User:Ramiro Logares

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-
Post-Doctoral Research Associate
 
-
Department of Ecology and Evolution,
 
-
Limnology
 
-
Uppsala University
 
-
Husargatan 3,  Box 573
 
-
SE-75 123 Uppsala
 
-
Sweden
 
-
ramiro.logares [at] ebc.uu.se
+
'''Institut de Ciències del Mar, CSIC''' [http://www.icm.csic.es/en]
-
Phone: ++46 (0) 18 471 2701 (office)
+
 
-
Fax: ++46 (0) 18 53 11 34
+
'''Passeig Marítim de la Barceloneta, 37-49'''
 +
 
 +
'''08003 Barcelona'''
 +
 +
'''Spain'''
 +
 
 +
 
 +
 
 +
'''Contact:'''
 +
 
 +
ramiro.logares at gmail.com
 +
 
 +
 
==Education==
==Education==
<!--Include info about your educational background-->
<!--Include info about your educational background-->
-
* 2007, PhD, Lund University, Sweden
+
* 2007, PhD, Lund University, Sweden [http://www.lu.se/o.o.i.s?id=12588&postid=600754]
-
* 2003, MS, Universidad Nacional del Comahue, Argentina
+
* 2003, MSc, Universidad Nacional del Comahue, Argentina
 +
 
 +
 
 +
 
 +
==Current position==
 +
 
 +
Institut de Ciències del Mar, CSIC, Barcelona.  Marie Curie Fellow
 +
 
 +
 
 +
==Previous positions==
 +
 
 +
Evolutionary Biology Centre [http://www.ebc.uu.se/index_eng.php], Limnology,
 +
Uppsala University [http://www.uu.se/en/],
 +
Uppsala, Sweden.  Post-Doc
 +
 
==Research interests==
==Research interests==
<!-- Feel free to add brief descriptions to your research interests as well -->
<!-- Feel free to add brief descriptions to your research interests as well -->
-
# Interest 1
+
# Microbial Ecology and Evolution
-
# Interest 2
+
# Population genetics and phylogenetics
-
# Interest 3
+
# Environmental transitions
 +
# Bioinformatics
 +
# Genomics
 +
 
 +
 
==Publications==
==Publications==
 +
-
'''Logares, R.''',Daugbjerg, N.,Boltovskoy, A., Kremp, A. Laybourn-Parry, J. Rengefors, K. 2008. Recent evolutionary diversification of a protist lineage. Environmental Microbiology, In press.
+
'''Logares, R.''', Lindstrom, 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.
-
'''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.
 
-
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. In press.
+
Massana, R., '''Logares, R.''' 2013. Eukaryotic versus prokaryotic marine picoplankton ecology. '''Environmental Microbiology'''. In press
-
'''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.
 
-
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.
+
Guillou L., D. Bachar, S. Audic, D. Bass, C. Berney, L. Bittner, C. Boutte, G. Burgaud, C. de Vargas, J. Decelle, J. del Campo, J.R. Dolan, M. Dunthorn, B. Edvardsen, M. Holzmann, W.H.C.F. Kooistra, E. Lara, N. Lebescot, '''R. Logares''', F. Mahé, R. Massana, M. Montresor, R. Morard, F. Not, J. Pawlowski, I. Probert, A.-L. Sauvadet, R. Siano, T. Stoeck, D. Vaulot Daniel, P. Zimmermann, R. Christen (in revision). 2013. The Protist Ribosomal Reference Database (PR2): a catalog of unicellular eukaryote small subunit rRNA sequences with curated taxonomy. '''Nucleic Acids Research'''. In press
-
'''Logares, R.''' 2006. Does the global microbiota consist of a few cosmopolitan species? Ecología Austral. 16:85-90.
 
-
'''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.
+
'''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.
-
'''Logares, R.''' and Úbeda, C.A. (2004): Alsodes gargola (Rana del Catedral). Overwintering Tadpoles. Herpetological Review 35: 368-369.
 
 +
Rengefors, K., '''Logares, R.''', Laybourn-Parry, J. 2012. Polar lakes may act as ecological islands to aquatic protists. '''Molecular Ecology''', In press
-
''Submitted''
+
'''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.
-
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.
 
-
'''Logares, R.''', Boltovskoy, A., Bensch, S., Laybourn-Parry, J., Rengefors, K. Genetic diversity within five phytoplankton species.  
+
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]
-
Leblond, J., Lasiter, A., Li, C., '''Logares, R.''', Rengefors, K., Evens, T. Correspondence between sterol composition and phylogeny in dinoflagellates.
+
 
 +
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.
 +
 
 +
 
 +
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 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.''', 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]
 +
 
 +
 
 +
'''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]
 +
 
 +
 
 +
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., 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.
 +
 
 +
 
 +
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.''', 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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
'''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]
 +
 
 +
 
 +
'''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]
 +
 
 +
 
 +
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
 +
 
 +
 
 +
'''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]
 +
 
 +
 
 +
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.
 +
 
 +
 
 +
'''Logares, R.''' 2006. Does the global microbiota consist of a few cosmopolitan species? '''Ecología Austral'''. 16:85-90.
 +
 
 +
 
 +
'''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.
 +
 
 +
 
 +
'''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 [http://www.aslo.org/books/ecodas8/ecodas8_017.pdf]
Line 61: Line 140:
'''PhD Thesis'''
'''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
+
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==
 +
 
 +
BioMarKs [http://www.sb-roscoff.fr/BioMarKs/]
 +
 
 +
MERG [http://www.merg.uio.no/]
 +
 
 +
Limnology Dept., Uppsala University [http://www.ebc.uu.se/limno/]
 +
 
 +
Limnology Dept., Lund University [http://www.limnol.lu.se/]
 +
 
 +
Antarctic videos [http://www.youtube.com/watch?v=RbAbfYooW14]
 +
 
 +
AAD [http://www.aad.gov.au/]
 +
 
==Useful links==
==Useful links==
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[Help|OpenWetWare help pages]]
*[[Help|OpenWetWare help pages]]

Revision as of 18:15, 10 November 2012

I am a new member of OpenWetWare!

Image:P1080349.JPG‎


Institut de Ciències del Mar, CSIC [1]

Passeig Marítim de la Barceloneta, 37-49

08003 Barcelona

Spain


Contact:

ramiro.logares at gmail.com



Contents

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

  1. Microbial Ecology and Evolution
  2. Population genetics and phylogenetics
  3. Environmental transitions
  4. Bioinformatics
  5. Genomics


Publications

Logares, R., Lindstrom, 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.


Massana, R., Logares, R. 2013. Eukaryotic versus prokaryotic marine picoplankton ecology. Environmental Microbiology. In press


Guillou L., D. Bachar, S. Audic, D. Bass, C. Berney, L. Bittner, C. Boutte, G. Burgaud, C. de Vargas, J. Decelle, J. del Campo, J.R. Dolan, M. Dunthorn, B. Edvardsen, M. Holzmann, W.H.C.F. Kooistra, E. Lara, N. Lebescot, R. Logares, F. Mahé, R. Massana, M. Montresor, R. Morard, F. Not, J. Pawlowski, I. Probert, A.-L. Sauvadet, R. Siano, T. Stoeck, D. Vaulot Daniel, P. Zimmermann, R. Christen (in revision). 2013. The Protist Ribosomal Reference Database (PR2): a catalog of unicellular eukaryote small subunit rRNA sequences with curated taxonomy. Nucleic Acids Research. In press


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.


Rengefors, K., Logares, R., Laybourn-Parry, J. 2012. Polar lakes may act as ecological islands to aquatic protists. Molecular Ecology, In press


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.


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]


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.


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]


Logares R. 2011. Population genetics: the next stop for microbial ecologists? Central European Journal of Biology 6(6):887-892 [7]


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]


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]


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., 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.


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., Boltovskoy, A., Bensch, S., Laybourn-Parry, J., Rengefors, K. 2009. Genetic diversity within five protist species. Protist. 160:301-317. [10]


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]


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]


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]


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


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]


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.


Logares, R. 2006. Does the global microbiota consist of a few cosmopolitan species? Ecología Austral. 16:85-90.


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.


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]


Useful links

Personal tools