10.1186/s12864-015-1988-0

Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes
Cited by: 40
Author(s): Mingyong Tang, Zhiwen Chen, Corrinne E. Grover, Yumei Wang, Shuangshuang Li, Guozheng Liu, Zhiying Ma, Jonathan F. Wendel, Jinping Hua
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-017-1038-y

Global identification, structural analysis and expression characterization of bHLH transcription factors in wheat
Cited by: 48
Author(s): Xiaojiang Guo, Jirui Wang
Software Mentions: 2
Published: over 9 years ago

10.1038/srep20650

Feature co-localization landscape of the human genome
Cited by: 11
Author(s): Siu-Kin Ng, Taobo Hu, Xi Long, Colin Chan, Suk Ying Tsang, Hong Xue
Software Mentions: 2
Published: over 10 years ago

10.1038/srep15443

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations
Cited by: 75
Author(s): Abdallah Abdallah, Grant A. Hill-Cawthorne, Thomas D. Otto, Francesc Español i Coll, José Afonso Guerra-Assunção, Ge Gao, Raeece Naeem, Hifzur Rahman Ansari, Tareq B. Malas, Sabir A. Adroub, Theo Verboom, Roy Ummels, Huoming Zhang, Aswini K. Panigrahi, Ruth McNerney, Roland Brosch, Taane G. Clark, Marcel A. Behr, Wilbert Bitter, Arnab Pain
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep28594

The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Cited by: 91
Author(s): Nyok-Sean Lau, Yuko Makita, Mika Kawashima, Todd D. Taylor, Shinji Kondo, Ahmad Sofiman Othman, Alexander Chong Shu‐Chien, Minami Matsui
Software Mentions: 2
Published: over 10 years ago

10.1038/srep32598

Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta)
Cited by: 2
Author(s): Xu Zhang, Zhilin Qu, Bing Su
Software Mentions: 2
Published: about 10 years ago

10.1186/s12870-021-02941-7

Genetic control of flowering in greater yam (Dioscorea alata L.)
Cited by: 10
Author(s): Fabien Cormier, Guillaume Martin, Hélène Vignes, Laurie Lachman, Denis Cornet, Yoana Faure, Erick Malédon, Pierre Mournet, Gemma Arnau, Hâna Chaïr
Software Mentions: 2
Published: over 5 years ago

10.1038/srep18227

MycoCAP - Mycobacterium Comparative Analysis Platform
Cited by: 4
Author(s): Siew Woh Choo, Mia Yang Ang, Avirup Dutta, Shi Tan, Cheuk Chuen Siow, Hamed Heydari, Naresh V.R. Mutha, Wei Yee Wee, George T.F. Wong
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-13-505

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma
Cited by: 31
Author(s): Jared J. Gartner, Sean Davis, Xiaomu Wei, Jimmy C. Lin, Niraj Trivedi, Jamie K. Teer, Paul S. Meltzer, Steven A. Rosenberg, Yardena Samuels
Software Mentions: 2
Published: about 14 years ago

10.1186/s12870-017-0979-5

Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa
Cited by: 58
Author(s): Md. Abdul Kayum, Jong-In Park, Ujjal Kumar Nath, Manosh Kumar Biswas, Hoy‐Taek Kim, Ill–Sup Nou
Software Mentions: 2
Published: over 9 years ago

10.1038/sdata.2015.72

Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus
Cited by: 50
Author(s): Thomas Schmutzer, Birgit Samans, Emmanuelle Dyrszka, Chris Ulpinnis, Stéphan Weise, Doreen Stengel, Christian Colmsee, Denis Lespinasse, Zeljko Micic, Stefan Abel, Peter Duchscherer, Frank Breuer, Amine Abbadi, Gunhild Leckband, Rod J. Snowdon, Uwe Scholz
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-020-02345-z

Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance
Cited by: 27
Author(s): Lu Long, Jing-Ruo Zhao, Dandan Guo, Xiaonan Ma, Fuchun Xu, Wenwen Yang, Wei Gao
Software Mentions: 2
Published: over 6 years ago

10.1186/s13104-020-05169-0

Autonomous replication sequences from the Amaranthus palmeri eccDNA replicon enable replication in yeast
Cited by: 12
Author(s): William T. Molin, Allison Yaguchi, Mark Blenner, Christopher A. Saski
Software Mentions: 2
Published: about 6 years ago

10.1186/1752-0509-8-S2-I1

Data integration in the era of omics: current and future challenges
Cited by: 295
Author(s): David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew E. Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam‐Rudloff, Ana Conesa, Jesper Tegnér
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13040-019-0207-y

Integrative analysis of genetic and epigenetic profiling of lung squamous cell carcinoma (LSCC) patients to identify smoking level relevant biomarkers
Cited by: 3
Author(s): Bidong Ma, Zhiyou Huang, Qian Wang, Jizhou Zhang, Bin Zhou, Jiaohong Wu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12284-019-0270-5

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection
Cited by: 8
Author(s): Zhenhui Zhong, Lian‐Yu Lin, Meilian Chen, Lili Lin, Xiaofeng Chen, Yunzhi Lin, Xi Chen, Zonghua Wang, Justice Norvienyeku, Huakun Zheng
Software Mentions: 2
Published: over 7 years ago

10.1126/sciadv.abh3032

Identification of SARS-CoV-2–induced pathways reveals drug repurposing strategies
Cited by: 26
Author(s): Namshik Han, Woochang Hwang, Konstantinos Tzelepis, Patrick Schmerer, Eliza Yankova, Méabh MacMahon, Winnie Lei, Nicholas M Katritsis, Anika Liu, Ulrike Felgenhauer, Alison Schuldt, Robert G. Harris, Kathryn Chapman, Frank McCaughan, Friedemann Weber, Tony Kouzarides
Software Mentions: 2
Published: over 5 years ago

10.1038/srep14941

Profiling RNA editing in human tissues: towards the inosinome Atlas
Cited by: 187
Author(s): Ernesto Picardi, Caterina Manzari, Francesca Mastropasqua, Italia Aiello, Anna Maria D’Erchia, Graziano Pesole
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep29017

Genome-scale DNA variant analysis and functional validation of a SNP underlying yellow fruit color in wild strawberry
Cited by: 64
Author(s): Charles Hawkins, Julie Caruana, Erin Schiksnis, Zhongchi Liu
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-017-07039-5

Transcriptomic signature of the follicular somatic compartment surrounding an oocyte with high developmental competence
Cited by: 22
Author(s): Satoshi Sugimura, Norio Kobayashi, Hiroaki Okae, T. Yamanouchi, Hideo Matsuda, Tatsuhiro Kojima, Akira Yajima, Y. Hashiyada, Masahiro Kaneda, Kei Sato, Kyoichi Imai, Kentaro Tanemura, Takahiro Arima, Robert B. Gilchrist
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-019-5462-2

Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken
Cited by: 52
Author(s): Manman Shen, Tingting Li, Genxi Zhang, Pengfei Wu, Fuxiang Chen, Qiuhong Lou, Lan Chen, Xiufeng Yin, Tao Zhang, Jinyu Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-6159-2

Genome-wide identification and transcript analysis of TCP transcription factors in grapevine
Cited by: 41
Author(s): Xiangpeng Leng, Hongru Wei, Xiaozhao Xu, Sandip A. Ghuge, Dongjie Jia, Gengsen Liu, Yongzhang Wang, Yuan Yang
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.ppat.1009886

A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road
Cited by: 7
Author(s): Xutong Wu, Chao Ning, Felix M. Key, Aida Andrades Valtueña, Aditya Kumar Lankapalli, Shizhu Gao, Yang Xuan, Fan Zhang, Linlin Liu, Zhongzhi Nie, Jian Ma, Johannes Krause, Alexander Herbig, Yinqiu Cui
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1009447

A heterochromatin inducing protein differentially recognizes self versus foreign genomes
Cited by: 7
Author(s): Eric Burton, Ibukun A. Akinyemi, Tiffany R. Frey, Huanzhou Xu, Xiaofan Li, Lai Jing Su, Jizu Zhi, Michael T. McIntosh, Sumita Bhaduri‐McIntosh
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-015-1906-5

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials
Cited by: 60
Author(s): Ming‐Cheng Luo, Frank M. You, Pingchuan Li, Jirui Wang, Tingting Zhu, Abhaya M. Dandekar, Charles A. Leslie, Mallikarjuna K. Aradhya, Patrick E. McGuire, Jan Dvořák
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2164-12-436

Analysis of high-identity segmental duplications in the grapevine genome
Cited by: 31
Author(s): Giuliana Giannuzzi, Pietro D’Addabbo, Marica Gasparro, M. Martinelli, Francesco Nicola Carelli, Donato Antonacci, Mario Ventura
Software Mentions: 2
Published: about 15 years ago

10.1186/s12870-021-03201-4

Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance
Cited by: 4
Author(s): Surendra Bhattarai, Yong‐Bi Fu, Bruce Coulman, Karen Tanino, Chithra Karunakaran, Bill Biligetu
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-019-5710-5

Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2
Cited by: 8
Author(s): Giorgio Gonnella, Nicole Adam, Mirjam Perner
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007461

The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence
Cited by: 30
Author(s): Indu Warrier, Nikhil Ram-Mohan, Zeyu Zhu, Ariana Hazery, Haley Echlin, Jason Rosch, Michelle M. Meyer, Tim van Opijnen
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2229-12-218

Identification and profiling of novel microRNAs in the Brassica rapagenome based on small RNA deep sequencing
Cited by: 36
Author(s): Bumjin Kim, Hee‐Ju Yu, Sin‐Gi Park, Ja Young Shin, Min Seok Oh, Namshin Kim, Jeong‐Hwan Mun
Software Mentions: 2
Published: almost 14 years ago

10.1155/2016/7823429

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
Cited by: 19
Author(s): Yiqing Xu, Changwei Bi, Guoxin Wu, Suyun Wei, Xiaogang Dai, Tongming Yin, Ning Ye
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.ppat.1004744

Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk
Cited by: 122
Author(s): Sebastian Schulz, Denitsa Eckweiler, Agata Bielecka, Tanja Nicolai, Raimo Franke, Andreas Dötsch, Klaus Hornischer, Sebastian Bruchmann, Juliane Düvel, Susanne Häußler
Software Mentions: 2
Published: over 11 years ago

10.1186/s12870-018-1526-8

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress
Cited by: 31
Author(s): Lingling Wang, Zhaoen Yang, Bin Zhang, Daoqian Yu, Ji Liu, Qian Gong, Ghulam Qanmber, Yi Li, Lili Lu, Yongjun Lin, Zuoren Yang, Fuguang Li
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1006582

Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing
Cited by: 53
Author(s): A.T. Shenoy, Terry Brissac, Ryan P. Gilley, Nikhil Kumar, Yong Wang, Norberto González-Juarbe, Whitney S. Hinkle, Sean C. Daugherty, Amol C. Shetty, Sandra Ott, Luke J. Tallon, Jessy Deshane, Hervé Tettelin, Carlos J. Orihuela
Software Mentions: 2
Published: about 9 years ago

10.1186/1742-4690-11-17

Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB
Cited by: 35
Author(s): Matthew S. Dahabieh, Marcel Ooms, Chanson J. Brumme, Jeremy M. G. Taylor, P. Richard Harrigan, Viviana Simon, Ivan Sadowski
Software Mentions: 2
Published: over 12 years ago

10.1186/s12870-019-1944-2

Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition
Cited by: 21
Author(s): Ying Wang, Zeyang Xiong, Qian Li, Yueyang Sun, Jing Jin, Hao Chen, Yu Zeng, Xingguo Huang, Yi Ding
Software Mentions: 2
Published: about 7 years ago

10.1155/2020/9381506

Metagenomic Analysis Exploring Taxonomic and Functional Diversity of Soil Microbial Communities in Sugarcane Fields Applied with Organic Fertilizer
Cited by: 11
Author(s): Ruoyu Li, Ziqin Pang, Yongmei Zhou, Nyumah Fallah, Chaohua Hu, Wenxiong Lin, Zhaonian Yuan
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-019-6388-4

Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome
Cited by: 24
Author(s): Konstantin V. Kuleshov, Gabriele Margos, Volker Fingerle, Joris Koetsveld, Irina A. Goptar, Mikhail L. Markelov, Nadezhda M. Kolyasnikova, Denis S. Sarksyan, Nina P. Kirdyashkina, German A. Shipulin, Joppe W. Hovius, Alexander E. Platonov
Software Mentions: 2
Published: over 6 years ago

10.1093/jxb/erx336

A disulfide bond A-like oxidoreductase is a strong candidate gene for self-incompatibility in apricot (Prunus armeniaca) pollen
Cited by: 20
Author(s): Juan Vicente Muñoz-Sanz, Elena Zuriaga, M. L. Badenes, Carlos Romero
Software Mentions: 2
Published: about 9 years ago

10.1186/s12870-014-0281-8

Non-specific lipid transfer proteins in maize
Cited by: 68
Author(s): Kaifa Wei, Xiaojun Zhong
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-13-429

Identification and analysis of pig chimeric mRNAs using RNA sequencing data
Cited by: 15
Author(s): Lei Ma, Shulin Yang, Weihua Zhao, Zhonglin Tang, Tingting Zhang, Kui Li
Software Mentions: 2
Published: about 14 years ago

10.1186/s12864-019-6146-7

DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori
Cited by: 15
Author(s): Haoling Huang, Ping Wu, Shaolun Zhang, Qi Shang, Haotong Yin, Qirui Hou, Jinbo Zhong, Xijie Guo
Software Mentions: 2
Published: almost 7 years ago

10.1093/jxb/erv203

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening
Cited by: 166
Author(s): Bin Zhu, Yanmin Yang, Ran Li, Daqi Fu, Liwei Wen, Yunbo Luo, Hongliang Zhu
Software Mentions: 2
Published: over 11 years ago

10.1093/jxb/erx384

Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatula
Cited by: 74
Author(s): Tianzuo Wang, Mingfeng Zhao, Xiuxiu Zhang, Min Liu, Chen-ge Yang, Yuhui Chen, Rujin Chen, Jiangqi Wen, Kirankumar S. Mysore, Wenhao Zhang
Software Mentions: 2
Published: almost 9 years ago

10.1534/genetics.117.300546

Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population
Cited by: 36
Author(s): Boby Mathew, Jens Léon, Wiebke Sannemann, Mikko J. Sillanpää
Software Mentions: 2
Published: over 8 years ago

10.1186/s13068-016-0440-2

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition
Cited by: 205
Author(s): Cheng Wang, Dan Dong, Haoshu Wang, Karin Müller, Yong Qin, Hailong Wang, Weixiang Wu
Software Mentions: 2
Published: over 10 years ago

10.1186/s12711-021-00657-8

Long-range linkage disequilibrium in French beef cattle breeds
Cited by: 7
Author(s): Abdelmajid El Hou, Dominique Rocha, Eric Venot, Véronique Blanquet, Romain Philippe
Software Mentions: 2
Published: about 5 years ago

10.1128/genomeA.00802-14

Whole-Genome Sequences of Three Symbiotic <i>Endozoicomonas</i> Strains
Cited by: 52
Author(s): Matthew J. Neave, Craig Michell, Amy Apprill, Christian R. Voolstra
Software Mentions: 2
Published: about 12 years ago

10.1590/1678-4685-GMB-2018-0235

Genome-wide identification and characterization of R2R3-MYB genes in Medicago truncatula
Cited by: 15
Author(s): Wei Li, Ying Liu, Jianfeng Zhao, Xin Zhen, Changhong Guo, Yongjun Shu
Software Mentions: 2
Published: about 7 years ago

10.1590/1678-4685-GMB-2020-0155

Genomic sequencing of two isolates of Ralstonia solanacearum causing Sergipe facies and comparative analysis with Bugtok disease isolates
Cited by: 3
Author(s): Jéssica Rodrigues da Silva, Ana Karolina Leite Pais, Greecy Mirian Rodrigues Albuquerque, Adriano Márcio Freire Silva, Wilson José Silva, Valdir de Queiroz Balbino, M. E. N. Fonseca, Marco Aurélio Siqueira da Gama, Elineide Barbosa de Souza, Rosa de Lima Ramos Mariano
Software Mentions: 2
Published: almost 7 years ago

10.1186/gb-2009-10-9-r94

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
Cited by: 141
Author(s): Scott DiGuistini, Nancy Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K. Chan, T. Roderick Docking, İnanç Birol, Robert A. Holt, Martin Hirst, Elaine R. Mardis, Marco A. Marra, Richard Hamelin, Jörg Bohlmann, Colette Breuil, Steven J.M. Jones
Software Mentions: 2
Published: almost 18 years ago

10.1186/s13568-021-01182-z

Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere
Cited by: 20
Author(s): Matthew Chekwube Enebe, Olubukola Oluranti Babalola
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12040608

Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles
Cited by: 2
Author(s): Sofia M. Kolchanova, Aleksey Komissarov, Sergei Kliver, Anyi Mazo‐Vargas, Yashira Afanador, Jafet Vélez-Valentín, Ricardo Valentín de la Rosa, Stephanie O Castro-Marquez, Israel Rivera-Colon, Audrey J. Majeske, Walter Wolfsberger, Taylor Hains, André Corvelo, Juan-Carlos Martinez-Cruzado, Travis C. Glenn, Orlando Robinson, Klaus Peter Koepfli, Tarás K. Oleksyk
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-018-1300-y

Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening
Cited by: 49
Author(s): Minghui Wang, Weihua Zhao, Lei Gao, Lingxia Zhao
Software Mentions: 2
Published: over 8 years ago

10.1186/s12870-017-0983-9

Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s
Cited by: 47
Author(s): LI Xu-yan, Xin Xie, Ji Li, Yuhai Cui, Yanming Hou, Lulu Zhai, Xiao Wang, Yanli Fu, Ranran Liu, Shaomin Bian
Software Mentions: 2
Published: over 9 years ago

10.3390/genes12030401

A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni
Cited by: 4
Author(s): Isa Schön, Fernando Rodríguez, Matthew Dunn, Koenraad Martens, Michael Shribak, Irina R. Arkhipova
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-021-03115-1

A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)
Cited by: 4
Author(s): Jianhua Zhao, Haoxia Li, Yuhui Xu, Yue Yin, Ting Huang, Bo Zhang, Yajun Wang, Yanlong Li, Yang Cao, Wei An
Software Mentions: 2
Published: about 5 years ago

10.3390/genes12040535

Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere
Cited by: 6
Author(s): Matthew Chekwube Enebe, Olubukola Oluranti Babalola
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12071022

The Influence of Soil Fertilization on the Distribution and Diversity of Phosphorus Cycling Genes and Microbes Community of Maize Rhizosphere Using Shotgun Metagenomics
Cited by: 12
Author(s): Matthew Chekwube Enebe, Olubukola Oluranti Babalola
Software Mentions: 2
Published: over 5 years ago

10.1093/jxb/erz541

Mutations of two FERONIA-like receptor genes enhance rice blast resistance without growth penalty
Cited by: 35
Author(s): Zhuhong Yang, Junjie Xing, Long Wang, Yue Liu, Jianing Qu, Yang Tan, Xiqin Fu, Qinlu Lin, Huafeng Deng, Feng Yu
Software Mentions: 2
Published: over 6 years ago

10.1186/1742-4690-10-126

Functional conservation of HIV-1 Gag: implications for rational drug design
Cited by: 56
Author(s): Guangdi Li, Jens Verheyen, Soo-Yon Rhee, Arnout Voet, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-016-2631-4

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding
Cited by: 48
Author(s): Pietro Gramazio, José Blanca, Peio Ziarsolo, Francisco Javier Herraiz, Jaime Prohens, Jaime Prohens, Santiago Vilanova
Software Mentions: 2
Published: over 10 years ago

10.3390/genes10100730

Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis
Cited by: 14
Author(s): Ruibin Sun, Shaohui Wang, Dan Ma, Yilin Li, Chuanliang Liu
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10020119

Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis
Cited by: 27
Author(s): Xianyan Zou, Àiyīng Liú, Zhen Zhang, Qún Gě, Senmiao Fan, Wànkuí Gǒng, Jùnwén Lǐ, Jǔwǔ Gōng, Yùzhēn Shí, Bin Tian, Yanling Wang, Ruixian Liu, Kang Lei, Qi Zhang, Xiao Jiang, Yulong Feng, Shuya Zhang, Tingting Jia, Lipeng Zhang, Yǒulù Yuán, Hǎihóng Shāng
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10070537

Genome-Wide Identification and Characterization of Xyloglucan Endotransglycosylase/Hydrolase in Ananas comosus during Development
Cited by: 15
Author(s): Qingyun Li, Huayang Li, Chongyang Yin, Xiaotong Wang, Qing Jiang, Rui Zhang, Fangfang Ge, Yudong Chen, Long Yang
Software Mentions: 2
Published: about 7 years ago

10.3390/genes11040353

Genome-Wide Identification, Classification, and Expression Profiling Reveals R2R3-MYB Transcription Factors Related to Monoterpenoid Biosynthesis in Osmanthus fragrans
Cited by: 18
Author(s): Haiyan Li, Yuanzheng Yue, Wenjie Ding, Gongwei Chen, Ling Li, Yuli Li, Tingting Shi, Xia Yang
Software Mentions: 2
Published: over 6 years ago

10.3390/genes10010071

Genome-Wide Identification and Expression Profiling of Sugar Transporter Protein (STP) Family Genes in Cabbage (Brassica oleracea var. capitata L.) Reveals their Involvement in Clubroot Disease Responses
Cited by: 29
Author(s): Wei Zhang, Shenyun Wang, Fangwei Yu, Jun Tang, Li Yu, Hong Wang, Jianbin Li
Software Mentions: 2
Published: over 7 years ago

10.3390/genes9110547

Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes
Cited by: 32
Author(s): Shuaibin Wang, Qingwei Song, Shanshan Li, Zhigang Hu, Dong Gao, Chi Song, Hongwen Huang, Yifei Liu
Software Mentions: 2
Published: almost 8 years ago

10.3390/genes10020081

Complete Genome Sequence Analysis and Characterization of Selected Iron Regulation Genes of Pasteurella Multocida Serotype A Strain PMTB2.1
Cited by: 7
Author(s): Shagufta Jabeen, Huan Yong Yap, Faez Firdaus Jesse Abdullah, Zunita Zakaria, Nurulfiza Mat Isa, Yung-Chie Tan, Yap S Joo, Dilan Amila Satharasinghe, Abdul Rahman Omar
Software Mentions: 2
Published: over 7 years ago

10.1186/s13568-017-0490-2

Metagenomic analysis reveals potential interactions in an artificial coculture
Cited by: 8
Author(s): Mei Ren, Guiying Zhang, Zi Ye, Zhixian Qiao, Meili Xie, Yan Lin, Tao Li, Jindong Zhao
Software Mentions: 2
Published: almost 9 years ago

10.3390/genes10020131

Evolution and Identification of the WRKY Gene Family in Quinoa (Chenopodium quinoa)
Cited by: 20
Author(s): Hong Yue, Xi Chang, Yongqiang Zhi, Lan Wang, Guangwei Xing, Weining Song, Xiaojun Nie
Software Mentions: 2
Published: over 7 years ago

10.3390/genes11050510

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)
Cited by: 17
Author(s): S.-H. Rong, Zhiyang Wu, Zizhang Cheng, Shan Zhang, Huan Liu, Qianming Huang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-020-02508-y

Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)
Cited by: 8
Author(s): Mengdi Li, Aqin Cao, Ruihua Wang, Zeyu Li, Shaoqing Li, Jianbo Wang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-5442-6

Identification of lncRNAs involved in rice ovule development and female gametophyte abortion by genome-wide screening and functional analysis
Cited by: 33
Author(s): Helian Liu, Ruihua Wang, Bigang Mao, Baisuo Zhao, Jianbo Wang
Software Mentions: 2
Published: over 7 years ago

10.3390/genes9020035

Genome-Wide Characterization of Heat-Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress
Cited by: 31
Author(s): Jianxia Liu, Runmei Wang, Wenying Liu, Hongli Zhang, Yi Guo, Rong Wen
Software Mentions: 2
Published: over 8 years ago

10.1186/s12870-015-0508-3

Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt
Cited by: 53
Author(s): Jie‐Yin Chen, Jinqun Huang, Nan‐Yang Li, Xuefeng Ma, Jinlong Wang, Chuan Liu, Yongfeng Liu, Yong Liang, Yuming Bao, Xiaofeng Dai
Software Mentions: 2
Published: over 11 years ago

10.1186/s12870-021-02999-3

A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era
Cited by: 14
Author(s): Wenxi Jiang, Chengzhi Jiang, Weiguang Yuan, Meijun Zhang, Zijie Fang, Yang Li, Chang-Jiu Li, Jia Ju, Zujun Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-017-4282-5

Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes
Cited by: 15
Author(s): Zhiwen Chen, Hushuai Nie, Yumei Wang, Haili Pei, Shuangshuang Li, Lida Zhang, Jinping Hua
Software Mentions: 2
Published: almost 9 years ago

10.3390/genes9020070

Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)
Cited by: 38
Author(s): Hong Yue, Duntao Shu, Meng Wang, Guangwei Xing, Haoshuang Zhan, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 2
Published: over 8 years ago

10.1093/g3journal/jkab209

Transcriptomic and photosynthetic responses to grafting of the <i>Nod1</i> gene in nodulated and non-nodulated soybeans
Cited by: 2
Author(s): Qingyuan He, Shihua Xiang, Wubin Wang, Yingjie Shu, Zhengpeng Li, Songhua Wang, Lei Chen, Xiao-Yan Yang, Tuanjie Zhao
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-016-2980-z

Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening
Cited by: 27
Author(s): Ophélie Jouffroy, Surya Saha, Lukas A. Mueller, Hadi Quesneville, Florian Maumus
Software Mentions: 2
Published: about 10 years ago

10.1093/g3journal/jkaa007

Genomic analyses of two Italian oyster mushroom <i>Pleurotus pulmonarius</i> strains
Cited by: 6
Author(s): Guillermo Vidal-Diez de Ulzurrun, Yi-Yun Lee, Jason E. Stajich, Erich M. Schwarz, Yu-Ting Hsueh
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes9040185

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
Cited by: 17
Author(s): Sergei Kliver, Mikhail Rayko, Alexey Komissarov, Evgeny Bakin, Daria V. Zhernakova, Kasavajhala V. S. K. Prasad, Catherine A. Rushworth, Ramamurthy Baskar, Dmitry Smetanin, Jeremy Schmutz, Daniel S. Rokhsar, Thomas Mitchell‐Olds, Ueli Grossniklaus, Vladimir Brukhin
Software Mentions: 2
Published: over 8 years ago

10.3390/genes11091026

Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence
Cited by: 17
Author(s): K N S Usha Kiranmayee, C. Tom Hash, Sivasubramani Selvanayagam, Punna Ramu, BhanuPrakash Amindala, Abhishek Rathore, P. B. Kavi Kishor, Rajeev Gupta, Santosh Deshpande
Software Mentions: 2
Published: about 6 years ago

10.1534/g3.118.200481

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes
Cited by: 12
Author(s): Yingpeng Hua, Ting Zhou, Qiong Liao, Haixing Song, Chunyun Guan, Zhenhua Zhang
Software Mentions: 2
Published: about 8 years ago

10.1534/g3.119.400262

Developing a High-Quality Linkage Map for the Atlantic Killifish<i>Fundulus heteroclitus</i>
Cited by: 10
Author(s): Jeffrey T. Miller, Noah M. Reid, Diane Nacci, Andrew Whitehead
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1007003

Genomics-enabled analysis of the emergent disease cotton bacterial blight
Cited by: 36
Author(s): Anne Z. Phillips, Jeffrey C. Berry, Mark C. Wilson, Anupama Vijayaraghavan, Jillian Burke, Jason Bunn, Tom Allen, Terry A. Wheeler, Rebecca Bart
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1000875

Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System
Cited by: 68
Author(s): Ana M. Tomljenovic-Berube, David T. Mulder, Matthew D. Whiteside, Fiona S. L. Brinkman, Brian K. Coombes
Software Mentions: 2
Published: over 16 years ago

10.1534/g3.120.401460

Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in <i>Brassica napus</i>
Cited by: 16
Author(s): Chuanji Zhao, Lijiang Liu, Luqman Bin Safdar, Meili Xie, Xiaohui Cheng, Yueying Liu, Yu‐Tao Xiang, Chaobo Tong, Jinxing Tu, Junyan Huang, Liu S
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1005001

Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells
Cited by: 71
Author(s): Fujun Qin, Zhenguo Song, Mihaela Babiceanu, Yansu Song, Loryn Facemire, Ritambhara Singh, Mazhar Adli, Hui Li
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1002070

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
Cited by: 492
Author(s): Stephen B. Goodwin, Sarrah Ben M’Barek, Braham Dhillon, Alexander H. J. Wittenberg, Charles F. Crane, James K. Hane, Andrew J. Foster, Theo A. J. van der Lee, Jane Grimwood, Andrea Aerts, J. F. Antoniw, Andy M. Bailey, Burt H. Bluhm, Judith Bowler, Jim Bristow, Ate van der Burgt, Blondy Canto-Canché, Alice C. L. Churchill, Laura Conde-Ferráez, H. J. Cools, Pedro M. Coutinho, Michael Csukai, Paramvir Dehal, P.J.G.M. de Wit, Bruno Giuliano Garisto Donzelli, H.C. van de Geest, Roeland C. H. J. van Ham, K. E. Hammond‐Kosack, Bernard Henrissat, Andrzej Kilian, Adilson Kenji Kobayashi, Edda Koopmann, Yiannis A. I. Kourmpetis, Arnold Kuzniar, Erika Lindquist, Vincent Lombard, Chris Maliepaard, N. F. Martins, Rahim Mehrabi, Jan Peter Nap, A. Ponomarenko, J. J. Rudd, Asaf Salamov, Jeremy Schmutz, Henk J. Schouten, Harris Shapiro, Ioannis Stergiopoulos, Stefano F. F. Torriani, Hank Tu, Ronald P. de Vries, C. Waalwijk, S.B. Ware, Ad Wiebenga, L.H. Zwiers, Richard P. Oliver, Igor V. Grigoriev, G.H.J. Kema
Software Mentions: 2
Published: over 15 years ago

10.1186/s12859-016-1148-9

IGDD: a database of intronless genes in dicots
Cited by: 21
Author(s): Hanwei Yan, Xiaogang Dai, Kai Feng, Qiuyue Ma, Tongming Yin
Software Mentions: 2
Published: about 10 years ago

10.1534/g3.114.015933

Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains
Cited by: 20
Author(s): Stephen L. Pearce, John G. Oakeshott, Gyanendra Pandey
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1009760

Genomic anatomy of male-specific microchromosomes in a gynogenetic fish
Cited by: 16
Author(s): Miao Ding, Xi-Yin Li, Zhixuan Zhu, Junhui Chen, Meng Lu, Qian Shi, Yang Wang, Zhi Li, Xin Zhao, Tao Wang, Wenxuan Du, Changxing Miao, Tian-Zi Yao, Mingtao Wang, Xiaojuan Zhang, Zhongwei Wang, Li Zhou, Jian‐Fang Gui
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-019-5454-2

Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses
Cited by: 43
Author(s): Wei Zhang, Shenyun Wang, Fangwei Yu, Jun Tang, Shibo Xi, Kan Bao, Li Yu, Hong Wang, Zhangjun Fei, Jianbin Li
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.115.017921

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon
Cited by: 33
Author(s): Yizhou Wang, Kristina M. Smith, John W. Taylor, Michael Freitag, Jason E. Stajich
Software Mentions: 2
Published: about 11 years ago

10.1534/g3.120.401361

Completed Genomic Sequence of<i>Bacillus thuringiensis</i>HER1410 Reveals a<i>Cry</i>-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage
Cited by: 15
Author(s): Ana Lechuga, Cédric Lood, Margarita Salas, Vera van Noort, Rob Lavigne, Modesto Redrejo-Rodríguez
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-15-699

Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes
Cited by: 81
Author(s): Mari Miyamoto, Daisuke Motooka, Kazuyoshi Gotoh, Takeshi Imai, Kazutoshi Yoshitake, Naohisa Goto, Tetsuya Iida, Teruo Yasunaga, Toshihiro Horii, Kazuharu Arakawa, Masahiro Kasahara, Shota Nakamura
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pgen.1000538

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution
Cited by: 87
Author(s): Lucia Carbone, R. Alan Harris, Gery M. Vessere, Alan R. Mootnick, Sean Humphray, Jane Rogers, Sung K. Kim, Jeffrey D. Wall, David I. K. Martin, Jerzy Jurka, Aleksandar Milosavljevic, Pieter J. de Jong
Software Mentions: 2
Published: over 17 years ago

10.18632/aging.103650

hsa_circRNA6448-14 promotes carcinogenesis in esophageal squamous cell carcinoma
Cited by: 5
Author(s): Yaowen Zhang, Xiang Yuan, Ning J. Yue, Lidong Wang, Junqi Liu, Ning Dai, Haijun Yang, Ruitai Fan, Fuyou Zhou
Software Mentions: 2
Published: about 6 years ago