bioconductor: ggtree | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000484

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
Cited by: 14
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ray, Nicholas M. Thomson, Sheikh Jarju, Brenda Kwambana-Adams, Arss Secka, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 4
Published: almost 4 years ago

10.3390/microorganisms9020438

Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir
Cited by: 10
Author(s): Eddie M. Wampande, Peter Waiswa, David J. Allen, Roger Hewson, Simon D. W. Frost, Sam Stubbs
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13073-021-00843-9

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
Cited by: 42
Author(s): Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 4
Published: almost 4 years ago

10.1002/ece3.7784

Spatial patterns in the size of Chinese lizards are driven by multiple factors
Cited by: 4
Author(s): Tao Liang, Zi Zhang, Wanting Dai, Lei Shi, Changhu Lu
Software Mentions: 4
Published: over 3 years ago

10.3390/genes12020138

Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius)
Cited by: 2
Author(s): Corey Kirkland, Marta Farré
Software Mentions: 4
Published: almost 4 years ago

10.1093/molbev/msaa324

Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases
Cited by: 8
Author(s): Elizabeth R. Ballou, Atlanta G. Cook, Eric Wallace
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2021.643731

Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives
Cited by: 11
Author(s): Rowena Hill, Theo Llewellyn, Elizabeth Downes, Joseph Oddy, Catriona MacIntosh, Simon Kallow, Bart Panis, John B. Dickie, Ester Gaya
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.02318-20

Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat
Cited by: 11
Author(s): Michael E. Hibbing, Karen W. Dodson, Vasilios Kalas, Swaine L. Chen, Scott J. Hultgren
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-019-1785-1

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center
Cited by: 21
Author(s): Matthew J. Ellington, Eva Heinz, Alexander M. Wailan, Matthew J. Dorman, Marcus C. de Goffau, Amy K. Cain, Sonal P. Henson, Nicholas Gleadall, Christine J. Boinett, Gordon Dougan, Nicholas M. Brown, Neil Woodford, Julian Parkhill, M. Estée Török, Sharon J. Peacock, Nicholas R. Thomson
Software Mentions: 4
Published: about 5 years ago

10.1093/gbe/evab202

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes
Cited by: 7
Author(s): Kirsten I. Verster, Rebecca L. Tarnopol, Saron M. Akalu, Noah K. Whiteman
Software Mentions: 4
Published: about 3 years ago

10.1002/ece3.6983

Foliar fungal endophyte community structure is independent of phylogenetic relatedness in an Asteraceae common garden
Cited by: 9
Author(s): Briana K. Whitaker, Natalie Christian, Qiang Chai, Keith Clay
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13068-021-01895-0

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
Cited by: 9
Author(s): Madhavi Latha Gandla, Niklas Mähler, Sacha Escamez, Tomas Skotare, Ogonna Obudulu, Linus Möller, Ilka Nacif Abreu, Joakim Bygdell, Magnus Hertzberg, Torgeir R. Hvidsten, Thomas Moritz, Gunnar Wingsle, Johan Trygg, Hannele Tuominen, Leif J. Jönsson
Software Mentions: 4
Published: almost 4 years ago

10.1002/ece3.4457

Habitat or temporal isolation: Unraveling herbivore-parasitoid speciation patterns using double digest RADseq
Cited by: 9
Author(s): Y. Miles Zhang, Amber Bass, Diana Catalina Fernández, Barbara J. Sharanowski
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.ppat.1006358

A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host
Cited by: 22
Author(s): Alison F. Feder, Christopher E. Kline, Patricia Polacino, Mackenzie L. Cottrell, Angela D. M. Kashuba, Brandon F. Keele, Shiu Lok Hu, Dmitri A. Petrov, Pleuni S. Pennings, Zandrea Ambrose
Software Mentions: 4
Published: over 7 years ago

10.1093/gbe/evz158

Geography Shapes the Population Genomics of Salmonella enterica Dublin
Cited by: 19
Author(s): Gavin Fenske, Anil J. Thachil, Patrick L. McDonough, Amy L. Glaser, Joy Scaria
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.00815-18

Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland
Cited by: 48
Author(s): Garrett J. Smith, Jordan C. Angle, Lindsey Solden, Mikayla A. Borton, Timothy H. Morin, Rebecca A. Daly, Michael D. Johnston, Kay C. Stefanik, Richard A. Wolfe, Gil Bohrer, Kelly Wrighton
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-020-07263-w

Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains
Cited by: 22
Author(s): Eva Wagner, Andreas Zaiser, Rebekka Leitner, Narciso M. Quijada, Nadja Pracser, Ariane Pietzka, Werner Ruppitsch, Stephan Schmitz‐Esser, Martin Wagner, Kathrin Rychli
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12866-020-02052-7

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae
Cited by: 6
Author(s): Sivkheng Kann, Sena Sao, Chanleakhena Phoeung, Youlet By, Juliet E. Bryant, Florence Komurian-Pradel, Vonthanak Saphonn, Monidarin Chou, Paul Turner
Software Mentions: 4
Published: almost 4 years ago

10.1093/gbe/evab073

Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation
Cited by: 8
Author(s): Gabriel Schweizer, Muhammad Bilal Haider, Gustavo Barroso, Nicole Rössel, Karin Münch, Regine Kahmann, Julien Dutheil
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.39231

Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera
Cited by: 24
Author(s): Michal Tupec, Aleš Buček, Václav Janous̆ek, Heiko Vogel, Darina Prchalová, Jiří Kindl, Tereza Pavlíčková, Petra Wenzelová, Ullrich Jahn, Irena Valterová, Iva Pichová
Software Mentions: 4
Published: almost 6 years ago

10.1155/2021/5585586

Epi-Gene: An R-Package for Easy Pan-Genome Analysis
Cited by: 1
Author(s): Furqan Awan, Muhammad Muddassir Ali, Muhammad Hamid, Muhammad Huzair Awan, Muhammad Mushtaq, Saeeda Kalsoom, Muhammad Ijaz, Khalid Mehmood, Yongjie Liu
Software Mentions: 4
Published: about 3 years ago

10.1126/science.abe3261

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
Cited by: 215
Author(s): Jacob E. Lemieux, Katherine J. Siddle, Bennett Shaw, Christine Loreth, Stephen F. Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H. Tomkins-Tinch, Lydia A. Krasilnikova, Katherine C. DeRuff, Melissa Rudy, Matthew R. Bauer, Kim A. Lagerborg, Erica Normandin, Sinéad B. Chapman, Steven K. Reilly, Melis N. Anahtar, Aaron E. Lin, Amber Carter, Cameron Myhrvold, Molly Kemball, Sushma Chaluvadi, Caroline Cusick, Katelyn Flowers, Anna Neumann, Felecia Cerrato, Maha Farhat, Damien Slater, Jason B. Harris, John A. Branda, David C. Hooper, Jessie M. Gaeta, Travis P. Baggett, James J. O’Connell, Andreas Gnirke, Tami D. Lieberman, Anthony Philippakis, Meagan Burns, Catherine Brown, Jeremy Luban, Edward T. Ryan, Sarah E Turbett, Regina C. LaRocque, William P. Hanage, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia Pierce, Eric S. Rosenberg, Pardis C. Sabeti, Daniel J. Park, Bronwyn MacInnis
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pcbi.1008518

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers
Cited by: 10
Author(s): Julian Libiseller-Egger, Jody Phelan, Susana Campino, Fady Mohareb, Taane G. Clark
Software Mentions: 4
Published: almost 4 years ago

10.1186/s40168-017-0331-1

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities
Cited by: 110
Author(s): Robert Danczak, Michael D. Johnston, Chris Kenah, Michael T. Slattery, Kelly Wrighton, Michael J. Wilkins
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-020-07171-z

A comprehensive analysis of cotton VQ gene superfamily reveals their potential and extensive roles in regulating cotton abiotic stress
Cited by: 14
Author(s): Pengyun Chen, Fei Wei, Shuaishuai Cheng, Liang Ma, Hantao Wang, Meng Zhang, Guangzhi Mao, Jianhua Lü, Pengbo Hao, Adeel Ahmad, Lijiao Gu, Qiang Ma, Aimin Wu, Hengling Wei, Shuang Yu
Software Mentions: 4
Published: about 4 years ago

10.1186/s12985-020-01394-y

Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria
Cited by: 21
Author(s): Cody Glickman, Sara M. Kammlade, Nabeeh A. Hasan, L. Elaine Epperson, Rebecca M. Davidson, Michael Strong
Software Mentions: 4
Published: over 4 years ago

10.1099/mgen.0.000338

Coinfinder: detecting significant associations and dissociations in pangenomes
Cited by: 33
Author(s): Fiona Whelan, Martin Rusilowicz, James O. McInerney
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pntd.0007241

Detection of classic and cryptic Strongyloides genotypes by deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities
Cited by: 26
Author(s): Meruyert Beknazarova, Joel Barratt, Richard S. Bradbury, Meredith Lane, Harriet Whiley, Kirstin Ross
Software Mentions: 4
Published: over 5 years ago

10.3389/fmed.2021.656827

Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
Cited by: 6
Author(s): Nitya Singh, Xiaolong Li, Elizabeth Beshearse, Jason Blanton, Jamie DeMent, Arie H. Havelaar
Software Mentions: 4
Published: over 3 years ago

10.3389/fmed.2020.00161

Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana
Cited by: 14
Author(s): Prince Asare, Isaac Darko Otchere, Edmund Bedeley, Daniela Brites, Chloé Loiseau, Nyonuku Akosua Baddoo, Adwoa Asante-Poku, Stephen Osei-Wusu, Diana Ahu Prah, Sònia Borrell, Miriam Reinhard, Audrey Forson, Kwadwo A. Koram, Sébastien Gagneux, Dorothy Yeboah-Manu
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2019.01432

Innate Immune Genes Associated With Newcastle Disease Virus Load in Chick Embryos From Inbred and Outbred Lines
Cited by: 9
Author(s): Megan A. Schilling, Sahar Memari, Isabella M. Cattadori, Robab Katani, Amandus P. Muhairwa, Joram Buza, Peter J. Hudson
Software Mentions: 4
Published: over 5 years ago

10.1089/phage.2020.0046

Isolation and Characterization of Klebsiella Phages for Phage Therapy
Cited by: 32
Author(s): Eleanor Townsend, L. Kelly, Lucy Gannon, George Muscatt, Rhys A. Dunstan, Slawomir Michniewski, Hari Sapkota, Saija Kiljunen, Anna Kolsi, Mikael Skurnik, Trevor Lithgow, Andrew Millard, Eleanor Jameson
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pntd.0007921

Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection
Cited by: 18
Author(s): Amin Addetia, Lauren C. Tantalo, Michelle J. Lin, Hong Xie, Meei‐Li Huang, Christina M. Marra, Alexander L. Greninger
Software Mentions: 4
Published: over 4 years ago

10.1098/rspb.2020.0489

Extreme genomic volatility characterizes the evolution of the immunoglobulin heavy chain locus in cyprinodontiform fishes
Cited by: 10
Author(s): William J. Bradshaw, Dario Riccardo Valenzano
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.669442

Association and Occurrence of Bifidobacterial Phylotypes Between Breast Milk and Fecal Microbiomes in Mother–Infant Dyads During the First 2 Years of Life
Cited by: 11
Author(s): Wenli Yan, Baolong Luo, Xu-Yao Zhang, Yuwen Ni, Fengwei Tian
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2020.01930

New Plasmodium vivax Genomes From the China-Myanmar Border
Cited by: 5
Author(s): Awtum Brashear, Adam C Huckaby, Qi Fan, Luke J Dillard, Yubing Hu, Yuling Li, Yan Zhao, Zenglei Wang, Yaming Cao, Jun Miao, Jennifer L. Guler, Liwang Cui
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.612432

Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic
Cited by: 13
Author(s): Santiago Justo Arévalo, Daniela Zapata Sifuentes, César J. Huallpa, Gianfranco Landa Bianchi, Adriana Castillo Chávez, Romina Garavito-Salini Casas, Guillermo Uceda-Campos, Roberto Pineda
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2020.00548

Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand
Cited by: 24
Author(s): Jessica Loraine, Eva Heinz, Rosesathorn Soontarach, Grace A. Blackwell, Richard A. Stabler, Supayang Piyawan Voravuthikunchai, Potjanee Srimanote, Pattarachai Kiratisin, Nicholas R. Thomson, Peter W. Taylor
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.620033

Population Genomic Analysis of Listeria monocytogenes From Food Reveals Substrate-Specific Genome Variation
Cited by: 6
Author(s): Tyler Bechtel, John G. Gibbons
Software Mentions: 3
Published: almost 4 years ago

10.1093/jxb/erab278

Rubisco substitutions predicted to enhance crop performance through carbon uptake modelling
Cited by: 16
Author(s): Wasim A Iqbal, Isabel G Miller, Rebecca L Moore, Iain J Hope, Daniel Cowan‐Turner, Maxim V. Kapralov
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-020-02674-z

Unlocking the relationships among population structure, plant architecture, growing season, and environmental adaptation in Henan wheat cultivars
Cited by: 3
Author(s): Jian Yang, Yanjie Zhou, Weiguo Hu, Yue Zhang, Yong Zhou, Yongxing Chen, Xicheng Wang, Hong Zhao, Tingjie Cao, Yong Li
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.5329

Genetic diversity of Microsporidia in the circulatory system of endemic amphipods from different locations and depths of ancient Lake Baikal
Cited by: 11
Author(s): Mariya Dimova, Ekaterina Madyarova, Anton Gurkov, Polina Drozdova, Yulia Lubyaga, Elizaveta Kondrateva, R. V. Adelshin, Maxim A. Timofeyev
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-020-02499-w

Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Cited by: 17
Author(s): Alexey A. Dmitriev, Parfait Kezimana, Tatiana A. Rozhmina, А. А. Жученко, Liubov V. Povkhova, Elena N. Pushkova, Roman O. Novakovskiy, Miroslav Pavelek, Gleb Vladimirov, Evgeny N. Nikolaev, Oxana Kovaleva, Yury Kostyukevich, Vitaliy Chagovets, Е. В. Романова, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, George S. Krasnov, Nataliya V. Melnikova
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2021.641280

Characterization of the Liriodendron Chinense MYB Gene Family and Its Role in Abiotic Stress Response
Cited by: 20
Author(s): Weihuang Wu, Sheng Zhu, Liming Zhu, Dandan Wang, Yang Liu, Siqin Liu, Jiaji Zhang, Zhaodong Hao, Ye Lu, Tielong Cheng, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2021.668623

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns
Cited by: 16
Author(s): Alexandre Hild Aono, Ricardo José Gonzaga Pimenta, Ana Letycia Basso Garcia, Fernando Henrique Correr, Guilherme Kenichi Hosaka, Marishani Marin Carrasco, Cláudio Benício Cardoso-Silva, Melina Cristina Mancini, Danilo Augusto Sforça, Lucas Borges dos Santos, James Shiniti Nagai, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Monalisa Sampaio Carneiro, Thiago Willian Almeida Balsalobre, Marcos G. Quiles, Welison Andrade Pereira, Gabriel Rodrigues Alves Margarido, Anete Pereira de Souza
Software Mentions: 3
Published: over 3 years ago

10.3897/phytokeys.171.55397

Taxonomic updates in Amphitecna (Bignoniaceae): A new Mexican species and the re-establishment of the giant-leaved A. megalophylla
Cited by: 2
Author(s): Héctor Gómez‐Domínguez, Andrés Ernesto Ortiz-Rodríguez, Delfilia Velasco-Espino, Rene Hernández-Burguete
Software Mentions: 3
Published: almost 4 years ago

10.1111/pbi.13136

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection
Cited by: 83
Author(s): Shan Wu, Xin Wang, Umesh K. Reddy, Honghe Sun, Kan Bao, Lei Gao, Linyong Mao, Takshay Patel, Carlos E. Ortíz, Venkata Lakshmi Abburi, Padma Nimmakayala, Sandra Branham, Patrick Wechter, Laura Massey, Kai-Shu Ling, Chandrasekar S. Kousik, Sue A. Hammar, Yaakov Tadmor, Vitaly Portnoy, Amit Gur, Nurit Katzir, Nihat Guner, Angela R. Davis, Alvaro G. Hernandez, Chris Wright, Cecilia McGregor, Robert L. Jarret, Xingping Zhang, Yong Xu, Todd C. Wehner, Rebecca Grumet, Amnon Levi, Zhangjun Fei
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-6459-6

A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion
Cited by: 7
Author(s): Shane Denecke, Panagiotis Ioannidis, Benjamin Buer, Aris Ilias, Vassilis Douris, Pantelis Topalis, Ralf Nauen, Sven Geibel, John Vontas
Software Mentions: 3
Published: almost 5 years ago

10.1093/ve/veab060

Integrating animal movements with phylogeography to model the spread of PRRSV in the USA
Cited by: 13
Author(s): Dennis N. Makau, Moh A. Alkhamis, Igor Adolfo Dexheimer Paploski, Cesar Corzo, Samantha Lycett, Kimberly VanderWaal
Software Mentions: 3
Published: over 3 years ago

10.1093/gigascience/giz015

Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations
Cited by: 22
Author(s): Kang Kang, Basti Bergdahl, Daniel Machado, Laura Dato, Ting-Li Han, Jun Li, Silas G. Villas‐Bôas, Markus J. Herrgård, Jochen Förster, Gianni Panagiotou
Software Mentions: 3
Published: almost 6 years ago

10.3390/microorganisms8121851

Analysis of Complete Genome Sequence of Acinetobacter baumannii Strain ATCC 19606 Reveals Novel Mobile Genetic Elements and Novel Prophage
Cited by: 13
Author(s): Mohammad Hamidian, Lucía Blasco, Lauren N Tillman, Joyce To, María Tomás, Garry Myers
Software Mentions: 3
Published: almost 4 years ago

10.3390/genes10110845

Evolution of Streptococcus pneumoniae Serotype 3 in England and Wales: A Major Vaccine Evader
Cited by: 47
Author(s): Natalie Groves, Carmen Sheppard, David Litt, Samuel Rose, Ana Silva, Nina Njoku, Sirlene Souza Rodrigues, Zahin Amin-Chowdhury, Nicholas Andrews, Shamez Ladhani, Norman K. Fry
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pbio.3000838

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions
Cited by: 55
Author(s): Felix L. Wu, Alva I. Strand, Laura A. Cox, Carole Ober, Jeffrey D. Wall, Priya Moorjani, Molly Przeworski
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-018-1552-8

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Cited by: 56
Author(s): Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin A. Huttley, Eldon E. Ball, Sylvain Forêt, David J. Miller
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-021-02409-9

Evolution of mouse circadian enhancers from transposable elements
Cited by: 29
Author(s): Julius Judd, Hayley Sanderson, Cédric Feschotte
Software Mentions: 3
Published: over 3 years ago

10.1093/gbe/evaa153

The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods
Cited by: 9
Author(s): Shane Denecke, Olympia Driva, Hằng Ngọc Bảo Lương, Panagiotis Ioannidis, Marc Linka, Ralf Nauen, Sven Geibel, John Vontas
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pntd.0007620

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers
Cited by: 58
Author(s): Danielle J. Ingle, Satheesh Nair, Hassan Hartman, Philip Ashton, Zoe A. Dyson, Martin Day, Joanne Freedman, Marie Anne Chattaway, Kathryn E. Holt, Timothy J. Dallman
Software Mentions: 3
Published: about 5 years ago

10.1093/infdis/jiab368

SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion
Cited by: 122
Author(s): Isabella Ferreira, Steven Kemp, Rawlings P. Datir, Akatsuki Saito, Bo Meng, Partha Rakshit, Akifumi Takaori‐Kondo, Yusuke Kosugi, Keiya Uriu, Izumi Kimura, Kotaro Shirakawa, Adam Abdullahi, Anurag Agarwal, Seiya Ozono, Kenzo Tokunaga, Kei Sato, Gupta Rk
Software Mentions: 3
Published: about 3 years ago

10.1099/mgen.0.000428

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
Cited by: 11
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ray, Gaëtan Thilliez, Nicholas M. Thomson, David Baker, Gemma L. Kay, Jennifer Danzy Cramer, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pntd.0007868

Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance
Cited by: 93
Author(s): Yogesh Hooda, Mohammad Saiful Islam Sajib, Hafizur Rahman, Stephen P. Luby, Joseph Bondy‐Denomy, Mathuram Santosham, Jason R Andrews, Samir K. Saha, Senjuti Saha
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0255326

Collection, genotyping and virus elimination of cassava landraces from Tanzania and documentation of farmer knowledge
Cited by: 3
Author(s): Morag Ferguson, Silver Tumwegamire, Charity Chidzanga, Trushar Shah, K. Mtunda, Heneriko Kulembeka, Bernadetta Kimata, S. Tollano, Mary Stephen, E. Mpayo, S. Mohamedi, Kasele Salum, E. Palangyo, J. Armachius, Abdullah Ali, Karoline Sichalwe, Dwasi Gambo Matondo, Festo Frank Masisila, Z. Matumbo, B. Kidunda, A. C. Arati, R. Muiruri, Florence Munguti, Adebayo Abass, Michael T. Abberton, Geoffrey Mkamilo
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0247348

Unexpected distribution of the 4-formylaminooxyvinylglycine (FVG) biosynthetic pathway in Pseudomonas and beyond
Cited by: 5
Author(s): Edward W. Davis, Rachel A. Okrent, Viola A. Manning, Kristin M. Trippe
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0248371

Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
Cited by: 30
Author(s): Massab Umair, Aamer Ikram, Muhammad Salman, Adnan Khurshid, Masroor Alam, Nazish Badar, R. Suleman, Faheem Tahir, Salman Sharif, Joel M. Montgomery, Shannon Whitmer, John D. Klena
Software Mentions: 3
Published: over 3 years ago

10.1016/j.ijppaw.2019.09.005

Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism
Cited by: 5
Author(s): G. Arias‐Robledo, Richard Wall, Krzysztof Szpila, Danny Shpeley, Terry L. Whitworth, Tariq Stark, R. Andrew King, Jamie R. Stevens
Software Mentions: 3
Published: almost 5 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

10.1371/journal.pone.0215396

Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting
Cited by: 17
Author(s): Natalia Maria Silva, Aline Márcia Silva Araújo de Oliveira, Stefania Pegorin, Camila Escandura Giusti, Vitor Baptista Ferrari, Deibs Barbosa, Luciane Martins, Carlos L. Morais, João Carlos Setúbal, Suzan Pantaroto de Vasconcellos, da Silva, Júlio Cézar Franco de Oliveira, Renata C. Pascon, Cristina Viana-Niero
Software Mentions: 3
Published: over 5 years ago

10.1093/ve/veaa084

Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000–18
Cited by: 20
Author(s): Zhaoxia Han, Yang Song, Jingwei Xiao, Lili Jiang, Wei E. Huang, Haiyan Wei, Jie Li, Hanri Zeng, Qingliang Yu, Jiameng Li, Deshan Yu, Yanjun Zhang, Chonghai Li, Zhifei Zhan, Yuanli Shi, Ying Xiong, Xianjun Wang, Tianjiao Ji, Qian Yang, Shuangli Zhu, Dongmei Yan, Wenbo Xu, Yong Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0253797

High-throughput sequencing reveals genetic determinants associated with antibiotic resistance in Campylobacter spp. from farm-to-fork
Cited by: 13
Author(s): Shaimaa F. Mouftah, José F. Cobo‐Díaz, Avelino Álvarez‐Ordóñez, Menattallah Elserafy, Nehal A. Saif, Asmaa Sadat, Ayman El-Shibiny, Mohamed Elhadidy
Software Mentions: 3
Published: over 3 years ago

10.1167/iovs.61.3.33

Expression and Localization ofKcne2in the Vertebrate Retina
Cited by: 1
Author(s): Moritz Lindner, Michael James Gilhooley, Teele Palumaa, A. Jennifer Morton, Steven Hughes, Mark W. Hankins
Software Mentions: 3
Published: over 4 years ago

10.1128/mSphere.00164-20

Accumulation of Antibiotic Resistance Genes in Carbapenem-Resistant Acinetobacter baumannii Isolates Belonging to Lineage 2, Global Clone 1, from Outbreaks in 2012–2013 at a Tehran Burns Hospital
Cited by: 21
Author(s): Masoumeh Douraghi, Johanna J. Kenyon, Parisa Aris, Mahla Asadian, Sedighe Ghourchian, Mohammad Hamidian
Software Mentions: 3
Published: over 4 years ago

10.1093/ve/veaa071

Large-scale survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants
Cited by: 15
Author(s): Vikas Sharma, Pierre Lefeuvre, Philippe Roumagnac, Denis Filloux, Pierre‐Yves Teycheney, Darren P. Martin, Florian Maumus
Software Mentions: 3
Published: over 4 years ago

10.1128/mSphere.00271-19

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints
Cited by: 36
Author(s): Andrés Gómez, Ashok Sharma, Elizabeth K. Mallott, Klára J. Petrželková, Carolyn A. Jost Robinson, Carl J. Yeoman, Franck Carbonero, Barbora Pafčo, Jessica M. Rothman, Alexander Ulanov, Klára Vlčková, Katherine R. Amato, Stephanie L. Schnorr, Nathaniel J. Dominy, David Modrý, Angelique Todd, Manolito Torralba, Karen E. Nelson, Michael B. Burns, Ran Blekhman, Melissa J. Remis, Rebecca M. Stumpf, Brenda A. Wilson, H. Rex Gaskins, Paul A. Garber, Bryan A. White, Steven R. Leigh
Software Mentions: 3
Published: about 5 years ago

10.1038/s42003-020-0779-6

Early high rates and disparity in the evolution of ichthyosaurs
Cited by: 28
Author(s): Benjamin C. Moon, Thomas L. Stubbs
Software Mentions: 3
Published: almost 5 years ago

10.3390/microorganisms7080218

Developing Gut Microbiota Exerts Colonisation Resistance to Clostridium (syn. Clostridioides) difficile in Piglets
Cited by: 20
Author(s): Łukasz Grześkowiak, Temesgen Hailemariam Dadi, Jürgen Zentek, Wilfried Vahjen
Software Mentions: 3
Published: over 5 years ago

10.3390/life11030219

SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave
Cited by: 7
Author(s): Maria Bousali, Aristea Dimadi, Evangelia Georgia Kostaki, Sotirios Tsiodras, Georgios K. Nikolopoulos, Dionyssios N. Sgouras, Gkikas Magiorkinis, George V. Papatheodoridis, Vasiliki Pogka, Giota Lourida, Aikaterini Argyraki, Emmanouil Angelakis, George Sourvinos, Apostolos Beloukas, Dimitrios Paraskevis, Timokratis Karamitros
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.01638-21

Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases
Cited by: 16
Author(s): Jun Kawasaki, Shohei Kojima, Keizō Tomonaga, Masayuki Horie
Software Mentions: 3
Published: about 3 years ago

10.3390/microorganisms9051006

Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates
Cited by: 6
Author(s): Merima Alispahic, Lukas Endler, Michael Heß, Claudia Heß
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.01490-21

Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia
Cited by: 31
Author(s): Brandon M. Murareanu, Ronesh Sukhdeo, Rui Qu, Jason Jiang, Aaron W. Reinke
Software Mentions: 3
Published: over 3 years ago

10.1093/molbev/msx304

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity
Cited by: 109
Author(s): Chris Wymant, Matthew Hall, Oliver Ratmann, David Bonsall, Tanya Golubchik, Mariateresa de Cesare, Astrid Gall, Marion Cornelissen, Christophe Fraser
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13068-021-01958-2

Zymomonas diversity and potential for biofuel production
Cited by: 8
Author(s): Magdalena M. Felczak, Robert M. Bowers, Tanja Woyke, Michaela A. TerAvest
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.01440-19

Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection
Cited by: 35
Author(s): Aleeza C. Gerstein, Katrina M. Jackson, Tami McDonald, Yina Wang, Benjamin D. Lueck, Sara Bohjanen, Kyle D. Smith, Andrew Akampurira, David B. Meya, Chaoyang Xue, David R. Boulware, Kirsten Nielsen
Software Mentions: 3
Published: about 5 years ago

10.1080/21505594.2017.1325064

Signatures of cytoplasmic proteins in the exoproteome distinguish community- and hospital-associated methicillin-resistantStaphylococcus aureusUSA300 lineages
Cited by: 18
Author(s): Solomon Mekonnen, Laura M Palma Medina, Corinna Glasner, Eleni Tsompanidou, Anne de Jong, Stefano Grasso, Marc Schaffer, Ulrike Mäder, Anders Rhod Larsen, Heidi Gumpert, Henrik Westh, Uwe Völker, Andreas Otto, Dörte Becher, Jan Maarten van Dijl
Software Mentions: 3
Published: over 7 years ago

10.3390/toxins13090666

Is Toxin-Producing Planktothrix sp. an Emerging Species in Lake Constance?
Cited by: 4
Author(s): Corentin Fournier, Eva Riehle, Daniel R. Dietrich, David Schleheck
Software Mentions: 3
Published: about 3 years ago

10.3390/toxins13020122

Genotypic and Phenotypic Characterization of Staphylococcus aureus Isolates from the Respiratory Tract in Mechanically-Ventilated Patients
Cited by: 6
Author(s): Alícia Lacoma, Maisem Laabei, José Francisco Sánchez-Herrero, Bernadette C. Young, Gerard Godoy-Tena, Meissiner Gomes-Fernandes, Lauro Sumoy, Oriol Plans, Fernándo Arméstar, Cristina Prat
Software Mentions: 3
Published: almost 4 years ago

10.1210/endocr/bqaa009

Protein Profile Changes in Circulating Placental Extracellular Vesicles in Term and Preterm Births: A Longitudinal Study
Cited by: 29
Author(s): Ramkumar Menon, Chirantan Debnath, Andrew Lai, Dominic Guanzon, Shinjini Bhatnagar, Pallavi Kshetrapal, Samantha Sheller‐Miller, Carlos Salomón
Software Mentions: 3
Published: almost 5 years ago

10.1210/en.2018-00836

Circulating Exosomal miRNA Profile During Term and Preterm Birth Pregnancies: A Longitudinal Study
Cited by: 84
Author(s): Ramkumar Menon, Chirantan Debnath, Andrew Lai, Dominic Guanzon, Shinjini Bhatnagar, Pallavi Kshetrapal, Samantha Sheller‐Miller, Carlos Salomón
Software Mentions: 3
Published: about 6 years ago

10.2807/1560-7917.ES.2019.24.37.1800627

Emergence of diversity in carbapenemase-producing Escherichia coli ST131, England, January 2014 to June 2016
Cited by: 18
Author(s): Nicholas Ellaby, Michel Doumith, Katie L. Hopkins, Neil Woodford, Matthew J. Ellington
Software Mentions: 3
Published: about 5 years ago

10.1186/s12862-019-1470-8

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species
Cited by: 11
Author(s): Anton Gurkov, Lorena Rivarola-Duarte, Daria Bedulina, Irene Fernández Casas, Hendrik Michael, Polina Drozdova, Anna Nazarova, E. B. Govorukhina, Maxim A. Timofeyev, Peter F. Stadler, Till Luckenbach
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-88132-8

Intra-host evolutionary dynamics of the hepatitis C virus among people who inject drugs
Cited by: 1
Author(s): Vincent Montoya, Anita Y.M. Howe, Weiyan Dong, Winnie Dong, Chanson J. Brumme, Andrea D. Olmstead, Kanna Hayashi, P. Richard Harrigan, Jeffrey B. Joy
Software Mentions: 3
Published: over 3 years ago

10.3897/BDJ.9.e59913

The Hummingbird Collection of the Natural History and Science Museum of the University of Porto (MHNC-UP), Portugal
Cited by: 1
Author(s): Ricardo J. Lopes, Pedro Faria, Daniela Gomes, Bárbara Freitas, Judit Málinger
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.50465

Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations
Cited by: 77
Author(s): Timothy A. Crombie, Stefan Zdraljevic, Daniel E. Cook, Robyn E. Tanny, Shannon C. Brady, Ye Wang, Kathryn Evans, Steffen Hahnel, Daehan Lee, Briana Rodriguez, Gaotian Zhang, Joost van der Zwagg, Karin Kiontke, Erik C. Andersen
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-75637-x

Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails
Cited by: 25
Author(s): Maria Kornienko, Nikita Kuptsov, Roman Gorodnichev, Dmitry Bespiatykh, Andrei Guliaev, Maria A. Letarova, Eugene E. Kulikov, Vladimir A. Veselovsky, М В Малахова, Andrey V. Letarov, Elena N. Ilina, Egor Shitikov
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2017.00543

Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus
Cited by: 52
Author(s): Zohorul Islam, Carmen Espinosa-Gongora, Peter Damborg, Raphael N. Sieber, Rikke Munk, Louise Husted, Arshnee Moodley, Robert Skov, Jesper Larsen, Luca Guardabassi
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.6580

Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caimanPaleosuchus trigonatus(Alligatoridae: Caimaninae)
Cited by: 26
Author(s): Pedro Bittencourt, Zilca Campos, Fábio Muniz, Boris Marioni, Bruno de Campos Souza, Ronis Da Silveira, Benoı̂t de Thoisy, Tomas Hrbek, Izeni Pires Farias
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.11439

Characterization of the gut microbiota in Chinese children with overweight and obesity using 16S rRNA gene sequencing
Cited by: 12
Author(s): Xiaowei Chen, Dawei Zhang, Haixiang Sun, Fei Jiang, Yan Shen, Pingmin Wei, Xiaobing Shen
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-020-07287-2

Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis
Cited by: 8
Author(s): Nancy Dong, Julia Bandura, Zhaolei Zhang, Yan Wang, Karine Labadie, Benjamin Noël, Angus Davison, Joris M. Koene, Hong Sun, Marie Agnès Coutellec, Feng Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-16810-7

Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering
Cited by: 78
Author(s): Richard G. J. Hodel, Shichao Chen, Adam C. Payton, Stuart F. McDaniel, Pamela S. Soltis, Douglas E. Soltis
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41597-020-0363-4

Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis
Cited by: 20
Author(s): Thomas Hackl, Roman Martin, Karina Barenhoff, Sarah Duponchel, Dominik Heider, Matthias Fischer
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12977-019-0510-1

Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study
Cited by: 10
Author(s): Hanwei Sudderuddin, Natalie N. Kinloch, Steven Jin, Rachel L. Miller, Bradley R. Jones, Chanson J. Brumme, Jeffrey B. Joy, Mark A. Brockman, Zabrina L. Brumme
Software Mentions: 3
Published: almost 5 years ago

10.21203/rs.3.rs-802084/v1

Immune responses in COVID-19 respiratory tract and blood reveal mechanisms of disease severity
Cited by: 0
Author(s): Wuji Zhang, Brendon Y Chua, Kevin J. Selva, Łukasz Kędzierski, Thomas Myles Ashhurst, Ebene R Haycroft, Suzanne K. Shoffner, Luca Hensen, David F. Boyd, Fiona James, Effie Mouhtouris, Jason C Kwong, Kyra Chua, George Drewett, Ana Copaescu, Julie E. Dobson, Louise C. Rowntree, Jennifer R Habel, Lilith F Allen, Hui‐Fern Koay, Jessica A. Neil, Matthew J. Gartner, Christina Y. Lee, Patiyan Andersson, Torsten Seemann, Norelle L Sherry, Fatima Amanat, Florian Krammer, Sarah L. Londrigan, Linda M. Wakim, Nöel King, Dale I. Godfrey, Laura K. Mackay, Paul G. Thomas, Suellen Nicholson, Kelly B. Arnold, Amy W. Chung, Natasha E Holmes, Olivia C Smibert, Jason A Trubiano, Claire L. Gordon, Thi H. O. Nguyen, Katherine Kedzierska
Software Mentions: 3
Published: about 3 years ago

Projects: bioconductor: ggtree

Papers Mentioning ggtree 474