Publications

2022

  • Baquero, F., Coque, T.M., Guerra-Pinto, N., Galán, J.C., Jiménez-Lalana, D., Tamames, J., Pedrós-Alió, C. The Influence of Coalescent Microbiotic Particles From Water and Soil on the Evolution and Spread of Antimicrobial Resistance (2022) Frontiers in Environmental Science, 10. DOI: 10.3389/fenvs.2022.824963
  • García-García, N., Tamames, J., Puente-Sánchez, F. M&Ms: A versatile software for building microbial mock communities (2022) Bioinformatics, 38 (7), pp. 2057-2059. DOI: 10.1093/bioinformatics/btab882
  • Lopez-Garcia, A., Saborio-Montero, A., Gutierrez-Rivas, M., Atxaerandio, R., Goiri, I., Garcia-Rodriguez, A., Jimenez-Montero, J.A., Gonzalez, C., Tamames, J., Puente-Sanchez, F., Serrano, M., Carrasco, R., Ovilo, C., Gonzalez-Recio, O. Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle (2022) GigaScience, 11. DOI: 10.1093/gigascience/giab088
  • Peña-Ocaña, B.A., Ovando-Ovando, C.I., Puente-Sánchez, F., Tamames, J., Servín-Garcidueñas, L.E., González-Toril, E., Gutiérrez-Sarmiento, W., Jasso-Chávez, R., Ruíz-Valdiviezo, V.M. Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake (2022) Environmental Research, 203, art. no. 111862, . DOI: 10.1016/j.envres.2021.111862
  • Puente-Sánchez, Fernando, Luis Macías, Karley L. Campbell, Marta Royo-Llonch, Vanessa Balagué, Pablo Sánchez, Javier Tamames, C.J. Mundy, Carlos Pedrós-Alió. 2022. Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean. BioRxiv, doi: https://doi.org/10.1101/2022.02.07.479392
  • Puente-Sánchez, Fernando, Alberto Pascual-García, Ugo Bastolla, Carlos Pedrós-Alió, Javier Tamames. 2022. Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity. BioRxiv doi: https://doi.org/10.1101/2022.09.11.507163

2021

  • Alcamán-Arias, M.E., Fuentes-Alburquenque, S., Vergara-Barros, P., Cifuentes-Anticevic, J., Verdugo, J., Polz, M., Farías, L., Pedrós-Alió, C., Díez, B. 2021. Coastal Bacterial Community Response to Glacier Melting in the Western Antarctic Peninsula. Microorganisms, 9, 88. https://doi.org/10.3390/microorganisms9010088
  • Royo-Llonch, Marta, Pablo Sánchez, Clara Ruiz-González, Guillem Salazar, Carlos Pedrós-Alió, Karine Labadie, Lucas Paoli, Federico Ibarbalz, Lucie Zinger, Benjamin Churcheward, Tara Oceans Coordinators, Samuel Chaffron, Damien Eveillard, Eric Karsenti, Shinichi Sunagawa, Patrick Wincker, Lee Karp-Boss, Chris Bowler and Silvia G Acinas. Ecogenomics of key prokaryotes in the Arctic Ocean. bioRxiv doi: https://doi.org/10.1101/2020.06.19.156794. Nature Microbiology, in press.
  • Acinas, Silvia G., Pablo Sánchez, Guillem Salazar, Francisco M. Cornejo-Castillo, Marta Sebastián, Ramiro Logares, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima-Mendez, Simon Roux, José M. González, Jesús M. Arrieta, Intikhab S. Alam, Allan Kamau, Chris Bowler, Jeroen Raes, Stéphane Pesant, Peer Bork, Susana Agustí, Takashi Gojobori, Vladimir B. Bajic, Dolors Vaqué, Matthew B. Sullivan, Carlos Pedrós-Alió, Ramon Massana, Carlos M. Duarte, Josep M. Gasol. Deep ocean metgenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology, 4: 604, doi.org/10.1038/s42003-021-02112.
  • Pedrós-Alió, Carlos. 2021. Time travel in microorganisms. Systematic and Applied Microbiolgoy, 44: 126227. doi: https://doi.org/10.1016/j.syapm.2021.12622.
  • Cifuentes-Anticevic, J., Alcamán-Arias, M.E., Alarcón-Schumacher, T., Tamayo-Leiva, J., Pedrós-Alió, C., Farías, L., Díez, B. 2021. Proteorhodopsin phototrophy in Antarctic coastal waters. mSphere 6:e00525-21. https://doi.org/10.1128/mSphere.00525-21.
  • Saborío-Montero, Alejandro, Adrián López-García, Mónica Gutiérrez-Rivas, Raquel Atxaerandio, Idoia Goiri, Aser García-Rodríguez, José A. Jiménez-Montero, Carmen González, Javier Tamames, Fernando Puente-Sánchez, Luis Varona, Magdalena Serrano, Cristina Ovilo, Oscar González-Recio. 2021. A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding. Journal of Dairy Science, 104 (7): 8135-8151.

2020

  • Puente-Sánchez F, García-García N, Tamames J. 2020. SQMtools: automated processing and visual analysis of ‘omics data with R and anvi’o. BMC Bioinformatics. Aug 14;21(1):358. doi: 10.1186/s12859-020-03703-2. PMID: 32795263; PMCID: PMC7430844.
  • Royo-Llonch, Marta, Pablo Sánchez, José M González, Carlos Pedrós-Alió & Silvia Acinas. 2020. Ecological and functional capabilities of an uncultured Kordia sp. Systematic and Applied Microbiology 43 (1): UNSP article number 126045. https://doi.org/10.1016/j.syapm.2019.126045
  • Lucena, Teresa, David R. Arahal, Isabel Sanz-Sáez, Silvia G. Acinas, Olga Sánchez, Rosa Aznar, Carlos Pedrós-Alió and María J. Pujalte. 2020. Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae. International Journal of Systematic and Evolutionary Microbiology, 70 (2): 1231-1239. DOI 10.1099/ijsem.0.003906.
  • Murray, Alison E., and 63 authors. 2020. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5: 987–994. DOI: 10.1038/s41564-020-0733-x
  • Lucena, Teresa, Isabel Sanz-Sáez, David R. Arahal, Silvia G. Acinas, Olga Sánchez, Carlos Pedrós-Alió, Rosa Aznar and María J. Pujalte. 2020. Mesonia oceanica sp. nov, isolated from oceans during Tara Oceans Expedition, with a preference for mesopelagic waters. International Journal of Systematic and Evolutionary Microbiology, 70 (7): 4329-4338. DOI:10.1099/ijsem.0.004296. IF 2.212
  • Sanz-Sáez, Isabel, Guillem Salazar, Pablo Sánchez, Elena Lara, Marta Royo-Llonch, Elisabet L. Sà, Teresa Lucena, María J. Pujalte, Dolors Vaqué, Carlos M. Duarte, Josep M. Gasol, Carlos Pedrós-Alió, Olga Sánchez, Silvia G. Acinas. 2020. Diversity and distribution of marine heterotrophic bacteria from a large culture collection. BMC Microbiology 20 (1), article number 207. https://doi.org/10.1186/s12866-020-01884-7. IF 2.989.
  • Lira, Felipe, Ivone Vaz-Moreira, Javier Tamames, Célia M. Manaia & José Luis Martínez. 2020. Metagenomic analysis of an urban resistome before and after wastewater treatment. Scientific Reports 10: 8174

2019

  • Boix-Amorós, A., Puente-Sánchez, F., Du Toit, E., Linderborg, K., Zhang, Y., Yang, B., Salminen, S., Isolauri, E., Tamames, J., Mira, A., Collado, MC. Mycobiome profiles in breast milk from healthy women depend on mode of delivery, geographic location and interaction with bacteria. Applied Env. Microbiol. 85(9). doi: 10.1128/AEM.02994-18
  • Tamames J, Puente-Sánchez F. SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline. Front. Microbiol. 9:3349. doi: 10.3389/fmicb.2018.03349.
  • González, José M., Laura Hernández, Iris Manzano, Carlos Pedrós-Alió. 2019. Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate. The ISME Journal, doi.org/10.1038/s41396-019-0347-6.
  • Díez-Vives, Cristina, Shaun Nielsen, Pablo Sánchez, Oswaldo Palenzuela, Isabel Ferrera, Marta Sebastián, Carlos Pedrós-Alió, Josep M. Gasol and Silvia G. Acinas. 2019. Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea. Molecular Ecology, doi: 10.1111/mec.15068.
  • Uribe-Lorío, Lorena, Laura Brenes, Walter Hernández-Ascencio, Raúl Mora-Amador, Gino González, Carlos Ramírez-Umaña, Beatriz Díez, Carlos Pedrós-Alió. 2019. The influence of temperature and pH on bacterial community composition of microbial mats in hot springs. Microbiology Open 8:e893, DOI:10.1002/mbo3.893.
  • García-García, Natalia, Javier Tamames, Alexandra M. Linz, Carlos Pedrós-Alió, Fernando Puente-Sánchez. 2019. Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions. The ISME Journal, 13: 2969-2983, d.o.i. https://doi.org/10.1038/s41396-019-0487-8

2018

  • Pedrós-Alió, C., Acinas, S.G., Logares, R., and Massana, R. 2018. The HTS contribution to marine microbial diversity. Chapter 3 In J.M. Gasol and D. Kirchman (eds.) Microbial Ecology of the Oceans, 3rd edition, Wiley Blackwell.
  • Fuentes-Valdés, J.J. ;Soto-Liebe, K. ;Pérez-Pantoja, D. ,Tamames, J., Belmar, L.,Pedrós-Alió, C.,Garrido, D.,Vásquez, M. Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay. Standards in Genomic Sciences, 13(1): 26. 10.1186/s40793-018-0323-1
  • Alcamán-Arias, M.E. ;Pedrós-Alió, C. ;Tamames, J. ;Fernández, C. ;Pérez-Pantoja, D. ;Vásquez, M. ;Díez, B. Diurnal changes in active carbon and nitrogen pathways along the temperature gradient in Porcelana hot spring microbial mat. Frontiers in Microbiology 9, 2353
  • Rocha, C., Vaz, I., Henriques, I., Tamames, J., Lira, F., Martínez, JL.,  ;Manaia, C. Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant. Environmental Int 118:179-188. doi: 10.1016/j.envint.2018.05.040.
  • Puente-Sánchez F., González-Silva C., Parro V., Tamames J., Azua-Bustos A. Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1. Genome Announc. 6(17). doi: 10.1128/genomeA.00216-18.
  • Guajardo-Leiva, Sergio, Carlos Pedrós-Alió, Oscar Salgado, Fabián Pinto, Beatriz Díez. 2018. Active crossfire between Cyanobacteria and Cyanophages in phototrophic mat communities within hot springs. Frontiers in Microbiology, 9:2039. doi: 10.3389/fmicb.2018.0203.

2017

  • Brussaard, Corina P.D., Kay D. Bidle, Carlos Pedrós-Alió, and Catherine Legrand (2016) The interactive microbial ocean. Nature Microbiology, article 16255, DOI: 10.1038/nmicrobiol.2016.255 2: 1-2.
  • Cobo-Simón, M., Tamames, J. (2017). Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. BMC Genomics, 18 (1), art. no. 499.DOI: 10.1186/s12864-017-3888-y.
  • Pedrós-Alió, Carlos (2017) Bajo la piel del océano. Plataforma Editorial, Barcelona.
  • Royo-Llonch, Marta, Ferrera I, Cornejo-Castillo FM, Sánchez P, Salazar G, Stepanauskas R, González JM, Sieracki, ME, Speich, S, Stemmann, L, Pedrós-Alió C and Acinas SG. (2017) Exploring microdiversity in novel Kordia spp. (Bacteroidetes) with proteorhodopsin from the tropical Indian Ocean via single amplified genomes. Frontiers in Microbiology, 8: article 1317: 1-14. doi: 10.3389/fmicb.2017.01317.

2016

  • Aguirre de Cárcer, Daniel, Carlos Pedrós-Alió, David A.Pearce and Antonio Alcamí (2016) Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones. Frontiers in Microbiology doi: 10.3389/fmicb.2016.00337 7: 1-11.
  • Barbosa, Andrés, Vanessa Balagué, Francisco Valera, Ana Martínez, Jesús Benzal, Miguel Motas, Julia I. Diaz, Alex Mira, Carlos Pedrós-Alió (2016) Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap penguins (Pygoscelis antarctica). PLoS ONE e0153215 1: 1-11.
  • Crespo, Bibiana G., Philip J. Wallhead, Ramiro Logares, Carlos Pedrós-Alió (2016) Probing the Rare Biosphere of the North-West Mediterranean Sea: An Experiment with High Sequencing Effort. PLoS ONE e0159195 11: 1-16.
  • Fuentes-Valdés, J.J., Plominsky, A.M., Allen, E.E., Tamames, J., Vásquez, M. (2016). Complete genome sequence of a cylindrospermopsin-producing cyanobacterium, Cylindrospermopsis raciborskii CS505, containing a circular chromosome and a single extrachromosomal element. Genome Announcements, 4 (4), art. no. e00823-16. DOI: 10.1128/genomeA.00823-16
  • Gasol, J.M., C. Cardelús, X.A.G. Morán, V. Balagué, I. Forn, C. Marrasé, R. Massana, C. Pedrós-Alió, M.M. Sala, R. Simó, D. Vaqué & M. Estrada (2016) Seasonal patterns in phytoplankton photosynthetic parameters and primary production in a coastal NW Mediterranean site. Sci. Mar. doi: 10.3989/scimar.04480.06E 80: 63-77.
  • Pedrós-Alió, Carlos, Susanna Manrubia (2016) The vast unknown microbial biosphere. Proc. Natl. Acad. Sci. USA, doi/10.1073/pnas.1606105113 113: 6585-6587.
  • Pinhassi, Jarone, Edward F. DeLong, Oded Béjà, José M. González, Carlos Pedrós-Alió (2016) Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology. Microbiology and Molecular Biology Reviews 80: 1-26. doi:10.1128/MMBR.00003-16.
  • Retamosa, G., de Pedro, L., González, I., Tamames, J. (2016). Prefiltering model for homology detection algorithms on GPU. Evolutionary Bioinformatics, 12, pp. 313-322. DOI: 10.4137/EBO.S40877
  • Tamames, Javier, Pablo D. Sánchez, Pablo Iván Nikel, Carlos Pedrós-Alió (2016) Quantifying The Relative Importance Of Phylogeny And Environmental Preferences As Drivers Of Gene Content In Prokaryotic Microorganisms. Frontiers in Microbiology http://dx.doi.org/10.3389/fmicb.2016.00433 7: 1-11.
  • Vaz-Moreira, I., Tamames, J., Martínez, J.L., Manaia, C.M. (2016). Draft genome sequences of two Ralstonia pickettii strains with different aminoglycoside resistance phenotypes. Genome Announcements, 4 (6), art. no. e01257-16. DOI: 10.1128/genomeA.01257-16
  • Yelton, Alexis P., Silvia G. Acinas, Shinichi Sunagawa, Peer Bork, Carlos Pedrós-Alió, Sallie Chisholm (2016) Global genetic capacity for mixotrophy in marine picocyanobacteria. The ISME journal 10: 2946-2957, doi:10.1038/ismej.2016.64 10: 2946-2957.

2015

  • Nguyen, D., R. Maranger, V. Balagué, M. Coll-Lladó, C. Lovejoy and C. Pedrós-Alió (2015) Winter diversity and expression of proteorhodopsin genes in a Polar Ocean. The ISME Journal doi:10.1038/ismej.2015.1 9: 1835-1845.
  • Pedrós-Alió, Carlos (2015) La vida en el hielo marino y en los lagos subglaciares. Drosophila 5: 25-26.
  • Pedrós-Alió, Carlos, Marianne Potvin, Connie Lovejoy (2015) Diversity of planktonic microorganisms in the Arctic Ocean. Progress in Oceanography http://dx.doi.org/10.1016/j.pocean.2015.07.009 139: 233-243.

2014

  • Alonso-Sáez, Laura, Michael Zeder, Tommy Harding, Jakob Pernthaler, Connie Lovejoy, Stefan Bertilsson, Carlos Pedrós-Alió (2014) Winter awakening of a rare betaproteobacterium in the Arctic Ocean. Frontiers in Microbiology, 5: 1-9. doi: 10.3389/fmicb.2014.00425.
  • Fernández-Gómez B., M. M. Sala, and C. Pedrós-Alió (2014) Seasonal changes in substrate utilization patterns by bacterioplankton in the Amundsen Gulf (western Arctic). Polar Biology 37: 1321-1329.
  • Lekunberri, I., J.M. Gasol, S.G. Acinas, L. Gómez-Consarnau, B.G. Crespo, E.O. Casamayor, R. Massana, C. Pedrós-Alió & J. Pinhassi (2014) The phylogenetic and ecological context of cultured and whole-genome-sequenced marine bacteria in the coastal NW Mediterranean Sea. Syst. Appl. Microbiol. 37: 216-228.
  • Palovaara, Joakim, Neelam Akram, Federico Baltar, Carina Bunse, Jeremy Forsberg, Carlos Pedrós-Alió, José M. González and Jarone Pinhassi (2014) Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria. Proceedings of the National Academy of Sciences USA 22: 3650-3658.
  • Pascual-García, A., Tamames, J., Bastolla, U. (2014). Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological. BMC Microbiology, 14 (1), art. no. 284. DOI: 10.1186/s12866-014-0284-5
  • Retamosa, G., de Pedro, L., Gonzalez, I., Tamames, J. (2014). High performance genomic sequencing: A filtered approach. Advances in Intelligent Systems and Computing, 294 (AISC), pp. 129-136. DOI: 10.1007/978-3-319-07581-5_16

2013

  • Crespo, Bibiana G., Thomas Pommier, Beatriz Fernández-Gómez, Carlos Pedrós-Alió (2013) Taxonomic composition of the particle attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbioloy open, in press 2: 1-10.
  • Escudero, L.V., E.O. Casamayor, G. Chong, C. Pedrós-Alió & C. Demergasso (2013) Distribution of microbial arsenic reduction, oxidation and extrusion genes along a wide range of environmental arsenic concentrations. PLOS one, e78890 8: 1-14.
  • Fernández-Gómez, Beatriz, Michael Richter, Margarete Schüler, Jarone Pinhassi, Silvia G Acinas, José M González and Carlos Pedrós-Alió (2013) Ecology of marine Bacteroidetes: a comparative genomics approach. The ISME Journal 7: 1026-1037.
  • Guazzaroni, M.-E., Herbst, F.-A., Lores, I., Tamames, J., Peláez, A.I., López-Cortés, N., Alcaide, M., Del Pozo, M.V., Vieites, J.M., Von Bergen, M., Gallego, J.L.R., Bargiela, R., López-López, A., Pieper, D.H., Rosselló-Móra, R., Sánchez, J., Seifert, J., Ferrer, M. (2013) Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation. ISME Journal, 7 (1), pp. 122-136. DOI: 10.1038/ismej.2012.82
  • Higuera, C., Pajares, G., Tamames, J., Morán, F. (2013) Expert system for clustering prokaryotic species by their metabolic features. Expert Systems with Applications, 40 (15), pp. 6185-6194. DOI: 10.1016/j.eswa.2013.05.013
  • Jiménez, G., Blanch, A.R., Tamames, J., Rosselló-Mora, R. (2013) Complete genome sequence of Bacillus toyonensis BCT-7112T, the active ingredient of the feed additive preparation Toyocerin. Genome Announcements, 1 (6), art. no. e01080-13. DOI: 10.1128/genomeA.01080-13
  • Jiménez, G., Urdiain, M., Cifuentes, A., López-López, A., Blanch, A.R., Tamames, J., Kämpfer, P., Kolstø, A.-B., Ramón, D., Martínez, J.F., Codoñer, F.M., Rosselló-Móra, R. (2013) Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Systematic and Applied Microbiology, 36 (6), pp. 383-391. DOI: 10.1016/j.syapm.2013.04.008
  • López-López, A., Richter, M., Peña, A., Tamames, J., Rosselló-Móra, R. (2013) New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach. Systematic and Applied Microbiology, 36 (3), pp. 205-214. DOI: 10.1016/j.syapm.2012.11.008
  • Mackenzie, Roy, Carlos Pedrós-Alió, Beatriz Díez (2013) Bacterial composition of microbial mats in hot springs in Northern Patagonia: variations with seasons and temperatura. Extremophiles 17: 123-136.
  • Pedrós-Alió, C. & J.M. Gasol (2013) Els bacteris i els arqueus Atles d’Ecosistemes dels Països Catalans. Ed. Enciclopedia Catalana, pp. 126-127.
  • Pedrós-Alió, Carlos (2013) La Vida al Límite CSIC – La Catarata, Madrid.
  • Pedrós-Alió, Carlos (2013) Rare biosphere. Chapter 407 in Levin SA (ed.) Encyclopedia of Biodiversity, second edition vol. 6: 345-351, Waltham, MA: Academic Press Encyclopedia of Biodiversity, Academic Press
  • Tamames, J., Durante-Rodríguez, G. (2013) Taxonomy becoming a driving force in genome sequencing projects. Systematic and Applied Microbiology, 36 (4), pp. 215-217. DOI: 10.1016/j.syapm.2013.01.002
  • Xavier JC, Barbosa A, Agustí S, Alonso-Sáez L, Duarte CM, Pedrós-Alió C, Vaqué D, et al (2013) Polar marine biology science in Portugal and Spain: Recent advances and future perspectives. Journal of Sea Research 83: 9-29.

2012

  • Alonso-Sáez, Laura, Alison S Waller, Daniel R Mende, Kevin Bakker, Hanna Farnelid, Patricia Yager, Connie Lovejoy, Jean-Éric Tremblay, Marianne Potvin, Friederike Heinrich, Marta Estrada, Lasse Riemann, Peer Bork, Carlos Pedrós-Alió, Stefan Bertilsson (2012) Role for urea in nitrification by polar marine Archaea. Proceedings of the National Academy of Sciences USA (doi 10.1073/pnas.1201914109) 109: 17989-17994.
  • Díez, B., B. Bergman, C. Pedrós-Alió, M. Antó, P. Snoeijs (2012) High cyanobacterial nifH gene diversity in Arctic seawater and sea ice brine. Environmental Microbiology Reports 4: 360-366.
  • Fernández-Gómez B.,Fernàndez-Guerra A., Casamayor EO., González JM., Pedrós-Alió C., and Silvia G. Acinas (2012) Patterns and Architecture of Genomic Islands in Marine Bacteria. BMC Genomics 13: 347-366.
  • Gasol, J.M., R. Massana, R. Simó, C. Marrasé, S. G. Acinas, C. Pedrós-Alió, C. Pelejero, M. M. Sala, E. Calvo, D. Vaqué, & F. Peters (2012) Blanes Bay (site 55) pp. 138-141 in O’Brien, T. D., Li, W. K. W., and Morán, X. A. G. (Eds). 2012. ICES Phytoplankton and Microbial Plankton Status Report 2009/2010. ICES Cooperative Research Report No. 313. 196 pp.
  • Ghiglione, Jean-François, Pierre E. Galand, Thomas Pommier, Carlos Pedrós-Alió, Elizabeth W Maas, Kevin Bakker, Stefan Bertilson, David L. Kirchman, Connie Lovejoy, Patricia L. Yager, Alison E. Murray (2012) Pole to pole biogeography of surface and deep marine bacterial communities. Proceedings of the National Academy of Sciences USA (doi 10.1073/pnas.1208160109). 109: 17633-17638.
  • Lara, J., L. Escudero, M. Ferrero, G. Chong, C. Pedrós-Alió, C. Demergasso (2012) Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile. Extremophiles 16: 523-538.
  • Pedrós-Alió, C., M. Felip, E.O. Casamayor, J. Catalan & J.M. Gasol (2012) Los amantes del frío: microorganismos en la criosfera. pp. 43-55. en E.O. Casamayor & J.M. Gasol (eds). Microbios en Acción: Biodiversidad invisible con efectos muy visibles. Ed. Los Libros de La Catarata/CSIC.
  • Pedrós-Alió, Carlos (2012) The rare bacterial biosphere. Annual Reviews in Marine Science 4: 449-466.
  • Silovic, Tina, Vanessa Balagué, Sandi Orlic, Carlos Pedrós-Alió (2012) Picoplankton seasonal variation and community structure in the northeast Adriatic coastal zone. FEMS Microbiology Ecology 82: 678-691.
  • Silva-Rocha, R., Tamames, J., de Lorenzo, V. (2012) The Logic of Decision Making in Environmental Bacteria. Biomolecular Information Processing: From Logic Systems to Smart Sensors and Actuators, pp. 279-302. DOI: 10.1002/9783527645480.ch15
  • Tamames, J., de la Peña, S., de Lorenzo, V. (2012) COVER: A priori estimation of coverage for metagenomic sequencing. Environmental Microbiology Reports, 4 (3), pp. 335-341. DOI: 10.1111/j.1758-2229.2012.00338.x
  • Tamames, J., Rosselló-Móra, R. (2012) On the fitness of microbial taxonomy. Trends in Microbiology, 20 (11), pp. 514-516. DOI: 10.1016/j.tim.2012.08.012

2011

  • Coll-Lladó, Montserrat, Silvia G. Acinas, Cristina Pujades and Carlos Pedrós-Alió (2011) Transcriptome Fingerprinting Analysis: an Approach to Explore Gene Expression Patterns in Marine Picoeukaryotic Communities PLOS one 6: 22950-22959.
  • Forest, Alexandre, Jean-Éric Tremblay, Dolors Vaqué, Cèlia Marrasé, Carlos Pedrós-Alió and others (2011) Biogenic carbon flows through the planktonic food web of the Amundsen Gulf (Arctic Ocean): A synthesis of field measurements and inverse modeling analyses Progress in Oceanography 91: 410-436.
  • González, José M., Jarone Pinhassi, Beatriz Fernández-Gómez,Montserrat Coll-Lladó, Mónica González-Velázquez, Pere Puigbò, Sebastian Jaenicke, Laura Gómez-Consarnau, Antoni Fernàndez-Guerra, Alexander Goesmann, and Carlos Pedrós-Alió (2011) Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134. Applied and Environmental Microbiology 77: 8676-8686.
  • Pedrós-Alió, C (2011) L’expulsió del paradís: els pinsans de Hawaii i la biologia de la conservació Omnis Cellula 27: 10-16.
  • Pedrós-Alió, C. (2011) Understanding the tsunami of sequences. Crystal Ball Envitonmental Microbiology Reports 3: 18-18.
  • Silva-Rocha, R., de Jong, H., Tamames, J., de Lorenzo, V. (2011) The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC Systems Biology, 5, art. no. 191. DOI: 10.1186/1752-0509-5-191
  • Silva-Rocha, R., Tamames, J., dos Santos, V.M., de Lorenzo, V. (2011) The logicome of environmental bacteria: Merging catabolic and regulatory events with Boolean formalisms. Environmental Microbiology, 13 (9), pp. 2389-2402. DOI: 10.1111/j.1462-2920.2011.02455.x

2010

  • Alonso-Sáez, Laura, Pierre E. Galand, Emilio O. Casamayor, Carlos Pedrós-Alió, Stefan Bertilsson (2010) High bicarbonate assimilation in the dark by Arctic bacteria The ISME Journal 4: 1581-1590.
  • Amaral-Zettler, Linda, Felipe Artigas, John Baross, Loka Bharathi, Antje Boetius, Dorairajasingam Chandramohan, Gerhard Herndl, Kazuhiro Kogure, Phillip Neal, Carlos Pedrós-Alió, and 6 other (2010) A global census of marine microbes Chapter 12 in McIntyre (ed) The International census of Marine Life
  • Ferrera, I., R. Massana, V. Balagué, C. Pedrós-Alió, O. Sánchez and J. Mas. 2010. (2010) Evaluation of DNA extraction methods from complex phototrophic biofilms Biofouling 26: 349-357.
  • Gasol, J.M., E.O. Casamayor & C. Pedrós-Alió (2010) Bacteris i arqueus al medi planctònic pp. 92. Història Natural dels Països Catalans. Fauna i Flora Suplement. Ed. Enciclopèdia Catalana.
  • Gerardo, N.M., Altincicek, B., Anselme, C., Atamian, H., Barribeau, S.M., de Vos, M., Duncan, E.J., Evans, J.D., Gabaldón, T., Ghanim, M., Heddi, A., Kaloshian, I., Latorre, A., Moya, A., Nakabachi, A., Parker, B.J., Pérez-Brocal, V., Pignatelli, M., Rahbé, Y., Ramsey, J.S., Spragg, C.J., Tamames, J., Tamarit, D., Tamborindeguy, C., Vincent-Monegat, C., Vilcinskas, A. (2010) Immunity and other defenses in pea aphids, Acyrthosiphon pisum. Genome Biology, 11 (2), art. no. r21. DOI: 10.1186/gb-2010-11-2-r21
  • Pedrós-Alió, C. (2010) La diversidá y la importancia ecolóxica de los procariotes pp. 11-35 en “La vida fonda, un océanu de diversidá”. III Día de les Ciencies Asturianes, Gobiernu del Principau d’Astúries, Xixón
  • Pommier, Thomas , P. R. Neal, Josep M. Gasol, Montserrat Coll, Silvia G. Acinas, Carlos Pedrós-Alió (2010) Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA Aquatic Microbial Ecology 61: 221-233.
  • Richards, S., Gibbs, R.A., Gerardo, N.M., Moran, N., Nakabachi, A., Stern, D., Tagu, D., Wilson, A.C.C., Muzny, D., Kovar, C., Cree, A., Chacko, J., Chandrabose, M.N., Dao, M.D., Dinh, H.H., Gabisi, R.A., Hines, S., Hume, J., Jhangian, S.N., Joshi, V., Lewis, L.R., Liu, Y.-S., Lopez, J., Morgan, M.B., Nguyen, N.B., Okwuonu, G.O., Ruiz, S.J., Santibanez, J., Wright, R.A., Fowler, G.R., Hitchens, M.E., Lozado, R.J., Moen, C., Steffen, D., Warren, J.T., Zhang, J., Nazareth, L.V., Chavez, D., Davis, C., Lee, S.L., Patel, B.M., Pu, L.-L., Bell, S.N., Johnson, A.J., Vattathil, S., Williams Jr., R.L., Shigenobu, S., Dang, P.M., Morioka, M., Fukatsu, T., Kudo, T., Miyagishima, S.-Y., Jiang, H., Worley, K.C., Legeai, F., Gauthier, J.-P., Collin, O., Zhang, L., Chen, H.-C., Ermolaeva, O., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Maglott, D., Murphy, T., Pruitt, K., Sapojnikov, V., Souvorov, A., Thibaud-Nissen, F., Câmara, F., Guigó, R., Stanke, M., Solovyev, V., Kosarev, P., Gilbert, D., Gabaldón, T., Huerta-Cepas, J., Marcet-Houben, M., Pignatelli, M., Moya, A., Rispe, C., Ollivier, M., Quesneville, H., Permal, E., Llorens, C., Futami, R., Hedges, D., Robertson, H.M., Alioto, T., Mariotti, M., Nikoh, N., McCutcheon, J.P., Burke, G., Kamins, A., Latorre, A., Ashton, P., Calevro, F., Charles, H., Colella, S., Douglas, A.E., Jander, G., Jones, D.H., Febvay, G., Kamphuis, L.G., Kushlan, P.F., Macdonald, S., Ramsey, J., Schwartz, J., Seah, S., Thomas, G., Vellozo, A., Cass, B., Degnan, P., Hurwitz, B., Leonardo, T., Koga, R., Altincicek, B., Anselme, C., Atamian, H., Barribeau, S.M., De Vos, M., Duncan, E.J., Evans, J., Ghanim, M., Heddi, A., Kaloshian, I., Vincent-Monegat, C., Parker, B.J., Pérez-Brocal, V., Rahbé, Y., Spragg, C.J., Tamames, J., Tamarit, D., Tamborindeguy, C., Vilcinskas, A., Bickel, R.D., Brisson, J.A., Butts, T., Chang, C.-C., Christiaens, O., Davis, G.K., Duncan, E., Ferrier, D., Iga, M., Janssen, R., Lu, H.-L., McGregor, A., Miura, T., Smagghe, G., Smith, J., Van Der Zee, M., Velarde, R., Wilson, M., Dearden, P., Edwards, O.R., Gordon, K., Hilgarth, R.S., Rider Jr., S.D., Srinivasan, D., Walsh, T.K., Ishikawa, A., Jaubert-Possamai, S., Fenton, B., Huang, W., Rizk, G., Lavenier, D., Nicolas, J., Smadja, C., Zhou, J.-J., Vieira, F.G., He, X.-L., Liu, R., Rozas, J., Field, L.M., Campbell, P., Carolan, J.C., Fitzroy, C.I.J., Reardon, K.T., Reeck, G.R., Singh, K., Wilkinson, T.L., Huybrechts, J., Abdel-Latief, M., Robichon, A., Veenstra, J.A., Hauser, F., Cazzamali, G., Schneider, M., Williamson, M., Stafflinger, E., Hansen, K.K., Grimmelikhuijzen, C.J.P., Price, D.R.G., Caillaud, M., Van Fleet, E., Ren, Q., Gatehouse, J.A., Brault, V., Monsion, B., Diaz, J., Hunnicutt, L., Ju, H.-J., Pechuan, X., Aguilar, J., Cortés, T., Ortiz-Rivas, B., Martínez-Torres, D., Dombrovsky, A., Dale, R.P., Davies, T.G.E., Williamson, M.S., Jones, A., Sattelle, D., Williamson, S., Wolstenholme, A., Cottret, L., Sagot, M.F., Heckel, D.G., Hunter, W. (2010) Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biology, 8 (2), art. no. e1000313, DOI: 10.1371/journal.pbio.1000313
  • Tamames, J., Abellán, J.J., Pignatelli, M., Camacho, A., Moya, A. (2010) Environmental distribution of prokaryotic taxa. BMC Microbiology, 10, art. no. 85. DOI: 10.1186/1471-2180-10-85
  • Tamames, J., de Lorenzo, V. (2010) EnvMine: A text-mining system for the automatic extraction of contextual information. BMC Bioinformatics, 11, art. no. 294. DOI: 10.1186/1471-2105-11-294
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