Publication list

Overall 46 papers are currently published under the BioMarKs umbrella (2011 - 2014), with 4 others submitted and an estimated 25 in preparation for submission in 2014/2015. 24 of the BioMarKs papers were published in journals having impact factors > 5, including Nature (2), Annual Reviews (2), PLoS Biology (1), Current Biology (1), Molecular Biology and Evolution (2), ISME (7), NAR (1), etc. Note that the number of completed BioMarKs papers (currently 50 and an estimated 70-80 by the end of 2015) is far above the number of 25 planned papers at the origin of the project.

List of scientific publications

Search returns 51 publications.

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Abstract Page Short title Yearsort ascending Complete Title Journal PDF
Massana et al. 2015 2015 Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing Environmental Microbiology PDF icon Massana et al 2015.pdf
Bendif et al. 2014 2014 Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta). Journal of Phycology, 50(1): 140-148 PDF icon Bendif et al 2014.pdf
Chambouvet et al. 2014 2014 Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments. BMC Microbiology 14:110 PDF icon Chambouvet-et-al-2014.pdf
Dunthorn et al. 2014 2014 Placing environmental next generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Molecular Biology and Evolution DOI:10.1093/molbev/msu055 PDF icon Dunthorn et al 2014.pdf
Nanjappa et al. 2014 2014 Mining metagenomic databases for the assessment of species diversity and distribution in an ancient diatom lineage. PLoS One, submitted
Forster et al. 2014 2014 Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic patterns as multicellular organisms. The ISME Journal, submitted
Glücksman et al. 2014 2014 Novel diversity of sulcozoan ciliary gliding protists (Apusomonadida, Planomonadida, Mantamonadida) and ecological patterns revealed by targeted probes, large-scale data mining, and metagenomics. Environmental Microbiology, submitted
Mahé et al. 2014 2014 Swarm: robust and fast clustering method for amplicon-based studies. Nature Methods, submitted
Hartikainen et al. 2014 2014 Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians. The ISME Journal 8:177-186 PDF icon Hartikainen et al 2014.pdf
Logares et al. 2014 2014 Patterns of Rare and Abundant Marine Microbial Eukaryotes Current Biology 24, 1-9 PDF icon Logares_etal_CurBio.pdf
Percopo et al. 2013 2013 A new potentially toxic Azadinium species (Dinophyceae) from the Mediterranean Sea, A. dexteroporum sp. nov. Journal of Phycology 49, 950-966 PDF icon Percopo et al 2013.pdf
Pernice et al. 2013 2013 General patterns of diversity in major marine microeukaryote lineages. PLoS ONE 8(2), e57170 PDF icon Pernice et al 2013.pdf
Bendif et al. 2013 2013 Microalgae systematics: can we still fit a square peg in a round hole when new evidence says it is a triangle? The Marine Biologist 1, 15-17 PDF icon Bendif et al 2013.pdf
Berney et al 2013 2013 Vampires in the oceans: predatory cercozoan amoebae in marine habitats The ISME Journal 7, 2387-2399 PDF icon Berney et al 2013.pdf
Bittner et al 2013 2013 Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay Molecular Ecology 22, 87-101 PDF icon Bittner et al 2013.pdf
del Campo et al. 2013 2013 Culturing Bias in Marine Heterotrophic Flagellates Analyzed Through Seawater Enrichment Incubations Microbial Ecology 66, 489-499 PDF icon del Campo et al 2013.pdf
Roy et al. 2013 2013 Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms Biogeosciences 10(1), 555-566 PDF icon Roy et al 2013.pdf
Egge et al 2013 2013 454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes PLoS ONE 8(9): e74371 PDF icon Egge et al 2013.pdf
Sperling et al. 2013 2013 Effect of elevated CO2 on the dynamics of particle-attached and free-living bacterioplankton communities in an Arctic fjord Biogeosciences 10(1), 181-191 PDF icon Sperling et al 2013.pdf
Hingamp et al. 2013 2013 Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. The ISME journal 7:1678–1695. PDF icon Hingamp et al 2013.pdf
André et al. 2013 2013 The cryptic and the apparent reversed : lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer. Paleobiology 39(1), 21-39 PDF icon André et al. 2013.pdf
Guillou et al. 2013 2013 The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy Nucleic Acids Research 41: 597-604 PDF icon Guillou et al 2013.pdf
Bendif et al. 2013 2013 On the description of Tisochrysis lutea gen. nov. sp. nov. and Isochrysis nuda sp. nov. in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta). Journal of Applied Phycology 10.1007/s10811-013-0037-0 PDF icon Bendif et al 2013b.pdf
Massana & Logares 2013 2013 Eukaryotic versus prokaryotic marine picoplankton ecology Environmental Microbiology 15(5), 1254-1261 PDF icon Massana & Logares 2013.pdf
del Campo et al. 2013 2013 Taming the smallest predators of the oceans The ISME Journal 7(2), 351-358 PDF icon del Campo et al 2013b.pdf
Ota et al. 2012 2012 Ultrastructure and molecular phylogeny of thaumatomonads (Cercozoa) with emphasis on Thaumatomastix salina from Oslofjorden, Norway. Protist 163 (4), 560-573 PDF icon Ota et al 2011.pdf
Pawlowski et al. 2012 2012 CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms PLoS Biology 10(11), e1001419 PDF icon Pawlowski et al 2012.pdf
Richards et al. 2012 2012 Marine Fungi: Their Ecology and Molecular Diversity Annual Review of Marine Science 4(1) 495-522 PDF icon Richards et al 2012.pdf
Rodriguez-Martinez et al. 2012 2012 Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). Molecular Biology and Evolution 29(5), 1393-1406 PDF icon Rodriguez-Martinez et al 2012.pdf
Ujiié et al. 2012 2012 Longitudinal differentiation among pelagic populations in a planktic foraminifer. Ecology and Evolution PDF icon Ujiié et al 2012.pdf
Nissimov et al. 2012 2012 Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. Journal of virology 86:2896–2897.
Nissimov et al. 2012b 2012 Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202 Journal of virology 86:2380–2381
Bass et al. 2012 2012 Reticulamoeba is a long-branched granofilosean (Cercozoa) that is missing from sequence databases PLoS One 7 (12) PDF icon Bass et al 2012.pdf
Logares et al. 2012 2012 Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing The ISME Journal 6(10), 1823-1833 PDF icon Logares et al 2012.pdf
Bass & Richards 2011 2011 Three reasons to re-evaluate fungal diversity 'on Earth and in the Ocean' Fungal Biology Reviews 25(4), 159-164 PDF icon Bass & Richards 2011.pdf
Beaufort et al. 2011 2011 Sensitivity of coccolithophores to carbonate chemistry and ocean acidification Nature 476(4), 80-83 PDF icon Beaufort et al 2011.pdf
Behnke et al. 2011 2011 Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions Environmental Microbiology 13(2), 340-349 PDF icon Behnke et al 2011.pdf
Pillet et al. 2011 2011 Molecular identification of sequestered diatom chloroplasts and kleptoplastidy in foraminifera. Protist 162(3), 394-404 PDF icon Pillet et al 2011.pdf
del Campo & Massana 2011 2011 Emerging Diversity within Chrysophytes, Choanoflagellates and Bicosoecids Based on Molecular Surveys Protist 162, 435-448 PDF icon del Campo & Massana 2011.pdf
Hagino et al. 2011 2011 New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliania huxleyi (Prymnesiophyceae) from the cox1b-ATP4 genes Journal of Phycology 47, 1164-1176 PDF icon Hagino et al 2011.pdf
Jones et al. 2011 2011 Discovery of novel intermediate forms redefines the fungal tree of life Nature 474, 200-205 PDF icon Jones et al 2011.pdf
Yoshida et al. 2011 2011 Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids. Virology Journal PDF icon Yoshida et al 2011.pdf
Lepère et al. 2011 2011 Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations FEMS Microbiology Ecology 76(3), 513-523 PDF icon Lepere et al 2011.pdf
Nissimov et al. 2011a 2011 Draft genome sequence of the coccolithovirus EhV-84. Standards in genomic sciences 5:1–11.
Nissimov et al. 2011b 2011 Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203. Journal of virology 85:13468–13469.
Massana 2011 2011 Eukaryotic picoplankton in surface oceans. Annual Review of Microbiology 65, 91-110 PDF icon Massana 2011.pdf
Massana et al. 2011 2011 Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean The ISME Journal 5(2), 184-195 PDF icon Massana et al 2011.pdf
Jones & Richards 2011 2011 Environmental DNA analysis and the expansion of the fungal tree of life. The Mycota. Springer, S & W. J (Eds.) PDF icon Jones & Richards 2011.pdf
Ogata et al. 2011 2011 Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment The ISME Journal 5(7), 1143-1151 PDF icon Ogata et al 2011.pdf
Siano et al. 2010 2010 Pelagodinium gen. nov. and P. béii comb. nov., a dinoflagellate symbiont of planktonic foraminifera Protist 161, 385-399 PDF icon Siano et al 2010.pdf
Stoeck et al. 2010 2010 Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water Molecular Ecology 19 (Suppl. 1), 21-31 PDF icon Stoeck et al 2010.pdf