bioconductor: ggtree | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.579802

A Biological Inventory of Prophages in A. baumannii Genomes Reveal Distinct Distributions in Classes, Length, and Genomic Positions
Cited by: 32
Author(s): Belinda Loh, Jiayuan Chen, Prasanth Manohar, Yunsong Yu, Xiaoting Hua, Sebastian Leptihn
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12985-021-01590-4

Temporal phylogeny and molecular characterization of echovirus 30 associated with aseptic meningitis outbreaks in China
Cited by: 6
Author(s): Xiaoling Tian, Zhaoxia Han, Yulong He, Qiang Sun, Wen-Rui Wang, Wenbo Xu, Hongying Li, Yong Zhang
Software Mentions: 2
Published: over 3 years ago

10.1093/ve/vez004

Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017–18
Cited by: 57
Author(s): Marjolein J Poen, Divya Venkatesh, Theo M. Bestebroer, Oanh Vuong, Rachel D Scheuer, Bas B. Oude Munnink, Dennis de Meulder, Mathilde Richard, Thijs Kuiken, Marion Koopmans, Leon Kelder, Yong Joo Kim, Youn‐Jeong Lee, Mieke Steensels, Bénédicte Lambrecht, Ádám Dán, Anne Pohlmann, Martin Beer, Vladimir Savić, Ian H. Brown, Ron A. M. Fouchier, Nicola S. Lewis
Software Mentions: 2
Published: almost 6 years ago

10.1093/ve/veaa102

Genomic epidemiology of a densely sampled COVID-19 outbreak in China
Cited by: 16
Author(s): Lily Geidelberg, Olivia Boyd, David A. Jorgensen, Igor Siveroni, Fabrícia F. Nascimento, Robert A. Johnson, Manon Ragonnet‐Cronin, Han Fu, Haowei Wang, Xiaoyue Xi, Wei Chen, Liu Dehui, Yingying Chen, Mengmeng Tian, Wenfeng Tan, Junjie Zai, Wanying Sun, Jiandong Li, Junhua Li, Erik Volz, Xingguang Li, Qing Nie
Software Mentions: 2
Published: almost 4 years ago

10.3390/v12060605

Regional Transmission and Reassortment of 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) Viruses in Bulgarian Poultry 2017/18
Cited by: 8
Author(s): Divya Venkatesh, Adam Brouwer, Gabriela V. Goujgoulova, Richard J. Ellis, James Seekings, Ian H. Brown, Nicola S. Lewis
Software Mentions: 2
Published: over 4 years ago

10.3390/v12090995

The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales
Cited by: 6
Author(s): Zhaoxia Han, Jingwei Xiao, Yang Song, Ming Hong, Guolong Dai, Huanhuan Lu, Man Zhang, Yueling Liang, Dongmei Yan, Shuangli Zhu, Wenbo Xu, Yong Zhang
Software Mentions: 2
Published: about 4 years ago

10.3390/v12111218

Metagenomic Approach with the NetoVIR Enrichment Protocol Reveals Virus Diversity within Ethiopian Honey Bees (Apis mellifera simensis)
Cited by: 15
Author(s): Haftom Gebremedhn, Ward Deboutte, Karel Schoonvaere, Peter Demaeght, Lina De Smet, Amssalu Bezabeh, Jelle Matthijnssens, Dirk C. de Graaf
Software Mentions: 2
Published: about 4 years ago

10.3390/v13061087

Replication Kinetics of B.1.351 and B.1.1.7 SARS-CoV-2 Variants of Concern Including Assessment of a B.1.1.7 Mutant Carrying a Defective ORF7a Gene
Cited by: 31
Author(s): Alyssa T. Pyke, Neelima Nair, Andrew van den Hurk, Peter Burtonclay, Son Hoang Nguyen, Jean Barcelon, Carol Kistler, Sanmarié Schlebusch, Jamie McMahon, Frederick Moore
Software Mentions: 2
Published: over 3 years ago

10.3390/v13071359

Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations
Cited by: 5
Author(s): Jean‐Paul Pirnay, Philippe Selhorst, Samuel L. Hong, Christel Cochez, Barney Potter, Piet Maes, Mauro Petrillo, Gytis Dudas, Vincent Claes, Yolien Van der Beken, Gilbert Verbeken, Julie Degueldre, Simon Dellicour, Lize Cuypers, France T’Sas, Guy Van den Eede, Bruno Verhasselt, Wouter Weuts, Cedric Smets, Jan Mertens, Philippe Geeraerts, Kevin K. Ariën, Emmanuel André, Pierre Neirinckx, Patrick Soentjens, Guy Baele
Software Mentions: 2
Published: over 3 years ago

10.3390/ijerph16193777

Anti-Biofouling Performance of an Immobilized Indigenous Quorum Quenching Bacterium Bacillus cereus HG10 and Its Influence on the Microbial Community in a Bioreactor
Cited by: 6
Author(s): Fangfang Xu, Chang Zhao, Chuang Hak Lee, Wenzhao Wang, Qiyong Xu
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.9591

Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis
Cited by: 24
Author(s): Xiang Li, Zewen Li, Yan He, Pan Li, Hongwei Zhou, Nianyi Zeng
Software Mentions: 2
Published: over 4 years ago

10.1186/s40168-020-0790-7

A pipeline for targeted metagenomics of environmental bacteria
Cited by: 33
Author(s): Anissa Grieb, Robert M. Bowers, Monike Oggerin, Danielle Goudeau, Janey Lee, Rex R. Malmstrom, Tanja Woyke, Bernhard M. Fuchs
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pbio.3000987

Daptomycin treatment impacts resistance in off-target populations of vancomycin-resistant Enterococcus faecium
Cited by: 10
Author(s): Clare L. Kinnear, Elsa Hansen, Valerie J. Morley, Kevin C. Tracy, Meghan Forstchen, Andrew F. Read, Robert J. Woods
Software Mentions: 2
Published: almost 4 years ago

10.1186/s40168-020-00902-0

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments
Cited by: 30
Author(s): Da-Shuai Mu, Shuo Wang, Qi-Yun Liang, Zhao-Zhong Du, Renmao Tian, Yang Ouyang, Xinpeng Wang, Aifen Zhou, Ya Gong, Guanjun Chen, Joy D. Van Nostrand, Yunfeng Yang, Jizhong Zhou, Zong‐Jun Du
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1007189

Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration
Cited by: 19
Author(s): Jing Yang, Nicola F. Müller, Remco R. Bouckaert, Bing Xu, Alexei J. Drummond
Software Mentions: 2
Published: over 5 years ago

10.1093/infdis/jiy747

High-Resolution Evolutionary Analysis of Within-Host Hepatitis C Virus Infection
Cited by: 9
Author(s): Jayna Raghwani, Chieh-Hsi Wu, Cynthia K. Y. Ho, Menno D. de Jong, Richard Molenkamp, Janke Schinkel, Oliver G. Pybus, Katrina A. Lythgoe
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0208852

Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem
Cited by: 47
Author(s): Eneas Aguirre‐von‐Wobeser, Jorge Rocha, Lori R. Shapiro, Mayra de la Torre
Software Mentions: 2
Published: almost 6 years ago

10.1099/mgen.0.000440

Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim
Cited by: 19
Author(s): Miquel Sánchez-Osuna, Pilar Cortés, Montserrat Llagostera, Jordi Barbé, Ivan Erill
Software Mentions: 2
Published: about 4 years ago

10.1099/mgen.0.000295

Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids
Cited by: 26
Author(s): Cameron J. Reid, Jessica McKinnon, Steven P. Djordjevic
Software Mentions: 2
Published: about 5 years ago

10.1099/mgen.0.000477

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history
Cited by: 68
Author(s): Mireia Coscollá, Sébastien Gagneux, Fabrizio Menardo, Chloé Loiseau, Paula Ruiz-Rodríguez, Sònia Borrell, Isaac Darko Otchere, Adwoa Asante-Poku, Prince Asare, Leonor Sánchez-Busó, Florian Gehre, C. N’Dira Sanoussi, Martín Antonio, Dissou Affolabi, Janet Fyfe, Patrick Beckert, Stefan Niemann, Abraham Alabi, Martin P. Grobusch, Robin Kobbe, Julian Parkhill, Christian Beisel, Lukas Fenner, Erik C. Böttger, Conor J. Meehan, Simon R. Harris, Bouke C. de Jong, Dorothy Yeboah-Manu, Daniela Brites
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0220981

Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding
Cited by: 18
Author(s): Hiroto Yamashita, Hideyuki Katai, Lina Kawaguchi, Atsushi J. Nagano, Yoriyuki Nakamura, Akio Morita, Takashi Ikka
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0235434

Characterizing the impact of an exotic soybean line on elite cultivar development
Cited by: 1
Author(s): Benjamin B. Stewart-Brown, Justin N. Vaughn, Thomas E. Carter, Zenglu Li
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0208735

Genome wide characterization of enterotoxigenic Escherichia coli serogroup O6 isolates from multiple outbreaks and sporadic infections from 1975-2016
Cited by: 8
Author(s): Vaishnavi Pattabiraman, Lee S. Katz, Jessica C. Chen, Andre McCullough, Eija Trees
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.chom.2018.04.017

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico
Cited by: 80
Author(s): Julien Thézé, Tony Li, Louis du Plessis, Jérôme Bouquet, Moritz U. G. Kraemer, Sneha Somasekar, Guixia Yu, Mariateresa de Cesare, Ángel Balmaseda, Guillermina Kuan, Eva Harris, Chieh-Hsi Wu, Azim Ansari, Rory Bowden, Nuno Rodrigues Faria, Shigeo Yagi, Sharon Messenger, Trevor Brooks, Mars Stone, Evan M. Bloch, Michael P. Busch, José Esteban Muñoz-Medina, César González-Bonilla, Steven M. Wolinsky, Susana López, David Bonsall, Charles Y. Chiu, Oliver G. Pybus
Software Mentions: 2
Published: over 6 years ago

10.1016/j.celrep.2021.109292

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Cited by: 343
Author(s): Bo Meng, Steven A Kemp, Guido Papa, Rawlings P. Datir, Isabella Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed A. Mohamed, Giulia Gallo, Nazia Thakur, Dami Collier, Petra Mlčochová, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. L. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra Gupta
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.62816

Structural basis for effector transmembrane domain recognition by type VI secretion system chaperones
Cited by: 24
Author(s): Shehryar Ahmad, Kara K. Tsang, Kartik Sachar, Dennis Quentin, Tahmid M Tashin, Nathan P Bullen, Stefan Raunser, Andrew G McArthur, Gerd Prehna, John C. Whitney
Software Mentions: 2
Published: almost 4 years ago

10.1038/s42003-020-01208-5

Diversity in the intrinsic apoptosis pathway of nematodes
Cited by: 3
Author(s): Neil D. Young, Tiffany J Harris, Marco Evangelista, Sharon Tran, Merridee A. Wouters, Tatiana P. Soares da Costa, Nadia J. Kershaw, Robin B. Gasser, Brian J. Smith, Erinna F. Lee, W. Douglas Fairlie
Software Mentions: 2
Published: about 4 years ago

10.3390/membranes10090211

The Best-Practice Organism for Single-Species Studies of Antimicrobial Efficacy against Biofilms Is Pseudomonas aeruginosa
Cited by: 3
Author(s): Anna Curtin, Matthew C. Thibodeau, Heather L. Buckley
Software Mentions: 2
Published: about 4 years ago

10.1002/ece3.5639

Environmental variables associated with Nothophaeocryptopus gaeumannii population structure and Swiss needle cast severity in Western Oregon and Washington
Cited by: 5
Author(s): Patrick Bennett, Jeffrey K. Stone
Software Mentions: 2
Published: about 5 years ago

10.1002/ece3.7673

Great chemistry between us: The link between plant chemical defenses and butterfly evolution
Cited by: 4
Author(s): Corné F H van der Linden, Michiel F. WallisDeVries, Sabrina Simon
Software Mentions: 2
Published: over 3 years ago

10.1038/s41426-018-0178-y

The molecular basis of antigenic variation among A(H9N2) avian influenza viruses
Cited by: 22
Author(s): Thomas P. Peacock, William T. Harvey, Jean-Rémy Sadeyen, Richard Reeve, Munir Iqbal
Software Mentions: 2
Published: about 6 years ago

10.3390/biology10080738

Egg Incubation Mechanics of Giant Birds
Cited by: 3
Author(s): An Yen, Hsiao-Jou Wu, Pin-Yi Chen, Hon‐Tsen Yu, Jia-Yang Juang
Software Mentions: 2
Published: over 3 years ago

10.1186/s13040-021-00270-x

Comparison of 16S and whole genome dog microbiomes using machine learning
Cited by: 3
Author(s): Scott A. Lewis, Andrea K. Nash, Qinghong Li, Tae-Hyuk Ahn
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.699140

Unlimited Cooperativity of Betatectivirus SSB, a Novel DNA Binding Protein Related to an Atypical Group of SSBs From Protein-Primed Replicating Bacterial Viruses
Cited by: 2
Author(s): Ana Lechuga, Darius Kazlauskas, Margarita Salas, Modesto Redrejo-Rodríguez
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.01137

A Large-Scale Outbreak of Echovirus 30 in Gansu Province of China in 2015 and Its Phylodynamic Characterization
Cited by: 12
Author(s): Jianhua Chen, Zhaoxia Han, Haizhuo Wu, Wenbo Xu, Deshan Yu, Yong Zhang
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2017.01345

Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar
Cited by: 51
Author(s): Chad R. Laing, Matthew D. Whiteside, Victor P. J. Gannon
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2021.687625

Evaluation of Virulence Determinants Using Whole-Genome Sequencing and Phenotypic Biofilm Analysis of Outbreak-Linked Staphylococcus aureus Isolates
Cited by: 10
Author(s): Jennifer Hait, Guojie Cao, George Kastanis, Liu Yin, James B. Pettengill, Sandra M. Tallent
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.588410

Acinetobacter Plasmids: Diversity and Development of Classification Strategies
Cited by: 11
Author(s): S. Z. Mindlin, Alexey V. Beletsky, Andrey L. Rakitin, Andrey V. Mardanov, Mayya Petrova
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2021.722838

Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka
Cited by: 8
Author(s): Chandima Jeewandara, Deshni Jayathilaka, D.M.S.H.K. Ranasinghe, Sharon Hsu, Dinuka Ariyaratne, Tibutius Jayadas, Deshan Madhusanka Panambara Arachchige, Benjamin B. Lindsey, Laksiri Gomes, Matthew Parker, Ananda Wijewickrama, Malika Karunaratne, Graham Ogg, Thushan I. de Silva, Gathsaurie Neelika Malavige
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2021.725414

Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers
Cited by: 19
Author(s): Fiona Valerie Franklin-Alming, Håkon Kaspersen, Marit Andrea Klokkhammer Hetland, Ragna-Johanne Bakksjø, Live L. Nesse, Thongpan Leangapichart, Iren Høyland Löhr, Amar A. Telke, Marianne Sunde
Software Mentions: 2
Published: about 3 years ago

10.3389/fonc.2020.584778

PA28γ, an Accomplice to Malignant Cancer
Cited by: 4
Author(s): Kexin Lei, Hetian Bai, Silu Sun, Chuan Xin, Jing Li, Qianming Chen
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2021.625416

Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica
Cited by: 7
Author(s): Nataliya V. Melnikova, Elena N. Pushkova, Ekaterina M. Dvorianinova, А. Д. Бениаминов, Roman O. Novakovskiy, Liubov V. Povkhova, Nadezhda L. Bolsheva, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, George S. Krasnov, Alexey A. Dmitriev
Software Mentions: 2
Published: about 3 years ago

10.1186/s12866-020-02071-4

Interaction study of Pasteurella multocida with culturable aerobic bacteria isolated from porcine respiratory tracts using coculture in conditioned media
Cited by: 2
Author(s): Nonzee Hanchanachai, Pramote Chumnanpuen, Teerasak E-kobon
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpubh.2019.00066

Clustering of Vibrio parahaemolyticus Isolates Using MLST and Whole-Genome Phylogenetics and Protein Motif Fingerprinting
Cited by: 6
Author(s): Kelsey J. Jesser, Willy Valdivia-Granda, Jessica Jones, Rachel T. Noble
Software Mentions: 2
Published: over 5 years ago

10.3389/fpubh.2019.00208

Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases
Cited by: 13
Author(s): Kristof Theys, Philippe Lemey, Anne-Mieke Vandamme, Guy Baele
Software Mentions: 2
Published: over 5 years ago

10.3389/fvets.2020.00027

Campylobacter jejuni Strain Dynamics in a Raccoon (Procyon lotor) Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover
Cited by: 6
Author(s): Steven K. Mutschall, Benjamin M. Hetman, Kristin J. Bondo, Victor P. J. Gannon, Claire M. Jardine, Eduardo Taboada
Software Mentions: 2
Published: almost 5 years ago

10.3389/fvets.2021.666767

Whole-Genome Comparative Analysis Reveals Association Between Salmonella Genomic Variation and Egg Production Systems
Cited by: 2
Author(s): Hamid Reza Sodagari, Shafi Sahibzada, Ian D. Robertson, Ihab Habib, Penghao Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fvets.2020.542724

Field-Adapted Full Genome Sequencing of Peste-Des-Petits-Ruminants Virus Using Nanopore Sequencing
Cited by: 5
Author(s): Emeli Torsson, Tebogo Kgotlele, Gerald Misinzo, Jonas Johansson Wensman, Mikael Berg, Oskar Karlsson Lindsjö
Software Mentions: 2
Published: about 4 years ago

10.1186/s12879-021-06142-3

A case report of endocarditis and spondylitis caused by Brucella melitensis biovar 3
Cited by: 5
Author(s): Huan Zhang, Sheng‐Xue Xie, Yue-Li Wang, Xiaoli Zhao, Jihai Yi, Zhen Wang, Qi Liu, Xiaoyu Deng, Bingjie Li, Buyun Cui, Yuanzhi Wang, Chuangfu Chen
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-020-6598-9

Insight into unique somitogenesis of yak (Bos grunniens) with one additional thoracic vertebra
Cited by: 6
Author(s): Yu Wang, Haoyang Cai, Xiaolin Luo, Yi Ai, Mingfeng Jiang, Yan Wen
Software Mentions: 2
Published: over 4 years ago

10.3390/genes10090687

The Genomics of Streptococcus Pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13
Cited by: 15
Author(s): Carmen Sheppard, Natalie Groves, Nicholas Andrews, David Litt, Norman K. Fry, Jo Southern, Elizabeth Miller
Software Mentions: 2
Published: about 5 years ago

10.3390/genes10110860

Transcriptional Structure of Petunia Clock in Leaves and Petals
Cited by: 6
Author(s): Marta I. Terry, Marta Carrera-Alesina, Julia Weiß, Marcos Egea‐Cortines
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-021-08004-3

The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome
Cited by: 16
Author(s): Zhongyu Mou, Yang Yi, Andrew Brantley Hall, Xiaofang Jiang
Software Mentions: 2
Published: about 3 years ago

10.1186/s12864-020-06905-3

Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe
Cited by: 10
Author(s): Tanvi Taparia, M.C. Krijger, Edward Haynes, J. G. Elphinstone, R. Noble, Jan van der Wolf
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-06791-9

Influence of genetic diversity of seventeen Beauveria bassiana isolates from different hosts on virulence by comparative genomics
Cited by: 12
Author(s): Zhengkun Zhang, Yuan Lü, Wenjing Xu, Li Sui, Qian Du, Yangzhou Wang, Yu Zhao, Qiyun Li
Software Mentions: 2
Published: over 4 years ago

10.1186/s13073-018-0574-x

Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia
Cited by: 42
Author(s): Stefano Giulieri, Sarah L. Baines, Romain Guérillot, Torsten Seemann, Anders Gonçalves da Silva, Mark B. Schultz, Ruth C. Massey, Natasha E Holmes, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 2
Published: over 6 years ago

10.1007/s11357-021-00443-w

Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort—correlation with disease characteristics
Cited by: 4
Author(s): Jonas Schmidt, Sandro Berghaus, Frithjof Blessing, Folker Wenzel, Holger Herbeck, J. Blessing, Peter Schierack, Stefan Rödiger, Dirk Roggenbuck
Software Mentions: 2
Published: about 3 years ago

10.7554/eLife.46402

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity
Cited by: 33
Author(s): Matthew Hall, Matthew T. G. Holden, Pramot Srisomang, Weera Mahavanakul, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Kay Fountain, Julian Parkhill, Emma K. Nickerson, Sharon J. Peacock, Christophe Fraser
Software Mentions: 2
Published: about 5 years ago

10.1111/irv.12782

Adenovirus infection in children hospitalized with pneumonia in Guangzhou, China
Cited by: 19
Author(s): Lirong Zou, Yi Liu, YU Jian-xiang, Yinchao Song, Lijun Liang, Qianfang Guo, Xue Zhuang, Yunqiang Zhang, Min Kang, Jie Wu
Software Mentions: 2
Published: over 4 years ago

10.1128/JB.00639-19

Nisin J, a Novel Natural Nisin Variant, Is Produced by Staphylococcus capitis Sourced from the Human Skin Microbiota
Cited by: 44
Author(s): Julie N O'Sullivan, Paula M. O’Connor, Mary C. Rea, Órla O’Sullivan, Calum J. Walsh, Brian Healy, Harsh Mathur, Des Field, Colin Hill, R. Paul Ross
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.56236

HA stabilization promotes replication and transmission of swine H1N1 gamma influenza viruses in ferrets
Cited by: 15
Author(s): Meng Hu, Guohua Yang, Jennifer DeBeauchamp, Jeri Carol Crumpton, Hyunsuh Kim, Lei Li, Xiu‐Feng Wan, Lisa Kercher, Andrew S. Bowman, Robert G. Webster, Richard J. Webby, Charles J. Russell
Software Mentions: 2
Published: over 4 years ago

10.1098/rspb.2018.2929

Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction
Cited by: 9
Author(s): Elena A. Ritschard, Robert R. Fitak, Oleg Simakov, Sönke Johnsen
Software Mentions: 2
Published: over 5 years ago

10.1098/rspb.2021.0069

Ecological opportunity and the rise and fall of crocodylomorph evolutionary innovation
Cited by: 28
Author(s): Thomas L. Stubbs, Stephanie E. Pierce, Armin Elsler, Philip S. L. Anderson, Emily J. Rayfield, Michael J. Benton
Software Mentions: 2
Published: over 3 years ago

10.5334/pb.1033

The Use of the Term Virtual Reality in Post-Stroke Rehabilitation: A Scoping Review and Commentary
Cited by: 21
Author(s): Hanne Huygelier, Emily Mattheus, Vero Vanden Abeele, Raymond van Ee, Céline R. Gillebert
Software Mentions: 2
Published: over 3 years ago

10.1126/sciadv.abe3868

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
Cited by: 32
Author(s): Liam P. Shaw, Kevin Chau, James Kavanagh, Manal AbuOun, Emma Stubberfield, Hyun S. Gweon, Leanne Barker, Gillian Rodger, Michael J. Bowes, Alasdair T. M. Hubbard, Hayleah Pickford, Jeremy Swann, Daniel Gilson, Richard P. Smith, Sarah Hoosdally, Robert Sebra, Howard Brett, Tim Peto, Mark Bailey, Derrick W. Crook, Daniel S. Read, Muna F. Anjum, A Sarah Walker, Nicole Stoesser
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-018-22660-8

Microbial metagenome of urinary tract infection
Cited by: 72
Author(s): Ahmed Moustafa, Weizhong Li, Harinder Singh, Kelvin Moncera, Manolito Torralba, Yonghao Yu, Oriol Manuel, William H. Biggs, J. Craig Venter, Karen E. Nelson, Rembert Pieper, Amalio Telenti
Software Mentions: 2
Published: over 6 years ago

10.1099/acmi.0.000143

Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
Cited by: 51
Author(s): Nicholas Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes, Leighton Pritchard
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-40168-7

Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains
Cited by: 25
Author(s): Alba Rey‐Iglesia, Ana García-Vázquez, Eve C. Treadaway, Johannes van der Plicht, Gennady Baryshnikov, Paul Szpak, Hervé Bocherens, Г. Г. Боескоров, Eline D. Lorenzen
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-4461-z

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses
Cited by: 7
Author(s): Xinrui Zhou, Jie Zheng, Fransiskus Xaverius Ivan, Rui Yin, Shoba Ranganathan, Vincent T. K. Chow, Chee-Keong Kwoh
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-78157-w

A horizontally acquired expansin gene increases virulence of the emerging plant pathogen Erwinia tracheiphila
Cited by: 6
Author(s): Jorge Rocha, Lori R. Shapiro, Roberto Kolter
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-82337-7

Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives
Cited by: 12
Author(s): Shingo Nishiki, Ken-ichi Lee, Mizue Kanai, Shuichi Nakayama, Makoto Ohnishi
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-86683-4

Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
Cited by: 6
Author(s): D. K. Arora, Krishnamoorthy Srikanth, Jongin Lee, Daehwan Lee, Nayoung Park, Suyeon Wy, Hyeonji Kim, Jong-Eun Park, Han-Ha Chai, Dajeong Lim, In-Cheol Cho, Jaebum Kim, Woncheoul Park
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-89650-1

Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
Cited by: 2
Author(s): Yue Wang, Paul M. Harrison
Software Mentions: 2
Published: over 3 years ago

10.1128/AEM.02769-19

Dissemination of Quinolone-Resistant Escherichia coli in the Norwegian Broiler and Pig Production Chains and Possible Persistence in the Broiler Production Environment
Cited by: 13
Author(s): Håkon Kaspersen, Camilla Sekse, Eve Zeyl Fiskebeck, Jannice Schau Slettemeås, Roger Simm, Madelaine Norström, Anne Margrete Urdahl, Karin Lagesen
Software Mentions: 2
Published: over 4 years ago

10.1128/AEM.02765-19

Emergence of Fluoroquinolone-Resistant Campylobacter jejuni and Campylobacter coli among Australian Chickens in the Absence of Fluoroquinolone Use
Cited by: 35
Author(s): Sam Abraham, Shafi Sahibzada, Kylie Hewson, Tanya Laird, Rebecca Abraham, Anthony Pavic, Alec Truswell, Terence Lee, Mark O’Dea, David Jordan
Software Mentions: 2
Published: over 4 years ago

10.1007/s00439-020-02132-8

Decoding a highly mixed Kazakh genome
Cited by: 4
Author(s): Madina Seidualy, Asta Blažytė, Sungwon Jeon, Youngjune Bhak, Yeonsu Jeon, Jung-Eun Kim, Anders Eriksson, Dan Bolser, Changhan Yoon, Andrea Manica, Semin Lee, Jong Bhak
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41396-021-00926-w

Genomic network analysis of environmental and livestock F-type plasmid populations
Cited by: 19
Author(s): William Matlock, Kevin Chau, Manal AbuOun, Emma Stubberfield, Leanne Barker, James Kavanagh, Hayleah Pickford, Daniel Gilson, Richard P. Smith, Hyun S. Gweon, Sarah Hoosdally, Jeremy Swann, Robert Sebra, Mark Bailey, Peto Tea., Derrick W. Crook, Muna F. Anjum, Daniel S. Read, A Sarah Walker, Nicole Stoesser, Liam Shaw, Howard Brett, Mike Bowes, Nicola De Maio, Nicholas Duggett, Duncan Wilson, Alasdair T. M. Hubbard, Hannah Jones, Anna E. Sheppard, Neil Woodford
Software Mentions: 2
Published: over 3 years ago

10.1093/molbev/msz053

Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
Cited by: 46
Author(s): Alvin X. Han, Edyth Parker, Frits Scholer, Sebastian Maurer‐Stroh, Colin A. Russell
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9061142

Molecular Analysis of East African Lumpy Skin Disease Viruses Reveals a Mixed Isolate with Features of Both Vaccine and Field Isolates
Cited by: 10
Author(s): Tesfaye Rufael, Melaku Sombo, Jacqueline Kasiiti Lichoti, Tajelser Adam, Yang Liu, Yazeed Abd Elraouf, Reingard Grabherr, Tirumala Bharani Kumar Settypalli, Francisco J. Berguido, Angelika Loitsch, Mesfin Sahle, Giovanni Cattoli, Adama Diallo, Charles Euloge Lamien
Software Mentions: 2
Published: over 3 years ago

10.3390/jof7070515

Cultivable Yeast Microbiota from the Marine Fish Species Genypterus chilensis and Seriolella violacea
Cited by: 10
Author(s): Benjamín Valderrama, José J. Ruiz, María Soledad Gutiérrez, Krisler Alveal, Mario Caruffo, Marcia Oliva, Héctor Flores, Alfonso Silva, Mauricio Toro, Angélica Reyes-Jara, Paola Navarrete
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8091376

Developmental, Dietary, and Geographical Impacts on Gut Microbiota of Red Swamp Crayfish (Procambarus clarkii)
Cited by: 36
Author(s): Zhenting Zhang, Jiali Liu, Xuexia Jin, Chao Liu, Chenwei Fan, Li Guo, Yunxiang Liang, Jinshui Zheng, Nan Peng
Software Mentions: 2
Published: about 4 years ago

10.3390/ani10091542

Analysis of Whole Genome Resequencing Datasets from a Worldwide Sample of Sheep Breeds to Identify Potential Causal Mutations Influencing Milk Composition Traits
Cited by: 5
Author(s): H. Marina, Beatriz Gutiérrez-Gil, Cristina Esteban-Blanco, R. Pelayo, Juan José Arranz
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-021-07805-w

Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response
Cited by: 2
Author(s): Shannon Woodhouse, Zhesi He, Hugh Woolfenden, Burkhard Steuernagel, Wilfried Haerty, Ian Bancroft, Judith A. Irwin, Richard J. Morris, Rachel Wells
Software Mentions: 1
Published: over 3 years ago

10.3390/pathogens9060480

Are Animals a Neglected Transmission Route of SARS-CoV-2?
Cited by: 28
Author(s): Marta Hernández, David Abad, José María Eiros, David Rodrı́guez-Lázaro
Software Mentions: 1
Published: over 4 years ago

10.1186/s12870-021-03170-8

Genome-wide identification and function analysis of HMAD gene family in cotton (Gossypium spp.)
Cited by: 2
Author(s): Qinqin Wang, Xuke Lu, Xiugui Chen, Lingxia Zhao, Mingge Han, Shuai Wang, Yuexin Zhang, Yapeng Fan, Wuwei Ye
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.669618

Novel Klebsiella pneumoniae K23-Specific Bacteriophages From Different Families: Similarity of Depolymerases and Their Therapeutic Potential
Cited by: 20
Author(s): Roman Gorodnichev, Nikolay V. Volozhantsev, Valentina M. Krasilnikova, И. Н. Бодоев, Maria Kornienko, Nikita Kuptsov, Anastasiya V. Popova, Г. И. Макаренко, Alexander I. Manolov, Pavel V. Slukin, Dmitry Bespiatykh, Vladimir V. Verevkin, Egor A. Denisenko, Eugene E. Kulikov, Vladimir A. Veselovsky, Maja V. Malakhova, I. A. Dyatlov, Elena Ilina, Egor Shitikov
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.704253

A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution
Cited by: 12
Author(s): Jing Qin Wu, Long Song, Yi Ding, Chongmei Dong, Mafruha T. Hasan, Robert Park
Software Mentions: 1
Published: over 3 years ago

10.1186/s12977-021-00556-2

Neutralization diversity of HIV-1 Indian subtype C envelopes obtained from cross sectional and followed up individuals against broadly neutralizing monoclonal antibodies having distinct gp120 specificities
Cited by: 1
Author(s): Ranajoy Mullick, Jyoti Sutar, Nitin Hingankar, Suprit Deshpande, Madhuri Thakar, Seema Sahay, Rajesh P. Ringe, Sampurna Mukhopadhyay, Ajit Patil, Shubhangi Bichare, Kailapuri G. Murugavel, Aylur K. Srikrishnan, Rajat Goyal, Devin Sok, Jayanta Bhattacharya
Software Mentions: 1
Published: over 3 years ago

10.1186/s13071-020-04097-z

Chagas vectors Panstrongylus chinai (Del Ponte, 1929) and Panstrongylus howardi (Neiva, 1911): chromatic forms or true species?
Cited by: 7
Author(s): Anita G. Villacís, Jean‐Pierre Dujardin, Francisco Panzera, César A. Yumiseva, Sebastián Pita, Soledad Santillán-Guayasamín, Marco I Orozco, Katherine D. Mosquera, Mario J. Grijalva
Software Mentions: 1
Published: over 4 years ago

10.1186/s12917-019-2226-9

Full genomic characterization of a porcine rotavirus strain detected in an asymptomatic piglet in Accra, Ghana
Cited by: 3
Author(s): Sam Stubbs, Osbourne Quaye, Maame Ekua Acquah, Samuel Mawuli Adadey, Iain Kean, Shefali Gupta, Barbara Blacklaws
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2019.02214

Memory CD4 + T-Cells Expressing HLA-DR Contribute to HIV Persistence During Prolonged Antiretroviral Therapy
Cited by: 36
Author(s): Eun-Ok Lee, Peter Bacchetti, J. Milush, Wei Shao, Eli Boritz, Daniel C. Douek, Rémi Fromentin, Teri Liegler, Rebecca Hoh, Steven G. Deeks, Frederick Hecht, Nicolas Chomont, Sarah Palmer
Software Mentions: 1
Published: about 5 years ago

10.1186/s13071-018-3006-2

The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts
Cited by: 15
Author(s): Elena Claudia Coipan, Gilian L. A. van Duijvendijk, Tim R. Hofmeester, Katsuhisa Takumi, Hein Sprong
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2020.01795

Coronaviruses in the Sea
Cited by: 29
Author(s): Gideon Mordecai, Ian Hewson
Software Mentions: 1
Published: over 4 years ago

10.1093/ve/vex034

Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution
Cited by: 9
Author(s): Jayna Raghwani, Robin N Thompson, Katia Koelle
Software Mentions: 1
Published: over 7 years ago

10.3390/v12070706

Recombination Analysis of Non-Poliovirus Members of the Enterovirus C Species: Restriction of Recombination Events to Members of the Same 3DPol Cluster
Cited by: 7
Author(s): Lieke Brouwer, Kimberley Benschop, Dung Nguyen, Everlyn Kamau, Dasja Pajkrt, Peter Simmonds, Katja C. Wolthers
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-019-43420-2

Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries
Cited by: 11
Author(s): Pedro Araújo, Alexandre Carvalho, Marta Pingarilho, Ana Abecasis, Nuno S. Osório
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.00938

Comparative Genome Analyses of Wild Type- and Quinolone Resistant Escherichia coli Indicate Dissemination of QREC in the Norwegian Broiler Breeding Pyramid
Cited by: 5
Author(s): Håkon Kaspersen, Eve Zeyl Fiskebeck, Camilla Sekse, Jannice Schau Slettemeås, Anne Margrete Urdahl, Madelaine Norström, Karin Lagesen, Roger Simm
Software Mentions: 1
Published: over 4 years ago

10.1186/s12917-021-02751-x

Molecular characterization of lumpy skin disease virus (LSDV) emerged in Bangladesh reveals unique genetic features compared to contemporary field strains
Cited by: 34
Author(s): Shukes Chandra Badhy, Mohammad Golam Azam Chowdhury, Tirumala Bharani Kumar Settypalli, Giovanni Cattoli, Charles Euloge Lamien, Mohamed Fakir, Shamima Akter, M. G. Osmani, Faisol Talukdar, Noorjahan Begum, Izhar Ahmed Khan, Bazlur Rashid, Mohammad Sadekuzzaman
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-019-50456-x

ICEKp2: description of an integrative and conjugative element in Klebsiella pneumoniae, co-occurring and interacting with ICEKp1
Cited by: 10
Author(s): Robeena Farzand, Kumar Rajakumar, Roxana Zamudio, Marco R. Oggioni, Michael R. Barer, Helen M. O’Hare
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2020.00775

Population Biology and Epidemiological Studies of Acinetobacter baumannii in the Era of Whole Genome Sequencing: Is the Oxford Scheme Still Appropriate?
Cited by: 9
Author(s): Xiaoting Hua, Linyue Zhang, Jintao He, Sebastian Leptihn, Yunsong Yu
Software Mentions: 1
Published: over 4 years ago

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Papers Mentioning ggtree 474