pypi: iRep | Projects | Ecosyste.ms: Papers

10.1186/s40168-019-0714-6

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments
Cited by: 78
Author(s): Jiarui Chen, Shelby E. McIlroy, Anand Asundi, David M. Baker, Gianni Panagiotou
Software Mentions: 11
Published: about 5 years ago

10.1186/s40793-019-0348-0

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom
Cited by: 13
Author(s): Srijak Bhatnagar, Elise S. Cowley, Sebastian Kopf, Sherlynette Pérez Castro, Sean M. Kearney, Scott C. Dawson, Kurt Hanselmann, S. Emil Ruff
Software Mentions: 7
Published: over 4 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single <i>Ctena orbiculata</i> (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2019.01313

A Bioinformatics Guide to Plant Microbiome Analysis
Cited by: 45
Author(s): Rares Calin Lucaciu, Claus Pelikan, Samuel M. Gerner, Christos Zioutis, Stephan Köstlbacher, Harald Marx, Craig W. Herbold, Hannes Schmidt, Thomas Rattei
Software Mentions: 7
Published: almost 5 years ago

10.1128/mSystems.00123-17

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome
Cited by: 62
Author(s): Sumayah F. Rahman, Matthew R. Olm, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 5
Published: over 6 years ago

10.1038/s41396-020-00773-1

Benchmarking microbial growth rate predictions from metagenomes
Cited by: 45
Author(s): Andrew M. Long, Songjun Hou, J. Cesar Ignacio‐Espinoza, Jed A. Fuhrman
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0221694

Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages
Cited by: 15
Author(s): Robert Danczak, Michael D. Johnston, Chris Kenah, Michael T. Slattery, Michael J. Wilkins
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00786-20

Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community
Cited by: 26
Author(s): Dimitri V. Meier, Stefanie Imminger, Osnat Gillor, Dagmar Woebken
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-020-00867-0

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Cited by: 394
Author(s): Kristopher Kieft, Zhichao Zhou, Karthik Anantharaman
Software Mentions: 4
Published: over 4 years ago

10.1038/s41396-020-0676-5

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium
Cited by: 27
Author(s): Hwee Sze Tee, David W. Waite, Leo S. Payne, Martin Middleditch, Susie Wood, Kim M. Handley
Software Mentions: 4
Published: over 4 years ago

10.1186/s13062-018-0225-6

Assessment of urban microbiome assemblies with the help of targeted in silico gold standards
Cited by: 9
Author(s): Samuel M. Gerner, Thomas Rattei, Alexandra B. Graf
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.42693

Extensive transmission of microbes along the gastrointestinal tract
Cited by: 270
Author(s): Thomas Sebastian Benedikt Schmidt, Matthew R. Hayward, Luís Pedro Coelho, Simone S. Li, Paul Igor Costea, Anita Y. Voigt, Jakob Wirbel, Oleksandr M. Maistrenko, Renato Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani, Anna Heintz‐Buschart, Shinichi Sunagawa, Georg Zeller, Paul Wilmes, Peer Bork
Software Mentions: 3
Published: over 5 years ago

10.1038/s41396-018-0332-5

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
Cited by: 55
Author(s): Adrian‐Ştefan Andrei, Michaela M. Salcher, Maliheh Mehrshad, Pavel Rychtecký, Petr Znachor, Rohit Ghai
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00889-21

A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients
Cited by: 7
Author(s): Inès Levade, Ashraful Islam Khan, Fahima Chowdhury, Stephen B. Calderwood, Edward T. Ryan, Jason B. Harris, Regina C. LaRocque, Taufiqur Rahman Bhuiyan, Firdausi Qadri, Ana A. Weil, Ben Shapiro
Software Mentions: 3
Published: about 3 years ago

10.1186/s13068-020-01679-y

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters
Cited by: 117
Author(s): Stefano Campanaro, Laura Treu, Luis M. Rodriguez-R, Adam Kovalovszki, Ryan M. Ziels, Irena Maus, Xinyu Zhu, Panagiotis Kougias, Arianna Basile, Gang Luo, Andreas Schlüter, Konstantinos T. Konstantinidis, Irini Angelidaki
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-64904-6

Novel clostridial lineages recovered from metagenomes of a hot oil reservoir
Cited by: 12
Author(s): Glenn D. Christman, Rosa León‐Zayas, Rui Zhao, Zarath M. Summers, Jennifer F. Biddle
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2019.02435

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake
Cited by: 37
Author(s): Jiro F. Mori, Lin-Xing Chen, Gerdhard L Jessen, Sarah B. Rudderham, Joyce McBeth, Matthew B.J. Lindsay, G. F. Slater, Jillian F. Banfield, Lesley A. Warren
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40168-020-0786-3

Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance
Cited by: 39
Author(s): Ray Keren, Jennifer Lawrence, Wei-Qin Zhuang, David Jenkins, Jillian F. Banfield, Lisa Alvarez‐Cohen, Lijie Zhou, Ke Yu
Software Mentions: 2
Published: over 4 years ago

10.1186/s40168-021-01130-w

Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans
Cited by: 14
Author(s): Christina Kumpitsch, Florian Ph. S. Fischmeister, Alexander Mahnert, Sonja Lackner, Marilena Wilding, Corina Sturm, Anna Springer, Tobias Madl, Sandra Holasek, Christoph Högenauer, Ivan A. Berg, Veronika Schoepf, Christine Moissl-Eichinger
Software Mentions: 2
Published: almost 3 years ago

10.1186/s40168-020-00989-5

Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites
Cited by: 12
Author(s): Alexandra Kristin Bashir, Lisa Wink, Stefanie Duller, Petra Schwendner, Charles S. Cockell, Petra Rettberg, Alexander Mahnert, Kristina Beblo‐Vranesevic, Maria Bohmeier, Elke Rabbow, F. Gaboyer, Francès Westall, Nicolas Walter, P. Cabezas, L. García-Descalzo, Felipe Gómez, M. Malki, Ricardo Amils, P. Ehrenfreund, E. Monaghan, P. Vannier, V. Marteinsson, Armin Erlacher, George Tanski, Jens Strauß, Mina Bashir, Andreas Riedo, Christine Moissl-Eichinger
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.8722

Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication
Cited by: 5
Author(s): Shinya Suzuki, Takuji Yamada
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-019-3301-8

LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics
Cited by: 5
Author(s): Chen Li, Yiqi Jiang, Shuai Cheng Li
Software Mentions: 2
Published: almost 5 years ago

10.1007/s12223-018-0658-4

Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology
Cited by: 38
Author(s): Lisa‐Maria Mauerhofer, Patricia Pappenreiter, Christian Paulik, Arne H. Seifert, Sébastien Bernacchi, Simon K.-M. R. Rittmann
Software Mentions: 1
Published: almost 6 years ago

10.1186/s40168-017-0285-3

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems
Cited by: 300
Author(s): Joanne B. Emerson, Rachel I. Adams, Clarisse M. Betancourt Román, Brandon Brooks, David A. Coil, Katherine E. Dahlhausen, Holly H. Ganz, Erica M. Hartmann, Tiffany Y. Hsu, Nicholas B. Justice, Ivan G. Paulino-Lima, Julia C. Luongo, Despoina S. Lymperopoulou, C. Gómez-Silván, Brooke Rothschild-Mancinelli, Melike Balk, Curtis Huttenhower, Andreas Nocker, Parag Vaishampayan, Lynn J. Rothschild
Software Mentions: 1
Published: about 7 years ago

10.3390/molecules25174023

Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia
Cited by: 9
Author(s): Roberta Iacono, Beatrice Cobucci‐Ponzano, Federica De Lise, Nicola Curci, Luisa Maurelli, Marco Moracci, Andrea Strazzulli
Software Mentions: 1
Published: about 4 years ago

10.1128/AEM.02224-17

Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus “Candidatus Sulfobium”
Cited by: 50
Author(s): Sarah Zecchin, Ralf Mueller, Jana Seifert, Ulrich Stingl, Karthik Anantharaman, Martin von Bergen, L. Cavalca, Michael Pester
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2021.692224

The sRNA Regulated Protein DdbA Is Involved in Development and Maintenance of the Chlamydia trachomatis EB Cell Form
Cited by: 5
Author(s): Nicole A. Grieshaber, Justin Runac, Sierra Turner, Marissa Dean, Cody Appa, Anders Omsland, Scott S. Grieshaber
Software Mentions: 1
Published: about 3 years ago

10.1073/pnas.2005917117

Geochemical transition zone powering microbial growth in subsurface sediments
Cited by: 28
Author(s): Rui Zhao, José M Mogollón, Sophie S. Abby, Christa Schleper, Jennifer F. Biddle, Desiree L. Roerdink, Ingunn H. Thorseth, Steffen Leth Jørgensen
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-017-03821-7

Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant
Cited by: 17
Author(s): Elizabeth K. Costello, Christine Sun, Erica M. Carlisle, Michael J. Morowitz, Jillian F. Banfield, David A. Relman
Software Mentions: 1
Published: over 7 years ago

Ecosyste.ms: Papers

Projects: pypi: iRep

Papers Mentioning iRep 29