Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
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The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology and human health. This dynamic research program integrates the powerful tools of genome science, molecular phylogenetics, and molecular ecology to advance our understanding of how living organisms are related to each other, to provide the tools to quantify and assess biodiversity, and to identify genes and underlying mechanisms of biomedical importance. Projects span all evolutionary time scales, ranging from deep phylogenetic divergence of ancient eukaryotic and prokaryotic lineages, to ecological analyses of how members of diverse communities contribute and respond to environmental change.
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Browsing Josephine Bay Paul Center in Comparative Molecular Biology and Evolution by Subject "Genomics"
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ArticleGenomic Standards Consortium projects(Genomic Standards Consortium, 2014) Field, Dawn ; Sterk, Peter ; Kottmann, Renzo ; De Smet, Wim ; Amaral-Zettler, Linda A. ; Cochrane, Guy R. ; James, Cole R. ; Davies, Neil ; Dawyndt, Peter ; Garrity, George M. ; Gilbert, Jack A. ; Glockner, Frank Oliver ; Hirschman, Lynette ; Klenk, Hans-Peter ; Knight, Rob ; Kyrpides, Nikos C. ; Meyer, Folker ; Karsch-Mizrachi, Ilene ; Morrison, Norman ; Robbins, Robert J. ; San Gil, Inigo ; Sansone, Susanna-Assunta ; Schriml, Lynn M. ; Tatusova, Tatiana ; Ussery, David W. ; Yilmaz, Pelin ; White, Owen ; Wooley, John ; Caporaso, J. GregoryThe Genomic Standards Consortium (GSC) is an open-membership community working towards the development, implementation and harmonization of standards in the field of genomics. The mission of the GSC is to improve digital descriptions of genomes, metagenomes and gene marker sequences. The GSC started in late 2005 with the defined task of establishing what is now termed the “Minimum Information about any Sequence” (MIxS) standard [1,2]. As an outgrowth of the activities surrounding the creation and implementation of the MixS standard there are now 18 projects within the GSC [3]. These efforts cover an ever widening range of standardization activities. Given the growth of projects and to promote transparency, participation and adoption the GSC has developed a “GSC Project Description Template”. A complete set of GSC Project Descriptions and the template are available on the GSC website. The GSC has an open policy of participation and continues to welcome new efforts. Any projects that facilitate the standard descriptions and exchange of data are potential candidates for inclusion under the GSC umbrella. Areas that expand the scope of the GSC are encouraged. Through these collective activities we hope to help foster the growth of the ‘bioinformatics standards’ community. For more information on the GSC and its range of projects, please see http://gensc.org/.
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ArticleIdentifying contamination with advanced visualization and analysis practices : metagenomic approaches for eukaryotic genome assemblies(PeerJ, 2016-03-29) Delmont, Tom O. ; Eren, A. MuratHigh-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.
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PreprintMobile genetic elements : in silico, in vitro, in vivo( 2015-11-30) Arkhipova, Irina R. ; Rice, Phoebe A.Mobile genetic elements (MGEs), also called transposable elements (TEs), represent universal components of most genomes and are intimately involved in nearly all aspects of genome organization, function, and evolution. However, there is currently a gap between fast-paced TE discovery in silico, stimulated by exponential growth of comparative genomic studies, and a limited number of experimental models amenable to more traditional in vitro and in vivo studies of structural, mechanistic, and regulatory properties of diverse MGEs. Experimental and computational scientists came together to bridge this gap at a recent conference, “Mobile Genetic Elements: in silico, in vitro, in vivo,” held at the Marine Biological Laboratory (MBL) in Woods Hole, MA, USA.
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ArticleThe ocean sampling day consortium(BioMed Central, 2015-06-19) Kopf, Anna ; Bicak, Mesude ; Kottmann, Renzo ; Schnetzer, Julia ; Kostadinov, Ivaylo ; Lehmann, Katja ; Fernandez-Guerra, Antonio ; Jeanthon, Christian ; Rahav, Eyal ; Ullrich, Matthias S. ; 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 ; Caçador, 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, Michail 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, Timothy ; 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 R. ; 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 D. ; Gidley, Maribeth Louise ; Zingone, Adriana ; Danovaro, Roberto ; Tsiamis, Georgios ; 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 OliverOcean 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. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
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ArticleReport of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012(Genomic Standards Consortium, 2014) 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, StevenThis 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 Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings.
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ArticleSimulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium(BioMed Central, 2016-03-17) Davies, Neil ; Field, Dawn ; Gavaghan, David ; Holbrook, Sally J. ; Planes, Serge ; Troyer, Matthias ; Bonsall, Michael ; Claudet, Joachim ; Roderick, George ; Schmitt, Russell J. ; Amaral-Zettler, Linda A. ; Berteaux, Veronique ; Bossin, Hervé C. ; Cabasse, Charlotte ; Collin, Antoine ; Deck, John ; Dell, Tony ; Dunne, Jennifer A. ; Gates, Ruth D. ; Harfoot, Mike ; Hench, James L. ; Hopuare, Marania ; Kirch, Patrick ; Kotoulas, Georgios ; Kosenkov, Alex ; Kusenko, Alex ; Leichter, James J. ; Lenihan, Hunter ; Magoulas, Antonios ; Martinez, Neo ; Meyer, Chris ; Stoll, Benoit ; Swalla, Billie ; Tartakovsky, Daniel M. ; Teavai Murphy, Hinano ; Turyshev, Slava ; Valdvinos, Fernanda ; Williams, Rich ; Wood, Spencer ; IDEA ConsortiumSystems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.