10.1371/journal.pcbi.1000200

Fusion and Fission of Genes Define a Metric between Fungal Genomes
Cited by: 23
Author(s): Pascal Durrens, Macha Nikolski, David James Sherman
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pgen.1001061

Telomere Disruption Results in Non-Random Formation of De Novo Dicentric Chromosomes Involving Acrocentric Human Chromosomes
Cited by: 61
Author(s): Kaitlin M. Stimpson, Ihn Young Song, Anna Jauch, Heidi Holtgreve-Grez, Karen Hayden, Joanna M. Bridger, Beth A. Sullivan
Software Mentions: 1
Published: about 16 years ago

10.1038/s41598-017-01082-y

Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids
Cited by: 34
Author(s): Tsuyoshi Sekizuka, Michihiro Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
Software Mentions: 1
Published: over 9 years ago

10.3390/biom9050188

Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica
Cited by: 20
Author(s): Weilong Kong, Ziyun Gong, Hua Zhong, Yue Zhang, Gangqing Zhao, Mayank Gautam, Xiaoxiao Deng, Chang Liu, Chenhao Zhang, Yangsheng Li
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms21218064

An Earliest Endosymbiont, Wolbachia massiliensis sp. nov., Strain PL13 from the Bed Bug (Cimex hemipterus), Type Strain of a New Supergroup T
Cited by: 20
Author(s): Younes Laidoudi, Anthony Levasseur, Hacène Medkour, Mossaab Maaloum, Mariem Ben Khedher, Masse Sambou, Hubert Bassène, Bernard Davoust, Florence Fénollar, Didier Raoult, Oleg Mediannikov
Software Mentions: 1
Published: almost 6 years ago

10.3390/biom9080317

Systematic Analysis of MYB Family Genes in Potato and Their Multiple Roles in Development and Stress Responses
Cited by: 50
Author(s): Xiaoxu Li, Chunfang Guo, Saboor Ahmad, Qi Wang, Jing Yu, Cheng Liu, Yongfeng Guo
Software Mentions: 1
Published: about 7 years ago

10.1155/2013/757490

Targeted Resequencing Reveals<i>ALK</i>Fusions in Non-Small Cell Lung Carcinomas Detected by FISH, Immunohistochemistry, and Real-Time RT-PCR: A Comparison of Four Methods
Cited by: 42
Author(s): Katja Tuononen, Virinder Sarhadi, Aino Wirtanen, Mikko Rönty, Kaisa Salmenkivi, Aija Knuuttila, Satu Maria Remes, Aino Telaranta-Keerie, Stuart Bloor, Pekka Ellonen, Sakari Knuutila
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1008116

Infection mechanisms and putative effector repertoire of the mosquito pathogenic oomycete Pythium guiyangense uncovered by genomic analysis
Cited by: 24
Author(s): Danyu Shen, Zhaoyang Tang, Wei Cong, Jing Wang, Yue Dong, Yang Chen, Yun Wei, Biao Cheng, Meiqian Zhang, Laura J. Grenville‐Briggs, Brett M. Tyler, Daolong Dou, Ai Xia
Software Mentions: 1
Published: over 7 years ago

10.1155/2020/6146104

Complete Genome Sequence and Biodegradation Characteristics of Benzoic Acid-Degrading Bacterium <i>Pseudomonas</i> sp. SCB32
Cited by: 7
Author(s): Wei Xiang, Xiaolan Wei, Hui Tang, Liangbo Li, Rong Huang
Software Mentions: 1
Published: over 6 years ago

10.1155/2019/2965035

Genome-Wide Identification, Evolution, and Transcriptional Profiling of<i>PP2C</i>Gene Family in<i>Brassica rapa</i>
Cited by: 25
Author(s): Nadeem Khan, Koeun Han, Chunmei Hu, Emal Naseri, Muhammad Salman Haider, Aliya Ayaz, Waleed Amjad Khan, Jianjun Wang, Xilin Hou
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1006025

Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome
Cited by: 37
Author(s): Hafez El Sayyed, Ludovic Le Chat, Elise Lebailly, Elise Vickridge, C. Pagès, François Cornet, Marco Cosentino Lagomarsino, Olivier Espéli
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1000714

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
Cited by: 152
Author(s): Paul J. McMurdie, Sebastian Behrens, Jochen A. Müller, Jonathan Göke, Kirsti M. Ritalahti, Ryan D. Wagner, Eugene Goltsman, Alla Lapidus, Susan Holmes, Frank E. Löffler, Alfred M. Spormann
Software Mentions: 1
Published: almost 17 years ago

10.1155/2018/9473542

Analysis of the Complete Genome Sequence of<i>Bacillus atrophaeus</i>GQJK17 Reveals Its Biocontrol Characteristics as a Plant Growth-Promoting Rhizobacterium
Cited by: 16
Author(s): Jinjin Ma, Chengqiang Wang, Haide Wang, Kai Liu, Tongrui Zhang, Liangtong Yao, Zhou Zhao, Binghai Du, Yuqiang Ding
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1005644

Absence of Maternal Methylation in Biparental Hydatidiform Moles from Women with NLRP7 Maternal-Effect Mutations Reveals Widespread Placenta-Specific Imprinting
Cited by: 78
Author(s): Marta Sánchez-Delgado, Alejandro Martin-Trujillo, Chiharu Tayama, Enrique Vidal, Manel Esteller, Isabel Iglesias-Platas, Nandita Deo, Olivia Barney, Ken Maclean, Kenichiro Hata, Kazuhiko Nakabayashi, Rosemary A. Fisher, David Gabriel Monk
Software Mentions: 1
Published: almost 11 years ago

10.1155/2021/9983858

Genome-Wide Identification and Evolutionary Analysis of Argonaute Genes in Hexaploid Bread Wheat
Cited by: 3
Author(s): Yan-Feng Liu, Limin Wang, Zhao Lizi, Wei Wang, Hongxia Zhang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1005072

The Role of China in the Global Spread of the Current Cholera Pandemic
Cited by: 71
Author(s): Xavier Didelot, Bo Pang, Zhemin Zhou, A. McCann, Peixiang Ni, Dongfang Li, Mark Achtman, Biao Kan
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1008365

Convergent evolution of linked mating-type loci in basidiomycete fungi
Cited by: 28
Author(s): Sheng Sun, Marco A. Coelho, Joseph Heitman, Minou Nowrousian
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1005721

Origins of De Novo Genes in Human and Chimpanzee
Cited by: 115
Author(s): Jorge Ruiz-Orera, Jessica Hernández-Rodríguez, Cristina Chiva, Eduard Sabidó, Ivanela Kondova, Ronald E. Bontrop, Tomàs Marquès-Bonet, M. Mar Albà
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-017-02364-1

Age-related penetrance of the C9orf72 repeat expansion
Cited by: 91
Author(s): Natalie A. Murphy, Karissa C. Arthur, Pentti J. Tienari, Henry Houlden, Adriano Chiò, Bryan J. Traynor
Software Mentions: 1
Published: over 9 years ago

10.1155/2021/3904120

A Complete Genome Sequence of the Wood Stem Endophyte Bacillus velezensis BY6 Strain Possessing Plant Growth-Promoting and Antifungal Activities
Cited by: 6
Author(s): Ping Zhang, Jian Diao, Guangqiang Xie, Ling Ma, Lihai Wang
Software Mentions: 1
Published: over 5 years ago

10.1155/2017/7904162

Characterization and Expression Profiling Analysis of Calmodulin Genes in Response to Salt and Osmotic Stresses in Pear (Pyrus bretschneideriRehd.) and in Comparison withArabidopsis
Cited by: 2
Author(s): Jun Tang, Jing Lin, Yong Li, Qiyun Yang, Qunkang Cheng, Zong‐Ming Cheng, Chang YouHong
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12938-019-0740-4

Analyzing brain structural differences associated with categories of blood pressure in adults using empirical kernel mapping-based kernel ELM+
Cited by: 3
Author(s): Xinying Yu, Bo Peng, Zeyu Xue, Hamidreza Saligheh Rad, Zhenlin Cai, Jun Shi, Jianbing Zhu, Yakang Dai
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-2656-8

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato
Cited by: 15
Author(s): Francisco Javier Herraiz, José Blanca, Peio Ziarsolo, Pietro Gramazio, Jaime Prohens, Gregory J. Anderson, Jaime Prohens, Santiago Vilanova
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1006630

Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants
Cited by: 107
Author(s): Sophie Lanciano, Marie-Christine Carpentier, Christel Llauro, Edouard Jobet, Dagmara Robakowska-Hyżorek, Éric Lasserre, Alain Ghesquière, Olivier Panaud, Marie Mirouze
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1004272

Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity
Cited by: 82
Author(s): Yoshikazu Furuta, Hiroe Namba-Fukuyo, Tomoko Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Yutaka Suzuki, Sumio Sugano, Mitsuyasu Hasebe, Ichizo Kobayashi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1003191

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution
Cited by: 94
Author(s): María Lluch‐Senar, Khai Luong, Verónica Lloréns‐Rico, Javier Delgado, Gang Fang, Kristi Spittle, Tyson A. Clark, Eric E. Schadt, Stephen W. Turner, Jonas Korlach, Luís Serrano
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-017-01857-3

Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization
Cited by: 14
Author(s): Xiaoming Wang, Ruochen Wang, Chuang Ma, Song Xue, Zhenshan Liu, Zhonghua Wang, Qixin Sun, Jun Cao, Shengbao Xu
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-020-07201-w

Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress
Cited by: 9
Author(s): Guodong Chen, Jizhong Wang, Xin Qiao, Can Jin, Weike Duan, Xiaochuan Sun, Juyou Wu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s40659-015-0038-3

Integrated analyses of copy number variations and gene differential expression in lung squamous-cell carcinoma
Cited by: 17
Author(s): Yang Zhao, Bing Zhuan, Yan Yan, Simin Jiang, Tao Wang
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-017-03330-7

Genome-wide mapping and characterization of microsatellites in the swamp eel genome
Cited by: 22
Author(s): Zhigang Li, Feng Chen, Chunhua Huang, Weiran Zheng, Chunlai Yu, Hanhua Cheng, Rongjia Zhou
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms21218262

Genome-Wide Identification and Functional Characterization of the Cation Proton Antiporter (CPA) Family Related to Salt Stress Response in Radish (Raphanus sativus L.)
Cited by: 18
Author(s): Yan Wang, Jiali Ying, Zhangping Yang, Liang Xu, Wanting Zhang, Meng Ni, Yuelin Zhu, Liwang Liu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1005391

Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates
Cited by: 42
Author(s): Jiayu Chen, Qing Sunny Shen, Wei‐Zhen Zhou, Jiguang Peng, Bin He, Yumei Li, Chu‐Jun Liu, Xuke Luan, Wanqiu Ding, Shuxian Li, Chunyan Chen, Bertrand Chin‐Ming Tan, Yong E. Zhang, Aibin He, Chuan-Yun Li
Software Mentions: 1
Published: about 11 years ago

10.1186/s13062-015-0085-2

Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm
Cited by: 31
Author(s): Aurélia Caputo, Vicky Merhej, Kalliopi Georgiades, Pierre‐Edouard Fournier, Olivier Croce, Caroline Robert, Didier Raoult
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-020-6501-8

Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress
Cited by: 21
Author(s): Man Zhang, Qing Liu, Qing-Yu He, Mengnan Chai, Youmei Huang, Fangqian Chen, Xiaomei Wang, Yeqiang Liu, Hanyang Cai, Yuan Qin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1005876

Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control
Cited by: 61
Author(s): Rafael Arango, Caucasella Díaz-Trujillo, Braham Dhillon, Andrea Aerts, Jean Carlier, Charles F. Crane, Tristan de Jong, Ineke de Vries, Robert A. Dietrich, Andrew Farmer, Claudia Fortes Fereira, Suzana Garcia, M. Guzmán, Richard Hamelin, Erika Lindquist, Rahim Mehrabi, O. Quirós, Jeremy Schmutz, Harris Shapiro, Elizabeth K. Reynolds, Gabriel Scalliet, M.T. Souza, Ioannis Stergiopoulos, Theo A. J. van der Lee, P.J.G.M. de Wit, M.F. Zapater, L.H. Zwiers, Igor V. Grigoriev, Stephen B. Goodwin, G.H.J. Kema
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pmed.1002750

Patterns of joint involvement in juvenile idiopathic arthritis and prediction of disease course: A prospective study with multilayer non-negative matrix factorization
Cited by: 35
Author(s): Simon Eng, Florence Aeschlimann, Mira van Veenendaal, Roberta Berard, Alan Rosenberg, Quaid Morris, Rae S. M. Yeung
Software Mentions: 1
Published: over 7 years ago

10.1093/bioinformatics/btv376

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications
Cited by: 14
Author(s): Matthew R. Laird, Morgan G. I. Langille, Fiona S. L. Brinkman
Software Mentions: 1
Published: over 11 years ago

10.1186/1752-0509-7-141

Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma
Cited by: 44
Author(s): Meeta Pradhan, Akshay Desai, Mathew Palakal
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0006839

Virulotyping of Salmonella enterica serovar Typhi isolates from Pakistan: Absence of complete SPI-10 in Vi negative isolates
Cited by: 12
Author(s): Sadia Liaquat, Yasra Sarwar, Aamir Ali, Abdul Haque, Muhammad Farooq, Ilargi Martínez-Ballesteros, Lorena Laorden, Javier Garaizar, Joseba Bikandi
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0002039

National Borders Effectively Halt the Spread of Rabies: The Current Rabies Epidemic in China Is Dislocated from Cases in Neighboring Countries
Cited by: 45
Author(s): Zhenyang Guo, Xiaoyan Tao, Chenghong Yin, Ning Han, Jinning Yu, Hao Li, Haizhou Liu, Fang Wei, J. Hume Adams, Jun Wang, Guodong Liang, Qing Tang, Simon Rayner
Software Mentions: 1
Published: over 13 years ago

10.1186/1756-0500-5-615

CooVar: Co-occurring variant analyzer
Cited by: 35
Author(s): Ismael A. Vergara, Christian Frech, Nansheng Chen
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12889-016-3630-8

The double burden of disease among mining workers in Papua, Indonesia: at the crossroads between Old and New health paradigms
Cited by: 15
Author(s): Rodrigo Rodríguez-Fernández, Nawi Ng, Dwidjo Susilo, John Prawira, Michael J. Bangs, Rachel M. Amiya
Software Mentions: 1
Published: about 10 years ago

10.3390/ani11040936

The Effect of Infertility on the Liver Structure, Endocrinology, and Gene Network in Japanese Flounder
Cited by: 3
Author(s): Qi Mang, Jilun Hou, Han Tian, Guixing Wang, Yufen Wang, Yufeng Liu, Yuqin Ren, Yaxian Zhao, Zhongwei He, Xiaoyan Zhang
Software Mentions: 1
Published: over 5 years ago

10.1186/1753-6561-6-S6-P37

AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations
Cited by: 3
Author(s): Hue Vuong, Robert M. Stephens, Natalia Volfovsky
Software Mentions: 1
Published: about 14 years ago

10.1038/s41598-017-04004-0

Genome-wide identification and characterization of genes involved in carotenoid metabolic in three stages of grapevine fruit development
Cited by: 35
Author(s): Xiangpeng Leng, Peipei Wang, Chen Wang, Xudong Zhu, Xiaopeng Li, Hongyan Li, Qian Mei, Ao Li, Zhongjie Liu, Jinggui Fang
Software Mentions: 1
Published: over 9 years ago

10.1186/1753-6561-6-S6-P17

Mining cancer genomes in COSMIC
Cited by: 1
Author(s): Mingming Jia, Simon Forbes, David Beare, Nidhi Bindal, Prasad Gunasekaran, Kenric Leung, Chai Yin Kok, Sally Bamford, Charlotte G. Cole, Sari Ward, Jon W. Teague, Michael R. Stratton, Peter J. Campbell, Andrew Futreal
Software Mentions: 1
Published: about 14 years ago

10.1186/s12870-021-03184-2

Genome-wide analysis of OSCA gene family members in Vigna radiata and their involvement in the osmotic response
Cited by: 17
Author(s): Lili Yin, Meiling Zhang, Ruigang Wu, Xiaoliang Chen, Fei Liu, Xing Bao-long
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-017-04833-z

Mitogenomic analyses support the recent division of the genus Orthotrichum (Orthotrichaceae, Bryophyta)
Cited by: 30
Author(s): Jakub Sawicki, Vítězslav Plášek, Ryszard Ochyra, Monika Szczecińska, Monika Ślipiko, Kamil Myszczyński, Tomasz Kulik
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0020090

Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting
Cited by: 60
Author(s): John Lamb, Chunsheng Zhang, Tao Xie, Kai Wang, Bin Zhang, Ke Hao, Eugene Chudin, Hunter B. Fraser, Joshua Millstein, Mark D. Ferguson, Christine Suver, Irena L. Ivanovska, Martin Scott, Ulrike Philippar, Dimple Bansal, Zhan Zhang, Julja Burchard, Ryan M. Smith, Danielle M. Greenawalt, Michele A. Cleary, Jonathan M.J. Derry, Andrey Loboda, James Watters, Ronnie T. P. Poon, Sheung Tat Fan, Chun Yeung, Nikki P.Y. Lee, Justin Guinney, Cliona Molony, Valur Emilsson, Carolyn Buser-Doepner, Jun Zhu, Stephen H. Friend, Mao Mao, Peter M. Shaw, Hongyue Dai, John M. Luk, Eric E. Schadt
Software Mentions: 1
Published: over 15 years ago

10.3390/nu13072326

Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans—Evidence from Targeted Nutrigenomic Studies
Cited by: 14
Author(s): Tatjana Ruskovska, Irena Budić-Leto, Karla Fabiola Corral-Jara, Vladimir Ajdžanović, Anna Arola‐Arnal, Francisca Isabel Bravo, Georgia-Eirini Deligiannidou, Jaroslav Havlík, Milkica Janeva, Elena Kistanova, Christos Kontogiorgis, Irèna Krga, Marika Massaro, Marko Miler, Verica Milošević, Christine Morand, Egeria Scoditti, Manuel Suárez, David Vauzour, Dragan Milenković
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0011748

The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications
Cited by: 161
Author(s): Hélène Falentin, Stéphanie-Marie Deutsch, Gwenaël Jan, Valentin Loux, Anne Thierry, Sandrine Parayre, Marie-Bernadette Maillard, Julien Dherbécourt, Fabien Cousin, Julien Jardin, Patricia Siguier, Arnaud Couloux, Valérie Barbe, Benoît Vacherie, Patrick Wincker, Jean‐François Gibrat, Claude Gaillardin, Sylvie Lortal
Software Mentions: 1
Published: about 16 years ago

10.1038/s41598-017-06160-9

Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation
Cited by: 8
Author(s): Hui Xu, Siyu Qin, Yanhong Lan, Mengjia Liu, Xiyue Cao, Dan Qiao, Yu Cao, Yi Cao
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-019-5789-8

Genome-wide analysis of the WRKY gene family and their positive responses to phytoplasma invasion in Chinese jujube
Cited by: 23
Author(s): Chaoling Xue, Hongtai Li, Zhiguo Liu, Lili Wang, Yitong Zhao, Ximeng Wei, Fang Hu, Mengjun Liu, Jin Zhao
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0171201

OxyR-activated expression of Dps is important for Vibrio cholerae oxidative stress resistance and pathogenesis
Cited by: 28
Author(s): Xiaoyun Xia, Jessie Larios-Valencia, Zhi Liu, Fu Xiang, Biao Kan, Hui Wang, Jun Zhu
Software Mentions: 1
Published: over 9 years ago

10.1186/s12870-019-1957-x

Genome-wide identification and expression analysis of the trihelix transcription factor family in tartary buckwheat (Fagopyrum tataricum)
Cited by: 26
Author(s): Zhaotang Ma, Moyang Liu, Wenjun Sun, Li Huang, Qi Wu, Tongliang Bu, Chenglei Li, Hui Chen
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0136101

Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle
Cited by: 19
Author(s): Pedro Manuel Martínez-García, Pablo Rodrı́guez-Palenzuela, Eva Arrebola, Víctor J. Carrión, José A. Gutiérrez‐Barranquero, Alejandro Pérez-Garcı́a, Cayo Ramos, Francisco M. Cazorla, Antonio de Vicente
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-016-2759-2

Transcriptome profiling of Diachasmimorpha longicaudata towards useful molecular tools for population management
Cited by: 3
Author(s): M. Constanza Mannino, Máximo Rivarola, Alejandra Carla Scannapieco, Sergio González, Marisa Diana Farber, Jorge Luis Cladera, Silvia Beatriz Lanzavecchia
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0211635

Metacaspase gene family in Rosaceae genomes: Comparative genomic analysis and their expression during pear pollen tube and fruit development
Cited by: 8
Author(s): Yunpeng Cao, Dong Meng, Tianzhe Chen, Yu Chen, Wei Zeng, Lei Zhang, Qi Wang, W Enchao C Hen, Qing Jin, Yi Lin, Yongping Cai
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms21228639

Whole Genome Sequencing and Tn5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease
Cited by: 1
Author(s): Wen-Jen Chen, Tzu-Yen Kuo, Chun-Yi Chen, Feng-Chia Hsieh, Yu Liang Yang, Je-Ruei Liu, Ming-Che Shih
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0087045

De novo Genome Assembly of the Fungal Plant Pathogen Pyrenophora semeniperda
Cited by: 20
Author(s): Marcus M. Soliai, Susan E. Meyer, Joshua A. Udall, David E. Elzinga, Russell A. Hermansen, Paul Bodily, Aaron A. Hart, Craig E. Coleman
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-14-22

Kerfuffle: a web tool for multi-species gene colocalization analysis
Cited by: 7
Author(s): Robert Aboukhalil, Bernard J. Fendler, Gurinder S. Atwal
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0067742

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species
Cited by: 116
Author(s): Kajal Kumari, Mehanathan Muthamilarasan, Gopal Misra, Sarika Gupta, A. Subramanian, Swarup K. Parida, Debasis Chattopadhyay
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0086852

Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (Setaria italica L.)
Cited by: 101
Author(s): Awdhesh Kumar Mishra, Mehanathan Muthamilarasan, Yusuf Khan, Swarup K. Parida
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0161369

Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors
Cited by: 5
Author(s): C Brunner, Bettina Brunner-Herglotz, Andrea Ziegler, Christian Frech, Gabriele Amann, Ruth Ladenstein, Inge M. Ambros, Peter F. Ambros
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0026742

Genome Analysis of a Highly Virulent Serotype 1 Strain of Streptococcus pneumoniae from West Africa
Cited by: 19
Author(s): Todd A. Williams, Nicholas J. Loman, Chinelo Ebruke, Daniel M. Musher, Richard A. Adegbola, Mark J. Pallen, George M. Weinstock, Martín Antonio
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0090087

New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs
Cited by: 79
Author(s): Isabel N. Sierra-García, Javier Correa Álvarez, Suzan Pantaroto de Vasconcellos, Anete Pereira de Souza, Eugênio Vaz dos Santos Neto, Valéria Maia de Oliveira
Software Mentions: 1
Published: over 12 years ago

10.1186/s12870-014-0253-z

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes
Cited by: 47
Author(s): Emma Mace, Shuaishuai Tai, David J. Innes, Ian D. Godwin, Wushu S. Hu, Bradley C. Campbell, Edward K. Gilding, Alan Cruickshank, Peter J. Prentis, Jun Wang, David R. Jordan
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0084713

Evidence for Site-Specific Occupancy of the Mitochondrial Genome by Nuclear Transcription Factors
Cited by: 33
Author(s): Georgi K. Marinov, Yun E. Wang, David C. Chan, B Wold
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-017-09397-6

Transcriptomic, biochemical and physio-anatomical investigations shed more light on responses to drought stress in two contrasting sesame genotypes
Cited by: 56
Author(s): Komivi Dossa, Donghua Li, Linhai Wang, Xiaomin Zheng, Aili Liu, Jingyin Yu, Xin Wei, Rong Zhou, Daniel Foncéka, Diaga Diouf, Boshou Liao, Ndiaga Cissé
Software Mentions: 1
Published: about 9 years ago

10.1186/s12870-019-1760-8

Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)
Cited by: 37
Author(s): Xin Gong, Liangyi Zhao, Xiaofei Song, Zekun Lin, Bingjie Gu, Jinxuan Yan, Shaoling Zhang, Shutian Tao, Xiaosan Huang
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0157901

Deciphering the Draft Genome of Toxoplasma gondii RH Strain
Cited by: 27
Author(s): Yee Ling Lau, Wenn-Chyau Lee, Ranganath Gudimella, Gui Ping Zhang, Xiao Teng Ching, Rozaimi Mohamad Razali, Farhanah Abdul Aziz, Arif Anwar, Mun Yik Fong
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0179073

Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens
Cited by: 28
Author(s): Yuzhe Wang, Xianglin Cao, Yaofeng Zhao, Fei Jing, Xiaoxiang Hu, Ning Li
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0080149

miRNA Signatures in Sera of Patients with Active Pulmonary Tuberculosis
Cited by: 65
Author(s): Paolo Miotto, Grace Mwangoka, Ilaria C. Valente, Luca Norbis, Giovanni Sotgiu, Roberta Bosu, Alessandro Ambrosi, Luigi Codecasa, Delia Goletti, Alberto Matteelli, Elias N. Ntinginya, Francesco Aloi, Norbert Heinrich, Klaus Reither, Daniela María Cirillo
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-015-1249-2

Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum)
Cited by: 83
Author(s): Jinyan Wang, Zhongze Hu, Tongmin Zhao, Youxin Yang, Tianzi Chen, Mali Yang, Wenbao Yu, Baolong Zhang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0164469

Whole-Genome Resequencing of a Cucumber Chromosome Segment Substitution Line and Its Recurrent Parent to Identify Candidate Genes Governing Powdery Mildew Resistance
Cited by: 18
Author(s): Qiang Xu, Yang Shi, Ting Yu, Xuewen Xu, Yali Yan, Xiaohua Qi, Xuehao Chen
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-017-10432-9

Mutational heterogeneity in non-serous ovarian cancers
Cited by: 35
Author(s): Jamie K. Teer, Sean Yoder, Anxhela Gjyshi, Santo V. Nicosia, Chaomei Zhang, Alvaro N.A. Monteiro
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0098986

Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)
Cited by: 48
Author(s): Cody E. Hinchliff, Stephen A. Smith
Software Mentions: 1
Published: over 12 years ago

10.1186/s12870-020-02752-2

Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus
Cited by: 25
Author(s): Weizhuo Zhu, Yiyi Guo, Yeke Chen, Dezhi Wu, Lixi Jiang
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0240908

Genomic divergence between Dickeya zeae strain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain
Cited by: 5
Author(s): Jingxin Zhang, Mohammad Arif, Huolin Shen, John Hu, Dan Sun, Xiaoming Pu, Qiyun Yang, Birun Lin
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0080835

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats
Cited by: 83
Author(s): Е. В. Лебедева, Roland Hatzenpichler, Éric Pelletier, Nathalie Schuster, Sandra Hauzmayer, А. Г. Булаев, N. V. Grigor’eva, Alexander Galushko, Markus Schmid, Márton Palatinszky, Denis Le Paslier, Holger Daims, Michael Wagner
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0154975

Complete Nucleotide Sequence of IncP-1β Plasmid pDTC28 Reveals a Non-Functional Variant of the blaGES-Type Gene
Cited by: 8
Author(s): Bingjun Dang, Daqing Mao, Yi Luo
Software Mentions: 1
Published: over 10 years ago

10.1186/s12870-018-1454-7

Characterization and subcellular localization of histone deacetylases and their roles in response to abiotic stresses in soybean
Cited by: 33
Author(s): Chao Yang, Wenjin Shen, Hongfeng Chen, Liutian Chu, Xu Yang, Xiaochen Zhou, Chuanliang Liu, Chunmiao Chen, Jiahui Zeng, Jin Liu, Qianfeng Li, Caiji Gao, Jean‐Benoît Charron, Ming Luo
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0155590

Characterization and Comparison of the CPK Gene Family in the Apple (Malus × domestica) and Other Rosaceae Species and Its Response to Alternaria alternata Infection
Cited by: 7
Author(s): Menghan Wei, Sanhong Wang, Hui Dong, Baiyan Cai, Jianmin Tao
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0189673

Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages
Cited by: 4
Author(s): Joshua Marc Cambridge, Alexandra Blinkova, Erick I. Salvador Rocha, Addys Bode Hernández, Maday Moreno, Edwin A. Gines-Candelaria, Benjamin M. Goetz, Scott Patrick Hunicke-Smith, Ed Satterwhite, Haley O. Tucker, James R. Walker
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0156281

Genome-Wide Comparative Analysis of the Phospholipase D Gene Families among Allotetraploid Cotton and Its Diploid Progenitors
Cited by: 19
Author(s): Kai Tang, C.Y. Dong, Jinyuan Liu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0099848

Genetic Architecture of Winter Hardiness and Frost Tolerance in Triticale
Cited by: 19
Author(s): Wenxin Liu, Hans Peter Maurer, Guoliang Li, Matthew R. Tucker, Manje Gowda, Elmar A. Weissmann, Volker Hahn, Tobias Würschum
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0092639

Mapping the Structure and Dynamics of Genomics-Related MeSH Terms Complex Networks
Cited by: 11
Author(s): J. Mario Siqueiros-García, Enrique Hernández‐Lemus, Rodrigo García-Herrera, Andrea Robina-Galatas
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2229-12-139

Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean
Cited by: 133
Author(s): Yang Jae Kang, Kil Hyun Kim, Sangrea Shim, Min Young Yoon, Shufeng Sun, Moon Young Kim, Kyujung Van, Suk-Ha Lee
Software Mentions: 1
Published: about 14 years ago

10.1186/s12870-018-1230-8

Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress
Cited by: 67
Author(s): Wei Gao, Fuchun Xu, Dandan Guo, Jing-Ruo Zhao, Liu Ji, Yawei Guo, Prashant Kumar Singh, Xiaonan Ma, Lu Long, José Ramón Botella, Chun‐Peng Song
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0194356

Whole-genome sequencing of Brassica oleracea var. capitata reveals new diversity of the mitogenome
Cited by: 8
Author(s): Kiwoung Yang, Ujjal Kumar Nath, Manosh Kumar Biswas, Abdul Kayum, Go-Eun Yi, Jonghoon Lee, Tae-Jin Yang, Ill Sup Nou
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-020-6573-5

Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis
Cited by: 7
Author(s): Vimla Kany G. Ami, Rami Balasubramanian, Shubhada R. Hegde
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-019-1891-y

Genome-wide identification and functional analysis of oleosin genes in Brassica napus L.
Cited by: 23
Author(s): Kang Chen, Yuping Yin, Si Liu, Zhenyi Guo, Kai Zhang, Liang Yu, Lina Zhang, Weiguo Zhao, Hongbo Chao, Maoteng Li
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0227716

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane
Cited by: 12
Author(s): Mingxing Cai, Jishan Lin, Zeyun Li, Zhicong Lin, Yaying Ma, Yibin Wang, Ray Ming
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0163635

The First Report of miRNAs from a Thysanopteran Insect, Thrips palmi Karny Using High-Throughput Sequencing
Cited by: 17
Author(s): K. B. Rebijith, R. Asokan, H. Ranjitha Hande, N. K. Krishna Kumar
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-020-6548-6

Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)
Cited by: 10
Author(s): Zhiguo Liu, Lixin Wang, Chaoling Xue, Yuetong Chu, Wei Gao, Yitong Zhao, Jin Zhao, Mengjun Liu
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0166341

Comparative Genome-Wide Analysis of the Malate Dehydrogenase Gene Families in Cotton
Cited by: 18
Author(s): Muhammad Imran, Kai Tang, Jinyuan Liu
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2105-13-S15-S7

IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis
Cited by: 43
Author(s): Fan Zhang, Renee Drabier
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0036939

Genomic Sequencing and Comparative Analysis of Epstein-Barr Virus Genome Isolated from Primary Nasopharyngeal Carcinoma Biopsy
Cited by: 78
Author(s): Hin‐Fai Kwok, Amy Tong, Chi-Ho Lin, Si Lok, Patrick J. Farrell, Dora Lai Wan Kwong, Alan Kwok Shing Chiang
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0217846

Genome-wide analysis identifies rare copy number variations associated with inflammatory bowel disease
Cited by: 15
Author(s): Svetlana Frenkel, Çharles N. Bernstein, Michael Sargent, Qin Kuang, Wenxin Jiang, John Wei, Bhooma Thiruvahindrapuram, Elizabeth L. Spriggs, Stephen W. Scherer, Pingzhao Hu
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-12988-y

Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes
Cited by: 22
Author(s): Yunduan Li, Yanxun Zhu, Jin Yao, Songlin Zhang, Li Wang, Chunfang Guo, Steve van Nocker, Xiping Wang
Software Mentions: 1
Published: about 9 years ago