pypi: GroopM | Projects | Ecosyste.ms: Papers

10.1186/s12859-020-03667-3

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
Cited by: 49
Author(s): Yi Yue, Hao Huang, Qi Zhao, Huimin Dou, Xinyi Liu, Tian-Fei Han, Yue Chen, Xiangjun Song, Youhua Zhang, Jing Tu
Software Mentions: 9
Published: about 4 years ago

10.1038/s41396-020-0622-6

Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes
Cited by: 35
Author(s): Bettina Glasl, Steven J. Robbins, Pedro R. Frade, Emma Marangon, Patrick W. Laffy, David G. Bourne, Nicole S. Webster
Software Mentions: 8
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

10.3389/fmicb.2016.00563

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
Cited by: 21
Author(s): Jeffrey J. Marlow, Connor T. Skennerton, Li Zhou, Karuna Chourey, Robert L. Hettich, Chongle Pan, Victoria J. Orphan
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-017-16375-5

Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico
Cited by: 45
Author(s): Adrien Vigneron, Eric Alsop, Perrine Cruaud, Gwenaelle Philibert, Benjamin L. King, Leslie Baksmaty, D. A. Lavallée, Bart P. Lomans, Nikos C. Kyrpides, Ian M. Head, Nicolas Tsesmetzis
Software Mentions: 5
Published: almost 7 years ago

10.7717/peerj.3035

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
Cited by: 132
Author(s): Elaina D. Graham, John F. Heidelberg, Benjamin J. Tully
Software Mentions: 5
Published: over 7 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: over 6 years ago

10.1128/mBio.00530-17

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea
Cited by: 53
Author(s): Connor T. Skennerton, Karuna Chourey, Ramsunder Iyer, Robert L. Hettich, Gene W. Tyson, Victoria J. Orphan
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-017-4294-1

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
Cited by: 44
Author(s): Bhavya Papudeshi, John M. Haggerty, Michael P. Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano L. Thompson, Robert A. Edwards, Elizabeth A. Dinsdale
Software Mentions: 4
Published: almost 7 years ago

10.1099/mgen.0.000212

Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures
Cited by: 19
Author(s): Luc Cornet, Amandine Bertrand, Marc Hanikenne, Emmanuelle Javaux, Annick Wilmotte, Denis Baurain
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.4075

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion.
Cited by: 17
Author(s): Miriam E. Shiffman, Rochelle M. Soo, Paul G. Dennis, Mark Morrison, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 4
Published: over 7 years ago

10.1016/j.csbj.2016.11.005

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
Cited by: 102
Author(s): Karel Sedlář, Kristyna Kupkova, Ivo Provazník
Software Mentions: 4
Published: over 7 years ago

10.1093/gbe/evu073

An Expanded Genomic Representation of the Phylum Cyanobacteria
Cited by: 260
Author(s): Rochelle M. Soo, Connor T. Skennerton, Yuji Sekiguchi, Michael Imelfort, Samuel J. Paech, Paul G. Dennis, Jason A. Steen, Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2016.00469

Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Cited by: 13
Author(s): Ankit Gupta, Sanjiv Kumar, Vishnu P. K. Prasoodanan, K. Harish, Ashok Sharma, Vineet K. Sharma
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-019-1643-1

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
Cited by: 60
Author(s): Matthew Z. DeMaere, Aaron E. Darling
Software Mentions: 3
Published: over 5 years ago

10.1186/s40168-016-0181-2

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
Cited by: 468
Author(s): Kate L. Ormerod, David Wood, Nancy Lachner, Shaan L. Gellatly, Joshua Daly, Jeremy Parsons, Cristiana G. O. Dal’Molin, Robin W. Palfreyman, Lars K. Nielsen, Matthew A. Cooper, Mark Morrison, Philip M. Hansbro, Philip Hugenholtz
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.603

GroopM: an automated tool for the recovery of population genomes from related metagenomes
Cited by: 228
Author(s): Michael Imelfort, Donovan H. Parks, Ben J. Woodcroft, Paul G. Dennis, Philip Hugenholtz, Gene W. Tyson
Software Mentions: 3
Published: almost 10 years ago

10.7717/peerj.740

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Cited by: 97
Author(s): Yuji Sekiguchi, Akiko Ohashi, Donovan H. Parks, Toshihiro Yamauchi, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 3
Published: over 9 years ago

10.1038/srep24175

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
Cited by: 181
Author(s): Hsin-Hung Lin, Yu-Chieh Liao
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-017-1653-5

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
Cited by: 20
Author(s): Bertjan Broeksema, Magdalena Całusińska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0200323

Consensus assessment of the contamination level of publicly available cyanobacterial genomes
Cited by: 38
Author(s): Luc Cornet, Loïc Meunier, Mick Van Vlierberghe, Raphaël R. Léonard, Benoit Durieu, Yannick Lara, Agnieszka Misztak, Damien Sirjacobs, Emmanuelle Javaux, Hervé Piégay, Annick Wilmotte, Denis Baurain
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-017-1835-1

Improving contig binning of metagenomic data using $$ {d}_2^S $$ oligonucleotide frequency dissimilarity
Cited by: 15
Author(s): Ying Wang, Kun Wang, Yang Lu, Fengzhu Sun
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2015.01469

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres
Cited by: 85
Author(s): Nurdyana Abdul Rahman, Donovan H. Parks, Inka Vanwonterghem, Mark Morrison, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 2
Published: over 8 years ago

10.1186/s13068-016-0441-1

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy
Cited by: 210
Author(s): Stefano Campanaro, Laura Treu, Panagiotis Kougias, Davide De Francisci, Giorgio Valle, Irini Angelidaki
Software Mentions: 2
Published: over 8 years ago

10.1128/mSystems.00651-19

Genomic and Transcriptomic Evidence Supports Methane Metabolism in <i>Archaeoglobi</i>
Cited by: 31
Author(s): Yifan Liu, Jing Chen, Livia S. Zaramela, Liying Wang, Serge Maurice Mbadinga, Zhenshan Hou, Xiaolin Wu, Ji‐Dong Gu, Karsten Zengler, Bo‐Zhong Mu
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2015.01451

gbtools: Interactive Visualization of Metagenome Bins in R
Cited by: 36
Author(s): Brandon K. B. Seah, Harald R. Gruber‐Vodicka
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.1165

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
Cited by: 1,336
Author(s): Dongwan Kang, Jeff Froula, Rob Egan, Zhong Wang
Software Mentions: 2
Published: about 9 years ago

10.1113/JP271942

Age decreases mitochondrial motility and increases mitochondrial size in vascular smooth muscle
Cited by: 31
Author(s): Susan Chalmers, Christopher D. Saunter, John M. Girkin, John G. McCarron
Software Mentions: 1
Published: over 8 years ago

10.1186/s40168-014-0066-1

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
Cited by: 255
Author(s): Cédric Christian Laczny, Tomasz Sternal, Valentin Plugaru, Piotr Gawron, Arash Atashpendar, Houry Hera Margossian, Sergio Coronado, Laurens van der Maaten, Nikos Vlassis, Paul Wilmes
Software Mentions: 1
Published: over 9 years ago

10.1098/rstb.2014.0328

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
Cited by: 40
Author(s): Jimmy H. Saw, Anja Spang, Katarzyna Zaremba-Niedźwiedzka, Lina Juzokaite, Jeremy A. Dodsworth, Senthil K. Murugapiran, Dan R. Colman, Cristina Takacs-Vesbach, Brian P. Hedlund, Lionel Guy, Thijs J. G. Ettema
Software Mentions: 1
Published: almost 9 years ago

10.1038/ismej.2017.142

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton
Cited by: 49
Author(s): Anny Cárdenas, Matthew J. Neave, Mohamed Fauzi Haroon, Claudia Pogoreutz, Nils Rädecker, Christian Wild, Astrid Gärdes, Christian R. Voolstra
Software Mentions: 1
Published: about 7 years ago

10.1186/s12859-019-2904-4

MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
Cited by: 13
Author(s): Jia Qian, Matteo Comin
Software Mentions: 1
Published: almost 5 years ago

Ecosyste.ms: Papers

Projects: pypi: GroopM

Papers Mentioning GroopM 32