212-25. PMID 20525631 DOI: 10.1093/Sysbio/Syp104  0.331
2010 Voges M, Bachmann V, Kammerer R, Gophna U, Hauck CR. CEACAM1 recognition by bacterial pathogens is species-specific. Bmc Microbiology. 10: 117. PMID 20406467 DOI: 10.1186/1471-2180-10-117  0.303
2010 Freilich S, Kreimer A, Borenstein E, Gophna U, Sharan R, Ruppin E. Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. Plos Computational Biology. 6: e1000690. PMID 20195496 DOI: 10.1371/Journal.Pcbi.1000690  0.33
2010 Kovacs A, Yacoby K, Gophna U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Research in Microbiology. 161: 192-7. PMID 20138144 DOI: 10.1016/J.Resmic.2010.01.006  0.349
2009 Albert EJ, Sommerfeld K, Gophna S, Marshall JS, Gophna U. The gut microbiota of toll-like receptor 2-deficient mice exhibits lineage-specific modifications. Environmental Microbiology Reports. 1: 65-70. PMID 23765722 DOI: 10.1111/J.1758-2229.2008.00006.X  0.308
2009 Freilich S, Kreimer A, Borenstein E, Yosef N, Sharan R, Gophna U, Ruppin E. Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biology. 10: R61. PMID 19500338 DOI: 10.1186/Gb-2009-10-6-R61  0.307
2009 Gophna U. Complexity Apparently Is Not a Barrier to Lateral Gene Transfers Microbe Magazine. 4: 549-553. DOI: 10.1128/Microbe.4.549.1  0.391
2008 Cohen O, Rubinstein ND, Stern A, Gophna U, Pupko T. A likelihood framework to analyse phyletic patterns. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3903-11. PMID 18852099 DOI: 10.1098/Rstb.2008.0177  0.362
2008 Wellner A, Gophna U. Neutrality of Foreign Complex Subunits in an Experimental Model of Lateral Gene Transfer Molecular Biology and Evolution. 25: 1835-1840. PMID 18550618 DOI: 10.1093/Molbev/Msn131  0.361
2007 Wellner A, Lurie MN, Gophna U. Complexity, connectivity, and duplicability as barriers to lateral gene transfer Genome Biology. 8. PMID 17678544 DOI: 10.1186/Gb-2007-8-8-R156  0.377
2006 Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJ. Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis. Journal of Clinical Microbiology. 44: 4136-41. PMID 16988016 DOI: 10.1128/Jcm.01004-06  0.527
2006 Gophna U, Charlebois RL, Doolittle WF. Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus. Trends in Microbiology. 14: 64-9. PMID 16413191 DOI: 10.1016/J.Tim.2005.12.008  0.57
2006 Gophna U, Thompson JR, Boucher Y, Doolittle WF. Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase. Molecular Biology and Evolution. 23: 168-78. PMID 16162862 DOI: 10.1093/Molbev/Msj019  0.648
2005 Ideses D, Gophna U, Paitan Y, Chaudhuri RR, Pallen MJ, Ron EZ. A Degenerate Type III Secretion System from Septicemic Escherichia coli Contributes to Pathogenesis Journal of Bacteriology. 187: 8164-8171. PMID 16291689 DOI: 10.1128/Jb.187.23.8164-8171.2005  0.376
2005 Mokady D, Gophna U, Ron EZ. Virulence factors of septicemic Escherichia coli strains. International Journal of Medical Microbiology. 295: 455-462. PMID 16238019 DOI: 10.1016/J.Ijmm.2005.07.007  0.345
2005 Ideses D, Biran D, Gophna U, Levy-Nissenbaum O, Ron EZ. The lpf operon of invasive Escherichia coli. International Journal of Medical Microbiology. 295: 227-236. PMID 16128397 DOI: 10.1016/J.Ijmm.2005.04.009  0.324
2005 Gophna U, Bapteste E, Doolittle WF, Biran D, Ron EZ. Evolutionary plasticity of methionine biosynthesis. Gene. 355: 48-57. PMID 16046084 DOI: 10.1016/J.Gene.2005.05.028  0.555
2005 Gophna U, Doolittle WF, Charlebois RL. Weighted genome trees: refinements and applications. Journal of Bacteriology. 187: 1305-16. PMID 15687194 DOI: 10.1128/Jb.187.4.1305-1316.2005  0.535
2005 Mokady D, Gophna U, Ron EZ. Extensive Gene Diversity in Septicemic Escherichia coli Strains Journal of Clinical Microbiology. 43: 66-73. PMID 15634952 DOI: 10.1128/Jcm.43.1.66-73.2005  0.334
2004 Gophna U, Ideses D, Rosen R, Grundland A, Ron EZ. OmpA of a septicemic Escherichia coli O78--secretion and convergent evolution. International Journal of Medical Microbiology. 294: 373-381. PMID 15595387 DOI: 10.1016/J.Ijmm.2004.08.004  0.324
2004 Gophna U, Charlebois RL, Doolittle WF. Have archaeal genes contributed to bacterial virulence? Trends in Microbiology. 12: 213-9. PMID 15120140 DOI: 10.1016/J.Tim.2004.03.002  0.586
2003 Gophna U, Ron EZ, Graur D. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene. 312: 151-63. PMID 12909351 DOI: 10.1016/S0378-1119(03)00612-7  0.384
2003 Adiri RS, Gophna U, Ron EZ. Multilocus sequence typing (MLST) of Escherichia coli O78 strains Fems Microbiology Letters. 222: 199-203. PMID 12770708 DOI: 10.1016/S0378-1097(03)00295-7  0.313
2003 Gophna U, Parket A, Hacker J, Ron EZ. A novel ColV plasmid encoding type IV pili. Microbiology. 149: 177-184. PMID 12576591 DOI: 10.1099/Mic.0.25858-0  0.363
2001 Gophna U, Oelschlaeger TA, Hacker J, Ron EZ. Yersinia HPI in septicemic Escherichia coli strains isolated from diverse hosts. Fems Microbiology Letters. 196: 57-60. PMID 11257548 DOI: 10.1111/J.1574-6968.2001.Tb10540.X  0.332
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