cran: genoPlotR | Projects | Ecosyste.ms: Papers

10.1186/s13073-021-00893-z

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers
Cited by: 18
Author(s): Alaric W. D’Souza, Manish Boolchandani, Sanket Patel, Gianluca Galazzo, Jarne M. van Hattem, Maris S Arcilla, Damian C. Melles∗, Menno D. de Jong, Constance Schultsz, Gautam Dantas, John Penders
Software Mentions: 13
Published: over 3 years ago

10.1128/mBio.01105-19

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
Cited by: 42
Author(s): Eike J. Steinig, Sebastián Duchêne, D. Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah A. Williamson, Angela Kearns, Richard V. Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V. N. O’Sullivan, Geoffrey W. Coombs, Andreas Petersen, Gráinne I. Brennan, Anna C. Shore, David C. Coleman, Annalisa Pantosti, Hermı́nia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J. Peacock, Derek S. Sarovich, Simon R. Harris, Julian Parkhill, Ruth C. Massey, Matthew T. G. Holden, Stephen D. Bentley, Steven Y. C. Tong
Software Mentions: 10
Published: almost 5 years ago

10.1093/molbev/msaa057

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
Cited by: 30
Author(s): Elizabeth J. Duncan, Megan Leask, Peter K. Dearden
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0205266

The evolution of UDP-glycosyl/glucuronosyltransferase 1E (UGT1E) genes in bird lineages is linked to feeding habits but UGT2 genes is not
Cited by: 4
Author(s): Yusuke Kawai, Yoshinori Ikenaka, Mayumi Ishizuka, Akira Kubota
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-014-0459-2

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi
Cited by: 106
Author(s): Xiaofang Jiang, Ashley Peery, Andrew Brantley Hall, Atashi Sharma, Xiaoguang Chen, Robert M. Waterhouse, Aleksey Komissarov, Michelle M. Riehle, Yogesh S. Shouche, Maria V. Sharakhova, Daniel Lawson, Nazzy Pakpour, Peter Arensburger, Victoria L M Davidson, Karin Eiglmeier, Scott J. Emrich, Phillip George, Ryan Kennedy, Shrinivasrao P. Mane, G. Maslen, Chioma Oringanje, Yumin Qi, Robert E. Settlage, Marta Tojo, José M. C. Tubío, Maria Unger, Bo Wang, Kenneth D. Vernick, José M. C. Ribeiro, Anthony A. James, Kristin Michel, Michael A. Riehle, Shirley Luckhart, Igor V. Sharakhov, Zhijian Tu
Software Mentions: 6
Published: about 10 years ago

10.1093/gbe/evu133

Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular Life
Cited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: over 10 years ago

10.1128/mSystems.00195-17

Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome
Cited by: 8
Author(s): Kathy N. Lam, Eric C. Martens, Trevor C. Charles
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.6448

The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont
Cited by: 10
Author(s): Stefanos Siozios, Jack Pilgrim, Alistair C. Darby, Matthew Baylis, Gregory D. D. Hurst
Software Mentions: 5
Published: over 5 years ago

10.1099/mgen.0.000050

Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward
Cited by: 44
Author(s): Mark B. Schultz, Duy Pham Thanh, Nhu Tran Do Hoan, Ryan R. Wick, Danielle J. Ingle, Jane Hawkey, D.J. Edwards, Johanna J. Kenyon, Nguyen Phu Huong Lan, James I. Campbell, Guy Thwaites, Nguyen Thi Khanh Nhu, Ruth M. Hall, Alexandre Fournier‐Level, Stephen Baker, Kathryn E. Holt
Software Mentions: 5
Published: over 8 years ago

10.3390/ijms22157928

A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups
Cited by: 3
Author(s): Daniel J. Goodall, Katie H. Jameson, Michelle Hawkins, Christian J. Rudolph
Software Mentions: 5
Published: over 3 years ago

10.3389/fpubh.2020.00451

Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumannii
Cited by: 6
Author(s): Chandler C. Roe, Charles H. D. Williamson, Adam J. Vazquez, Kristen Kyger, Michael Valentine, Jolene R. Bowers, P.D. Phillips, Veronica Harrison, Elizabeth M. Driebe, David M. Engelthaler, Jason W. Sahl
Software Mentions: 4
Published: about 4 years ago

10.3390/ijms21041543

A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (Prunus persica) Chilling Requirement
Cited by: 9
Author(s): Li-Dek Chou, Shih-Jie Huang, Chen Yu Hsieh, Ming-Te Lu, Chia-Wei Song, Fu-Chiun Hsu
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-40883-1

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
Cited by: 13
Author(s): Jonna Teikari, Rafael Vicentini Popin, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000456

Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone
Cited by: 14
Author(s): Eleonora Tassinari, Matt Bawn, Gaëtan Thilliez, Oliver J. Charity, Luke Acton, Mark Kirkwood, Liljana Petrovska, Timothy J. Dallman, Catherine M. Burgess, Neil Hall, Geraldine Duffy, Robert A. Kingsley
Software Mentions: 4
Published: about 4 years ago

10.1128/JCM.00190-19

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus
Cited by: 30
Author(s): Stephen C. Watts, Kathryn E. Holt
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.49002

Dynamic turnover of centromeres drives karyotype evolution in Drosophila
Cited by: 57
Author(s): Ryan Bracewell, Kamalakar Chatla, Matthew J. Nalley, Doris Bachtrog
Software Mentions: 4
Published: about 5 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

10.1093/gbe/evaa216

Portiera Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their Endosymbionts
Cited by: 12
Author(s): Diego Santos-García, Natividad Mestre-Rincon, David Ouvrard, Einat Zchori-Fein, Shai Morin
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0223680

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Cited by: 51
Author(s): Xiaofang Jiang, Andrew Brantley Hall, Ramnik J. Xavier, Eric J. Alm
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-018-4663-4

Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome
Cited by: 17
Author(s): Gleb N. Artemov, Semen M. Bondarenko, Anastasia N. Naumenko, V. N. Stegniy, Igor V. Sharakhov
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2015.00265

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions
Cited by: 46
Author(s): Cheryl-Emiliane T. Chow, Danielle M. Winget, Richard Allen White, Steven J. Hallam, Curtis A. Suttle
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2015.00955

Direct sequencing of human gut virome fractions obtained by flow cytometry
Cited by: 18
Author(s): Mária Džunková, Giuseppe D’Auria, Andrés Moya
Software Mentions: 3
Published: about 9 years ago

10.3389/fmicb.2020.01699

Genomic and Phenotypic Analysis of an ESBL-Producing E. coli ST1159 Clonal Lineage From Wild Birds in Mongolia
Cited by: 7
Author(s): Peter Schierack, Stefan E. Heiden, Muhammad Moman Khan, Lena Nikolaus, Rafał Kolenda, Michael Stubbe, Davaa Lkhagvasuren, Stefan Rödiger, Sebastian Guenther, Katharina Schaufler
Software Mentions: 3
Published: over 4 years ago

10.1186/s13073-020-00814-6

A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition
Cited by: 69
Author(s): Stefan E. Heiden, Nils–Olaf Hübner, Jürgen A. Bohnert, Claus–Dieter Heidecke, Axel Krämer, Veronika Balau, Wolfgang Gierer, Stephan Schaefer, Tim Eckmanns, Sören Gatermann, Elias Eger, Sebastian Guenther, Karsten Becker, Katharina Schaufler
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2017.00218

The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species
Cited by: 27
Author(s): Daniel Wüthrich, Hélène Berthoud, Daniel Wechsler, Elisabeth Eugster, Stefan Irmler, Rémy Bruggmann
Software Mentions: 3
Published: almost 8 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

10.1371/journal.pone.0065793

Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing
Cited by: 41
Author(s): Alma Brolund, Oscar Franzén, Öjar Melefors, Karin Tegmark-Wisell, Linus Sandegren
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0202279

Organellar genome analysis reveals endosymbiotic gene transfers in tomato
Cited by: 13
Author(s): Hyoung Tae Kim, Je Min Lee
Software Mentions: 3
Published: about 6 years ago

10.1038/srep32590

Snapshots of a shrinking partner: Genome reduction in Serratia symbiotica
Cited by: 61
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 3
Published: about 8 years ago

10.1093/gbe/evw111

Host-Associated Genomic Features of the Novel Uncultured Intracellular PathogenCa.Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts
Cited by: 12
Author(s): Weihong Qi, Lloyd Vaughan, Pantelis Katharios, Ralph Schlapbach, Helena M. B. Seth-Smith
Software Mentions: 3
Published: over 8 years ago

10.1186/s13099-020-00394-1

Comparative genomics of Helicobacter pullorum from different countries
Cited by: 4
Author(s): Guilan Zhou, Hao Liang, Yixin Gu, Changyan Ju, Lihua He, Pengbo Guo, Zhujun Shao, Jianzhong Zhang, Maojun Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1093/gigascience/giab017

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis
Cited by: 10
Author(s): Anton Zamyatin, Pavel Avdeyev, Jiangtao Liang, Atashi Sharma, Chujia Chen, Varvara Lukyanchikova, Nikita Alexeev, Zhijian Tu, Max A. Alekseyev, Igor V. Sharakhov
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.01515-19

Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens
Cited by: 60
Author(s): Megan C. McDonald, Adam P. Taranto, Erin Hill, Benjamin Schwessinger, Zhaohui Liu, S. Simpfendorfer, Andrew Milgate, Peter S. Solomon
Software Mentions: 3
Published: about 5 years ago

10.1099/mgen.0.000208

Characterization of capsule genes in non-pathogenic Neisseria species
Cited by: 14
Author(s): Marianne E. A. Clemence, Martin Maiden, Odile B. Harrison
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2148-12-65

A genome-wide study of recombination rate variation in Bartonella henselae
Cited by: 18
Author(s): Lionel Guy, Björn Nystedt, Yu Sun, Kristina Näslund, Eva Berglund, Siv G. E. Andersson
Software Mentions: 2
Published: over 12 years ago

10.3390/life8020017

Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions
Cited by: 2
Author(s): David J. Martínez-Cano, Gil Bor, Andrés Moya, Luis Delaye
Software Mentions: 2
Published: over 6 years ago

10.1128/AAC.00209-18

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain
Cited by: 25
Author(s): Stefan Sütterlin, Carlos J. Téllez-Castillo, Leticia Anselem, Huan Yin, James E. Bray, Martin C. J. Maiden
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9071345

Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany
Cited by: 1
Author(s): Stefan E. Heiden, Katharina Sydow, Stephan Schaefer, I. Klempien, Veronika Balau, Péter Bauer, Nils–Olaf Hübner, Katharina Schaufler
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8111740

In Silico Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria Pseudomonas fluorescens F113 and Other Pseudomonads
Cited by: 17
Author(s): Esther Blanco-Romero, Daniel Garrido‐Sanz, Rafael Rivilla, Miguel Redondo‐Nieto, Marta Martín
Software Mentions: 2
Published: about 4 years ago

10.1093/molbev/msu227

Massive Expansion of Ubiquitination-Related Gene Families within the Chlamydiae
Cited by: 33
Author(s): Daryl Domman, Astrid Collingro, Ilias Lagkouvardos, Lena Gehre, Thomas Weinmaier, Thomas Rattei, Agathe Subtil, Matthias Horn
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1003393

A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella
Cited by: 82
Author(s): Lionel Guy, Björn Nystedt, Christina Toft, Katarzyna Zaremba-Niedźwiedzka, Eva Berglund, Fredrik Granberg, Kristina Näslund, Ann‐Sofie Eriksson, Siv G. E. Andersson
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0155441

Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication
Cited by: 18
Author(s): Alejandro Oceguera‐Figueroa, Alejandro Manzano-Marı́n, Sebastian Kvist, Andrés Moya, Mark E. Siddall, Amparo Latorre
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0063027

Adaptive Mutations and Replacements of Virulence Traits in the Escherichia coli O104:H4 Outbreak Population
Cited by: 14
Author(s): Lionel Guy, Cecilia Jernberg, Jenny Arvén Norling, Sofie Ivarsson, Ingela Hedenström, Öjar Melefors, Ulrika Liljedahl, Lars Engstrand, Siv G. E. Andersson
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0053440

Microevolution of the Chromosomal Region of Acute Disease Antigen A (adaA) in the Query (Q) Fever Agent Coxiella burnetii
Cited by: 17
Author(s): Dimitrios Frangoulidis, Wolf D. Splettstoesser, Olfert Landt, Jasmin Dehnhardt, Klaus Henning, Angela Hilbert, Tilman Bauer, Markus Antwerpen, Hermann Meyer, Mathias C. Walter, J Knobloch
Software Mentions: 2
Published: almost 12 years ago

10.3389/fcell.2021.633195

DNA Topoisomerase 3α Is Involved in Homologous Recombination Repair and Replication Stress Response in Trypanosoma cruzi
Cited by: 7
Author(s): Héllida Marina Costa-Silva, Bruno Carvalho Resende, Adriana Castilhos Souza Umaki, Willian Andrade Prado, Marcelo Santos da Silva, Stela Virgílio, Andréa Mara Macedo, Sérgio Danilo Junho Pena, Erich Birelli Tahara, Luíz Ricardo Orsini Tosi, Maria Carolina Elias, Luciana O. Andrade, João Luís Reis-Cunha, Glória Regina Franco, Stênio Perdigão Fragoso, Carlos Renato Machado
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.00504

Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems
Cited by: 25
Author(s): Hanna Koch, Heike M. Freese, Richard L. Hahnke, Meinhard Simon, Matthias Wietz
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.02933

Genome Analysis of Haplotype D of Candidatus Liberibacter Solanacearum
Cited by: 9
Author(s): Leron Katsir, Zhepu Ruan, Diego Santos-García, Alon Piasezky, Jiandong Jiang, Noa Sela, Shiri Freilich, Ofir Bahar
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2021.662575

Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda
Cited by: 13
Author(s): Elias Eger, Stefan E. Heiden, Katja Korolew, Claude Bayingana, Jules Ndoli, Augustin Sendegeya, Jean Bosco Gahutu, Mathis S. E. Kurz, Frank P. Mockenhaupt, Julia Müller, Stefan Simm, Katharina Schaufler
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.00381

Nucleotide Second Messenger-Based Signaling in Extreme Acidophiles of the Acidithiobacillus Species Complex: Partition Between the Core and Variable Gene Complements
Cited by: 14
Author(s): Ana Moya-Beltrán, Camila Rojas-Villalobos, Mauricio Díaz, Nicolás Guiliani, Raquel Quatrini, Matías Castro
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.00045

Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes (mpeBA and cpeBA)
Cited by: 45
Author(s): Patricia Sánchez‐Baracaldo, Giorgio Bianchini, Andrea Di Cesare, Cristiana Callieri, Nathan Chrismas
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpls.2015.01126

Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation
Cited by: 67
Author(s): Sophie Cesbron, Martial Briand, Salwa Essakhi, Sophie Gironde, Tristan Boureau, Charles Manceau, Marion Fischer-Le Saux, Marie‐Agnès Jacques
Software Mentions: 2
Published: almost 9 years ago

10.1534/g3.114.015933

Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains
Cited by: 20
Author(s): Stephen L. Pearce, John G. Oakeshott, Gyanendra Pandey
Software Mentions: 2
Published: over 9 years ago

10.3390/genes12091359

Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain
Cited by: 6
Author(s): Esther Camacho, Sandra González-de la Fuente, José Carlos Solana, Alberto Rastrojo, Fernando Carrasco-Ramiro, José Marı́a Requena, Begoña Aguado
Software Mentions: 2
Published: about 3 years ago

10.1186/gb-2013-14-11-r130

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade
Cited by: 73
Author(s): Katarzyna Zaremba-Niedźwiedzka, Jenny Viklund, Weizhou Zhao, Jennifer C. Ast, Alexander Sczyrba, Tanja Woyke, Katherine D. McMahon, Stefan Bertilsson, Ramunas Stepanauskas, Siv G. E. Andersson
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.ppat.1002151

Transformation of Natural Genetic Variation into Haemophilus Influenzae Genomes
Cited by: 69
Author(s): Joshua Chang Mell, Svetlana Shumilina, Ira M. Hall, Rosemary J. Redfield
Software Mentions: 2
Published: over 13 years ago

10.1038/s41598-020-60120-4

Systematic analysis of the Hippo pathway organization and oncogenic alteration in evolution
Cited by: 13
Author(s): Yuxuan Chen, Han Han, Gayoung Seo, Rebecca Vargas, Bing Yang, Kimberly Chuc, Huabin Zhao, Wenqi Wang
Software Mentions: 2
Published: over 4 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/s41396-019-0362-7

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems
Cited by: 25
Author(s): Vera Bischoff, Boyke Bunk, Jan P. Meier‐Kolthoff, Cathrin Spröer, Anja Poehlein, Marco Dogs, Mary Nguyen, Jörn Petersen, Rolf Daniel, Jörg Overmann, Markus Göker, Meinhard Simon, Thorsten Brinkhoff, Cristina Moraru
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2017.01512

Whole Genome Sequencing of Danish Staphylococcus argenteus Reveals a Genetically Diverse Collection with Clear Separation from Staphylococcus aureus
Cited by: 33
Author(s): Thomas Arn Hansen, Mette Damkjær Bartels, Silje Vermedal Høgh, Lone Dons, Michael Pedersen, Thøger Gorm Jensen, Michael Kemp, Marianne Nielsine Skov, Heidi Gumpert, Peder Worning, Henrik Westh
Software Mentions: 1
Published: over 7 years ago

10.3389/fphys.2017.00539

Phylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions
Cited by: 17
Author(s): Xiaomei Wu, Fei-Hua Wu, Qian-Rong Wu, Shu Zhang, Suping Chen, Matthew Sima
Software Mentions: 1
Published: over 7 years ago

10.1128/mSystems.00182-18

Loss of Bacitracin Resistance Due to a Large Genomic Deletion among Bacillus anthracis Strains
Cited by: 7
Author(s): Yoshikazu Furuta, Hayato Harima, Emiko Ito, Fumito Maruyama, Naomi Ohnishi, Ken Osaki, Hirohito Ogawa, David Squarre, Bernard M. Hang’ombe, Hideaki Higashi
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0156104

Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species
Cited by: 37
Author(s): Aquillah M. Kanzi, Brenda D. Wingfield, Emma Theodora Steenkamp, Sanushka Naidoo, Nicolaas Albertus Van der Merwe
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms22179196

Hypervirulent Klebsiella pneumoniae Sequence Type 420 with a Chromosomally Inserted Virulence Plasmid
Cited by: 13
Author(s): Elias Eger, Stefan E. Heiden, Karsten Becker, Andrea Rau, Katharina Geisenhainer, Evgeny A. Idelevich, Katharina Schaufler
Software Mentions: 1
Published: about 3 years ago

10.1186/1471-2156-14-51

Linking the potato genome to the conserved ortholog set (COS) markers
Cited by: 5
Author(s): Hannele Lindqvist‐Kreuze, Kwang-Soo Cho, Leticia Portal, Flor Rodríguez, Reinhard Simon, Lukas A. Mueller, David M. Spooner, Merideth Bonierbale
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13756-020-00828-0

Colonization of a hand washing sink in a veterinary hospital by an Enterobacter hormaechei strain carrying multiple resistances to high importance antimicrobials
Cited by: 12
Author(s): Kanishka Indiwari Kamathewatta, Rhys N. Bushell, Fannana Rafa, Glenn F. Browning, Helen Billman‐Jacobe, Marc S. Marenda
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0035097

The Chlamydia psittaci Genome: A Comparative Analysis of Intracellular Pathogens
Cited by: 84
Author(s): Anja Voigt, Gerhard Schöfl, Hans Peter Saluz
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0047274

Comparative Genomics of Serratia spp.: Two Paths towards Endosymbiotic Life
Cited by: 28
Author(s): Alejandro Manzano-Marı́n, Araceli Lamelas, Andrés Moya, Amparo Latorre
Software Mentions: 1
Published: about 12 years ago

10.1093/gbe/evv108

Distinctive Genome Reduction Rates Revealed by Genomic Analyses of TwoCoxiella-Like Endosymbionts in Ticks
Cited by: 129
Author(s): Yuval Gottlieb, Itai Lalzar, Lisa Klasson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0147492

Origin and Evolution of Rickettsial Plasmids
Cited by: 24
Author(s): Khalid El Karkouri, Pierre Pontarotti, Didier Raoult, Pierre‐Edouard Fournier
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0187104

Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae) and the utility of molecular markers
Cited by: 8
Author(s): Louis Graf, Yae Jin Kim, Ga Youn Cho, Kathy Ann Miller, Hwan Su Yoon
Software Mentions: 1
Published: about 7 years ago

10.1186/s13071-021-04821-3

Comparison of mitochondrial genome and development of specific PCR primers for identifying two scuticociliates, Pseudocohnilembus persalinus and Uronema marinum
Cited by: 2
Author(s): Yuxi Huang, Sen Wang, Yanqi Gao, Jie-Hu Chen, Xiuli Wang, Ruijun Li
Software Mentions: 1
Published: over 3 years ago

10.3390/microorganisms9020348

Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer
Cited by: 4
Author(s): Florian Tagini, Trestan Pillonel, Claire Bertelli, Katia Jaton, Gilbert Greub
Software Mentions: 1
Published: almost 4 years ago

10.3390/microorganisms8050634

Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.
Cited by: 28
Author(s): Zhenxing Xu, Yoko Masuda, Chie Hayakawa, Natsumi Ushijima, Kimiko Kawano, Yutaka Shiratori, Keishi Senoo, Hideomi Itoh
Software Mentions: 1
Published: over 4 years ago

10.1186/s13099-017-0219-4

Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan
Cited by: 5
Author(s): Haruo Suzuki, Masaru Tomita, Pei-Jane Tsai, Wen Chien Ko, Yuan‐Pin Hung, I-Hsiu Huang, Jenn Wei Chen
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms9092001

Preclinical Development of a Bacteriophage Cocktail for Treating Multidrug Resistant Pseudomonas aeruginosa Infections
Cited by: 8
Author(s): Sophie Camens, Liu Sha, Karen Hon, George Bouras, Alkis James Psaltis, Peter‐John Wormald, Sarah Vreugde
Software Mentions: 1
Published: about 3 years ago

10.1186/s40168-019-0737-z

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut
Cited by: 55
Author(s): Yoshihiko Suzuki, Suguru Nishijima, Yoshikazu Furuta, Junichi Yoshimura, Wataru Suda, Koichiro Oshima, Masahira Hattori, Shinichi Morishita
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms21093160

Isolation and Characterization of Two Klebsiella pneumoniae Phages Encoding Divergent Depolymerases
Cited by: 17
Author(s): Pilar Domingo‐Calap, Beatriz Beamud, Lucas Mora-Quilis, Fernando Gónzález-Candelas, Rafael Sanjuán
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00030-20

Complete Genome Sequence of Moraxella osloensis Strain YV1, Isolated from an Australian Wastewater Treatment Plant
Cited by: 2
Author(s): Steven Batinovic, Daniel T. F. Rice, Robert J. Seviour, Steve Petrovski
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-017-18374-y

Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs
Cited by: 42
Author(s): Sandra González-de la Fuente, Ramón Peiró‐Pastor, Alberto Rastrojo, Javier Moreno, Fernando Carrasco-Ramiro, José Marı́a Requena, Begoña Aguado
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12936-017-1888-7

Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae
Cited by: 10
Author(s): Yun Wei, Biao Cheng, Guoding Zhu, Danyu Shen, Jiangtao Liang, Cong Wang, Jing Wang, Jianxia Tang, Jun Cao, Igor V. Sharakhov, Ai Xia
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms21249562

Evolution of MicroRNA Biogenesis Genes in the Sterlet (Acipenser ruthenus) and Other Polyploid Vertebrates
Cited by: 2
Author(s): Mikhail V Fofanov, Dmitry Prokopov, Heiner Kuhl, Manfred Schartl, Vladimir A. Trifonov
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-60308-8

Identification of a molecular marker associated with lignotuber in Eucalyptus ssp
Cited by: 4
Author(s): Tânia Mara Bortoloto, Maria Cecília P. Fuchs-Ferraz, Karine Kettener, Lígia Martins Rubio, E. R. González, Izabel Christina Gava de Souza, Shinitiro Oda, Bruno César Rossini, Celso Luís Marino
Software Mentions: 1
Published: over 4 years ago

10.1186/s13756-021-00941-8

Novel chromosomal insertions of ISEcp1-blaCTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli
Cited by: 18
Author(s): Misheck Shawa, Yoshikazu Furuta, Gillan Mulenga, Maron Mubanga, Evans Mulenga, Tuvshinzaya Zorigt, Christone Kaile, Manyando Simbotwe, Atmika Paudel, Bernard M. Hang’ombe, Hideaki Higashi
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.687985

Comparative Genomics of Closely Related Tetragenococcus halophilus Strains Elucidate the Diversity and Microevolution of CRISPR Elements
Cited by: 3
Author(s): Minenosuke Matsutani, Takura Wakinaka, Jun Watanabe, Masafumi Tokuoka, Akihiro Ohnishi
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.00105-18

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins
Cited by: 404
Author(s): Elizabeth J. Klemm, Sadia Shakoor, Andrew J. Page, Farah Naz Qamar, Kim Judge, Dania Khalid Saeed, Vanessa Wong, Timothy J. Dallman, Satheesh Nair, Stephen Baker, Ghazala Shaheen, Shahida Qureshi, Mohammad Tahir Yousafzai, Muhammad Khalid Saleem, Zahra Hasan, Gordon Dougan, Rumina Hasan
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2021.672448

The Complete Mitochondrial DNA of Trypanosoma cruzi: Maxicircles and Minicircles
Cited by: 11
Author(s): Francisco Callejas-Hernández, Alfonso Herreros-Cabello, Javier Del Moral-Salmoral, Manuel Fresno, Núria Gironés
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.01531

Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis
Cited by: 21
Author(s): Shu-Ting Cho, Hsiang‐Fu Kung, Weijie Huang, Saskia A. Hogenhout, Chih-Horng Kuo
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2229-11-42

Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity
Cited by: 66
Author(s): Agustín Lucas Arce, Jesica Raineri, Matías Capella, Julieta Virginia Cabello, Raquel L. Chan
Software Mentions: 1
Published: over 13 years ago

10.1128/mBio.02039-19

Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki - and Thorarchaeota
Cited by: 16
Author(s): Lokeshwaran Manoharan, Jessica A. Kozlowski, Robert W. Murdoch, Frank E. Löffler, Filipa L. Sousa, Christa Schleper
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2020.546150

Genetic Structure, Function, and Evolution of Capsule Biosynthesis Loci in Vibrio parahaemolyticus
Cited by: 5
Author(s): Shengzhe Bian, Wenhong Zeng, Qiwen Li, Yinghui Li, Nai-Kei Wong, Min Jiang, Le Zuo, Qinghua Hu, Liqiang Li
Software Mentions: 1
Published: almost 4 years ago

10.12688/f1000research.2-63.v1

Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
Cited by: 8
Author(s): Michel Abanto, Ana Carolina Paulo Vicente
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0032231

Primitive Duplicate Hox Clusters in the European Eel's Genome
Cited by: 127
Author(s): Christiaan V. Henkel, Erik Burgerhout, Daniëlle L. de Wijze, Ron P. Dirks, Yuki Minegishi, Hans J. Jansen, Herman P. Spaink, Sylvie Dufour, Finn‐Arne Weltzien, Katsumi Tsukamoto, Guido E.E.J.M. van den Thillart
Software Mentions: 1
Published: over 12 years ago

10.3389/fmicb.2021.636396

High-Level Aminoglycoside Resistance in Human Clinical Klebsiella pneumoniae Complex Isolates and Characteristics of armA-Carrying IncHI5 Plasmids
Cited by: 7
Author(s): Xueya Zhang, Qiaoling Li, Hailong Lin, Wangxiao Zhou, Changrui Qian, Zhewei Sun, Li Lin, Hongmao Liu, Jing Lü, Xiangmin Lin, Kewei Li, Teng Xu, Hailin Zhang, Changchong Li, Qiyu Bao
Software Mentions: 1
Published: over 3 years ago

10.1186/s12866-019-1481-z

Characterization of a bacteriophage with broad host range against strains of Pseudomonas aeruginosa isolated from domestic animals
Cited by: 33
Author(s): Anna Cristhina Carmine de Melo, Amanda da Mata Gomes, Fernando Lucas Melo, Daniel Mendes Pereira Ardisson-Araújo, Águeda Castagna de Vargas, Valessa Lunkes Ely, Elliot Watanabe Kitajima, Bergmann Morais Ribeiro, José Luiz Caldas Wolff
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-286

Plastid and mitochondrion genomic sequences from Arctic Chlorella sp. ArM0029B
Cited by: 27
Author(s): Heisawn Jeong, Jong‐Min Lim, Jihye Park, Young Mi Sim, Han-Gu Choi, Jung-Ho Lee, Won-Joong Jeong
Software Mentions: 1
Published: almost 11 years ago

10.3389/fmicb.2018.00369

Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains
Cited by: 13
Author(s): Marina Sánchez‐Hidalgo, Ignacio González, Christian Díaz-Muñoz, Gabriel García Martínez, Olga Genilloud
Software Mentions: 1
Published: over 6 years ago

Projects: cran: genoPlotR

Papers Mentioning genoPlotR 96