cran: Nonpareil | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.587972

DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil
Cited by: 11
Author(s): Julian Yu, Michael J. Pavia, Lauren M. Deem, Susan E. Crow, Jonathan Deenik, C. Ryan Penton
Software Mentions: 9
Published: about 4 years ago

10.1186/s12866-020-01907-3

The gut mycobiota of rural and urban individuals is shaped by geography
Cited by: 23
Author(s): Mubanga Hellen Kabwe, Surendra Vikram, Khodani Mulaudzi, Janet K. Jansson, Thulani P. Makhalanyane
Software Mentions: 7
Published: over 4 years ago

10.1186/s40168-020-00813-0

Disinfection exhibits systematic impacts on the drinking water microbiome
Cited by: 37
Author(s): Zihan Dai, Maria C. Sevillano-Rivera, Szymon T. Calus, Quyen Melina Bautista-de los Santos, A. Murat Eren, P.W.J.J. van der Wielen, Umer Zeeshan Ijaz, Ameet J. Pinto
Software Mentions: 7
Published: over 4 years ago

10.1186/s40168-016-0154-5

Recovering complete and draft population genomes from metagenome datasets
Cited by: 195
Author(s): Naseer Sangwan, Fangfang Xia, Jack A. Gilbert
Software Mentions: 7
Published: over 8 years ago

10.1128/mBio.02634-20

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study
Cited by: 22
Author(s): Nastassia V. Patin, Angela Peña-Gonzalez, Janet K. Hatt, Christine L. Moe, Amy Kirby, Konstantinos T. Konstantinidis
Software Mentions: 6
Published: almost 4 years ago

10.1038/sdata.2019.8

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining
Cited by: 33
Author(s): Markus Gastauer, Mabel Patricia Ortiz Vera, Kleber Padovani de Souza, Eder S. Pires, Ronnie Alves, Cecílio Fróis Caldeira, Sílvio Júnio Ramos, Guilherme Oliveira
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.11721

Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms
Cited by: 10
Author(s): Taylor Priest, Luis H. Orellana, Bruno Huettel, Bernhard M. Fuchs, Rudolf Amann
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giaa125

Localized effect of treated wastewater effluent on the resistome of an urban watershed
Cited by: 17
Author(s): Christopher N Thornton, Windy Tanner, James VanDerslice, William J. Brazelton
Software Mentions: 5
Published: about 4 years ago

10.1186/s40168-017-0392-1

Metabolic capability and in situ activity of microorganisms in an oil reservoir
Cited by: 61
Author(s): Yi Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S. Zaramela, Ji Dong Gu, Bo Zhong Mu, Karsten Zengler
Software Mentions: 5
Published: almost 7 years ago

10.3390/v12111204

Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake
Cited by: 4
Author(s): Catherine Girard, Valérie Langlois, Adrien Vigneron, Warwick F. Vincent, Alexander I. Culley
Software Mentions: 5
Published: about 4 years ago

10.1128/mSphere.00194-18

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community
Cited by: 19
Author(s): Adit Chaudhary, Imrose Kauser, Anirban Ray, Rachel Poretsky
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-017-00896-0

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis
Cited by: 55
Author(s): Daniel Kurth, Ariel Fernando Amadío, Omar Federico Ordoñez, Virginia Helena Albarracín, Wolfgang Gärtner, Marı́a Eugenia Farı́as
Software Mentions: 4
Published: over 7 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: about 6 years ago

10.3390/v11060484

Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
Cited by: 24
Author(s): René Kallies, Martin Hölzer, Rodolfo Brizola Toscan, Ulisses Nunes da Rocha, John C. Anders, Antonis Chatzinotas
Software Mentions: 4
Published: over 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

10.3389/fmicb.2016.00579

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem
Cited by: 61
Author(s): Eric R. Johnston, Luis M. Rodriguez-R, Chengwei Luo, Mengting Yuan, Liyou Wu, Zhili He, Edward A. G. Schuur, Yiqi Luo, James M. Tiedje, Jizhong Zhou, Konstantinos T. Konstantinidis
Software Mentions: 4
Published: over 8 years ago

10.1128/mSystems.00003-16

Differential Functional Constraints Cause Strain-Level Endemism in <i>Polynucleobacter</i> Populations
Cited by: 18
Author(s): Naseer Sangwan, Iratxe Zarraonaindia, Jarrad Hampton-Marcell, Herbert Ssegane, Tifani W. Eshoo, Geeta Rijal, M. Cristina Negri, Jack A. Gilbert
Software Mentions: 4
Published: over 8 years ago

10.1128/mSystems.00441-21

Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics
Cited by: 18
Author(s): Byung Hee Chun, Dong Han, Hyung Min Kim, Dongbin Park, Da Min Jeong, Hyun Ah Kang, Che Ok Jeon
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-020-57464-2

Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach
Cited by: 38
Author(s): Mario Moreno-Pino, Antonia Cristi, James F. Gillooly, Nicole Trefault
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-017-3918-9

Assembling metagenomes, one community at a time
Cited by: 83
Author(s): A.J. van der Walt, Marc W. Van Goethem, Jean‐Baptiste Ramond, Thulani P. Makhalanyane, Oleg N. Reva, Don A. Cowan
Software Mentions: 2
Published: over 7 years ago

10.1111/1751-7915.13532

Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide‐producing bacteria during soil formation
Cited by: 26
Author(s): Miljenka Vuko, Barbara Cania, Cordula Vogel, Susanne Kublik, Michael Schloter, Stefanie Schulz
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40168-019-0632-7

Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus
Cited by: 91
Author(s): Johan S. Sáenz, Tadeu Alcides Marques, Rafael Simões Coelho Barone, José Eurico Possebon Cyrino, Susanne Kublik, Joseph Nesme, Michael Schloter, Susanne Rath, Gisle Vestergaard
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40168-020-00983-x

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota
Cited by: 8
Author(s): Ryan A. Blaustein, Lisa Marie Michelitsch, A. Glawe, Hansung Lee, Stefanie Huttelmaier, Nancy Hellgeth, Sarah Ben Maamar, Erica M. Hartmann
Software Mentions: 2
Published: almost 4 years ago

10.1128/mSphere.00274-20

Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs
Cited by: 22
Author(s): Sarah Potgieter, Zihan Dai, Stephanus N. Venter, Makhosazana Sigudu, Ameet J. Pinto
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.00234-20

Phages Actively Challenge Niche Communities in Antarctic Soils
Cited by: 15
Author(s): Oliver Bezuidt, Pedro H. Lebre, Rian Pierneef, Carlos León‐Sobrino, Evelien M. Adriaenssens, Don A. Cowan, Yves Van de Peer, Thulani P. Makhalanyane
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-08783-4

From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments
Cited by: 18
Author(s): Cinzia Corinaldesi, Michael Tangherlini, Antonio Dell’Anno
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.ppat.1008211

Mobilizable antibiotic resistance genes are present in dust microbial communities
Cited by: 20
Author(s): Sarah Ben Maamar, A. Glawe, Taylor K Brown, Nancy Hellgeth, Jinglin Hu, Ji Ping Wang, Curtis Huttenhower, Erica M. Hartmann
Software Mentions: 1
Published: almost 5 years ago

10.1021/acs.est.0c01945

Insights into Ammonia Adaptation and Methanogenic Precursor Oxidation by Genome-Centric Analysis
Cited by: 44
Author(s): Yanqing Miao, Laura Treu, Xinyu Zhu, Hailin Tian, Arianna Basile, Ioannis A. Fotidis, Irini Angelidaki
Software Mentions: 1
Published: about 4 years ago

10.1093/gigascience/giy166

Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur
Cited by: 14
Author(s): Saskia Hiltemann, Stefan A. Boers, Peter J. van der Spek, Ruud Jansen, John P. Hays, Andrew Stubbs
Software Mentions: 1
Published: over 6 years ago

10.1128/mSystems.00039-18

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity
Cited by: 124
Author(s): Luis M. Rodriguez-R, Santosh Gunturu, James M. Tiedje, James R. Cole, Konstantinos T. Konstantinidis
Software Mentions: 1
Published: over 6 years ago

10.1038/s42003-021-01810-1

The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles
Cited by: 15
Author(s): Karin Holmfeldt, Emelie Nilsson, Domenico Simone, Margarita López-Fernández, Xiaofen Wu, Ino de Bruijn, Daniel Lundin, Anders F. Andersson, Stefan Bertilsson, Mark Dopson
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-019-53679-0

Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer
Cited by: 16
Author(s): Luis H. Orellana, Janet K. Hatt, Ramsunder Iyer, Karuna Chourey, Robert L. Hettich, Jim C. Spain, Wendy H. Yang, Joanne C. Chee‐Sanford, Robert A. Sanford, Frank E. Löffler, Konstantinos T. Konstantinidis
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-36567-x

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment
Cited by: 27
Author(s): Boryoung Shin, Minjae Kim, Karsten Zengler, Kuk-Jeong Chin, Will A. Overholt, Lisa M. Gieg, Konstantinos T. Konstantinidis, Joel E. Kostka
Software Mentions: 1
Published: almost 6 years ago

Ecosyste.ms: Papers

Projects: cran: Nonpareil

Papers Mentioning Nonpareil 33