Characterization of a sponge microbiome using an integrative genome-centric approach
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Title
Characterization of a sponge microbiome using an integrative genome-centric approach
Authors
Keywords
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Journal
ISME Journal
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2020-01-29
DOI
10.1038/s41396-020-0591-9
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Note: Only part of the references are listed.- Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta
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- (2018) Donovan H Parks et al. NATURE BIOTECHNOLOGY
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- (2018) Lauren Speare et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Sponges to Be Winners under Near-Future Climate Scenarios
- (2018) James J Bell et al. BIOSCIENCE
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- (2018) Sheila Podell et al. ISME Journal
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- (2018) Kristina Bayer et al. mSystems
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- (2017) Carmen Astudillo-García et al. ENVIRONMENTAL MICROBIOLOGY
- metaSPAdes: a new versatile metagenomic assembler
- (2017) Sergey Nurk et al. GENOME RESEARCH
- dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
- (2017) Matthew R Olm et al. ISME Journal
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- (2017) Beate M Slaby et al. ISME Journal
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- (2017) Lucas Moitinho-Silva et al. ISME Journal
- Expression of eukaryotic-like protein in the microbiome of sponges
- (2017) C. Díez-Vives et al. MOLECULAR ECOLOGY
- Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges
- (2017) Gerald Lackner et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2016) Holly M. Bennett et al. GLOBAL CHANGE BIOLOGY
- Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
- (2016) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- The Sponge Hologenome
- (2016) Nicole S. Webster et al. mBio
- MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
- (2015) Yu-Wei Wu et al. BIOINFORMATICS
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
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- (2015) Tiago R. D. Costa et al. NATURE REVIEWS MICROBIOLOGY
- KEGG as a reference resource for gene and protein annotation
- (2015) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- The Pfam protein families database: towards a more sustainable future
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
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- (2015) M. Moriyama et al. mBio
- Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange
- (2015) Cara L. Fiore et al. Frontiers in Microbiology
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
- (2015) Dongwan D. Kang et al. PeerJ
- Revealing microbial functional activities in the Red Sea spongeStylissa carteriby metatranscriptomics
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- (2014) Micheal C. Wilson et al. NATURE
- The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features
- (2014) Janine Kamke et al. PLoS One
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- (2014) Kristin K. Jernigan et al. PeerJ
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- (2014) Michael Imelfort et al. PeerJ
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- (2013) Vladimir Bondarev et al. ENVIRONMENTAL MICROBIOLOGY
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- (2013) Ana I.S. Esteves et al. FEMS MICROBIOLOGY ECOLOGY
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- (2012) Michael Liu et al. ISME Journal
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- (2012) L. Fan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean
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- pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
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- (2010) Alexander Siegl et al. ISME Journal
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Complex nitrogen cycling in the spongeGeodia barretti
- (2009) Friederike Hoffmann et al. ENVIRONMENTAL MICROBIOLOGY
- Evidence of nitrification and denitrification in high and low microbial abundance sponges
- (2009) Marie-Lise Schläppy et al. MARINE BIOLOGY
- CERBERUS, a novel U-box protein containing WD-40 repeats, is required for formation of the infection thread and nodule development in the legume-Rhizobiumsymbiosis
- (2009) Koji Yano et al. PLANT JOURNAL
- Functional diversity of ankyrin repeats in microbial proteins
- (2009) Souhaila Al-Khodor et al. TRENDS IN MICROBIOLOGY
- Physiology, phylogeny andin situevidence for bacterial and archaeal nitrifiers in the marine spongeAplysina aerophoba
- (2008) Kristina Bayer et al. ENVIRONMENTAL MICROBIOLOGY
- Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
- (2008) José R. de la Torre et al. ENVIRONMENTAL MICROBIOLOGY
- The functional roles of marine sponges
- (2008) James J. Bell ESTUARINE COASTAL AND SHELF SCIENCE
- Ankyrin Repeat Proteins Comprise a Diverse Family of Bacterial Type IV Effectors
- (2008) X. Pan et al. SCIENCE
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