pypi: PhyloPhlAn | Projects | Ecosyste.ms: Papers

10.1128/mSystems.00316-20

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
Cited by: 8
Author(s): Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia
Software Mentions: 11
Published: almost 4 years ago

10.7554/eLife.65088

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Cited by: 604
Author(s): Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Léonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Vallès-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
Software Mentions: 10
Published: over 3 years ago

10.1186/s40168-021-01078-x

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
Cited by: 85
Author(s): Fei Xie, Wei Jin, Huazhe Si, Yuan Yuan, Ye Tao, Junhua Liu, Xiaoxu Wang, Chengjian Yang, Qiushuang Li, Xiu-Tian Yan, Limei Lin, Qian Jiang, Lei Zhang, Chang Guo, Chris Greening, Rasmus Heller, Le Luo Guan, Phillip B. Pope, Zhiliang Tan, Weiyun Zhu, Min Wang, Qiang Qiu, Zhipeng Li, Shengyong Mao
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-020-02144-7

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding
Cited by: 32
Author(s): Toby Wilkinson, Daniel Korir, Moses Ogugo, Robert D. Stewart, Mick Watson, Edith Paxton, John P. Goopy, Christelle Robert
Software Mentions: 7
Published: about 4 years ago

10.1186/s13059-021-02427-7

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Cited by: 56
Author(s): Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Vallès-Colomer, Willem M. de Vos, Nicola Segata
Software Mentions: 7
Published: about 3 years ago

10.1038/s41598-021-81668-9

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen
Cited by: 23
Author(s): Laura Glendinning, Buğra Genç, R. J. Wallace, Mick Watson
Software Mentions: 7
Published: over 3 years ago

10.1128/mSystems.00063-20

Genomic Analysis of Bovine Staphylococcus aureus Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
Cited by: 31
Author(s): Sohail Naushad, Diego Nobrega, Syed Ali Raza Naqvi, Herman W. Barkema, Jeroen De Buck
Software Mentions: 7
Published: about 4 years ago

10.7717/peerj.1029

Compact graphical representation of phylogenetic data and metadata with GraPhlAn
Cited by: 584
Author(s): Francesco Asnicar, George Weingart, Timothy L. Tickle, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: about 9 years ago

10.1038/s41396-020-00736-6

The saccharibacterium TM7x elicits differential responses across its host range
Cited by: 26
Author(s): Daniel R. Utter, Xuesong He, Colleen M. Cavanaugh, Jeffrey S. McLean, Batbileg Bor
Software Mentions: 6
Published: about 4 years ago

10.1016/j.cell.2019.01.001

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Cited by: 956
Author(s): Edoardo Pasolli, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, Paolo Manghi, Adrian Tett, Paolo Ghensi, María Carmen Collado, Benjamin L. Rice, Casey DuLong, Xochitl C. Morgan, Christopher D. Golden, Christopher Quince, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-020-02042-y

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
Cited by: 60
Author(s): Nicolai Karcher, Edoardo Pasolli, Francesco Asnicar, Kun Huang, Adrian Tett, Serena Manara, Federica Armanini, D. J. G. Bain, Sylvia H. Duncan, Petra Louis, Moreno Zolfo, Paolo Manghi, Mireia Vallès-Colomer, Roberta Raffaetà, Omar Rota‐Stabelli, María Carmen Collado, Georg Zeller, Daniel Falush, Frank Maixner, Alan W. Walker, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: over 4 years ago

10.1093/gbe/evu149

Small but Powerful, the Primary Endosymbiont of Moss Bugs, Candidatus Evansia muelleri, Holds a Reduced Genome with Large Biosynthetic Capabilities
Cited by: 33
Author(s): Diego Santos-García, Amparo Latorre, Andrés Moya, George Gibbs, Viktor Hartung, Konrad Dettner, Stefan Martin Kuechler, Francisco J. Silva
Software Mentions: 6
Published: about 10 years ago

10.1371/journal.pone.0227639

Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing
Cited by: 15
Author(s): Federica Antonelli, Alfonso Esposito, Ludovica Calvo, Valerio Licursi, Philippe Tisseyre, Sandra Ricci, Manuela Romagnoli, Silvano Piazza, Francesca Guerrieri
Software Mentions: 6
Published: over 4 years ago

10.1099/mgen.0.000207

Taxonogenomics reveal multiple novel genomospecies associated with clinical isolates of Stenotrophomonas maltophilia
Cited by: 20
Author(s): Prabhu B. Patil, Sanjeet Kumar, Samriti Midha, Vikas Gautam
Software Mentions: 5
Published: about 6 years ago

10.7717/peerj.10941

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
Cited by: 59
Author(s): Rachel Gilroy, Anuradha Ray, María Getino, Isabella Pursley, Daniel L. Horton, Nabil-Fareed Alikhan, Dave Baker, Karim Gharbi, Neil Hall, Mick Watson, Evelien M. Adriaenssens, Ebenezer Foster-Nyarko, Sheikh Jarju, Arss Secka, Martín Antonio, Aharon Oren, Roy R. Chaudhuri, Roberto La Ragione, Falk Hildebrand, Mark J. Pallen
Software Mentions: 5
Published: over 3 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

10.3389/fmicb.2020.01979

Genomic Comparison and Spatial Distribution of Different Synechococcus Phylotypes in the Black Sea
Cited by: 11
Author(s): Andrea Di Cesare, Nina Dzhembekova, Pedro J. Cabello‐Yeves, Ester M. Eckert, Violeta Slabakova, Nataliya Slabakova, Elisaveta Peneva, Roberto Bertoni, Gianluca Corno, Michaela M. Salcher, Lyudmila Kamburska, Filippo Bertoni, Francisco Rodrı́guez-Valera, Snejana Moncheva, Cristiana Callieri
Software Mentions: 4
Published: about 4 years ago

10.1128/mSystems.00939-20

Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut
Cited by: 15
Author(s): Jacobo de la Cuesta-Zuluaga, Tim D. Spector, Nicholas D. Youngblut, Ruth E. Ley
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2021.692453

Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping
Cited by: 12
Author(s): Amar Ćosić, Eva Leitner, Christian Petternel, Herbert Galler, Franz F. Reinthaler, Kathrin A. Herzog-Obereder, Elisabeth Tatscher, Sandra Raffl, Gebhard Feierl, Christoph Högenauer, Ellen L. Zechner, Sabine Kienesberger
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2018.00280

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification
Cited by: 14
Author(s): Mingwei Cai, Siu-Kin Ng, Chee Kent Lim, Hsu Feng Lu, Yangyang Jia, Patrick K. H. Lee
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00522-20

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants
Cited by: 69
Author(s): John Leech, Raúl Cabrera‐Rubio, Aaron M. Walsh, Guerrino Macori, Calum J. Walsh, Wiley Barton, Laura Finnegan, Fiona Crispie, Órla O’Sullivan, Marcus J. Claesson, Paul D. Cotter
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.3162

The genomic sequence ofExiguobacterium chiriqhuchastr. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Cited by: 14
Author(s): Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar Federico Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, Marı́a Eugenia Farı́as, Amparo Latorre, Valeria Souza
Software Mentions: 4
Published: over 7 years ago

10.1128/mSystems.00236-18

Using Core Genome Alignments To Assign Bacterial Species
Cited by: 51
Author(s): Matthew Chung, James B. Munro, Hervé Tettelin, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 6 years ago

10.1128/mBio.00916-18

Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake
Cited by: 13
Author(s): Sari Peura, Moritz Buck, Sanni L. Aalto, Sergio E. Morales, Hannu Nykänen, Alexander Eiler
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-60623-0

First evidence of production of the lantibiotic nisin P
Cited by: 29
Author(s): Enriqueta García-Gutiérrez, Paula M. O’Connor, Gerhard Saalbach, Calum J. Walsh, James W. Hegarty, Caitriona M. Guinane, Melinda J. Mayer, Arjan Narbad, Paul D. Cotter
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-39787-x

A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the Rosaceae infecting strains
Cited by: 7
Author(s): Ivan Polsinelli, Luigimaria Borruso, Rosanna Caliandro, Luca Triboli, Alfonso Esposito, Stefano Benini
Software Mentions: 4
Published: over 5 years ago

10.1099/acmi.0.000015

Phylogenomics insights into order and families of Lysobacterales
Cited by: 19
Author(s): Sanjeet Kumar, Kanika Bansal, Prashant P. Patil, Prabhu B. Patil
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms8111663

Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut
Cited by: 11
Author(s): Hiroki Nishiyama, Hisashi Endo, Romain Blanc-Mathieu, Hiroyuki Ogata
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2018.00344

Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis
Cited by: 11
Author(s): Anne Busch, Prasad Thomas, Eric Zuchantke, Holger Brendebach, Kerstin Neubert, Josephine Gruetzke, Sascha Al Dahouk, Martin C. Peters, Helmut Hotzel, Heinrich Neubauer, Herbert Tomaso
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.01045-20

Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity
Cited by: 38
Author(s): Nicholas D. Youngblut, Jacobo de la Cuesta-Zuluaga, Georg H. Reischer, Chris Walzer
Software Mentions: 3
Published: over 3 years ago

10.3390/molecules26082387

Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia
Cited by: 8
Author(s): Nadezhda Chernysheva, Evgeniya Bystritskaya, G. N. Likhatskaya, Olga I. Nedashkovskaya, Marina Isaeva
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2016.01759

Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates
Cited by: 32
Author(s): Taya Forde, Karin Orsel, Ruth N. Zadoks, Roman Biek, Layne G. Adams, Sylvia Checkley, Tracy Davison, Jeroen De Buck, Mathieu Dumond, Brett Elkin, Laura Finnegan, Bryan Macbeth, Cait Nelson, Amanda Niptanatiak, Shane Sather, Helen Schwantje, Frank van der Meer, Susan Kutz
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.01202

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
Cited by: 1,372
Author(s): Jose U. Scher, Andrew Sczesnak, Randy S. Longman, Nicola Segata, Carles Úbeda, Craig M. Bielski, Tim Rostron, Vincenzo Cerundolo, Eric G. Pamer, Steven B. Abramson, Curtis Huttenhower, Dan R. Littman
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.37182

A selective gut bacterial bile salt hydrolase alters host metabolism
Cited by: 156
Author(s): Lina Yao, Sarah C. Seaton, Sula Ndousse-Fetter, Arijit A. Adhikari, Nicholas DiBenedetto, Amir I. Mina, Alexander S. Banks, Lynn Bry, A. Sloan Devlin
Software Mentions: 3
Published: about 6 years ago

10.1186/s40168-021-01117-7

Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Cited by: 23
Author(s): Wisnu Adi Wicaksono, Tomislav Cernava, Christian Berg, Gabriele Berg
Software Mentions: 3
Published: about 3 years ago

10.1186/s40168-020-00846-5

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse
Cited by: 43
Author(s): Marcel van de Wouw, Aaron M. Walsh, Fiona Crispie, Lucas van Leuven, Joshua M. Lyte, Marcus Boehme, Gerard Clarke, Timothy G. Dinan, Paul D. Cotter
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-021-02482-0

The influence of the gut microbiome on BCG-induced trained immunity
Cited by: 15
Author(s): Martin Stražar, Vera P. Mourits, Valerie A C M Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A. B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea, Ramnik J. Xavier
Software Mentions: 3
Published: almost 3 years ago

10.1186/s12859-020-03831-9

Tissue-associated microbial detection in cancer using human sequencing data
Cited by: 6
Author(s): Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez, Youping Deng
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2019.00053

Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa
Cited by: 29
Author(s): Utkarsh Sood, Princy Hira, Roshan Kumar, Abhay Bajaj, D. L. N. Rao, Rup Lal, Mallikarjun Shakarad
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2018.02254

To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies
Cited by: 44
Author(s): Diego Santos-García, Ksenia Juravel, Shiri Freilich, Einat Zchori-Fein, Amparo Latorre, Andrés Moya, Shai Morin, Francisco J. Silva
Software Mentions: 3
Published: almost 6 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.00038-17

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
Cited by: 23
Author(s): Valerie Hubalek, Moritz Buck, BoonFei Tan, Julia M. Foght, Annelie Wendeberg, David Berry, Stefan Bertilsson, Alexander Eiler
Software Mentions: 3
Published: almost 7 years ago

10.3390/microorganisms9030657

Bacterial Dimethylsulfoniopropionate Biosynthesis in the East China Sea
Cited by: 9
Author(s): Ji Liu, Yunhui Zhang, Jingli Liu, Haohui Zhong, Beth T. Williams, Yanfen Zheng, Andrew R. J. Curson, Chuang Sun, Hao Sun, Delei Song, Brett Wagner Mackenzie, Ana Bermejo Martínez, Jonathan D. Todd, Xiaohua Zhang
Software Mentions: 3
Published: over 3 years ago

10.1128/mSystems.00187-18

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract
Cited by: 302
Author(s): Isabel F. Escapa, Tsute Chen, Yanmei Huang, Prasad Gajare, Floyd E. Dewhirst, Katherine P. Lemon
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.28842

Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators
Cited by: 59
Author(s): Jutta Nesper, Isabelle Hug, Setsu Kato, Chee-Seng Hee, Judith Habazettl, Pablo Manfredi, Stephan Grzesiek, Tilman Schirmer, Thierry Emonet, Urs Jenal
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13059-019-1923-9

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
Cited by: 52
Author(s): Serena Manara, Francesco Asnicar, Francesco Beghini, Davide Bazzani, Fabio Cumbo, Moreno Zolfo, Eleonora Nigro, Nicolai Karcher, Paolo Manghi, Marisa Isabell Metzger, Edoardo Pasolli, Nicola Segata
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-017-17640-3

Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment
Cited by: 18
Author(s): Qifan Zeng, Xiangli Tian, Luxin Wang
Software Mentions: 2
Published: almost 7 years ago

10.1128/AEM.00139-16

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone
Cited by: 8
Author(s): Kevin C. Lee, Matthew B. Stott, Peter F. Dunfield, Curtis Huttenhower, Ian R. McDonald, Xochitl C. Morgan
Software Mentions: 2
Published: over 8 years ago

10.1186/s12862-014-0207-y

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam
Cited by: 16
Author(s): Juanjuan Chai, Guruprasad Kora, Tae-Hyuk Ahn, Doreene R. Hyatt, Chongle Pan
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-015-1542-0

Using the taxon-specific genes for the taxonomic classification of bacterial genomes
Cited by: 16
Author(s): Ankit Gupta, Vineet K. Sharma
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-019-5751-9

Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family
Cited by: 7
Author(s): Yinzhao Wang, Giorgio Casaburi, Wei Lin, Ying Liu, Fengping Wang, Yongxin Pan
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-016-2643-0

Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution
Cited by: 36
Author(s): Taya Forde, Roman Biek, Ruth N. Zadoks, Matthew L. Workentine, Jeroen De Buck, Susan Kutz, Tanja Opriessnig, Hannah Trewby, Frank van der Meer, Karin Orsel
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-016-2380-4

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami
Cited by: 17
Author(s): Satoshi Hiraoka, Asako Machiyama, Minoru Ijichi, Kentaro Inoue, Koichiro Oshima, Masahira Hattori, Susumu Yoshizawa, Kazuhiro Kogure, Wataru Iwasaki
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

10.1186/s40168-019-0780-9

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem
Cited by: 76
Author(s): Xinyu Zhu, Stefano Campanaro, Laura Treu, Rekha Seshadri, Natalia Ivanova, Panagiotis Kougias, Nikos C. Kyrpides, Irini Angelidaki
Software Mentions: 2
Published: over 4 years ago

10.1186/s40168-020-0794-3

Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes
Cited by: 38
Author(s): Lin Ye, Renwei Mei, Wen Tso Liu, Hongqiang Ren, Xu Xiang Zhang
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms7070211

Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment
Cited by: 2
Author(s): Liang Shen, Yongqin Liu, Ninglian Wang, Namita Paudel Adhikari
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0126124

Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species
Cited by: 88
Author(s): Ana Gutiérrez-Preciado, Alfredo G. Torres, Enrique Merino, Hernán Ruy Bonomi, Fernando A. Goldbaum, Víctor Antonio García-Angulo
Software Mentions: 2
Published: over 9 years ago

10.1016/j.chom.2020.05.013

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level
Cited by: 131
Author(s): Douglas J. Kenny, Damian R. Plichta, Dmitry Shungin, Nitzan Koppel, Andrew Brantley Hall, Beverly Fu, Ramachandran S. Vasan, Stanley Y. Shaw, Hera Vlamakis, Emily P. Balskus, Ramnik J. Xavier
Software Mentions: 2
Published: about 4 years ago

10.1016/j.chom.2019.08.018

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
Cited by: 248
Author(s): Adrian Tett, Kun Huang, Francesco Asnicar, Hannah Fehlner-Peach, Edoardo Pasolli, Nicolai Karcher, Federica Armanini, Paolo Manghi, Kevin S. Bonham, Moreno Zolfo, Francesca De Filippis, Cara Magnabosco, Richard Bonneau, John Lusingu, John Amuasi, Karl J. Reinhard, Thomas Rattei, Fredrik Boulund, Lars Engstrand, Albert Zink, María Carmen Collado, Dan R. Littman, Daniel Eibach, Omar Rota‐Stabelli, Curtis Huttenhower, Frank Maixner, Nicola Segata
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.celrep.2016.03.015

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants
Cited by: 136
Author(s): Doyle V. Ward, Matthias Scholz, Moreno Zolfo, Diana H. Taft, Kurt Schibler, Adrian Tett, Nicola Segata, Ardythe L. Morrow
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2020.01500

Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake
Cited by: 8
Author(s): Leyden Fernández, Sari Peura, Alexander Eiler, A. Linz, Katherine D. McMahon, Stefan Bertilsson
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2017.02036

Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems
Cited by: 13
Author(s): Ya Ping Zhang, Masaaki Kitajima, Andrew J. Whittle, Wen Tso Liu
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2018.03067

Antimicrobial Susceptibility and Genomic Structure of Arcobacter skirrowii Isolates
Cited by: 12
Author(s): Ingrid Hänel, Helmut Hotzel, Herbert Tomaso, Anne Busch
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.00636

Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping
Cited by: 6
Author(s): Natalie Witt, Sandro Andreotti, Anne Busch, Kerstin Neubert, Knut Reinert, Herbert Tomaso, David Meierhofer
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.606612

Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes
Cited by: 40
Author(s): Yonghui Zeng, Nupur Nupur, Naicheng Wu, Anne Mette Madsen, Xihan Chen, Alastair T. Gardiner, Michal Koblížek
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2017.01296

In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas
Cited by: 36
Author(s): Phuong Tran, Michael A. Savka, Han Ming Gan
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2017.02131

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs
Cited by: 66
Author(s): Pedro J. Cabello‐Yeves, Rohit Ghai, Maliheh Mehrshad, Antonio Picazo, Antonio Camacho, Francisco Rodrı́guez-Valera
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2020.608832

Genomic Insights of “Candidatus Nitrosocaldaceae” Based on Nine New Metagenome-Assembled Genomes, Including “Candidatus Nitrosothermus” Gen Nov. and Two New Species of “Candidatus Nitrosocaldus”
Cited by: 11
Author(s): Zhen-Hao Luo, Manik Prabhu Narsing Rao, Hao Chen, Zheng-Shuang Hua, Qi Li, Brian P. Hedlund, Zhou-Yan Dong, Bingbing Liu, Shuxian Guo, Wen‐Sheng Shu, Wenjun Li
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2017.00644

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting
Cited by: 42
Author(s): Leandro Nascimento Lemos, Roberta Verciano Pereira, Ronaldo Bento Quaggio, Luciane Martins, Livia Maria Silva Moura, Amanda R da Silva, Luciana Principal Antunes, da Silva, João Carlos Setúbal
Software Mentions: 2
Published: over 7 years ago

10.1128/genomeA.00009-18

Draft Genome Sequences of Novel Pseudomonas , Flavobacterium , and Sediminibacterium Species Strains from a Freshwater Ecosystem
Cited by: 3
Author(s): Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Bruno Adriano, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata
Software Mentions: 2
Published: over 6 years ago

10.1111/1346-8138.15536

Skin microbiota in health and disease: From sequencing to biology
Cited by: 15
Author(s): Thomas H. A. Ederveen, Jos P.H. Smits, Jos Boekhorst, Joost Schalkwijk, Ellen H. van den Bogaard, Patrick L.J.M. Zeeuwen
Software Mentions: 2
Published: about 4 years ago

10.1038/srep42252

The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures
Cited by: 39
Author(s): Ilnam Kang, Suhyun Kim, Md. Rashedul Islam, Jang-Cheon Cho
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-40830-0

Metatranscriptomic evidence for classical and RuBisCO-mediated CO2 reduction to methane facilitated by direct interspecies electron transfer in a methanogenic system
Cited by: 28
Author(s): Peixian Yang, Giin-Yu Amy Tan, Muhammad Aslam, Jeong‐Hwan Kim, Po‐Heng Lee
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.00433-18

A Genome-Wide Screen Identifies Genes in Rhizosphere-Associated Pseudomonas Required to Evade Plant Defenses
Cited by: 69
Author(s): Zhexian Liu, Polina Beskrovnaya, Ryan A. Melnyk, Sarzana S. Hossain, Sophie Khorasani, Lucy O'Sullivan, Christina L. Wiesmann, Jen Bush, Joël D Richard, Cara H. Haney
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00342-19

Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs
Cited by: 7
Author(s): Juan C. Villada, Maria F. Duran, Patrick K. H. Lee
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.00651-19

Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi
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

10.1038/s41396-020-0632-4

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining
Cited by: 153
Author(s): Jie-Liang Liang, Jun Liu, Pu Jia, Tong Yang, Qingwei Zeng, Sheng-Chang Zhang, Bin Liao, Wen‐Sheng Shu, Jintian Li
Software Mentions: 2
Published: over 4 years ago

10.1038/s41396-017-0009-5

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling
Cited by: 82
Author(s): Maliheh Mehrshad, Francisco Rodríguez‐Valera, Mohammad Ali Amoozegar, Purificación López‐García, Rohit Ghai
Software Mentions: 2
Published: almost 7 years ago

10.1099/ijsem.0.003942

Comparative genome sequence analysis of several species in the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov.
Cited by: 7
Author(s): Luciana Albuquerque, Nadine Castelhano, Pedro Raposo, Hugo J.C. Froufe, Igor Tiago, Rita Severino, Inês Roxo, Inês Gregório, Cristina Barroso, Conceição Egas, Milton S. da Costa
Software Mentions: 2
Published: over 4 years ago

10.3389/fcimb.2017.00028

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics
Cited by: 24
Author(s): Tsute Chen, Huma Siddiqui, Ingar Olsen
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2016.00362

Identification and Partial Characterization of a Novel UDP-N-Acetylenolpyruvoylglucosamine Reductase/UDP-N-Acetylmuramate:l-Alanine Ligase Fusion Enzyme from Verrucomicrobium spinosum DSM 4136T
Cited by: 6
Author(s): Kubra F. Naqvi, Delphine Patin, Matthew S. Wheatley, Michael A. Savka, Renwick C. J. Dobson, Han Ming Gan, Hélène Barreteau, Didier Blanot, Dominique Mengin‐Lecreulx, André O. Hudson
Software Mentions: 1
Published: over 8 years ago

10.1038/s41396-019-0448-2

Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’ (JS1) inferred from genomics
Cited by: 56
Author(s): Yifan Liu, Zhen-Zhen Qi, Li-Bin Shou, Jinfeng Liu, Shi‐Zhong Yang, Ji‐Dong Gu, Bo‐Zhong Mu
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.00333

Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates
Cited by: 5
Author(s): Shikha Sharma, Vasvi Chaudhry, Sanjeet Kumar, Prabhu B. Patil
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2018.02945

A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer
Cited by: 13
Author(s): Gaofeng Ni, Domenico Simone, D. De Palma, Elias Broman, Xiaofen Wu, Stephanie Turner, Mark Dopson
Software Mentions: 1
Published: almost 6 years ago

10.3389/fbioe.2018.00184

Enrichment and Genomic Characterization of a N2O-Reducing Chemolithoautotroph From a Deep-Sea Hydrothermal Vent
Cited by: 4
Author(s): Sayaka Mino, N. Yoneyama, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2021.652766

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis
Cited by: 14
Author(s): Liping Wang, Zongze Shao
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2017.01969

Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association
Cited by: 10
Author(s): Hong Chen, Matthew D. Hitchings, José Enrique Mendoza, Virginia Balanza, Paul D. Facey, Paul Dyson, Pablo Bielza, Ricardo Del Sol
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2017.01410

Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes
Cited by: 16
Author(s): Charu Tripathi, Harshita Mishra, Himani Khurana, Vatsala Dwivedi, Komal Kamra, Ram Krishan Negi, Rup Lal
Software Mentions: 1
Published: about 7 years ago

10.1186/s12866-020-01993-3

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community
Cited by: 17
Author(s): Ga Gong, Saisai Zhou, Runbo Luo, Zhuoma Gesang, Suolang Sizhu
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.dib.2021.107364

Draft genome sequence data of methanotrophic Methylovulum psychrotolerans strain S1L and Methylomonas paludis strain S2AM isolated from hypoxic water column layers of boreal lakes
Cited by: 4
Author(s): Antti J. Rissanen, Rahul Mangayil, Mette M. Svenning, Ramita Khanongnuch
Software Mentions: 1
Published: almost 3 years ago

10.1371/journal.pbio.2004920

Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly
Cited by: 11
Author(s): Tu Anh Nguyen, Jamie Greig, Asif Khan, Cara Goh, Gregory Jedd
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2017.02149

Entomopathogenicity to Two Hemipteran Insects Is Common but Variable across Epiphytic Pseudomonas syringae Strains
Cited by: 12
Author(s): Melanie R. Smee, David A. Baltrus, Tory A. Hendry
Software Mentions: 1
Published: over 6 years ago

10.1128/genomeA.01040-16

Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria )
Cited by: 5
Author(s): Brian Klein, Katherine P. Lemon, Lina L. Faller, Guillaume Jospin, Jonathan A. Eisen, David A. Coil
Software Mentions: 1
Published: almost 8 years ago

10.1128/genomeA.01652-16

Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility
Cited by: 2
Author(s): Brian Klein, Katherine P. Lemon, Prasad Gajare, Guillaume Jospin, Jonathan A. Eisen, David A. Coil
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.00394-17

Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi
Cited by: 6
Author(s): Mats Töpel, Matthew I. M. Pinder, Ola Johansson, Olga Kourtchenko, Anna Godhe, Adrian K. Clarke
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.01294-17

Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater
Cited by: 6
Author(s): Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Bruno Adriano, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41396-017-0001-0

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
Cited by: 62
Author(s): Sarahi L. Garcia, Sarah Stevens, Benjamin C. Crary, Manuel Martínez‐García, Ramunas Stepanauskas, Tanja Woyke, Susannah G. Tringe, Siv G. E. Andersson, Stefan Bertilsson, Rex R. Malmstrom, Katherine D. McMahon
Software Mentions: 1
Published: almost 7 years ago

10.1128/genomeA.01558-17

Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain-Forming Diatom Skeletonema marinoi
Cited by: 5
Author(s): Mats Töpel, Matthew I. M. Pinder, Ola Johansson, Olga Kourtchenko, Anna Godhe, Adrian K. Clarke
Software Mentions: 1
Published: over 6 years ago

10.3390/microorganisms9040781

European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen
Cited by: 8
Author(s): Jérémy Cigna, Angélique Laurent, Małgorzata Waleron, Krzysztof Waleron, Pauline Dewaegeneire, Jan van der Wolf, Didier Andrivon, Denis Faure, Valérie Hélias
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: PhyloPhlAn

Papers Mentioning PhyloPhlAn 144