Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: PhyloPhlAn
https://packages.ecosyste.ms/registries/pypi.org/packages/PhyloPhlAn
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
4 versions
Latest release: about 2 years ago
1 dependent package
331 downloads last month
Papers Mentioning PhyloPhlAn 144
10.3390/microorganisms8101590
Microbiota of the Therapeutic Euganean Thermal Muds with a Focus on the Main Cyanobacteria SpeciesCited by: 17
Author(s): Barbara Gris, Laura Treu, Raffaella Margherita Zampieri, Fabrizio Caldara, Chiara Romualdi, Stefano Campanaro, Nicoletta La Rocca
Software Mentions: 1
Published: about 4 years ago
10.3390/microorganisms9061299
Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn’s Disease Patients and Healthy IndividualsCited by: 6
Author(s): Maria Siniagina, Maria Markelova, Eugenia A. Boulygina, Alexander Laikov, Dilyara Khusnutdinova, С. Р. Абдулхаков, Natalia Danilova, Alfiya Odintsova, Р. А. Абдулхаков, Tatiana V. Grigoryeva
Software Mentions: 1
Published: over 3 years ago
10.3390/microorganisms9020407
Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic PlasticityCited by: 5
Author(s): Riccardo Rosselli, Nicola La Porta, Rosella Muresu, Piergiorgio Stevanato, Giuseppe Concheri, Andrea Squartini
Software Mentions: 1
Published: almost 4 years ago
10.1186/s40168-015-0121-6
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoiresCited by: 40
Author(s): Eugen Bauer, Cédric Christian Laczny, Stefanía Magnúsdóttir, Paul Wilmes, Ines Thiele
Software Mentions: 1
Published: almost 9 years ago
10.1186/s40168-019-0773-8
Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysisCited by: 40
Author(s): Qifan Zeng, Chao Liao, Jeffery S. Terhune, Luxin Wang
Software Mentions: 1
Published: almost 5 years ago
10.1099/acmi.0.000199
Bacterial gastroenteritis caused by the putative zoonotic pathogen Campylobacter lanienae: First reported case in GermanyCited by: 7
Author(s): Juliane Fornefett, Anne Busch, Sandra Döpping, Helmut Hotzel, Dagmar Rimek
Software Mentions: 1
Published: over 3 years ago
10.7150/jgen.39039
Whole Genome Sequence of <i>Marinobacter salarius</i> Strain SMR5, Shown to Promote Growth in its Diatom HostCited by: 6
Author(s): Mats Töpel, Matthew I. M. Pinder, Ola Johansson, Olga Kourtchenko, Anna Godhe, Adrian K. Clarke
Software Mentions: 1
Published: almost 6 years ago
10.1186/s40168-020-00877-y
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomesCited by: 34
Author(s): Sheila Podell, Jessica M. Blanton, Aaron Oliver, Michelle A. Schorn, Vinayak Agarwal, Jason S. Biggs, Bradley S. Moore, Eric E. Allen
Software Mentions: 1
Published: over 4 years ago
10.1186/s40168-019-0652-3
Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana TrenchCited by: 110
Author(s): Jiwen Liu, Yanfen Zheng, Heyu Lin, Xuchen Wang, Meng Li, Yang Liu, Yu Meng, Meixun Zhao, Nikolai Pedentchouk, David J. Lea‐Smith, Jonathan D. Todd, Clayton R. Magill, Weijia Zhang, Shun Zhou, Delei Song, Haohui Zhong, Yu Xin, Min Yu, Jie Tian, Xiaohua Zhang
Software Mentions: 1
Published: over 5 years ago
10.1155/2019/7586430
Complete Genome Sequence of the Plant Growth-Promoting Bacterium<i>Hartmannibacter diazotrophicus</i>Strain E19<sup>T</sup>Cited by: 15
Author(s): Christian Suarez, Stefan Ratering, Torsten Hain, Moritz Fritzenwanker, Alexander Goesmann, Jochen Blom, Trinad Chakraborty, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Sylvia Schnell
Software Mentions: 1
Published: about 5 years ago
10.1186/s40168-019-0637-2
Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed familyCited by: 402
Author(s): Ilias Lagkouvardos, Till Robin Lesker, Thomas C. A. Hitch, Eric Galvez, Nathiana Smit, Klaus Neuhaus, Jun Wang, John F. Baines, Birte Abt, Bärbel Stecher, Jörg Overmann, Till Strowig, Thomas Clavel
Software Mentions: 1
Published: almost 6 years ago
10.1128/MRA.00482-19
Complete Genome Sequence of the Diatom-Associated Bacterium Sphingorhabdus sp. Strain SMR4yCited by: 1
Author(s): Mats Töpel, Matthew I. M. Pinder, Ola Johansson, Olga Kourtchenko, Anna Godhe, Adrian K. Clarke
Software Mentions: 1
Published: over 5 years ago
10.1128/mBio.01033-18
Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid AnglerfishesCited by: 44
Author(s): Tory A. Hendry, Lindsay L Freed, Dana Fader, Danté B. Fenolio, Tracey Sutton, Jose V. Lopez
Software Mentions: 1
Published: over 6 years ago
10.1128/MRA.01461-18
Genome Sequence of Arenibacter algicola Strain SMS7, Found in Association with the Marine Diatom Skeletonema marinoiCited by: 2
Author(s): Mats Töpel, Matthew I. M. Pinder, Ola Johansson, Olga Kourtchenko, Anna Godhe, Adrian K. Clarke
Software Mentions: 1
Published: almost 6 years ago
10.3390/ijms21218128
Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskia baicalensisCited by: 5
Author(s): Ivan S. Petrushin, С. И. Беликов, Lubov Chernogor
Software Mentions: 1
Published: about 4 years ago
10.1128/mSphere.00202-18
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater BacteriaCited by: 19
Author(s): Sarahi L. Garcia, Moritz Buck, Joshua J. Hamilton, Christian Wurzbacher, Hans‐Peter Grossart, Katherine D. McMahon, Alexander Eiler
Software Mentions: 1
Published: over 6 years ago
10.1128/mSphere.00087-20
Phylogenomic Insights into Diversity and Evolution of Nonpathogenic <i>Xanthomonas</i> Strains Associated with CitrusCited by: 16
Author(s): Kanika Bansal, Sanjeet Kumar, Prabhu B. Patil
Software Mentions: 1
Published: over 4 years ago
10.1128/MRA.00972-18
Draft Genome Sequence of Bacillus anthracis Strain Sterne 09RA8929Cited by: 1
Author(s): Anne Busch, Mandy C. Elschner, Daniela Jacob, Roland Grunow, Herbert Tomaso
Software Mentions: 1
Published: about 6 years ago
10.1128/mSystems.00190-17
On the Road to Strain-Resolved Comparative MetagenomicsCited by: 97
Author(s): Nicola Segata
Software Mentions: 1
Published: over 6 years ago
10.1128/MRA.00107-21
Complete Genome Sequence of Rhodococcus qingshengii Strain VKM Ac-2784D, Isolated from Elytrigia repens RhizosphereCited by: 4
Author(s): Ivan S. Petrushin, Yu. A. Markova, Marina S. Karepova, Yulia V. Zaytseva, Л. А. Беловежец
Software Mentions: 1
Published: over 3 years ago
10.1128/MRA.01584-18
Genome Sequence of <i>Rhizobium jaguaris</i> CCGE525 <sup>T</sup> , a Strain Isolated from <i>Calliandra grandiflora</i> Nodules from a Rain Forest in MexicoCited by: 3
Author(s): Luis E. Servín-Garcidueñas, Gabriela Guerrero, Marco Antonio Rogel-Hernández, Esperanza Martı́nez-Romero
Software Mentions: 1
Published: over 5 years ago
10.1186/s12864-015-1980-8
Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteomeCited by: 34
Author(s): Vartul Sangal, Jochen Blom, Iain C. Sutcliffe, Christina von Hunolstein, Andreas Burkovski, Paul A. Hoskisson
Software Mentions: 1
Published: about 9 years ago
10.1099/mgen.0.000592
Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene clusterCited by: 9
Author(s): Preetha Shibu, Frazer McCuaig, Anne L. McCartney, Magdalena Kujawska, Lindsay J. Hall, Lesley Hoyles
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-021-07632-z
Comparative genomics and physiological investigation supported safety, cold adaptation, efficient hydrolytic and plant growth-promoting potential of psychrotrophic Glutamicibacter arilaitensis LJH19, isolated from night-soil compostCited by: 15
Author(s): Shruti Sinai Borker, Abhishek Thakur, Sanjeet Kumar, Sareeka Kumari, Rakshak Kumar, Sanjay Kumar
Software Mentions: 1
Published: over 3 years ago
10.1186/s13068-018-1121-0
Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestionCited by: 26
Author(s): Yangyang Jia, Siu-Kin Ng, Hsu Feng Lu, Mingwei Cai, Patrick K. H. Lee
Software Mentions: 1
Published: over 6 years ago
10.3390/biology10090924
Microorganisms of Two Thermal Pools on Kunashir Island, RussiaCited by: 2
Author(s): А. С. Розанов, Anton V. Korzhuk, Sergei V. Shekhovtsov, Gennady V. Vasiliev, S. E. Peltek
Software Mentions: 1
Published: about 3 years ago
10.1093/bioinformatics/btz848
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy DatabaseCited by: 1,815
Author(s): Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks
Software Mentions: 1
Published: about 5 years ago
10.1186/s13104-021-05589-6
Genomic characterization of bacteria from the ultra-oligotrophic Madison aquifer: insight into the archetypical LuxI/LuxR and identification of novel LuxR solosCited by: 3
Author(s): Peter C. Wengert, Narayan H. Wong, Hazel A. Barton, Han Ming Gan, André O. Hudson, Michael A. Savka
Software Mentions: 1
Published: over 3 years ago
10.1186/s13104-019-4704-3
Genome sequence of a pathogenic Corynebacterium ulcerans strain isolated from a wild boar with necrotizing lymphadenitisCited by: 4
Author(s): Anne Busch, Jens Möller, Andreas Burkovski, Helmut Hotzel
Software Mentions: 1
Published: about 5 years ago
10.3389/fmicb.2016.01090
Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing BacteriaCited by: 72
Author(s): Jessica A. Kozlowski, K. Dimitri Kits, Lisa Y. Stein
Software Mentions: 1
Published: over 8 years ago
10.1038/s41396-018-0098-9
Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolutionCited by: 85
Author(s): Wei Lin, Wensi Zhang, Xiang Zhao, Andrew P. Roberts, Greig A. Paterson, Dennis A. Bazylinski, Yongxin Pan
Software Mentions: 1
Published: over 6 years ago
10.3389/fmicb.2020.00688
Genotypic and Phenotypic Characterization of Fecal Staphylococcus epidermidis Isolates Suggests Plasticity to Adapt to Different Human Body SitesCited by: 17
Author(s): Enriqueta García-Gutiérrez, Calum J. Walsh, Lizbeth Sayavedra, Teresa Diaz-Calvo, Dinesh Thapa, Patricia Ruas‐Madiedo, Melinda J. Mayer, Paul D. Cotter, Arjan Narbad
Software Mentions: 1
Published: over 4 years ago
10.3389/fmicb.2019.01828
Friends With Benefits: Exploring the Phycosphere of the Marine Diatom Skeletonema marinoiCited by: 35
Author(s): Ola Johansson, Matthew I. M. Pinder, Fredrik Ohlsson, Jenny Egardt, Mats Töpel, Adrian K. Clarke
Software Mentions: 1
Published: over 5 years ago
10.3389/fmicb.2019.02926
Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using MetagenomicsCited by: 15
Author(s): Jose M. Haro‐Moreno, Francisco Rodrı́guez-Valera, Mario López‐Pérez
Software Mentions: 1
Published: almost 5 years ago
10.3389/fmicb.2016.01990
Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome SequencingCited by: 42
Author(s): Sohail Naushad, Herman W. Barkema, Christopher D. Luby, Larissa Anuska Zeni Condas, Diego Nobrega, Domonique A. Carson, Jeroen De Buck
Software Mentions: 1
Published: almost 8 years ago
10.3389/fmicb.2017.01584
Comparative Genomic Analysis of Neutrophilic Iron(II) Oxidizer Genomes for Candidate Genes in Extracellular Electron TransferCited by: 93
Author(s): Shaomei He, Roman A. Barco, David Emerson, Eric E. Roden
Software Mentions: 1
Published: over 7 years ago
10.1038/s41396-019-0378-z
The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global “deep red fluorescence”Cited by: 33
Author(s): Cristiana Callieri, Violeta Slabakova, Nina Dzhembekova, Nataliya Slabakova, Elisaveta Peneva, Pedro J. Cabello‐Yeves, Andrea Di Cesare, Ester M. Eckert, Roberto Bertoni, Gianluca Corno, Michaela M. Salcher, Lyudmila Kamburska, Filippo Bertoni, Snejana Moncheva
Software Mentions: 1
Published: over 5 years ago
10.3389/fmicb.2018.03187
Genome Sequencing and Pan-Genome Analysis of 23 Corallococcus spp. Strains Reveal Unexpected Diversity, With Particular Plasticity of Predatory Gene SetsCited by: 59
Author(s): Paul Livingstone, Russell M. Morphew, David E. Whitworth
Software Mentions: 1
Published: almost 6 years ago
10.3389/fmicb.2018.00834
Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidisCited by: 37
Author(s): Inwoo Baek, Min‐Cheol Kim, Imchang Lee, Seong-In Na, Michael Goodfellow, Jongsik Chun
Software Mentions: 1
Published: over 6 years ago
10.1186/s12864-019-6206-z
Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GPCited by: 12
Author(s): Ana C. Reis, Boris A. Kolvenbach, Mohamed Chami, Luı́s Gales, Conceição Egas, Philippe F.-X. Corvini, Olga C. Nunes
Software Mentions: 1
Published: about 5 years ago
10.3389/fcimb.2014.00188
Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae familyCited by: 29
Author(s): Han Ming Gan, Huan You Gan, Nurul Hawa Ahmad, Nazrin A. Aziz, André O. Hudson, Michael A. Savka
Software Mentions: 1
Published: almost 10 years ago
10.3389/fmicb.2018.01079
Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric MetagenomicsCited by: 52
Author(s): Laura Treu, Stefano Campanaro, Panagiotis Kougias, Cristina Sartori, Ilaria Bassani, Irini Angelidaki
Software Mentions: 1
Published: over 6 years ago
10.3389/fmicb.2020.595066
Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan PigCited by: 27
Author(s): Saisai Zhou, Runbo Luo, Ga Gong, Yifei Wang, Zhuoma Gesang, Kai Wang, Xu Zhao, Suolang Sizhu
Software Mentions: 1
Published: almost 4 years ago
10.3389/fmicb.2018.02458
A Novel Alkaliphilic Streptomyces Inhibits ESKAPE PathogensCited by: 27
Author(s): Luciana Terra, Paul Dyson, Matthew D. Hitchings, Lloyd E. Thomas, Alyaa Abdelhameed, İbrahim M. Banat, Salvatore A. Gazzè, Dušica Vujaklija, Paul D. Facey, Lewis Francis, Gerry A. Quinn
Software Mentions: 1
Published: about 6 years ago