Ecosyste.ms: Papers

10.3389/fmicb.2017.01654

Environmental Bacteriophages of the Emerging Enterobacterial Phytopathogen, Dickeya solani, Show Genomic Conservation and Capacity for Horizontal Gene Transfer between Their Bacterial Hosts
Cited by: 15
Author(s): Alison M. Day, Jiyoon Ahn, Xinzhe Fang, George P. C. Salmond
Software Mentions: 1
Published: over 6 years ago

10.1093/gbe/evu037

Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence
Cited by: 60
Author(s): Simon Renny‐Byfield, Joseph P. Gallagher, Corrinne E. Grover, Emmanuel Szadkowski, Justin T. Page, Joshua A. Udall, Xiyin Wang, Andrew H. Paterson, Jonathan F. Wendel
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2017.01673

An Anthropocentric View of the Virosphere-Host Relationship
Cited by: 25
Author(s): Rodrigo Araújo Lima Rodrigues, Aron José Pazin de Andrade, Paulo Victor de Miranda Boratto, Giliane de Souza Trindade, Erna Geessien Kroon, Jônatas Santos Abrahão
Software Mentions: 1
Published: over 6 years ago

10.1155/2019/4242653

Complete Genome Sequence of<i>Photobacterium damselae</i>Subsp.<i>damselae</i>Strain SSPD1601 Isolated from Deep-Sea Cage-Cultured<i>Sebastes schlegelii</i>with Septic Skin Ulcer
Cited by: 7
Author(s): Yongxiang Yu, Zheng Zhang, Yingeng Wang, Meijie Liao, Xiaojun Rong, Bin Li, Kai Wang, Jing Chen, Hao Zhang
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2020.580719

Metabolic Contributions of an Alphaproteobacterial Endosymbiont in the Apicomplexan Cardiosporidium cionae
Cited by: 8
Author(s): Elizabeth Sage Hunter, Christopher Paight, Christopher E. Lane
Software Mentions: 1
Published: over 3 years ago

10.1093/gbe/evu175

Genomic Signatures of Distributive Conjugal Transfer among Mycobacteria
Cited by: 38
Author(s): Tatum D Mortimer, Caitlin S. Pepperell
Software Mentions: 1
Published: over 9 years ago

10.1093/gbe/evu201

Genomic Evolution of Saccharomyces cerevisiae under Chinese Rice Wine Fermentation
Cited by: 27
Author(s): Yudong Li, Weiping Zhang, Dao-Qiong Zheng, Zhan Zhou, Wenwen Yu, Lei Zhang, Lei Feng, Xinmiao Liang, Wenjun Guan, Jingwen Zhou, Jian Chen, Zhenguo Lin
Software Mentions: 1
Published: over 9 years ago

10.1093/gbe/evu222

Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex
Cited by: 37
Author(s): Mark Sistrom, Benjamin R. Evans, Robert Bjornson, Wendy Gibson, Oliver Balmer, Pascal Mäser, Serap Aksoy, Adalgisa Caccone
Software Mentions: 1
Published: over 9 years ago

10.1093/gbe/evu262

Genomic Diversification in Strains of Rickettsia felis Isolated from Different Arthropods
Cited by: 66
Author(s): Joseph J. Gillespie, Timothy Driscoll, Victoria I. Verhoeve, Tadanobu Utsuki, Claudia Husseneder, Vladimir N. Chouljenko, Abdu F. Azad, Kevin R. Macaluso
Software Mentions: 1
Published: over 9 years ago

10.1093/gbe/evv092

Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity
Cited by: 76
Author(s): Jana Sperschneider, Donald M. Gardiner, Louise F. Thatcher, Rebecca Lyons, Karam B. Singh, John M. Manners, Jennifer Taylor
Software Mentions: 1
Published: about 9 years ago

10.1155/2019/2804134

Genomic Analysis of a New Estrogen-Degrading Bacterial Strain,<i>Acinetobacter</i>sp. DSSKY-A-001
Cited by: 8
Author(s): Qing Qiu, Ping Wang, Hui Kang, Yu Wang, Kejian Tian, Hongliang Huo
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2016.01541

Genome Sequencing and Comparative Genomics Analysis Revealed Pathogenic Potential in Penicillium capsulatum as a Novel Fungal Pathogen Belonging to Eurotiales
Cited by: 9
Author(s): Ying Yang, Min Chen, Zongwei Li, Abdullah M. S. Al‐Hatmi, Sybren de Hoog, Weihua Pan, Qiang Ye, Xiaochen Bo, Zhen Li, Shengqi Wang, Junzhi Wang, Huipeng Chen, Wanqing Liao
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2019.01003

Guarani Virophage, a New Sputnik-Like Isolate From a Brazilian Lake
Cited by: 15
Author(s): Saïd Mougari, Meriem Bekliz, Jônatas Santos Abrahão, Fabrizio Di Pinto, Anthony Levasseur, Bernard La Scola
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2019.01373

Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China
Cited by: 16
Author(s): Xing Liu, Miaomiao Xing, Chunli Kong, Zhiyuan Fang, Limei Yang, Yangyong Zhang, Yong Wang, Jian Ling, Youyou Yang, Honghao Lv
Software Mentions: 1
Published: almost 5 years ago

10.1093/gbe/evz006

An Annotated Genome for <i>Haliotis rufescens</i> (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species
Cited by: 32
Author(s): Rick E. Masonbrink, Catherine Purcell, Sara E. Boles, Andrew Whitehead, John R. Hyde, Arun S. Seetharam, Andrew J. Severin
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms18102040

Genome-Wide Analysis of CCA1-Like Proteins in Soybean and Functional Characterization of GmMYB138a
Cited by: 16
Author(s): Shaomin Bian, Dong Jin, Ruihua Li, Xin Xie, Guangzhen Gao, Weikang Sun, Yuejia Li, Lulu Zhai, Xuyan Li
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2020.00785

Complete Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma atroviride: Genomic Features, Comparative Analysis and Insight Into the Mitochondrial Evolution in Trichoderma
Cited by: 8
Author(s): Yunyoung Kwak
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2021.674147

Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil
Cited by: 12
Author(s): Roberta Torres de Melo, Newton Nascentes Galvão, Micaela Guidotti Takeuchi, Phelipe Augusto Borba Martins Peres, Belchiolina Beatriz Fonseca, Rodrigo Profeta, Vasco Azevedo, Guilherme Paz Monteiro, Bertram Brenig, Daise Aparecida Rossi
Software Mentions: 1
Published: almost 3 years ago

10.3389/fmicb.2021.696102

Description, Taxonomy, and Comparative Genomics of a Novel species, Thermoleptolyngbya sichuanensis sp. nov., Isolated From Hot Springs of Ganzi, Sichuan, China
Cited by: 13
Author(s): Jie Tang, Liheng Li, Meijin Li, Lianming Du, Mahfuzur Rahman Shah, Małgorzata Waleron, Krzysztof Waleron, Maurycy Daroch
Software Mentions: 1
Published: over 2 years ago

10.3389/fmicb.2019.01044

Exopolysaccharide, Isolated From a Novel Strain Bifidobacterium breve lw01 Possess an Anticancer Effect on Head and Neck Cancer – Genetic and Biochemical Evidences
Cited by: 26
Author(s): Lin Wang, Yifei Wang, Qingxiang Li, Kai Tian, Le Xu, Guorong Liu, Chuanbin Guo
Software Mentions: 1
Published: about 5 years ago

10.1093/gbe/evab177

Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution
Cited by: 10
Author(s): Tim Regan, Lewis Stevens, Carolina Peñaloza, Ross D. Houston, Diego Robledo, Tim P. Bean
Software Mentions: 1
Published: almost 3 years ago

10.3389/fmicb.2021.686008

Highly Efficient CRISPR-Mediated Base Editing in Sinorhizobium meliloti
Cited by: 4
Author(s): Longxiang Wang, Yuan Xiao, Xiaowei Wei, Jimin Pan, Deqiang Duanmu
Software Mentions: 1
Published: almost 3 years ago

10.3389/fmicb.2021.618649

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales
Cited by: 9
Author(s): Abdullah Zubaer, Alvan Wai, Nikita Patel, Jordan Perillo, Georg Hausner
Software Mentions: 1
Published: over 3 years ago

10.1186/s13073-015-0164-0

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
Cited by: 299
Author(s): Francesc Español i Coll, Ruth McNerney, Mark D. Preston, José Afonso Guerra-Assunção, Andrew Warry, Grant A. Hill-Cawthorne, Kim Mallard, Mridul Nair, Armandina Miranda, Adriana Alves, João Perdigão, Miguel Viveiros, Isabel Portugal, Zahra Hasan, Rumina Hasan, Judith R. Glynn, Nigel Martin, Arnab Pain, Taane G. Clark
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13073-017-0399-z

Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells
Cited by: 21
Author(s): Sjors Middelkamp, Sebastiaan van Heesch, Arie Koen Braat, Joep de Ligt, Maarten van Iterson, Marieke Simonis, Markus J. van Roosmalen, Martijn J. E. Kelder, Evelien Kruisselbrink, Ron Hochstenbach, Nienke E. Verbeek, Elly F. Ippel, Youri Adolfs, R. Jeroen Pasterkamp, Wigard P. Kloosterman, Ewart Kuijk, Edwin Cuppen
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2020.611143

Impact of Bacillus on Phthalides Accumulation in Angelica sinensis (Oliv.) by Stoichiometry and Microbial Diversity Analysis
Cited by: 5
Author(s): Wei-Meng Feng, Pei Liu, Hui Yan, Sen Zhang, Erxin Shang, Guang Yu, Shu Jiang, Dawei Qian, Junwei Ma, Jin‐Ao Duan
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.749218

Complete Genome Sequence of Weissella confusa LM1 and Comparative Genomic Analysis
Cited by: 4
Author(s): Shenglei Yuan, Yundan Wang, Fangqing Zhao, Le Kang
Software Mentions: 1
Published: over 2 years ago

10.3389/fmicb.2020.02047

Structural and Proteomic Studies of the Aureococcus anophagefferens Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing
Cited by: 4
Author(s): Eric R. Gann, Yuejiao Xian, Paul E. Abraham, Robert L. Hettich, Todd B. Reynolds, Chuan Xiao, Steven W. Wilhelm
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2018.01573

The Identification of DepB: An Enzyme Responsible for the Final Detoxification Step in the Deoxynivalenol Epimerization Pathway in Devosia mutans 17-2-E-8
Cited by: 41
Author(s): Jason Carere, Yousef I. Hassan, Dion Lepp, Ting Zhou
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.gpb.2020.05.002

MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals
Cited by: 8
Author(s): Xiaoxu Yang, Chengliang Yang, Xianing Zheng, Luoxing Xiong, Yu‐Tian Tao, Meng Wang, Adam Yongxin Ye, Qixi Wu, Yanmei Dou, Junyu Luo, Liping Wei, August Yue Huang
Software Mentions: 1
Published: about 4 years ago

10.1186/2047-217X-3-19

iReport: a generalised Galaxy solution for integrated experimental reporting
Cited by: 4
Author(s): Saskia Hiltemann, Youri Hoogstrate, Peter van der Spek, Guido Jenster, Andrew Stubbs
Software Mentions: 1
Published: over 9 years ago

10.1186/2047-217X-1-14

A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education
Cited by: 41
Author(s): Tarás K. Oleksyk, Jean‐François Pombert, Daniel Siu, Anyi Mazo‐Vargas, Brian P. Ramos, Wilfried Guiblet, Yashira Afanador, Christina Ruiz-Rodriguez, Michael L. Nickerson, David M. Logue, Michael Dean, L. Figueroa, Ricardo Valentin, Juan-Carlos Martinez-Cruzado
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2016.00340

Genomic Insights into a New Citrobacter koseri Strain Revealed Gene Exchanges with the Virulence-Associated Yersinia pestis pPCP1 Plasmid
Cited by: 11
Author(s): Fabrice Armougom, Idir Bitam, Olivier Croce, Vicky Merhej, Lina Barassi, Ti-Thien Nguyen, Bernard La Scola, Didier Raoult
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2015.00349

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population
Cited by: 52
Author(s): Jessica M. Labonté, Erin K. Field, Maggie C. Y. Lau, Dylan Chivian, Esta van Heerden, K. Eric Wommack, Thomas L. Kieft, Tullis C. Onstott, Ramunas Stepanauskas
Software Mentions: 1
Published: about 9 years ago

10.3389/fmicb.2020.01934

Comparative Genomic and Secretomic Analysis Provide Insights Into Unique Agar Degradation Function of Marine Bacterium Vibrio fluvialis A8 Through Horizontal Gene Transfer
Cited by: 5
Author(s): Chunsheng Li, Chi Li, Laihao Li, Xianqing Yang, Shengjun Chen, Qi Bo, Yongqiang Zhao
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2014.00084

A Glimpse of the genomic diversity of haloarchaeal tailed viruses
Cited by: 17
Author(s): Ana Senčilo, Elina Roine
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2019.02104

Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio
Cited by: 17
Author(s): Rafael R. de la Haba, Clara López-Hermoso, Cristina Sánchez‐Porro, Konstantinos T. Konstantinidis, António Ventosa
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2021.731711

Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri
Cited by: 4
Author(s): Chang‐Jen Huang, Ting-Li Wu, Po Xing Zheng, Jheng-Yang Ou, Hui-Fang Ni, Yao‐Cheng Lin
Software Mentions: 1
Published: over 2 years ago

10.3389/fmicb.2019.01616

Bacterial Acid Resistance Toward Organic Weak Acid Revealed by RNA-Seq Transcriptomic Analysis in Acetobacter pasteurianus
Cited by: 24
Author(s): Haoran Yang, Yongjian Yu, Caixia Fu, Fusheng Chen
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2017.00443

A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins
Cited by: 28
Author(s): Charles Coluzzi, Gérard Guédon, Marie‐Dominique Devignes, Chloé Ambroset, Valentin Loux, Thomas Lacroix, Sophie Payot, Nathalie Leblond‐Bourget
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2020.581802

Mechanism of the Potential Therapeutic Candidate Bacillus subtilis BSXE-1601 Against Shrimp Pathogenic Vibrios and Multifunctional Metabolites Biosynthetic Capability of the Strain as Predicted by Genome Analysis
Cited by: 6
Author(s): Dongdong Wang, Jiahui Li, Guoliang Zhu, Kun Zhao, Wenwen Jiang, Haidong Li, Wenjun Wang, Vikash Kumar, Shuanglin Dong, Weiming Zhu, Xiangli Tian
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.01806

Genetic and Biochemical Evidence That Enterococcus faecalis Gr17 Produces a Novel and Sec-Dependent Bacteriocin, Enterocin Gr17
Cited by: 9
Author(s): Guorong Liu, Yao Wang, Xue Li, Hao Xu, Duoxia Xu, Yuguang Zhou, Arshad Mehmood
Software Mentions: 1
Published: almost 5 years ago

10.1093/gigascience/giz038

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing
Cited by: 23
Author(s): Ruby Dhar, Ashikh Seethy, Karthikeyan Pethusamy, Sunil Kumar Singh, Vishwajeet Rohil, Kakali Purkayastha, Indrani Mukherjee, Sandeep Goswami, Rakesh Singh, Ankita Raj, Tryambak Srivastava, Sovon Acharya, Balaji Rajashekhar, Subhradip Karmakar
Software Mentions: 1
Published: about 5 years ago

10.1093/gigascience/giz063

A chromosome-scale assembly of the major African malaria vector Anopheles funestus
Cited by: 44
Author(s): Jay Ghurye, Sergey Koren, Scott T. Small, Seth Redmond, Paul Howell, Adam M. Phillippy, Nora J. Besansky
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms19102914

Gummy Stem Blight Resistance in Melon: Inheritance Pattern and Development of Molecular Markers
Cited by: 17
Author(s): Zahid Hassan, Abdur Rahim, Sathishkumar Natarajan, Arif Hasan Khan Robin, Hoy‐Taek Kim, Jong-In Park, Ill–Sup Nou
Software Mentions: 1
Published: over 5 years ago

10.1093/gigascience/giaa020

Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly
Cited by: 3
Author(s): Fanming Meng, Zhuoying Liu, Han Han, Dmitrijs Finkelbergs, Yangshuai Jiang, Mingfei Zhu, Yang Wang, Zongyi Sun, Chao Chen, Yadong Guo, Jifeng Cai
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2018.02099

Deciphering Resistome and Virulome Diversity in a Porcine Slaughterhouse and Pork Products Through Its Production Chain
Cited by: 16
Author(s): Guillermo Campos Calero, Natacha Caballero Gómez, Nabil Benomar, Beatriz Pérez Montoro, Charles W. Knapp, Antonio Gálvez, Hikmate Abriouel
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2021.696588

A High Starch Diet Alters the Composition of the Intestinal Microbiota of Largemouth Bass Micropterus salmoides, Which May Be Associated With the Development of Enteritis
Cited by: 10
Author(s): Xiaoli Huang, Zhong Liu, Qin Kang, Sha Li, Yun Feng, Yi Geng, Defang Chen, Yangping Ou, Shiyong Yang, Lizi Yin, Wei Luo
Software Mentions: 1
Published: almost 3 years ago

10.1093/gigascience/giaa092

Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)
Cited by: 5
Author(s): Feng Shao, Arne Ludwig, Yang Mao, Geoffrey Liu, Zuogang Peng
Software Mentions: 1
Published: almost 4 years ago

10.1093/gigascience/giaa099

Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods
Cited by: 10
Author(s): Damien Courtine, Jan Provazník, Jérôme Reboul, Guillaume Blanc, Vladimír Beneš, Jonathan J. Ewbank
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.610698

Anti-Foc RT4 Activity of a Newly Isolated Streptomyces sp. 5–10 From a Medicinal Plant (Curculigo capitulata)
Cited by: 16
Author(s): Tao Yun, Miaoyi Zhang, Dengbo Zhou, Jing Tao, Xiaoping Zang, Defeng Qi, Yufeng Chen, Kai Li, Yanbin Zhao, Wen Tang, Jiaquan Huang, Wei Wang, Jianghui Xie
Software Mentions: 1
Published: over 3 years ago