pypi: ete3 | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1009065

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: about 4 years ago

10.3390/ijms22052244

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis
Cited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 3 years ago

10.1186/s12859-021-04057-z

Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Cited by: 21
Author(s): Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Software Mentions: 13
Published: over 3 years ago

10.7717/peerj.4395

COREMIC: a web-tool to search for a niche associated CORE MICrobiome
Cited by: 17
Author(s): Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams
Software Mentions: 11
Published: almost 7 years ago

10.1128/mSystems.00065-20

Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk
Cited by: 19
Author(s): Justine W. Debelius, Tingting Huang, Yonglin Cai, Alexander Ploner, Donal Barrett, Xiaoying Zhou, Xue Xiao, Yancheng Li, Jian Liao, Yuming Zheng, Guangwu Huang, Hans‐Olov Adami, Yi Xin Zeng, Zhe Zhang, Ye W
Software Mentions: 10
Published: about 4 years ago

10.1128/mSystems.00474-21

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

10.1186/s13059-020-02195-w

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Cited by: 107
Author(s): Alon Shaiber, Amy Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch, A. Murat Eren
Software Mentions: 8
Published: almost 4 years ago

10.7554/eLife.31035

Phenotype inference in an Escherichia coli strain panel
Cited by: 36
Author(s): Marco Galardini, Alexandra Koumoutsi, Lucía Herrera-Domínguez, Juan Antonio Cordero Varela, Anja Telzerow, Omar Wagih, Morgane Wartel, Olivier Clermont, Erick Denamur, Athanasios Typas, Pedro Beltrão
Software Mentions: 8
Published: almost 7 years ago

10.3389/fmicb.2020.591093

NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
Cited by: 8
Author(s): David Dylus, Trestan Pillonel, Onya Opota, Daniel Wüthrich, Helena M. B. Seth-Smith, Adrian Egli, Stefano Leo, Vladimir Lazarević, Jacques Schrenzel, Sacha Laurent, Claire Bertelli, Dominique Blanc, Stefan Neuenschwander, Alban Ramette, Laurent Falquet, Frank Imkamp, Peter M. Keller, André Kahles, Simone Oberhaensli, Valérie Barbié, Christophe Dessimoz, Gilbert Greub, Aitana Lebrand
Software Mentions: 6
Published: almost 4 years ago

10.1002/ece3.7959

BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection
Cited by: 2
Author(s): Giobbe Forni, Angelo Ruggieri, Giovanni Piccinini, Andrea Luchetti
Software Mentions: 6
Published: about 3 years ago

10.1111/pbi.13210

The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley
Cited by: 39
Author(s): Miao Liu, Yan Li, Yanling Ma, Qiang Zhao, Jiri Stiller, Qi Feng, Qifeng Tian, Dengcai Liu, Bin Han, Chunji Liu
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-021-04309-y

airpg: automatically accessing the inverted repeats of archived plastid genomes
Cited by: 2
Author(s): Tilman Mehl, Michael Gruenstaeudl
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2019.02273

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre
Cited by: 15
Author(s): Daniel Mende, Dominique Le Bœuf, Edward F. DeLong
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.26580

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
Cited by: 56
Author(s): Feiqiao Brian Yu, Paul C. Blainey, Frederik Schulz, Tanja Woyke, Mark Horowitz, Stephen R. Quake
Software Mentions: 4
Published: over 7 years ago

10.1128/JVI.00828-17

Cooperation between Strain-Specific and Broadly Neutralizing Responses Limited Viral Escape and Prolonged the Exposure of the Broadly Neutralizing Epitope
Cited by: 35
Author(s): Colin Anthony, Talita York, Valerie Bekker, David Matten, Philippe Selhorst, Roux-Cil. Ferreria, Nigel Garrett, Salim S. Abdool Karim, Lynn Morris, Natasha T. Wood, Penny L. Moore, Carolyn Williamson
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2018.01402

Cholecystectomy Damages Aging-Associated Intestinal Microbiota Construction
Cited by: 47
Author(s): Wenxue Wang, Junfeng Wang, Julan Li, Peng Yan, Jimmy Yun, Ruyi Zhang, Wei Yue, Qiang Guo, Jiawei Geng
Software Mentions: 3
Published: over 6 years ago

10.3906/biy-2005-35

Phylogenetic analysis of SARS-CoV-2 genomes in Turkey
Cited by: 13
Author(s): Ogün Adebali, Aylin Bircan, Defne Circi, Burak İŞlek, Zeynep Kilinc, Berkay Selçuk, Berk Turhan
Software Mentions: 3
Published: over 4 years ago

10.1126/sciimmunol.abi6950

Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals after mRNA vaccination
Cited by: 504
Author(s): Rishi R. Goel, Sokratis A. Apostolidis, Mark M. Painter, Divij Mathew, Ajinkya Pattekar, Oliva Kuthuru, Sigrid Gouma, Philip Hicks, Wenzhao Meng, Aaron M. Rosenfeld, Sarah Dysinger, Kendall A. Lundgreen, Leticia Kuri-Cervantes, Sharon Adamski, Amanda Hicks, Scott Korte, Derek A. Oldridge, Amy E. Baxter, Josephine R. Giles, Madison E. Weirick, Christopher M. McAllister, Jeanette Dougherty, Sherea Long, Kurt D’Andrea, Jacob T. Hamilton, Michael R. Betts, Eline T. Luning Prak, Paul Bates, Scott E. Hensley, Allison R. Greenplate, E. John Wherry
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-10640-3

Riparian plant litter quality increases with latitude
Cited by: 50
Author(s): Luz Boyero, Manuel A. S. Graça, Alan M. Tonin, Javier Jiménez Pérez, Austin D. Swafford, Verónica Ferreira, Andrea Landeira-Dabarca, Markos A. Alexandrou, Mark O. Gessner, Brendan G. McKie, Ricardo Albariño, Leon A. Barmuta, Marcos Callisto, Julián Chará, Éric Chauvet, Checo Colón-Gaud, David Dudgeon, Andrea C. Encalada, Ricardo Figueroa, Alexander S. Flecker, Tadeusz Fleituch, André Frainer, José F. Gonçalves, Julie E. Helson, Tomoya Iwata, Jude M. Mathooko, Charles Mwithali M’Erimba, Catherine M. Pringle, Alonso Ramírez, Christopher M. Swan, Catherine M. Yule, Richard G. Pearson
Software Mentions: 2
Published: about 7 years ago

10.1093/bib/bbaa206

Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
Cited by: 19
Author(s): Eva S. Deutekom, Berend Snel, Teunis J. P. van Dam
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2020.570825

Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes
Cited by: 11
Author(s): Ho Jin Gwak, Mina Rho
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2020.00840

Reduced Genome of the Gut Symbiotic Bacterium “Candidatus Benitsuchiphilus tojoi” Provides Insight Into Its Possible Roles in Ecology and Adaptation of the Host Insect
Cited by: 6
Author(s): Shakhinur Islam Mondal, Arzuba Akter, Ryuichi Koga, Takahiro Hosokawa, Mehmet Dayı, Kazunori Murase, Ryusei Tanaka, Shuji Shigenobu, Takema Fukatsu, Taisei Kikuchi
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.00293-21

High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System
Cited by: 22
Author(s): Anh D. Ha, Mohammad Moniruzzaman, Frank O. Aylward
Software Mentions: 2
Published: about 3 years ago

10.3390/v12111270

Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes
Cited by: 12
Author(s): Léo Blanca, Eugène Christo-Foroux, Sofia Rigou, Matthieu Legendre
Software Mentions: 2
Published: about 4 years ago

10.1111/1755-0998.13277

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (<i>Emys orbicularis</i>, L. 1758)
Cited by: 3
Author(s): Charlotte Ducotterd, Julien Crovadore, François Lefort, Jean‐François Rubin, Sylvain Ursenbacher
Software Mentions: 2
Published: about 4 years ago

10.1186/s13059-018-1479-0

Impact of transposable elements on genome structure and evolution in bread wheat
Cited by: 182
Author(s): Thomas Wicker, Heidrun Gundlach, Manuel Spannagl, Cristóbal Uauy, Philippa Borrill, Ricardo H. Ramírez-González, Romain De Oliveira, Klaus Mayer, Etienne Paux, Frédéric Choulet
Software Mentions: 1
Published: over 6 years ago

10.1038/s41396-020-00825-6

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
Cited by: 55
Author(s): M. Consuelo Gazitúa, Dean Vik, Simon Roux, Ann C. Gregory, Benjamin Bolduc, Brittany Widner, Margaret R. Mulholland, Steven J. Hallam, Osvaldo Ulloa, Matthew B. Sullivan
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2019.01148

Switching the Post-translational Modification of Translation Elongation Factor EF-P
Cited by: 14
Author(s): Wolfram Volkwein, Ralph Krafczyk, Pravin Kumar Ankush Jagtap, Marina Parr, Elena Mankina, Jakub Macošek, Zhenghuan Guo, Maximilian J. L. J. Fürst, Miriam Pfab, Dmitrij Frishman, Janosch Hennig, Kirsten Jung, Jürgen Lassak
Software Mentions: 1
Published: over 5 years ago

Ecosyste.ms: Papers

Projects: pypi: ete3

Papers Mentioning ete3 28