User:Ramiro Logares: Difference between revisions
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ramiro.logares at gmail.com | ramiro.logares at gmail.com | ||
https://twitter.com/ramalok | |||
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Institut de Ciències del Mar, CSIC, Barcelona. Marie Curie Fellow | Institut de Ciències del Mar, CSIC, Barcelona. Marie Curie Fellow | ||
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==Previous positions== | ==Previous positions== | ||
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==Publications== | ==Publications== | ||
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27. '''Logares, R.''', Sunagawa,S., Salazar, G., Cornejo-Castillo, F.M., Ferrera, I., Sarmento, H., Hingamp, P., Ogata, H., de Vargas, C., Lima-Mendez, G., Raes, J., Poulain, J., Jaillon, J., Wincker, P., Kandels-Lewis, S., Karsenti, E., Bork, P., Acinas, S.G. 2013. Metagenomic 16S rDNA Illumina Tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. '''Environmental Microbiology'''. In Press. | |||
26. '''Logares, R.''', Lindström, E., Langenheder, S., Logue J.B., Paterson, H., Laybourn-Parry, J., Rengefors, K., Tranvik, L., Bertilsson, S. 2013. Biogeography of bacterial communities exposed to progressive long- term environmental | |||
change. '''The ISME journal'''. In press. | |||
25. Pernice, M.C., '''Logares, R.''', Guillou, L. Massana, R. 2013. General patterns of diversity in major marine microeukaryote lineages. '''PLOS ONE'''. In press | |||
'''Logares R.''' | 24. Massana, R., '''Logares, R.''' 2013. Eukaryotic versus prokaryotic marine picoplankton ecology. '''Environmental Microbiology'''. In press | ||
'''Logares, R.''', | 23. Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J.R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W.H.C.F., Lara, E., Lebescot, N., '''Logares, R.''', Mahé, F., Massana, R., Montresor, M., Morard, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A.-L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P., Christen, R. 2013. The Protist Ribosomal Reference Database (PR2): a catalog of unicellular eukaryote small subunit rRNA sequences with curated taxonomy. '''Nucleic Acids Research'''. 41:597-604. | ||
'''Logares, R.''', | 22. '''Logares, R.''', Audic, S., Santini, S., Pernice, M. C., de Vargas, C., Massana, R. 2012. Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. '''The ISME journal'''. In press. | ||
21. Rengefors, K., '''Logares, R.''', Laybourn-Parry, J. 2012. Polar lakes may act as ecological islands to aquatic protists. '''Molecular Ecology''', In press | |||
20. '''Logares.R.''', Haverkamp, T.H.A., Kumar, S., Lanzén, A., Nederbragt, A.J., Quince, C., Kauserud, H. 2012. Environmental microbiology through the lens of High-Throughput DNA Sequencing: synopsis of current platforms and bioinformatics approaches. ''' The Journal of Microbiological Methods''', In press. | |||
19. Rodriguez-Martinez R, Rocap G, '''Logares R''', Romac S, Massana R. 2012. Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). '''Molecular Biology and Evolution '''. In press. [http://mbe.oxfordjournals.org/content/early/2011/12/13/molbev.msr303.abstract?%253Cbr%253Eijkey=AbqtqTTBzrpdMwb&keytype=ref] | |||
'''Logares, R.''' | 18. Nuñez, M., '''Logares, R.''' 2012. Black Swans in ecology and evolution: The importance of improbable but highly influential events. '''Ideas in Ecology and Evolution''', In Press. | ||
17. Grote J., Altunkaya A., Bayindirli C., Bergauer K., Moraes P., Chen H., D’Ambrosio L., Edwards B., Fernández-Gomez B., Hamisi M., '''Logares R'''., Nguyen D., Rii S., Saeck E., Schutte C., Widner B., Church M.J., Steward G.F., Karl D.M., DeLong E.F., Eppley J.M., Schuster S., Kyrpides N.C., Rappé M.S. 2012. Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. '''Standards in Genomic Sciences''' In Press [http://sigen.org/index.php/sigen] | |||
'''Logares | 16. '''Logares R.''' 2011. Population genetics: the next stop for microbial ecologists? '''Central European Journal of Biology''' 6(6):887-892 [http://www.springerlink.com/content/t726l42433441363/] | ||
'''Logares, R.''', Shalchian-Tabrizi, K., | 15. '''Logares, R.''', Bråte, J., Heinrich, F., Shalchian-Tabrizi, K., Bertilsson, S. 2010. Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). '''Molecular Biology and Evolution'''. 27:347-357. [http://www.ncbi.nlm.nih.gov/pubmed/19808864?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1] | ||
14. '''Logares, R.''', Bråte, J., Bertilsson, S., Clasen, J.L., Shalchian-Tabrizi, K., Rengefors, K. 2009. Infrequent marine-freshwater transitions in the microbial world. '''Trends in Microbiology'''. 17:414-422. [http://www.ncbi.nlm.nih.gov/pubmed/19726194?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2] | |||
'''Logares, R.''', | 13. Bråte, J., '''Logares, R.''', Berney, C., Klaveness, D., Jakobsen, K., Shalchian-Tabrizi, K. 2010. Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. '''ISME journal''' In press. | ||
Leblond,J., | 12. Leblond, J., Lasiter, A., Li, C., '''Logares, R.''', Rengefors, K., Evens, T. Applying Clustering and Phylogeny Analysis to Study Dinoflagellates based on Sterol Composition. '''International Journal of Data Mining and Bioinformatics'''. In press. | ||
'''Logares, R.''' | 11. Szabo, K., Kiss, K., '''Logares, R.''', Eiler, A., Acs, E., Toth, B., Bertilsson, S. 2010. Composition and dynamics of microeukaryote communities in the River Danube. '''Fottea'''. In press. | ||
'''Logares, R.''' | 10. '''Logares, R.''', Boltovskoy, A., Bensch, S., Laybourn-Parry, J., Rengefors, K. 2009. Genetic diversity within five protist species. '''Protist'''. 160:301-317. [http://www.ncbi.nlm.nih.gov/pubmed/19162540?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=3] | ||
'''Logares, R.''' and Úbeda, C.A. (2004): Alsodes gargola (Rana del Catedral). Overwintering Tadpoles. '''Herpetological Review''' 35: 368-369. | 9. Shalchian-Tabrizi, K., Bråte, J., '''Logares, R.''', Klaveness, D., Berney, C., Jakobsen, K. Diversification in unicellular eukaryotes: Cryptomonad colonizations of marine and freshwaters inferred from revised 18S rRNA phylogeny. 2008. '''Environmental Microbiology''', 10: 1231–1243. [http://www.ncbi.nlm.nih.gov/pubmed/18643928?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4] | ||
8. '''Logares, R.''',Daugbjerg, N.,Boltovskoy, A., Kremp, A. Laybourn-Parry, J. Rengefors, K. 2008. Recent evolutionary diversification of a protist lineage. '''Environmental Microbiology'''. 10: 1231–1243. [http://www.ncbi.nlm.nih.gov/pubmed/18294207?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=5] | |||
7. '''Logares, R.''', Shalchian-Tabrizi, K., Boltovskoy, A., Rengefors, K. 2007. Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions. '''Molecular Phylogenetics and Evolution''', 45: 887-903. [http://www.ncbi.nlm.nih.gov/pubmed/17928239?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=6] | |||
6. Rengefors, K., Laybourn-Parry, J., '''Logares, R.''', Hansen, G. 2008.Marine-derived dinoflagellates in Antarctic saline lakes: annual dynamics and community composition. '''Journal of Phycology'''. 44: 592-604 | |||
5. '''Logares, R.''', Rengefors, K., Kremp, A., Shalchian-Tabrizi, K., Boltovskoy, A.,Tengs, T. Shurtleff, A. and Klaveness, D. 2007. Phenotypically different microalgal morphospecies with identical ribosomal DNA: A case of rapid adaptive evolution? '''Microbial Ecology'''. 53: 549-561. [http://www.ncbi.nlm.nih.gov/pubmed/17410396?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=7] | |||
4. Leblond,J., Anderson, B., Kofink, D., '''Logares, R.''', Rengefors, K. and Kremp, A. 2006. Lipid Composition of Two Cold-Adapted Dinoflagellate (Dinophyceae) Species from Scandinavian Waters: Comparison with Dinoflagellates from Warmer Environments. '''European Journal of Phycology'''. 41: 303-311. | |||
3. '''Logares, R.''' 2006. Does the global microbiota consist of a few cosmopolitan species? '''Ecología Austral'''. 16:85-90. | |||
2. '''Logares, R.''' and Úbeda, C.A. 2006. First insights into the overwintering biology of Alsodes gargola frogs and tadpoles in harsh Andean-Patagonian alpine environments. '''Amphibia-Reptilia''' 27: 263-267. | |||
1. '''Logares, R.''' and Úbeda, C.A. (2004): Alsodes gargola (Rana del Catedral). Overwintering Tadpoles. '''Herpetological Review''' 35: 368-369. | |||
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Logares , R. E. 2007. Microbial evolution: patterns of diversity in aquatic protists. PhD thesis, Lund University, Sweden ISBN: 978-91-7105-263-6 [http://www.lu.se/o.o.i.s?id=12588&postid=600754] | Logares , R. E. 2007. Microbial evolution: patterns of diversity in aquatic protists. PhD thesis, Lund University, Sweden ISBN: 978-91-7105-263-6 [http://www.lu.se/o.o.i.s?id=12588&postid=600754] | ||
==Misc== | ==Misc== | ||
Latest revision as of 09:55, 16 September 2013
Institut de Ciències del Mar, CSIC [1]
Passeig Marítim de la Barceloneta, 37-49
08003 Barcelona
Spain
Contact:
ramiro.logares at gmail.com
Education
- 2007, PhD, Lund University, Sweden [2]
- 2003, MSc, Universidad Nacional del Comahue, Argentina
Current position
Institut de Ciències del Mar, CSIC, Barcelona. Marie Curie Fellow
Previous positions
Evolutionary Biology Centre [3], Limnology, Uppsala University [4], Uppsala, Sweden. Post-Doc
Research interests
- Microbial Ecology and Evolution
- Population genetics and phylogenetics
- Environmental transitions
- Bioinformatics
- Genomics
Publications
27. Logares, R., Sunagawa,S., Salazar, G., Cornejo-Castillo, F.M., Ferrera, I., Sarmento, H., Hingamp, P., Ogata, H., de Vargas, C., Lima-Mendez, G., Raes, J., Poulain, J., Jaillon, J., Wincker, P., Kandels-Lewis, S., Karsenti, E., Bork, P., Acinas, S.G. 2013. Metagenomic 16S rDNA Illumina Tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environmental Microbiology. In Press.
26. Logares, R., Lindström, E., Langenheder, S., Logue J.B., Paterson, H., Laybourn-Parry, J., Rengefors, K., Tranvik, L., Bertilsson, S. 2013. Biogeography of bacterial communities exposed to progressive long- term environmental
change. The ISME journal. In press.
25. Pernice, M.C., Logares, R., Guillou, L. Massana, R. 2013. General patterns of diversity in major marine microeukaryote lineages. PLOS ONE. In press
24. Massana, R., Logares, R. 2013. Eukaryotic versus prokaryotic marine picoplankton ecology. Environmental Microbiology. In press
23. Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J.R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W.H.C.F., Lara, E., Lebescot, N., Logares, R., Mahé, F., Massana, R., Montresor, M., Morard, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A.-L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P., Christen, R. 2013. The Protist Ribosomal Reference Database (PR2): a catalog of unicellular eukaryote small subunit rRNA sequences with curated taxonomy. Nucleic Acids Research. 41:597-604.
22. Logares, R., Audic, S., Santini, S., Pernice, M. C., de Vargas, C., Massana, R. 2012. Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. The ISME journal. In press.
21. Rengefors, K., Logares, R., Laybourn-Parry, J. 2012. Polar lakes may act as ecological islands to aquatic protists. Molecular Ecology, In press
20. Logares.R., Haverkamp, T.H.A., Kumar, S., Lanzén, A., Nederbragt, A.J., Quince, C., Kauserud, H. 2012. Environmental microbiology through the lens of High-Throughput DNA Sequencing: synopsis of current platforms and bioinformatics approaches. The Journal of Microbiological Methods, In press.
19. Rodriguez-Martinez R, Rocap G, Logares R, Romac S, Massana R. 2012. Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). Molecular Biology and Evolution . In press. [5]
18. Nuñez, M., Logares, R. 2012. Black Swans in ecology and evolution: The importance of improbable but highly influential events. Ideas in Ecology and Evolution, In Press.
17. Grote J., Altunkaya A., Bayindirli C., Bergauer K., Moraes P., Chen H., D’Ambrosio L., Edwards B., Fernández-Gomez B., Hamisi M., Logares R., Nguyen D., Rii S., Saeck E., Schutte C., Widner B., Church M.J., Steward G.F., Karl D.M., DeLong E.F., Eppley J.M., Schuster S., Kyrpides N.C., Rappé M.S. 2012. Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Standards in Genomic Sciences In Press [6]
16. Logares R. 2011. Population genetics: the next stop for microbial ecologists? Central European Journal of Biology 6(6):887-892 [7]
15. Logares, R., Bråte, J., Heinrich, F., Shalchian-Tabrizi, K., Bertilsson, S. 2010. Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Molecular Biology and Evolution. 27:347-357. [8]
14. Logares, R., Bråte, J., Bertilsson, S., Clasen, J.L., Shalchian-Tabrizi, K., Rengefors, K. 2009. Infrequent marine-freshwater transitions in the microbial world. Trends in Microbiology. 17:414-422. [9]
13. Bråte, J., Logares, R., Berney, C., Klaveness, D., Jakobsen, K., Shalchian-Tabrizi, K. 2010. Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME journal In press.
12. Leblond, J., Lasiter, A., Li, C., Logares, R., Rengefors, K., Evens, T. Applying Clustering and Phylogeny Analysis to Study Dinoflagellates based on Sterol Composition. International Journal of Data Mining and Bioinformatics. In press.
11. Szabo, K., Kiss, K., Logares, R., Eiler, A., Acs, E., Toth, B., Bertilsson, S. 2010. Composition and dynamics of microeukaryote communities in the River Danube. Fottea. In press.
10. Logares, R., Boltovskoy, A., Bensch, S., Laybourn-Parry, J., Rengefors, K. 2009. Genetic diversity within five protist species. Protist. 160:301-317. [10]
9. Shalchian-Tabrizi, K., Bråte, J., Logares, R., Klaveness, D., Berney, C., Jakobsen, K. Diversification in unicellular eukaryotes: Cryptomonad colonizations of marine and freshwaters inferred from revised 18S rRNA phylogeny. 2008. Environmental Microbiology, 10: 1231–1243. [11]
8. Logares, R.,Daugbjerg, N.,Boltovskoy, A., Kremp, A. Laybourn-Parry, J. Rengefors, K. 2008. Recent evolutionary diversification of a protist lineage. Environmental Microbiology. 10: 1231–1243. [12]
7. Logares, R., Shalchian-Tabrizi, K., Boltovskoy, A., Rengefors, K. 2007. Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions. Molecular Phylogenetics and Evolution, 45: 887-903. [13]
6. Rengefors, K., Laybourn-Parry, J., Logares, R., Hansen, G. 2008.Marine-derived dinoflagellates in Antarctic saline lakes: annual dynamics and community composition. Journal of Phycology. 44: 592-604
5. Logares, R., Rengefors, K., Kremp, A., Shalchian-Tabrizi, K., Boltovskoy, A.,Tengs, T. Shurtleff, A. and Klaveness, D. 2007. Phenotypically different microalgal morphospecies with identical ribosomal DNA: A case of rapid adaptive evolution? Microbial Ecology. 53: 549-561. [14]
4. Leblond,J., Anderson, B., Kofink, D., Logares, R., Rengefors, K. and Kremp, A. 2006. Lipid Composition of Two Cold-Adapted Dinoflagellate (Dinophyceae) Species from Scandinavian Waters: Comparison with Dinoflagellates from Warmer Environments. European Journal of Phycology. 41: 303-311.
3. Logares, R. 2006. Does the global microbiota consist of a few cosmopolitan species? Ecología Austral. 16:85-90.
2. Logares, R. and Úbeda, C.A. 2006. First insights into the overwintering biology of Alsodes gargola frogs and tadpoles in harsh Andean-Patagonian alpine environments. Amphibia-Reptilia 27: 263-267.
1. Logares, R. and Úbeda, C.A. (2004): Alsodes gargola (Rana del Catedral). Overwintering Tadpoles. Herpetological Review 35: 368-369.
e-Book
Dupont, C., Chappell, D., Logares, R.,Vila-Costa, M. A hitchhiker’s guide to the new molecular toolbox for ecologists. Chapter 2, p. 17-29. In: P.F. Kemp [ed.] 2010. Eco-DAS VIII Symposium Proceedings. Waco, TX, US:American Society of Limnology and Oceanography. doi:10.4319/ecodas.2010.978-0-9845591-1-4 [15]
PhD Thesis
Logares , R. E. 2007. Microbial evolution: patterns of diversity in aquatic protists. PhD thesis, Lund University, Sweden ISBN: 978-91-7105-263-6 [16]
Misc
BioMarKs [17]
MERG [18]
Limnology Dept., Uppsala University [19]
Limnology Dept., Lund University [20]
Antarctic videos [21]
AAD [22]
