pypi: barrnap | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1008866

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli
Cited by: 119
Author(s): Marie Touchon, Perrin Amandine, Jorge Moura de Sousa, Belinda Vangchhia, Samantha Burn, Claire O’Brien, Erick Denamur, David M. Gordon, Eduardo P. C. Rocha
Software Mentions: 16
Published: over 4 years ago

10.1093/femsec/fiab127

Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost
Cited by: 1
Author(s): Gilda Varliero, Muhammad Rafiq, Swati Singh, Annabel Summerfield, Fotis Sgouridis, Donald A. Cowan, Gary Barker
Software Mentions: 10
Published: about 3 years ago

10.1128/mSystems.00474-21

Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics
Cited by: 12
Author(s): Elizabeth A. McDaniel, Francisco Moya-Flores, Natalie K. Beach, Pamela Y. Camejo, Ben O. Oyserman, Matthew Kizaric, Eng Hoe Khor, Daniel R. Noguera, Katherine D. McMahon
Software Mentions: 9
Published: about 3 years ago

10.1128/mSystems.00264-19

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex
Cited by: 46
Author(s): Stijn Wittouck, Sander Wuyts, Conor J. Meehan, Vera van Noort, Sarah Lebeer
Software Mentions: 7
Published: about 5 years ago

10.1098/rstb.2019.0086

Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes
Cited by: 22
Author(s): David M. Needham, Camille Poirier, Elisabeth Hehenberger, Valeria Jiménez, Jarred Swalwell, Alyson E. Santoro, Alexandra Z. Worden
Software Mentions: 7
Published: about 5 years ago

10.1093/g3journal/jkab255

Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce’s disease
Cited by: 8
Author(s): Cassandra L. Ettinger, Frank J. Byrne, Matthew A. Collin, Derreck Carter-House, Linda L. Walling, Peter W. Atkinson, Rick A Redak, Jason E. Stajich
Software Mentions: 7
Published: over 3 years ago

10.12688/f1000research.28608.2

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Cited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2019.00904

Advances and Challenges in Metatranscriptomic Analysis
Cited by: 217
Author(s): Migun Shakya, Chien‐Chi Lo, Patrick Chain
Software Mentions: 6
Published: about 5 years ago

10.1186/s40168-020-00836-7

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer
Cited by: 46
Author(s): Ohana Y.A. Costa, Mattias de Hollander, Agata Pijl, Binbin Liu, Eiko E. Kuramae
Software Mentions: 6
Published: over 4 years ago

10.1093/g3journal/jkab177

New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species
Cited by: 8
Author(s): Lauren J. Frazee, Joanna L. Rifkin, Dinusha C. Maheepala, Alannie‐Grace Grant, Stephen I. Wright, Susan Kalisz, Amy Litt, Rachel B. Spigler
Software Mentions: 6
Published: over 3 years ago

10.1016/j.xcrm.2020.100077

Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study
Cited by: 108
Author(s): Cristina Alcon-Giner, Matthew J. Dalby, Shabhonam Caim, Jennifer Ketskemety, Alexander Shaw, Kathleen Sim, Melissa A. Lawson, Raymond Kiu, Charlotte Leclaire, Lisa Chalklen, Magdalena Kujawska, Suparna Mitra, Fahmina Fardus‐Reid, Gusztav Belteki, Katherine McColl, Jonathan R. Swann, J. Simon Kroll, Paul Clarke, Lindsay J. Hall
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-021-04154-z

Tamock: simulation of habitat-specific benchmark data in metagenomics
Cited by: 0
Author(s): Samuel M. Gerner, Alexandra B. Graf, Thomas Rattei
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.711359

Circulating Levels of the Short-Chain Fatty Acid Acetate Mediate the Effect of the Gut Microbiome on Visceral Fat
Cited by: 67
Author(s): Ana Nogal, Panayiotis Louca, Mengjie Zhang, Philippa M Wells, Claire J. Steves, Tim D. Spector, Mario Falchi, Ana M. Valdes, Cristina Menni
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2016.01221

Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales
Cited by: 23
Author(s): John Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2021.660779

Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia
Cited by: 4
Author(s): Mario Moreno-Pino, Juan A. Ugalde, Jorge Hernández Valdés, Susana Rodríguez-Marconi, Génesis Parada-Pozo, Nicole Trefault
Software Mentions: 5
Published: over 3 years ago

10.1038/s41396-020-0600-z

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity
Cited by: 61
Author(s): Oleksandr M. Maistrenko, Daniel Mende, Mechthild Lϋetge, Falk Hildebrand, Thomas Schmidt, Simone S. Li, João F. Matias Rodrigues, Christian von Mering, Luís Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.01869

Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance
Cited by: 20
Author(s): Erika Corretto, Livio Antonielli, Angela Sessitsch, Christoph Höfer, Markus Puschenreiter, Siegrid Widhalm, Karivaradharajan Swarnalakshmi, Günter Brader
Software Mentions: 4
Published: over 4 years ago

10.1186/s40168-019-0722-6

Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease
Cited by: 28
Author(s): Samuel S. Minot, Amy Willis
Software Mentions: 4
Published: over 5 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

10.1128/mBio.02863-20

Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis
Cited by: 10
Author(s): Marija Dmitrijeva, Christian Kahlert, Rounak Feigelman, Rebekka Kleiner, Oliver Nolte, Werner C. Albrich, Florent Baty, Christian von Mering
Software Mentions: 4
Published: over 3 years ago

10.1128/AEM.00134-18

Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria
Cited by: 54
Author(s): Sander Wuyts, Wannes Van Beeck, Eline Oerlemans, Stijn Wittouck, Ingmar Claes, Ilke De Boeck, Stefan Weckx, Bart Lievens, Luc De Vuyst, Sarah Lebeer
Software Mentions: 3
Published: over 6 years ago

10.1007/s00253-021-11133-0

Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains
Cited by: 5
Author(s): Małgorzata Ryngajłło, Tomasz Boruta, Marcin Bizukojć
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41684-021-00831-x

Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system
Cited by: 7
Author(s): Mónica J.B. Amorim, Yannick Gansemans, Susana I. L. Gomes, Filip Van Nieuwerburgh, Janeck J. Scott-Fordsmand
Software Mentions: 3
Published: about 3 years ago

10.1038/s42003-021-02510-6

Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach
Cited by: 9
Author(s): Yu-Hsiang Chen, Pei‐Wen Chiang, D. Yu. Rogozin, Andrey G. Degermendzhy, Hsiu‐Hui Chiu, Sen‐Lin Tang
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.686998

Comparative Genomics Reveals Potential Mechanisms of Plant Beneficial Effects of a Novel Bamboo-Endophytic Bacterial Isolate Paraburkholderia sacchari Suichang626
Cited by: 4
Author(s): Kai Wang, Ying Wu, Mengyuan Ye, Yifan Yang, Fred O. Asiegbu, Kirk Overmyer, Shenkui Liu, Fuqiang Cui
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.708782

Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics
Cited by: 14
Author(s): Jose M. Haro‐Moreno, Mario López‐Pérez, Francisco Rodrı́guez-Valera
Software Mentions: 3
Published: about 3 years ago

10.1111/1462-2920.14902

A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone
Cited by: 36
Author(s): Saara Suominen, Nina Dombrowski, Jaap S. Sinninghe Damsté, Laura Villanueva
Software Mentions: 2
Published: almost 5 years ago

10.1007/s00284-017-1349-0

Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications
Cited by: 14
Author(s): Martinus J. A. Daas, Bastienne Vriesendorp, Antonius H. P. van de Weijer, John van der Oost, Richard van Kranenburg
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2018.01520

Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism
Cited by: 30
Author(s): Yuanchan Luo, Yuejuan Cheng, Jincui Yi, Zhijun Zhang, Qian Luo, Daojing Zhang, Yuanguang Li
Software Mentions: 2
Published: over 6 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

10.1128/mBio.02975-19

Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria
Cited by: 32
Author(s): Jimmy H. Saw, Takuro Nunoura, Miho Hirai, Yoshihiro Takaki, Rachel Parsons, Michelle L. Michelsen, Krista Longnecker, Elizabeth B. Kujawinski, Ramunas Stepanauskas, Zachary C. Landry, Craig A. Carlson, Stephen J. Giovannoni
Software Mentions: 2
Published: over 4 years ago

10.1186/s40168-018-0556-7

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake
Cited by: 37
Author(s): Keith Arora‐Williams, Scott W. Olesen, Benjamin P. Scandella, Kyle Delwiche, Sarah J. Spencer, Elise McKenna Myers, Sonali Abraham, Alyssa Sooklal, Sarah P. Preheim
Software Mentions: 2
Published: about 6 years ago

10.1128/mSphere.00333-18

Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95
Cited by: 55
Author(s): Stine Jørgensen, Marc Stegger, Eglė Kudirkienė, Berit Lilje, Louise K. Poulsen, Troels Ronco, Teresa Pires dos Santos, Kristoffer Kiil, Magne Bisgaard, Karl Pedersen, Lisa K. Nolan, Lance B. Price, Rikke Heidemann Olsen, Paal Skytt Andersen, Henrik Christensen
Software Mentions: 2
Published: over 5 years ago

10.1128/MRA.01703-18

Complete Genome Sequence of Shewanella sp. Strain TH2012, Isolated from Shrimp in a Cultivation Pond Exhibiting Early Mortality Syndrome
Cited by: 8
Author(s): Piyanuch Wechprasit, Muthita Panphloi, Siripong Thitamadee, Kallaya Sritunyalucksana, Anuphap Prachumwat
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00415-20

Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean
Cited by: 42
Author(s): Frank O. Aylward, Alyson E. Santoro
Software Mentions: 2
Published: over 4 years ago

10.3390/md16050140

Genome-Wide Comparison Reveals a Probiotic Strain Lactococcus Lactis WFLU12 Isolated from the Gastrointestinal Tract of Olive Flounder (Paralichthys Olivaceus) Harboring Genes Supporting Probiotic Action
Cited by: 14
Author(s): Thanh Luan Nguyen, Do-Hyung Kim
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2021.661798

Global Expansion of Linezolid-Resistant Coagulase-Negative Staphylococci
Cited by: 8
Author(s): Vladimir Gostev, Semen A. Leyn, Alexander Kruglov, Daria Likholetova, Olga Kalinogorskaya, Marina Baykina, Н. В. Дмитриева, Z. V. Grigorievskaya, Tatiana V. Priputnevich, L A Lyubasovskaya, Alexey B. Gordeev, С В Сидоренко
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2020.01549

Genomic Analysis and Antimicrobial Resistance of Aliarcobacter cryaerophilus Strains From German Water Poultry
Cited by: 8
Author(s): Eva Müller, Helmut Hotzel, Christine Ahlers, Ingrid Hänel, Herbert Tomaso, Mostafa Y. Abdel-Glil
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.7775

Whole genome sequencing of a novel, dichloromethane-fermentingPeptococcaceaefrom an enrichment culture
Cited by: 11
Author(s): Sophie I. Holland, Richard Edwards, Haluk Ertan, Yie Kuan Wong, Tonia Russell, Nandan P. Deshpande, Michael Manefield, Matthew Lee
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms7040107

Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake
Cited by: 3
Author(s): Alvaro S. Villalobos, Jutta Wiese, Johannes F. Imhoff, Cristina Dorador, Alexander Keller, Ute Hentschel
Software Mentions: 1
Published: over 5 years ago

10.1186/s13073-021-00950-7

Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes
Cited by: 37
Author(s): Chan Yeong Kim, Muyoung Lee, Sunmo Yang, Kyungnam Kim, Dongeun Yong, Hye Ryun Kim, Insuk Lee
Software Mentions: 1
Published: about 3 years ago

10.1080/19490976.2020.1829449

Lactobacillus lactis CKDB001 ameliorate progression of nonalcoholic fatty liver disease through of gut microbiome: addendum
Cited by: 8
Author(s): Na Young Lee, Hyun Chae Joung, Byoung Kook Kim, Byung Yong Kim, Tae Sik Park, Ki Tae Suk
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-019-45886-6

Whole genome sequencing revealed new molecular characteristics in multidrug resistant staphylococci recovered from high frequency touched surfaces in London
Cited by: 22
Author(s): Rory Cave, Raju Misra, Jiazhen Chen, Shiyong Wang, Hermine V. Mkrtchyan
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-66792-2

Novel keratinolytic enzymes, discovered from a talented and efficient bacterial keratin degrader
Cited by: 14
Author(s): Yuhong Huang, Mateusz Łężyk, Florian-Aleksander Herbst, Peter Kamp Busk, Lene Lange
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-86196-0

Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water
Cited by: 5
Author(s): William S. Marsh, Brenden W. Heise, Mark J. Krzmarzick, Robert W. Murdoch, Babu Z. Fathepure
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-98588-3

A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure
Cited by: 7
Author(s): Maria Dalgaard Mikkelsen, Cao Thi Thuy Hang, Thomas Roret, Nanna Rhein‐Knudsen, Jesper Holck, Van Thi Thanh Tran, Thuan Thi Nguyen, Van Thi Thanh Tran, Mateusz Łężyk, Jan Muschiol, Thinh Duc Pham, Mirjam Czjzek, Anne S. Meyer
Software Mentions: 1
Published: about 3 years ago

10.3389/fmicb.2021.621161

Taxonomic and Enzymatic Characterization of Flocculibacter collagenilyticus gen. nov., sp. nov., a Novel Gammaproteobacterium With High Collagenase Production
Cited by: 10
Author(s): Jian Li, Junhui Cheng, Zhao-Jie Teng, Zhuo Sun, Xiaoyan He, Peng Wang, Mei Shi, Xiao‐Yan Song, Xiu-Lan Chen, Yuzhong Zhang, Xiaoli Tian, Xiying Zhang
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.02170

Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces
Cited by: 35
Author(s): Marc G. Chevrette, Camila Carlos‐Shanley, Katherine Louie, Benjamin P. Bowen, Trent Northen, Cameron R. Currie
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2021.576696

Comparative Genomics Analysis Demonstrated a Link Between Staphylococci Isolated From Different Sources: A Possible Public Health Risk
Cited by: 2
Author(s): Rory Cave, Raju Misra, Jiazhen Chen, Shiyong Wang, Hermine V. Mkrtchyan
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.725755

Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1
Cited by: 13
Author(s): Nan Xu, Caian Qiu, Qiyuan Yang, Yunzeng Zhang, Mingqi Wang, Chao Ye, Minliang Guo
Software Mentions: 1
Published: about 3 years ago

10.1186/s12879-019-3821-x

Identifying the mechanism underlying treatment failure for Salmonella Paratyphi A infection using next-generation sequencing – a case report
Cited by: 3
Author(s): Hye-Ran Park, Dong-Min Kim, Na-Ra Yun, Choon-Mee Kim
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.01937-20

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor
Cited by: 21
Author(s): Aurèle Vuillemin, Sergio Vargas, Ömer K. Coskun, R. A. Pockalny, Richard W Murray, David C. Smith, Steven Dhondt, William D. Orsi
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2018.03349

SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline
Cited by: 175
Author(s): Javier Tamames, Fernando Puente-Sánchez
Software Mentions: 1
Published: almost 6 years ago

10.3390/jof7040289

Genomic Analysis and Assessment of Melanin Synthesis in Amorphotheca resinae KUC3009
Cited by: 4
Author(s): Jeong Joo Oh, Young Jun Kim, Jee Young Kim, Sun Lul Kwon, Changsu Lee, Myeong Eun Lee, Jung Ho Kim, Gyu Hyeok Kim
Software Mentions: 1
Published: over 3 years ago

10.1099/ijsem.0.004609

Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller
Cited by: 21
Author(s): Boas C L van der Putten, Sébastien Matamoros, Daniel R. Mende, Edwin R. Scholl, Constance Schultsz
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pntd.0007934

Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017
Cited by: 17
Author(s): Yaovi Mahuton Gildas Hounmanou, Pimlapas Leekitcharoenphon, Eglé Kudirkiene, Robinson H. Mdegela, René S. Hendriksen, John Elmerdahl Olsen, Anders Dalsgaard
Software Mentions: 1
Published: almost 5 years ago

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Papers Mentioning barrnap 56