Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

[1]  Kevin Y. Yip,et al.  Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. , 2010, Genome research.

[2]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[3]  John C. Wooley,et al.  A Primer on Metagenomics , 2010, PLoS Comput. Biol..

[4]  Randy Showstack,et al.  World Ocean Database , 2009 .

[5]  Dawn Field,et al.  The seasonal structure of microbial communities in the Western English Channel. , 2009, Environmental microbiology.

[6]  Matthew Z. DeMaere,et al.  The genomic basis of trophic strategy in marine bacteria , 2009, Proceedings of the National Academy of Sciences.

[7]  Shulei Sun,et al.  Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome , 2009, Applied and Environmental Microbiology.

[8]  C. Fraser,et al.  The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity , 2009, Science.

[9]  Jan O. Korbel,et al.  Quantifying environmental adaptation of metabolic pathways in metagenomics , 2009, Proceedings of the National Academy of Sciences.

[10]  P. Bork,et al.  Molecular eco-systems biology: towards an understanding of community function , 2008, Nature Reviews Microbiology.

[11]  James H Brown,et al.  A latitudinal diversity gradient in planktonic marine bacteria , 2008, Proceedings of the National Academy of Sciences.

[12]  Peer Bork,et al.  Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat , 2008, Molecular systems biology.

[13]  B. Bohannan,et al.  Microbial Biogeography: From Taxonomy to Traits , 2008, Science.

[14]  Lawrence A. David,et al.  Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton , 2008, Science.

[15]  S. Giovannoni,et al.  SAR11 marine bacteria require exogenous reduced sulphur for growth , 2008, Nature.

[16]  Rick L. Stevens,et al.  Functional metagenomic profiling of nine biomes , 2008, Nature.

[17]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples , 2008, PloS one.

[18]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[19]  P. Bork,et al.  Get the most out of your metagenome: computational analysis of environmental sequence data. , 2007, Current opinion in microbiology.

[20]  J. Kuever,et al.  Molecular analysis of the distribution and phylogeny of dissimilatory adenosine-5'-phosphosulfate reductase-encoding genes (aprBA) among sulfur-oxidizing prokaryotes. , 2007, Microbiology.

[21]  Sarah C. Goslee,et al.  The ecodist Package for Dissimilarity-based Analysis of Ecological Data , 2007 .

[22]  E. Delong,et al.  Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes , 2007, The ISME Journal.

[23]  J. Raes,et al.  Quantitative assessment of protein function prediction from metagenomics shotgun sequences , 2007, Proceedings of the National Academy of Sciences.

[24]  R. Knight,et al.  Global patterns in bacterial diversity , 2007, Proceedings of the National Academy of Sciences.

[25]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.

[26]  S. Kravitz,et al.  CAMERA: A Community Resource for Metagenomics , 2007, PLoS biology.

[27]  Benjamin J. Raphael,et al.  The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families , 2007, PLoS biology.

[28]  S. Tringe,et al.  Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments , 2007, Science.

[29]  P. Vandamme,et al.  Multilocus Sequence Typing Breathes Life into a Microbial Metagenome , 2006, PloS one.

[30]  L. Riemann,et al.  Global patterns of diversity and community structure in marine bacterioplankton , 2006, Molecular ecology.

[31]  David A. Siegel,et al.  Climate-driven trends in contemporary ocean productivity , 2006, Nature.

[32]  Christian von Mering,et al.  STRING 7—recent developments in the integration and prediction of protein interactions , 2006, Nucleic Acids Res..

[33]  H. Birks,et al.  Dispersal Limitations Matter for Microbial Morphospecies , 2006, Science.

[34]  B. Enquist,et al.  Rebuilding community ecology from functional traits. , 2006, Trends in ecology & evolution.

[35]  Sallie W. Chisholm,et al.  Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients , 2006, Science.

[36]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.

[37]  James H. Brown,et al.  Microbial biogeography: putting microorganisms on the map , 2006, Nature Reviews Microbiology.

[38]  E. Delong,et al.  Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior , 2006, Science.

[39]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide , 2005, Nucleic Acids Res..

[40]  K. Arrigo Marine microorganisms and global nutrient cycles , 2005, Nature.

[41]  Edward M. Rubin,et al.  Metagenomics: DNA sequencing of environmental samples , 2005, Nature Reviews Genetics.

[42]  D. Gevers,et al.  Re-evaluating prokaryotic species , 2005, Nature Reviews Microbiology.

[43]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[44]  Richard A. Feely,et al.  A global ocean carbon climatology: Results from Global Data Analysis Project (GLODAP) , 2004 .

[45]  P. Bork,et al.  Genome evolution reveals biochemical networks and functional modules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[46]  B. Finlay Global Dispersal of Free-Living Microbial Eukaryote Species , 2002, Science.

[47]  J. P. Grime,et al.  Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges , 2001, Science.

[48]  M. Kondoh Unifying the relationships of species richness to productivity and disturbance , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[49]  J. Randerson,et al.  Primary production of the biosphere: integrating terrestrial and oceanic components , 1998, Science.

[50]  P. Falkowski,et al.  Biogeochemical Controls and Feedbacks on Ocean Primary Production , 1998, Science.

[51]  P. Reich,et al.  The Influence of Functional Diversity and Composition on Ecosystem Processes , 1997 .

[52]  R. Olson,et al.  Growth of Prochlorococcus, a Photosynthetic Prokaryote, in the Equatorial Pacific Ocean , 1995, Science.

[53]  E. Delong,et al.  Phylogenetic diversity of aggregate‐attached vs. free‐living marine bacterial assemblages , 1993 .

[54]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[55]  A. Magurran Ecological Diversity and Its Measurement , 1988, Springer Netherlands.

[56]  C. Krebs Ecology: The Experimental Analysis of Distribution and Abundance , 1973 .

[57]  H. Hotelling Relations Between Two Sets of Variates , 1936 .

[58]  Peer Bork,et al.  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..

[59]  Alexander F. Auch,et al.  Access the most recent version at doi: 10.1101/gr.5969107 References Open Access , 2007 .

[60]  Timothy P. Boyer,et al.  World ocean database 2009 , 2006 .

[61]  Tom Coenye,et al.  Opinion: Re-evaluating prokaryotic species. , 2005, Nature reviews. Microbiology.

[62]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[63]  A. Chao Nonparametric estimation of the number of classes in a population , 1984 .

[64]  P. Colinvaux Introduction to ecology , 1973 .

[65]  United Nations Food and Agriculture Organisation , 1950, Nature.

[66]  Raymond L. Lindeman Experimental Simulation of Winter Anaerobiosis in a Senescent Lake , 1942 .