Now showing items 1-10 of 10

    • Anvi’o : an advanced analysis and visualization platform for ‘omics data 

      Eren, A. Murat; Esen, Ozcan C.; Quince, Christopher; Vineis, Joseph H.; Morrison, Hilary G.; Sogin, Mitchell L.; Delmont, Tom O. (PeerJ, 2015-10-08)
      Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively ...
    • Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria 

      Anantharaman, Karthik; Breier, John A.; Sheik, Cody S.; Dick, Gregory J. (2012-11-08)
      Hydrothermal vents are a well-known source of energy that powers chemosynthesis in the deep sea. Recent work suggests that microbial chemosynthesis is also surprisingly pervasive throughout the dark oceans, serving as a ...
    • Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica 

      Delmont, Tom O.; Eren, A. Murat; Vineis, Joseph H.; Post, Anton F. (Frontiers Media, 2015-10-26)
      Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis ...
    • Meeting report : Ocean ‘omics science, technology and cyberinfrastructure : current challenges and future requirements (August 20-23, 2013) 

      Gilbert, Jack A.; Dick, Gregory J.; Jenkins, Bethany D.; Heidelberg, John F.; Allen, Eric E.; Mackey, Katherine R. M.; DeLong, Edward F. (Genomic Standards Consortium, 2014)
      The National Science Foundation’s EarthCube End User Workshop was held at USC’s Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterise the needs ...
    • A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters 

      Grzymski, Joseph J.; Riesenfeld, Christian S.; Williams, Timothy J.; Dussaq, Alex M.; Ducklow, Hugh W.; Erickson, Matthew; Cavicchioli, Ricardo; Murray, Alison E. (Nature Publishing Group, 2012-04-26)
      Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant ...
    • The ocean sampling day consortium 

      Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Georgios; Siam, Rania; Abdallah, Rehab Z.; Sonnenschein, Eva C.; Cariou, Thierry; O’Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-Clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhaes; Luna, Gian Marco; Quero, Grazia Marina; Loscher, Carolin R.; Kremp, Anke; DeLorenzo, Marie E.; Øvreås, Lise; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ramos, Sandra; Magalhaes, Catarina; Jude-Lemeilleur, Florence; Aguirre-Macedo, Ma Leopoldina; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A.; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M.; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion M. F.; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C.; Kandil, Mahrous M.; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-Ezpeleta, Naiara; Berteaux-Lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; ten Hoopen, Petra; Cochrane, Guy; L’Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M.; Martin, Patrick; Jensen, Rachelle M.; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; dos Santos, Antonina; Villar, Emilie; Pesant, Stephane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Herrera Silveira, Jorge A.; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Fronth Nyhus, Paul Anders; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N.; Gasol, Josep M.; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S.; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M.; Collins, R. Eric; Ducluzeau, Anne-Lise; Martinez, Jonathan; Costello, Mark J.; Amaral-Zettler, Linda A.; Gilbert, Jack A.; Davies, Neil; Field, Dawn; Glockner, Frank Oliver (BioMed Central, 2015-06-19)
      Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. ...
    • Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics 

      Delmont, Tom O.; Eren, A. Murat; Maccario, Lorrie; Prestat, Emmanuel; Esen, Ozcan C.; Pelletier, Eric; Le Paslier, Denis; Simonet, Pascal; Vogel, Timothy M. (Frontiers Media, 2015-04-30)
      Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution ...
    • Recovering complete and draft population genomes from metagenome datasets 

      Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A. (BioMed Central, 2016-03-08)
      Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. ...
    • Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012 

      Davies, Neil; Field, Dawn; Amaral-Zettler, Linda A.; Bicak, Mesude; Bourlat, Sarah; Coddington, Jonathan; Deck, John; Drummond, Alexei; Gilbert, Jack A.; Glockner, Frank Oliver; Kottmann, Renzo; Meyer, Chris; Morrison, Norman; Obst, Matthias; Robbins, Robert J.; Schriml, Lynn M.; Sterk, Peter; Stones-Havas, Steven (Genomic Standards Consortium, 2014)
      This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The workshop’s primary goal was to work towards the launch of the ...
    • Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics 

      Lee, Sonny T. M.; Kahn, Stacy A.; Delmont, Tom O.; Shaiber, Alon; Esen, Ozcan C.; Hubert, Nathaniel A.; Morrison, Hilary G.; Antonopoulos, Dionysios A.; Rubin, David T.; Eren, A. Murat (BioMed Central, 2017-05-04)
      Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack ...