2022

• Gordeliy V, Kovalev K, Bamberg E, Rodriguez-Valera F, Zinovev E, Zabelskii D, Alekseev A, Rosselli R, Gushchin I, Okhrimenko I. Microbial Rhodopsins. Methods Mol Biol. 2022 [PubMed]


• Rodriguez-Valera F, Pushkarev A, Rosselli R, Béjà O. Searching Metagenomes for New Rhodopsins Methods Mol Biol. 2022;2501:101-108. [PubMed]


• Cabello-Yeves PJ, Scanlan DJ, Callieri C, Picazo A, Schallenberg L, Huber P, Roda-Garcia JJ, Bartosiewicz M, Belykh OI, Tikhonova IV, Torcello-Requena A, De Prado PM, Millard AD, Camacho A, Rodriguez-Valera F, Puxty RJ. α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats. ISME J. 2022 Jul 18. [PubMed]


• Zaragoza-Solas A, Haro-Moreno JM, Rodriguez-Valera F, López-Pérez M. Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples. mSystems. 2022 Jun 28;7(3):e0019222 [PubMed]

2021

• Roda-Garcia JJ, Haro-Moreno JM, Huschet LA, Rodriguez-Valera F, López-Pérez M. Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle. mSystems. 2021 Oct 26;6(5):e0094421 [PubMed]


• Haro-Moreno JM, López-Pérez M, Rodriguez-Valera F.Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics. Front Microbiol. 2021 Aug 27;12:708782. [PubMed]


• Coutinho FH, Zaragoza-Solas A, López-Pérez M, Barylski J, Zielezinski A, Dutilh BE, Edwards R, Rodriguez-Valera F. RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content. Patterns (N Y). 2021 Jun 15;2(7):100274. [PubMed]


• Cabello-Yeves PJ, Callieri C, Picazo A, Mehrshad M, Haro-Moreno JM, Roda-Garcia JJ, Dzhembekova N, Slabakova V, Slabakova N, Moncheva S, Rodriguez-Valera F. The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics. Environ Microbiome. 2021 Mar 16;16(1):5. [PubMed]

2020

• López-Pérez M, Haro-Moreno JM, Iranzo J, Rodriguez-Valera F. Genomes of the "Candidatus Actinomarinales" Order: Highly Streamlined Marine Epipelagic Actinobacteria. mSystems. 2020 Dec 15;5(6):e01041-20 [PubMed]


• Coutinho FH, Cabello-Yeves PJ, Gonzalez-Serrano R, Rosselli R, López-Pérez M, Zemskaya TI, Zakharenko AS, Ivanov VG, Rodriguez-Valera F. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. Microbiome. 2020 Nov 19;8(1):163. [PubMed]


• Zabelskii D, Alekseev A, Kovalev K, Rankovic V, Balandin T, Soloviov D, Bratanov D, Savelyeva E, Podolyak E, Volkov D, Vaganova S, Astashkin R, Chizhov I, Yutin N, Rulev M, Popov A, Eria-Oliveira AS, Rokitskaya T, Mager T, Antonenko Y, Rosselli R, Armeev G, Shaitan K, Vivaudou M, Büldt G, Rogachev A, Rodriguez-Valera F, Kirpichnikov M, Moser T, Offenhäusser A, Willbold D, Koonin E, Bamberg E, Gordeliy V. Viral rhodopsins 1 are an unique family of light-gated cation channels. Nat Commun. 2020 Nov 11;11(1):5707. [PubMed]


• López-Pérez M, Haro-Moreno JM, Coutinho FH, Martinez-Garcia M, Rodriguez-Valera F. Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective. mSystems. 2020 Oct 6;5(5):e00605-20. [PubMed]


• Rodriguez-Valera F. Introduction to saline environments. The biology of halophilic bacteria.2020 Aug 19: 1-23.
  


• Di Cesare A, Dzhembekova N, Cabello-Yeves PJ, Eckert EM, Slabakova V, Slabakova N, Peneva E, Bertoni R, Corno G, Salcher MM, Kamburska L, Bertoni F, Rodriguez-Valera F, Moncheva S, Callieri C. Genomic Comparison and Spatial Distribution of Different Synechococcus Phylotypes in the Black Sea. Front Microbiol. 2020 Aug 12;11:1979. [PubMed]


• Zemskaya TI, Cabello-Yeves PJ, Pavlova ON, Rodriguez-Valera F. Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth. Appl Microbiol Biotechnol. 2020 Jul;104(14):6079-6090. [PubMed]


• Gonzalez-Serrano R, Dunne M, Rosselli R, Martin-Cuadrado AB, Grosboillot V, Zinsli LV, Roda-Garcia JJ, Loessner MJ, Rodriguez-Valera F. Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. mSystems. 2020 Jun 9;5(3):e00217-20 [PubMed]


• Haro-Moreno JM, Rodriguez-Valera F, Rosselli R, Martinez-Hernandez F, Roda-Garcia JJ, Gomez ML, Fornas O, Martinez-Garcia M, López-Pérez M. Ecogenomics of the SAR11 clade. Environ Microbiol. 2020 May;22(5):1748-1763. [PubMed]


• Kovalev K, Volkov D, Astashkin R, Alekseev A, Gushchin I, Haro-Moreno JM, Chizhov I, Siletsky S, Mamedov M, Rogachev A, Balandin T, Borshchevskiy V, Popov A, Bourenkov G, Bamberg E, Rodriguez-Valera F, Büldt G, Gordeliy V. High-resolution structural insights into the heliorhodopsin family. Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4131-4141. [PubMed]


• Zaragoza-Solas A, Rodriguez-Valera F, López-Pérez M. Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments. mSystems. 2020 Feb 18;5(1):e00905-19. [PubMed]


• Göller PC, Haro-Moreno JM, Rodriguez-Valera F, Loessner MJ, Gómez-Sanz E. Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil. Microbiome. 2020 Feb 11;8(1):17 [PubMed]

2019

• Pedro J. Cabello-Yeves, Tamara I. Zemskaya, Alexandra S. Zakharenko, Mariya V. Sakirko, Vyacheslav G. Ivanov, Rohit Ghai, Francisco Rodriguez-Valera. . Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat. Limnology and Oceanography. 2019 Dec 30. [aslopubs]


• Coutinho FH, Edwards RA, Rodríguez-Valera F. Charting the diversity of uncultured viruses of Archaea and Bacteria BMC Biol. 2019 Dec 29;17(1):109. [PubMed]


• Haro-Moreno JM, Rodriguez-Valera F, López-Pérez M. Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics. Front Microbiol. 2019 Dec 19;10:2926 [PubMed]


• Coutinho FH, Rosselli R, Rodríguez-Valera F. Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean. mSystems. 2019 Nov 5;4(6):e00554-19. [PubMed]


• Bratanov D, Kovalev K, Machtens JP, Astashkin R, Chizhov I, Soloviov D, Volkov D, Polovinkin V, Zabelskii D, Mager T, Gushchin I, Rokitskaya T, Antonenko Y, Alekseev A, Shevchenko V, Yutin N, Rosselli R, Baeken C, Borshchevskiy V, Bourenkov G, Popov A, Balandin T, Büldt G, Manstein DJ, Rodriguez-Valera F, Fahlke C, Bamberg E, Koonin E, Gordeliy V. Unique structure and function of viral rhodopsins. Nat Commun. 2019 Oct 30;10(1):4939. [PubMed]


• Cabello-Yeves PJ, Rodriguez-Valera F. Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome. Microbiome. 2019 Aug 22;7(1):117 [PubMed]


• Kim JG, Kim SJ, Cvirkaite-Krupovic V, Yu WJ, Gwak JH, López-Pérez M, Rodriguez-Valera F, Krupovic M, Cho JC, Rhee SK. Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea. Proc Natl Acad Sci U S A. 2019 Jul 30;116(31):15645-15650. [PubMed]


• López-Pérez M, Haro-Moreno JM, de la Torre JR, Rodriguez-Valera F. Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes. Environ Microbiol. 2019 Jun;21(6):1980-1988. [PubMed]


• Kim SJ, Kim JG, Lee SH, Park SJ, Gwak JH, Jung MY, Chung WH, Yang EJ, Park J, Jung J, Hahn Y, Cho JC, Madsen EL, Rodriguez-Valera F, Hyun JH, Rhee SK. F. Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya. I Thaumarchaeota assembled from metagenomes. Microbiome. 2019 Feb 20;7(1):29. [PubMed]


• López-Pérez M, Jayakumar JM, Haro-Moreno JM, Zaragoza-Solas A, Reddi G, Rodriguez-Valera F, Shapiro OH, Alam M, Almagro-Moreno S. Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype. mBio. 2019 Feb 19;10(1):e02852-18. [PubMed]


• Mizuno CM, Guyomar C, Roux S, Lavigne R, Rodriguez-Valera F, Sullivan MB, Gillet R, Forterre P, Krupovic M. Numerous cultivated and uncultivated viruses encode ribosomal proteins. Nat Commun. 2019 Feb 14;10(1):752 [PubMed]


• Díez-Villaseñor C, Rodriguez-Valera F. CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans. Nat Commun. 2019 Jan 17;10(1):294. [PubMed]


• Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol. 2019 Jan;37(1):29-37. [PubMed]


• Martinez-Hernandez F, Fornas Ò, Lluesma Gomez M, Garcia-Heredia I, Maestre-Carballa L, López-Pérez M, Haro-Moreno JM, Rodriguez-Valera F, Martinez-Garcia M. Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean. ISME J. 2019 Jan;13(1):232-236. [PubMed]


• Karen E Nelson, Sarah K Highlander, Francisco Rodriguez-Valera, Bryan A White. Encyclopedia of metagenomics. Springer New York. 2019. [Springer]

2018

• Cabello-Yeves PJ, Picazo A, Camacho A, Callieri C, Rosselli R, Roda-Garcia JJ, Coutinho FH, Rodriguez-Valera F.Ecological and genomic features of two widespread freshwater picocyanobacteria. Environ Microbiol. 2018 Oct;20(10):3757-3771. [PubMed]


• Haro-Moreno JM, López-Pérez M, de la Torre JR, Picazo A, Camacho A, Rodriguez-Valera F. Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment. Microbiome. 2018 Jul 10;6(1):128. [PubMed]


• Fernández-Ruiz I, Coutinho FH, Rodriguez-Valera F. Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes. Front Microbiol. 2018 May 18;9:1033. [PubMed]


• Hou S, López-Pérez M, Pfreundt U, Belkin N, Stüber K, Huettel B, Reinhardt R, Berman-Frank I, Rodriguez-Valera F, Hess WR.Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise. ISME J. 2018 Apr;12(4):981-996. [PubMed]


• Mehrshad M, Rodriguez-Valera F, Amoozegar MA, López-García P, Ghai R.The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. ISME J. 2018 Mar;12(3):655-668. [PubMed]

2017

• Carda-Diéguez M, Ghai R, Rodríguez-Valera F, Amaro C. Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. Microbiome. 2017 Dec 21;5(1):162. [PubMed]


• Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F. Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Appl Environ Microbiol. 2017 Dec 15;84(1). [PubMed]


• Cabello-Yeves PJ, Ghai R, Mehrshad M, Picazo A, Camacho A, Rodriguez-Valera F. Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs. ront Microbiol. 2017 Nov 2;8:2131. [PubMed]


• López-Pérez M, Haro-Moreno JM, Gonzalez-Serrano R, Parras-Moltó M, Rodriguez-Valera F. Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters. PLoS Genet. 2017 Sep 25;13(9):e1007018. [PubMed]


• Shevchenko V, Mager T, Kovalev K, Polovinkin V, Alekseev A, Juettner J, Chizhov I, Bamann C, Vavourakis C, Ghai R, Gushchin I, Borshchevskiy V, Rogachev A, Melnikov I, Popov A, Balandin T, Rodriguez-Valera F, Manstein DJ, Bueldt G, Bamberg E, Gordeliy V. Inward H+ pump xenorhodopsin: Mechanism and alternative optogenetic approach. Sci Adv. 2017 Sep 22;3(9):e1603187. [PubMed]


• Bolhuis H, Martín-Cuadrado AB, Rosselli R, Pašić L, Rodriguez-Valera F.Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface. BMC Genomics. 2017 Jul 3;18(1):510. [PubMed]


• Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun. 2017 Jun 23;8:15892. [PubMed]


• Cabello-Yeves PJ, Haro-Moreno JM, Martin-Cuadrado AB, Ghai R, Picazo A, Camacho A, Rodriguez-Valera F. Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs. Front Microbiol. 2017 Jun 21;8:1151. [PubMed]


• Melnikov I, Polovinkin V, Kovalev K, Gushchin I, Shevtsov M, Shevchenko V, Mishin A, Alekseev A, Rodriguez-Valera F, Borshchevskiy V, Cherezov V, Leonard GA, Gordeliy V, Popov A. Fast iodide-SAD phasing for high-throughput membrane protein structure determination. Sci Adv. 2017 May 12;3(5):e1602952. [PubMed]


• Haro-Moreno JM, Rodriguez-Valera F, López-García P, Moreira D, Martin-Cuadrado AB. New insights into marine group III Euryarchaeota, from dark to light. ISME J. 2017 May;11(5):1102-1117. [PubMed]


• López-Pérez M, Ramon-Marco N, Rodriguez-Valera F. Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. BMC Genomics. 2017 Jan 5;18(1):36. [PubMed]

2016

• Ghai R, Mehrshad M, Mizuno CM, Rodriguez-Valera F. Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria. ISME J. 2016 Aug 9. [PubMed]


• Mizuno CM, Ghai R, Saghaï A, López-García P, Rodriguez-Valera F.Genomes of Abundant and Widespread Viruses from the Deep Ocean. MBio. 2016 Jul 26;7(4). [PubMed]


• López-Pérez M, Kimes NE, Haro-Moreno JM, Rodriguez-Valera F.Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea. Front Microbiol. 2016 Jun 22;7:996. [PubMed]


• Mojica FJ, Rodriguez-Valera F. The discovery of CRISPR in archaea and bacteria. FEBS J. 2016 Sep;283(17):3162-9. [PubMed]


• López-Pérez M, Rodriguez-Valera F.Pangenome Evolution in the Marine Bacterium Alteromonas. Genome Biol Evol. 2016 Jun 3;8(5):1556-70. [PubMed]


• Ivanova EP, López-Pérez M, Webb HK, Ng HJ, Dang TH, Zhukova NV, Mikhailov VV, Crawford RJ, Rodriguez-Valera F. Thalassospira australica sp. nov. isolated from sea water. Antonie Van Leeuwenhoek. 2016 Aug;109(8):1091-100. [PubMed]


• Rodriguez-Valera F, Martin-Cuadrado AB, López-Pérez M. Flexible genomic islands as drivers of genome evolution. Curr Opin Microbiol. 2016 Jun;31:154-60. [PubMed]


• Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G.Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Front Microbiol. 2016 Feb 25;7:211. [PubMed]


• Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F. Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea. Appl Environ Microbiol. 2016 Jan 4;82(5):1599-612. [PubMed]

2015

• Zhang CL, Xie W, Martin-Cuadrado AB, Rodriguez-Valera F. Marine Group II Archaea, potentially important players in the global ocean carbon cycle. Front Microbiol. 2015 Oct 13;6:1108. [PubMed]


• León MJ, Rodríguez-Olmos A, Sánchez-Porro C, López-Pérez M, Rodríguez-Valera F, Soliveri J, Ventosa A, Copa-Patiño JL.Spiribacter curvatus sp. nov., a moderately halophilic bacterium isolated from a saltern. Int J Syst Evol Microbiol. 2015 Dec;65(12):4638-43. [PubMed]


• Martin-Cuadrado AB, Pašić L, Rodriguez-Valera F. Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi. BMC Genomics. 2015 Aug 13;16:603. [PubMed]


• Kimes NE, López-Pérez M, Flores-Félix JD, Ramírez-Bahena MH, Igual JM, Peix A, Rodriguez-Valera F, Velázquez E. Pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic Mediterranean zone. Syst Appl Microbiol. 2015 Jul;38(5):293-9. [PubMed]


• Carda-Diéguez M, Mizuno CM, Ghai R, Rodriguez-Valera F, Amaro C. Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla). Front Microbiol. 2015 Jan 29;6:3. [PubMed]


• Mizuno CM, Rodriguez-Valera F, Ghai R.Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics. MBio. 2015 Feb 10;6(1). [PubMed]


• Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME J. 2015 Jul;9(7):1619-34. [PubMed]


• Ivanova EP, López-Pérez M, Zabalos M, Nguyen SH, Webb HK, Ryan J, Lagutin K, Vyssotski M, Crawford RJ, Rodriguez-Valera F.Ecophysiological diversity of a novel member of the genus Alteromonas, and description of Alteromonas mediterranea sp. nov. Antonie Van Leeuwenhoek. 2015 Jan;107(1):119-32. [PubMed]

2014

• López-Pérez M, Rodriguez-Valera F, Webb HK, Crawford RJ, Ivanova EP. Genome Sequence of "Thalassospira australica" NP3b2T Isolated from St. Kilda Beach, Tasman Sea. Genome Announc. 2014 Nov 13;2(6). [PubMed]. Erratum in Genome Announc. 2015 Jan 22;3(1). [PubMed]


• Carda-Diéguez M, Ghai R, Rodriguez-Valera F, Amaro C. Metagenomics of the mucosal microbiota of European eels. Genome Announc. 2014 Nov 6;2(6). [PubMed]


• Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F.Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing. Mol Ecol. 2014 Dec;23(24):6073-90. [PubMed]


• Kimes NE, López-Pérez M, Ausó E, Ghai R, Rodriguez-Valera F. RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages. BMC Genomics. 2014 Oct 26;15:938. [PubMed]


• Guo MY, Huo DQ, Ghai R, Rodriguez-Valera F, Shen CH, Zhang N, Zhang SY, Hou CJ. Metagenomics of ancient fermentation pits used for the production of chinese strong-aroma liquor. Genome Announc. 2014 Oct 23;2(5). [PubMed]


• Ventosa A, Fernández AB, León MJ, Sánchez-Porro C, Rodriguez-Valera F.The Santa Pola saltern as a model for studying the microbiota of hypersaline environments. Extremophiles. 2014 Sep;18(5):811-24. [PubMed]


• López-Pérez M, Gonzaga A, Ivanova EP, Rodriguez-Valera F.Genomes of Alteromonas australica, a world apart. BMC Genomics. 2014 Jun 18;15:483. [PubMed]


• Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P. Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota. Genome Biol Evol. 2014 Jun 12;6(7):1549-63. [PubMed]


• López-Pérez M, Martin-Cuadrado AB, Rodriguez-Valera F. Homologous recombination is involved in the diversity of replacement flexible genomic islands in aquatic prokaryotes. Front Genet. 2014 May 22;5:147. [PubMed]


• Fernández AB, Vera-Gargallo B, Sánchez-Porro C, Ghai R, Papke RT, Rodriguez-Valera F, Ventosa A.Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach. Front Microbiol. 2014 May 8;5:196. [PubMed]


• Park SJ, Ghai R, Martín-Cuadrado AB, Rodríguez-Valera F, Chung WH, Kwon K, Lee JH, Madsen EL, Rhee SK.Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments. PLoS One. 2014 May 5;9(5):e96449. [PubMed]


• León MJ, Fernández AB, Ghai R, Sánchez-Porro C, Rodriguez-Valera F, Ventosa A.From metagenomics to pure culture: isolation and characterization of the moderately halophilic bacterium Spiribacter salinus gen. nov., sp. nov. Appl Environ Microbiol. 2014 Jul;80(13):3850-7. [PubMed]


• Fernández AB, Ghai R, Martin-Cuadrado AB, Sánchez-Porro C, Rodriguez-Valera F, Ventosa A. Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics. FEMS Microbiol Ecol. 2014 Jun;88(3):623-35. [PubMed]


• Rodriguez-Valera F, Mizuno CM, Ghai R. Tales from a thousand and one phages. Bacteriophage. 2014 Jan 1;4(1):e28265 [PubMed]


• Mizuno CM, Ghai R, Rodriguez-Valera F. Evidence for metaviromic islands in marine phages. Front Microbiol. 2014 Feb 3;5:27. [PubMed]


• Syutkin AS, Pyatibratov MG, Galzitskaya OV, Rodríguez-Valera F, Fedorov OV.Haloarcula marismortui archaellin genes as ecoparalogs. Extremophiles. 2014 Mar;18(2):341-9. [PubMed]

2013

• Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R. Expanding the marine virosphere using metagenomics. PLoS Genet. 2013;9(12):e1003987. [PubMed]


• Fernandez AB, Ghai R, Martin-Cuadrado AB, Sanchez-Porro C, Rodriguez-Valera F, Ventosa A. Metagenome sequencing of prokaryotic microbiota from two hypersaline ponds of a marine saltern in santa pola, Spain. Genome Announc. 2013 Nov 14;1(6). [PubMed]


• Garcia-Heredia I, Rodriguez-Valera F, Martin-Cuadrado AB. Novel group of podovirus infecting the marine bacterium Alteromonas macleodii. Bacteriophage. 2013 Apr 1;3(2):e24766. [PubMed]


• López-Pérez M, Ghai R, Leon MJ, Rodríguez-Olmos Á, Copa-Patiño JL, Soliveri J, Sanchez-Porro C, Ventosa A, Rodriguez-Valera F. Genomes of "Spiribacter", a streamlined, successful halophilic bacterium. BMC Genomics. 2013 Nov 13;14:787. [PubMed]


• Mizuno CM, Kimes NE, López-Pérez M, Ausó E, Rodriguez-Valera F, Ghai R. A hybrid NRPS-PKS gene cluster related to the bleomycin family of antitumor antibiotics in Alteromonas macleodii strains. PLoS One. 2013 Sep 19;8(9):e76021. [PubMed]


• Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F. Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria. Sci Rep. 2013; 3:2471. [PubMed]


• López-Pérez M, Gonzaga A, Rodriguez-Valera F. Genomic diversity of "deep ecotype" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames. Genome Biol Evol. 2013; 5(6):1220-32. [PubMed]


• Leon MJ, Ghai R, Fernandez AB, Sanchez-Porro C, Rodriguez-Valera F, Ventosa A.Draft Genome of Spiribacter salinus M19-40, an Abundant Gammaproteobacterium in Aquatic Hypersaline Environments. Genome Announc. 2013 Jan;1(1). [PubMed]


• López-Pérez M, Gonzaga A, Martin-Cuadrado AB, López-García P, Rodriguez-Valera F, Kimes NE.Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains. Microb Ecol. 2013 Apr;65(3):720-30. [PubMed]


• Mizuno CM, Rodriguez-Valera F, Garcia-Heredia I, Martin-Cuadrado AB, Ghai R. Reconstruction of novel cyanobacterial siphovirus genomes from Mediterranean metagenomic fosmids. Appl Environ Microbiol. 2013 Jan;79(2):688-95. [PubMed]

2012

• Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F. Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biol Evol. 2012;4(12):1360-74. [PubMed]


• Gonzaga A, López-Pérez M, Martin-Cuadrado AB, Ghai R, Rodriguez-Valera F. Complete genome sequence of the copiotrophic marine bacterium Alteromonas macleodii strain ATCC 27126T. J Bacteriol. 2012 Dec;194(24):6998. [PubMed]


• Park SJ, Kim JG, Jung MY, Kim SJ, Cha IT, Ghai R, Martín-Cuadrado AB, Rodríguez-Valera F, Rhee SK.Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle. J Bacteriol. 2012 Dec;194(24):6948-9. [PubMed]


• López-Pérez M, Gonzaga A, Martin-Cuadrado AB, Onyshchenko O, Ghavidel A, Ghai R, Rodriguez-Valera F.Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph. Sci Rep. 2012;2:696. [PubMed]


• Park SJ, Ghai R, Martín-Cuadrado AB, Rodríguez-Valera F, Jung MY, Kim JG, Rhee SK.Draft genome sequence of the sulfur-oxidizing bacterium "Candidatus Sulfurovum sediminum" AR, which belongs to the Epsilonproteobacteria. J Bacteriol. 2012 Aug;194(15):4128-9. [PubMed]


• Ghai R, Hernandez CM, Picazo A, Mizuno CM, Ininbergs K, Díez B, Valas R, DuPont CL, McMahon KD, Camacho A, Rodriguez-Valera F.Metagenomes of Mediterranean coastal lagoons. Sci Rep. 2012; 2:490. [PubMed]


• Garcia-Heredia I, Martin-Cuadrado AB, Mojica FJ, Santos F, Mira A, Antón J, Rodriguez-Valera F.Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS One. 2012; 7(3):e33802. [PubMed]


• Ghai R, McMahon KD, Rodriguez-Valera F.Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC. Environ Microbiol Rep. 2012 Feb;4(1):29-35. [PubMed]


• Rodriguez-Valera F, Ussery DW. Is the pan-genome also a pan-selectome? F1000Res. 2012 Sep 21;1:16. [PubMed]

2011

• Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F. New abundant microbial groups in aquatic hypersaline environments. Sci Rep. 2011; 1:135. [PubMed]


• Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, Wagner Garcia J, Pellon de Miranda F, Henrique-Silva F. Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS One. 2011; 6(8):e23785. [PubMed]. Erratum in PLoS One. 2014;9(5):e97393. [PubMed]


• Brochier-Armanet C, Deschamps P, López-García P, Zivanovic Y, Rodríguez-Valera F, Moreira D. Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea. ISME J. 2011 Aug;5(8):1291-302. [PubMed]

2010

• Mira A, Martín-Cuadrado AB, D'Auria G, Rodríguez-Valera F. The bacterial pan-genome:a new paradigm in microbiology. Int Microbiol. 2010 Jun;13(2):45-57. [PubMed]


• Ghai R, Martin-Cuadrado AB, Molto AG, Heredia IG, Cabrera R, Martin J, Verdú M, Deschamps P, Moreira D, López-García P, Mira A, Rodriguez-Valera F.Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J. 2010 Sep;4(9):1154-66. [PubMed]


• Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, Felts B, Haynes M, Liu H, Lipson D, Mahaffy J, Martin-Cuadrado AB, Mira A, Nulton J, Pasić L, Rayhawk S, Rodriguez-Mueller J, Rodriguez-Valera F, Salamon P, Srinagesh S, Thingstad TF, Tran T, Thurber RV, Willner D, Youle M, Rohwer F.Viral and microbial community dynamics in four aquatic environments. ISME J. 2010 Jun;4(6):739-51. [PubMed]

2009

• Pasić L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera F.Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC Genomics. 2009 Dec 1;10:570. [PubMed]


• Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasić L, Thingstad TF, Rohwer F, Mira A. Explaining microbial population genomics through phage predation. Nat Rev Microbiol. 2009 Nov;7(11):828-36. [PubMed]


• Martin-Cuadrado AB, Ghai R, Gonzaga A, Rodriguez-Valera F. CO dehydrogenase genes found in metagenomic fosmid clones from the deep mediterranean sea. Appl Environ Microbiol. 2009 Dec;75(23):7436-44. [PubMed]

2008

• Ivars-Martínez E, D'Auria G, Rodríguez-Valera F, Sânchez-Porro C, Ventosa A, Joint I, Mühling M. Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Mol Ecol. 2008 Sep;17(18):4092-106. [PubMed]


• Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J. 2008 Dec;2(12):1194-212. [PubMed]


• Quaiser A, López-García P, Zivanovic Y, Henn MR, Rodriguez-Valera F, Moreira D.Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ Microbiol. 2008 Oct;10(10):2704-17. [PubMed]


• Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J. 2008 Aug;2(8):865-86. [PubMed]


• Sanchez-Perez G, Mira A, Nyiro G, Pasić L, Rodriguez-Valera F.Adapting to environmental changes using specialized paralogs. Trends Genet. 2008 Apr;24(4):154-8. [PubMed]

2007

• Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D'Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F.Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J. 2007 Jul;1(3):235-45. [PubMed]


• López-López A, Benlloch S, Bonfá M, Rodríguez-Valera F, Mira A. Intragenomic 16S rDNA divergence in Haloarcula marismortui is an adaptation to different temperatures. J Mol Evol. 2007 Dec;65(6):687-96. [PubMed]


• Martín-Cuadrado AB, López-García P, Alba JC, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodríguez-Valera F. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One. 2007 Sep 19;2(9):e914. [PubMed]


• Sharma AK, Walsh DA, Bapteste E, Rodriguez-Valera F, Ford Doolittle W, Papke RT.Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol. 2007 May 18;7:79. [PubMed]


• Burns DG, Janssen PH, Itoh T, Kamekura M, Li Z, Jensen G, Rodríguez-Valera F, Bolhuis H, Dyall-Smith ML. Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain. Int J Syst Evol Microbiol. 2007 Feb;57(Pt 2):387-92. [PubMed]

2006

• Legault BA, Lopez-Lopez A, Alba-Casado JC, Doolittle WF, Bolhuis H, Rodriguez-Valera F, Papke RT. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics. 2006 Jul 4;7:171. [PubMed]


• Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D.The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity. BMC Genomics. 2006 Jul 4;7:169. [PubMed]


• Zaballos M, López-López A, Ovreas L, Bartual SG, D'Auria G, Alba JC, Legault B, Pushker R, Daae FL, Rodríguez-Valera F.Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea. FEMS Microbiol Ecol. 2006 Jun;56(3):389-405. [PubMed]


• Mira A, Pushker R, Rodríguez-Valera F.The Neolithic revolution of bacterial genomes. Trends Microbiol. 2006 May;14(5):200-6. [PubMed]


• Moreira D, Rodríguez-Valera F, López-García P. Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group. Microbiology. 2006 Feb;152(Pt 2):505-17. [PubMed]


• D'Auria G, Pushker R, Rodriguez-Valera F.IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships. Bioinformatics. 2006 Mar 1;22(5):527-31. [PubMed]

2005

• Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbø CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18147-52. [PubMed]


• Onyshchenko OM, Kiprianova OA, Rodriguez-Valera F, Benlloch S.[Taxonomical study of bacteria from genera Alteromonas and Pseudoalteromonas isolated from Black Sea water and invertebrates]. Mikrobiol Z. 2005 Jul-Aug;67(4):3-13. [PubMed]


• Pushker R, D'Auria G, Alba-Casado JC, Rodríguez-Valera F. Micro-Mar: a database for dynamic representation of marine microbial biodiversity. BMC Bioinformatics. 2005 Sep 9;6:222. [PubMed]


• Bartual SG, Seifert H, Hippler C, Luzon MA, Wisplinghoff H, Rodríguez-Valera F. Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii. J Clin Microbiol. 2005 Sep;43(9):4382-90. [PubMed]. Erratum in J Clin Microbiol. 2007 Jun;45(6):2101. [PubMed]


• López-López A, Bartual SG, Stal L, Onyshchenko O, Rodríguez-Valera F. Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea. Environ Microbiol. 2005 May;7(5):649-59. [PubMed]

2004

• Papke RT, Koenig JE, Rodríguez-Valera F, Doolittle WF. Frequent recombination in a saltern population of Halorubrum. Science. 2004 Dec 10;306(5703):1928-9. [PubMed]


• Mira A, Pushker R, Legault BA, Moreira D, Rodríguez-Valera F.Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol Biol. 2004 Nov 26;4:50. [PubMed]


• Bolhuis H, Poele EM, Rodriguez-Valera F.Isolation and cultivation of Walsby's square archaeon. Environ Microbiol. 2004 Dec;6(12):1287-91. [PubMed]


• Moreira D, Rodríguez-Valera F, López-García P. Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes. Environ Microbiol. 2004 Sep;6(9):959-69. [PubMed]


• Pushker R, Mira A, Rodríguez-Valera F. Comparative genomics of gene-family size in closely related bacteria. Genome Biol. 2004;5(4):R27. [PubMed]


• Rodríguez-Valera F. Environmental genomics, the big picture? FEMS Microbiol Lett. 2004 Feb 16;231(2):153-8. [PubMed]


• López-García P, Brochier C, Moreira D, Rodríguez-Valera F.Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ Microbiol. 2004 Jan;6(1):19-34. [PubMed]

2003

• Papke RT, Douady CJ, Doolittle WF, Rodríguez-Valera F. Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern. Environ Microbiol. 2003 Nov;5(11):1039-45. [PubMed]


• Ruiz M, Rodríguez JC, Rodríguez-Valera F, Royo G.Amplified-fragment length polymorphism as a complement to IS6110-based restriction fragment length polymorphism analysis for molecular typing of Mycobacterium tuberculosis. J Clin Microbiol. 2003 Oct;41(10):4820-2. [PubMed]


• Cifuentes A, Antón J, De Wit R, Rodríguez-Valera F. Diversity of bacteria and Archaea in sulphate-reducing enrichment cultures inoculated from serial dilution of Zostera noltii rhizosphere samples. Environ Microbiol. 2003 Sep;5(9):754-64. [PubMed]


• Øvreås L, Daae FL, Torsvik V, Rodríguez-Valera F.Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol. 2003 Oct;46(3):291-301. [PubMed]

2002

• Rodríguez-Valera F. Approaches to prokaryotic biodiversity: a population genetics perspective. Environ Microbiol. 2002 Nov;4(11):628-33. [PubMed]


• Pérez-Luz S, Fernandez J, Rodríguez-Valera F, Pascual L, Moreno C, Amo A, Apraiz D, Catalán V.Sequence diversity of the internal transcribed spacer (ITS) region of the rRNA operons among different serogroups of Legionella pneumophila isolates. Syst Appl Microbiol. 2002 Aug;25(2):212-9. [PubMed]


• López-López A, Pujalte MJ, Benlloch S, Mata-Roig M, Rosselló-Mora R, Garay E, Rodríguez-Valera F.Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the alpha-Proteobacteria. Int J Syst Evol Microbiol. 2002 Jul;52(Pt 4):1277-83. [PubMed].


• Such J, Francés R, Muñoz C, Zapater P, Casellas JA, Cifuentes A, Rodríguez-Valera F, Pascual S, Sola-Vera J, Carnicer F, Uceda F, Palazón JM, Pérez-Mateo M.Detection and identification of bacterial DNA in patients with cirrhosis and culture-negative, nonneutrocytic ascites. Hepatology. 2002 Jul;36(1):135-41. [PubMed]


• Benlloch S, López-López A, Casamayor EO, Øvreås L, Goddard V, Daae FL, Smerdon G, Massana R, Joint I, Thingstad F, Pedrós-Alió C, Rodríguez-Valera F.Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environ Microbiol. 2002 Jun;4(6):349-60. [PubMed]


• Casamayor EO, Massana R, Benlloch S, Øvreås L, Díez B, Goddard VJ, Gasol JM, Joint I, Rodríguez-Valera F, Pedrós-Alió C.Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environ Microbiol. 2002 Jun;4(6):338-48. [PubMed]


• García-Martínez J, Acinas SG, Massana R, Rodríguez-Valera F. Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions. Environ Microbiol. 2002 Jan;4(1):42-50. [PubMed]


• Antón J, Oren A, Benlloch S, Rodríguez-Valera F, Amann R, Rosselló-Mora R. Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):485-91. [PubMed]


• Ruiz M, Rodríguez JC, García-Martínez J, Escribano I, Sirvent E, Gutiérrez F, Rodríguez-Valera F, Royo G.Molecular characterization of a Spanish isolate of Mycobacterium malmoense. Res Microbiol. 2002 Jan-Feb;153(1):33-6. [PubMed]


• López-García P, Rodríguez-Valera F, Moreira D. Toward the monophyly of Haeckel's radiolaria: 18S rRNA environmental data support the sisterhood of polycystinea and acantharea. Mol Biol Evol. 2002 Jan;19(1):118-21. [PubMed]

2001

• Ruíz M, Rodríguez JC, Escribano I, García-Martínez J, Rodríguez-Valera F, Royo G. Application of molecular biology techniques to the diagnosis of nontuberculous mycobacterial infections. APMIS. 2001 Dec;109(12):857-64. [PubMed]


• Moreira D, López-García P, Rodríguez-Valera F. New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence. Int J Syst Evol Microbiol. 2001 Nov;51(Pt 6):2211-9. [PubMed]


• Anton AI, Martinez-Murcia AJ, Rodriguez-Valera F, Dalet F. Sequence microdiversity at the ribosomal RNA operons of Escherichia coli pyelonephritogenic strains. Clin Microbiol Infect. 2001 Jul;7(7):345-51. [PubMed]


• López-García P, López-López A, Moreira D, Rodríguez-Valera F. Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiol Ecol. 2001 Jul;36(2-3):193-202. [PubMed]


• Oren A, Rodríguez-Valera F. The contribution of halophilic Bacteria to the red coloration of saltern crystallizer ponds(1). FEMS Microbiol Ecol. 2001 Jul;36(2-3):123-130. [PubMed]


• Benlloch S, Acinas SG, Antón J, López-López A, Luz SP, Rodríguez-Valera F. Archaeal Biodiversity in Crystallizer Ponds from a Solar Saltern: Culture versus PCR. Microb Ecol. 2001 Jan;41(1):12-19. [PubMed]


• López-García P, Moreira D, López-López A, Rodríguez-Valera F. A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions.Environ Microbiol. 2001 Jan;3(1):72-8. [PubMed]


• López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D.Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature. 2001 Feb 1;409(6820):603-7. [PubMed]


• García-Martínez J, Bescós I, Rodríguez-Sala JJ, Rodríguez-Valera F.RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acids Res. 2001 Jan 1;29(1):178-80. [PubMed]

2000

• Moreira D, Rodríguez-Valera F. A mitochondrial origin for eukaryotic C2H2 zinc finger regulators? Trends Microbiol. 2000 Oct;8(10):448-50. [PubMed]


• Rodríguez JC, Royo G, Rodríguez-Valera F. Application of four molecular techniques for typing outbreak-associated Mycobacterium tuberculosis strains. APMIS. 2000 Mar;108(3):231-6. [PubMed]


• Díez B, Antón J, Guixa-Boixereu N, Pedrós-Alió C, Rodríguez-Valera F. Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment. Int Microbiol. 2000 Sep;3(3):159-64. [PubMed]


• García-Martínez J, Rodríguez-Valera F. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Mol Ecol. 2000 Jul;9(7):935-48. [PubMed]


• Antón J, Rosselló-Mora R, Rodríguez-Valera F, Amann R. Extremely halophilic bacteria in crystallizer ponds from solar salterns. Appl Environ Microbiol. 2000 Jul;66(7):3052-7. [PubMed]


• Cifuentes A, Antón J, Benlloch S, Donnelly A, Herbert RA, Rodríguez-Valera F. Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol. 2000 Apr;66(4):1715-9. [PubMed]

1999

• Antón J, Llobet-Brossa E, Rodríguez-Valera F, Amann R. Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds.Environ Microbiol. 1999 Dec;1(6):517-23. [PubMed]


• Parolis LA, Parolis H, Paramonov NA, Boán IF, Antón J, Rodríguez-Valera F. Structural studies on the acidic exopolysaccharide from Haloferax denitrificans ATCC 35960. Carbohydr Res. 1999 Jun 30;319(1-4):133-40. [PubMed]


• García-Martínez J, Acinas SG, Antón AI, Rodríguez-Valera F. Use of the 16S--23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods. 1999 May;36(1-2):55-64. [PubMed]


• Martínez-Murcia AJ, Antón AI, Rodríguez-Valera F. Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli. Int J Syst Bacteriol. 1999 Apr;49 Pt 2:601-10. [PubMed]


• Antón AI, Martínez-Murcia AJ, Rodríguez-Valera F. Intraspecific diversity of the 23S rRNA gene and the spacer region downstream in Escherichia coli. J Bacteriol. 1999 May;181(9):2703-9. [PubMed]


• Hurtado A, Rodríguez-Valera F. Accessory DNA in the genomes of representatives of the Escherichia coli reference collection. J Bacteriol. 1999 Apr;181(8):2548-54. [PubMed]


• Lopez-Lopez A, Exposito E, Anton J, Rodriguez-Valera F, Aldaz A. Use of thiobacillus ferrooxidans in a coupled microbiological-electrochemical system for wastewater detoxification . Biotechnol Bioeng. 1999 Apr 5;63(1):79-86. [PubMed]


• Acinas SG, Antón J, Rodríguez-Valera F. Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl Environ Microbiol. 1999 Feb;65(2):514-22. [PubMed]

1998

• Paramonov NA, Parolis LA, Parolis H, Boán IF, Antón J, Rodríguez-Valera F. The structure of the exocellular polysaccharide produced by the Archaeon Haloferax gibbonsii (ATCC 33959). Carbohydr Res. 1998 Jun;309(1):89-94. [PubMed]


• Antón AI, Martínez-Murcia AJ, Rodríguez-Valera F. Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. J Mol Evol. 1998 Jul;47(1):62-72. [PubMed]


• Pérez Luz S, Rodríguez-Valera F, Lan R, Reeves PR. Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies. J Bacteriol. 1998 Apr;180(8):2144-51. [PubMed]

1997

• Mojica FJ, Cisneros E, Ferrer C, Rodríguez-Valera F, Juez G. Osmotically induced response in representatives of halophilic prokaryotes: the bacterium Halomonas elongata and the archaeon Haloferax volcanii.J Bacteriol. 1997 Sep;179(17):5471-81. [PubMed]


• Zavaleta AI, Martínez-Murcia AJ, Rodríguez-Valera F. Intraspecific genetic diversity of Oenococcus oeni as derived from DNA fingerprinting and sequence analyses. Appl Environ Microbiol. 1997 Apr;63(4):1261-7. [PubMed]

1996

• Parolis H, Parolis LA, Boán IF, Rodríguez-Valera F, Widmalm G, Manca MC, Jansson PE, Sutherland IW. The structure of the exopolysaccharide produced by the halophilic Archaeon Haloferax mediterranei strain R4 (ATCC 33500). Carbohydr Res. 1996 Dec 13;295:147-56. [PubMed]


• García-Martínez J, Martínez-Murcia A, Antón AI, Rodríguez-Valera F. Comparison of the small 16S to 23S intergenic spacer region (ISR) of the rRNA operons of some Escherichia coli strains of the ECOR collection and E. coli K-12. J Bacteriol. 1996 Nov;178(21):6374-7. [PubMed]


• Zavaleta AI, Martínez-Murcia AJ, Rodríguez-Valera F. 16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. Microbiology. 1996 Aug;142 ( Pt 8):2105-14. [PubMed]


• García-Martínez J, Martínez-Murcia AJ, Rodríguez-Valera F, Zorraquino A. Molecular evidence supporting the existence of two major groups in uropathogenic Escherichia coli. FEMS Immunol Med Microbiol. 1996 Jul;14(4):231-44. [PubMed]


• Ferrer C, Mojica FJ, Juez G, Rodríguez-Valera F. Differentially transcribed regions of Haloferax volcanii genome depending on the medium salinity. Bacteriol. 1996 Jan;178(1):309-13. [PubMed]

1995

• Rodríguez-Valera F, García Martínez J, Martínez-Murcia AJ. Intraspecific diversity in Bacteria. The case of Escherichia coli. Microbiologia. 1995 Sep;11(3):379-82. [PubMed]


• Mojica FJ, Ferrer C, Juez G, Rodríguez-Valera F. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol Microbiol. 1995 Jul;17(1):85-93. [PubMed]

1994

• Martínez-Murcia AJ, Rodríguez-Valera F. The use of arbitrarily primed PCR (AP-PCR) to develop taxa specific DNA probes of known sequence. FEMS Microbiol Lett. 1994 Dec 15;124(3):265-9. [PubMed]


• Mojica FJ, Charbonnier F, Juez G, Rodríguez-Valera F, Forterre P. Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii. J Bacteriol. 1994 Aug;176(16):4966-73. [PubMed]

1993

• Mojica FJ, Juez G, Rodríguez-Valera F. Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites. Mol Microbiol. 1993 Aug;9(3):613-21. [PubMed]


• Rodriguez-Valera F. Biotechnological potential of halobacteria. Biochem Soc Symp. 1992;58:135-47. [PubMed]

1990

• Juez G, Rodriguez-Valera F, Herrero N, Mojica FJ. Evidence for salt-associated restriction pattern modifications in the archaeobacterium Haloferax mediterranei. J Bacteriol. 1990 Dec;172(12):7278-81. [PubMed]


• Lillo JG, Rodriguez-Valera F. Effects of Culture Conditions on Poly(beta-Hydroxybutyric Acid) Production by Haloferax mediterranei. Appl Environ Microbiol. 1990 Aug;56(8):2517-2521. [PubMed]

1988

• Antón J, Meseguer I, Rodríguez-Valera F. Production of an Extracellular Polysaccharide by Haloferax mediterranei. Appl Environ Microbiol. 1988 Oct;54(10):2381-6. [PubMed]

1986

• Pérez-Fillol M, Rodríguez-Valera F. Potassium ion accumulation in cells of different halobacteria. Microbiologia. 1986 Oct;2(2):73-80. [PubMed]


• Fernandez-Castillo R, Rodriguez-Valera F, Gonzalez-Ramos J, Ruiz-Berraquero F. Accumula tion of Poly (beta-Hydroxybutyrate) by Halobacteria. Appl Environ Microbiol. 1986 Jan;51(1):214-6. [PubMed]

1985

• Pérez-Fillol M, Rodríguez-Valera F, Ferry JG. Isolation of methanogenic bacteria able to grow in high salt concentration. Microbiologia. 1985 Sep;1(1-2):29-33. [PubMed]


• Rodriguez-Valera F, Ventosa A, Juez G, Imhoff JF. Variation of environmental features and microbial populations with salt concentrations in a multi-pond saltern. Microb Ecol. 1985 Jun;11(2):107-15. [PubMed]

1983

• Rodriguez-Valera F, Nieto JJ, Ruiz-Berraquero F. Light as an energy source in continuous cultures of bacteriorhodopsin-containing halobacteria. Appl Environ Microbiol. 1983 Mar;45(3):868-71. [PubMed]


• Rodriguez-Valera F, Juez G, Kushner DJ. Halobacterium mediterranei spec, nov., a New Carbohydrate-Utilizing Extreme Halophile. Syst Appl Microbiol. 1983; 4(3):369-81. [PubMed]

1981

• Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations. Microb Ecol. 1981 Sep;7(3):235-43. [PubMed]

1980

• Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Behaviour of mixed populations of halophilic bacteria in continuous cultures. Can J Microbiol. 1980 Nov;26(11):1259-63. [PubMed]

1979

• Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Isolation of extreme halophiles from seawater. Environ Microbiol. 1979 Jul;38(1):164-5. [PubMed]