10.3390/ijms22094326

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly
Cited by: 10
Author(s): Parwinder Kaur, Christopher Lui, Olga Dudchenko, Raja Sekhar Nandety, Bhavna Hurgobin, Melanie Pham, E Aiden, Jiangqi Wen, Kirankumar S. Mysore
Software Mentions: 3
Published: over 5 years ago

10.1186/s12951-021-01047-4

An atherosclerotic plaque-targeted single-chain antibody for MR/NIR-II imaging of atherosclerosis and anti-atherosclerosis therapy
Cited by: 15
Author(s): Liwei Zhang, Sheng Xue, Feng Ren, Si-Yang Huang, Ruizhi Zhou, Yu Wang, Chunxiao Zhou, Zhen Li
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.20739

Biomarkers identified for prostate cancer patients through genome-scale screening
Cited by: 10
Author(s): Lei‐Yun Wang, Jiajia Cui, Tao Zhu, Wei Shao, Yi Zhao, Qianqian Wang, Yupeng Zhang, Ji-Chu Wu, Le Zhang
Software Mentions: 3
Published: about 9 years ago

10.3390/ijms21238934

Identification and Characterization of PLATZ Transcription Factors in Wheat
Cited by: 20
Author(s): Yuxin Fu, Mengping Cheng, Maolian Li, Xiaojiang Guo, Yongrui Wu, Jirui Wang
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21103529

Soil Microbiome Response to Contamination with Bisphenol A, Bisphenol F and Bisphenol S
Cited by: 28
Author(s): Magdalena Zaborowska, Jadwiga Wyszkowska, Agata Borowik
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms21103660

Genome-Wide Dissection of the CRF Gene Family in Brassica napus Indicates that BnaCRF8s Specifically Regulate Root Architecture and Phosphate Homeostasis against Phosphate Fluctuation in Plants
Cited by: 7
Author(s): Sheliang Wang, Hao Zhang, Lei Shi, Fangsen Xu, Guangda Ding
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms20184593

Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry (Fragaria vesca)
Cited by: 16
Author(s): Hong Chen, Huihui Li, Xiaoyan Lu, Longzheng Chen, Jing Liu, Hongmiao Wu
Software Mentions: 3
Published: about 7 years ago

10.3390/ijms19092525

Opposite Polarity Monospore Genome De Novo Sequencing and Comparative Analysis Reveal the Possible Heterothallic Life Cycle of Morchella importuna
Cited by: 28
Author(s): Wei Liu, LianFu Chen, Yingli Cai, Qianqian Zhang, Yinbing Bian
Software Mentions: 3
Published: about 8 years ago

10.3390/ijms21020483

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes
Cited by: 25
Author(s): Wei Liu, Yingli Cai, Qianqian Zhang, Shu Fang, Lianfu Chen, Xiaolong Ma, Yinbing Bian
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0010433

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments
Cited by: 259
Author(s): Paul Janssen, Rob Van Houdt, Hugo Moors, Pieter Monsieurs, Nicolas Morin, Arlette Michaux, Mohammed Abderrafi Benotmane, Natalie Leys, Tatiana Vallaeys, Alla Lapidus, Sébastien Monchy, Claudine Médigue, Safiyh Taghavi, S. McCorkle, John J. Dunn, Daniël van der Lelie, Max Mergeay
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0201854

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice
Cited by: 21
Author(s): Xiang Li, Hang Yu, Yamin Jiao, Muhammad Qasim Shahid, Jinwen Wu, Xiangdong Liu
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0010795

Identification of Novel Pathogenicity Loci in Clostridium perfringens Strains That Cause Avian Necrotic Enteritis
Cited by: 90
Author(s): Dion Lepp, Bryan Roxas, Valeria R. Parreira, Pradeep Reddy Marri, Everett L. Rosey, Joshua Gong, J. Glenn Songer, Gayatri Vedantam, John F. Prescott
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0196588

FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer
Cited by: 42
Author(s): Priyabrata Panigrahi, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.19084

Two subunits of human ORC are dispensable for DNA replication and proliferation
Cited by: 32
Author(s): Etsuko Shibata, Manjari Kiran, Yoshiyuki Shibata, Samarendra Kumar Singh, Shashi Kiran, Anindya Dutta
Software Mentions: 3
Published: almost 10 years ago

10.1155/2017/1278932

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis
Cited by: 39
Author(s): Georgios A. Pavlopoulos, David Páez-Espino, Nikos C. Kyrpides, Ioannis Iliopoulos
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0129396

Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome
Cited by: 26
Author(s): Ching-Ping Lin, Chih‐Yuan Ko, Ching-I Kuo, Mao-Sen Liu, Roland Schafleitner, Long-Fang Oliver Chen
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-15-255

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans
Cited by: 19
Author(s): Ismael A. Vergara, Maja Tarailo‐Graovac, Christian Frech, Jun Wang, Zhaozhao Qin, Ting Zhang, Rong She, Jeffrey Shih-Chieh Chu, Ke Wang, Nansheng Chen
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-021-07378-8

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton
Cited by: 19
Author(s): Dou Liu, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Hǎihóng Shāng, Hongbin Li, Gao Xiao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-6319-4

Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae
Cited by: 14
Author(s): Jing Li, Xiaotong Gao, Shiye Sang, Changning Liu
Software Mentions: 3
Published: almost 7 years ago

10.1111/tpj.14115

High intraspecific diversity of <i>Restorer‐of‐fertility‐like</i> genes in barley
Cited by: 21
Author(s): Joanna Melonek, Ruonan Zhou, Philipp E. Bayer, David Edwards, Nils Stein, Ian Small
Software Mentions: 3
Published: almost 8 years ago

10.1111/tpj.12600

The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression
Cited by: 31
Author(s): Katie Baker, Micha Bayer, Nicola Cook, Steven Dreißig, Taniya Dhillon, Joanne Russell, Pete E. Hedley, Jenny Morris, Luke Ramsay, Isabelle Colas, Robbie Waugh, Brian J. Steffenson, Iain Milne, Gordon Stephen, David Marshall, Andrew J. Flavell
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pntd.0001512

Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing
Cited by: 85
Author(s): Adriano C. Coelho, Sébastien Boisvert, Avinaba Mukherjee, Philippe Leprohon, Jacques Corbeil, Marc Ouellette
Software Mentions: 3
Published: over 14 years ago

10.3390/ijerph17031009

Geographical Patterns of Algal Communities Associated with Different Urban Lakes in China
Cited by: 15
Author(s): Shengnan Chen, Hao He, Rongrong Zong, Kaiwen Liu, Miaomiao Yan, Lei Xu, Yutian Miao
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-13-545

Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens
Cited by: 98
Author(s): Jihye Park, Ying Zhang, Anne M. Buboltz, Xuqing Zhang, Stephan C. Schuster, Umesh Ahuja, Minghsun Liu, Jeff F. Miller, Mohammed Sebaihia, Stephen D. Bentley, Julian Parkhill, Eric T. Harvill
Software Mentions: 3
Published: almost 14 years ago

10.1155/2016/1562041

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max
Cited by: 2
Author(s): Kevin Lambirth, Adam M. Whaley, Jessica A. Schlueter, Kenneth J. Piller, Kenneth L. Bost
Software Mentions: 3
Published: almost 10 years ago

10.1155/2021/6289174

Comparative Analysis of the Glutathione S-Transferase Gene Family of Four Triticeae Species and Transcriptome Analysis of GST Genes in Common Wheat Responding to Salt Stress
Cited by: 24
Author(s): Yongchao Hao, Shoushen Xu, Zhongfan Lyu, Hong Wei Wang, Lingrang Kong, Silong Sun
Software Mentions: 3
Published: over 5 years ago

10.1111/acel.13357

Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions
Cited by: 8
Author(s): Xiao Dong, Shixiang Sun, Lei Zhang, Seung-Soo Kim, Zhidong Tu, Cristina Montagna, Alexander Y. Maslov, Yousin Suh, Tao Wang, Judith Campisi, Jan Vijg
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0008935

Dual RNAseq analyses at soma and germline levels reveal evolutionary innovations in the elephantiasis-agent Brugia malayi, and adaptation of its Wolbachia endosymbionts
Cited by: 3
Author(s): Germain Chevignon, Vincent Foray, Mercedes M. Pérez‐Jiménez, Silvia Libro, Matthew Chung, Jeremy M. Foster, Frédéric Landmann
Software Mentions: 3
Published: over 5 years ago

10.3390/ijerph15040708

Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China
Cited by: 29
Author(s): Xiaojuan Wang, Jie Gu, Hua Gao, Xiaoqing Qian, Haichao Li
Software Mentions: 3
Published: over 8 years ago

10.1128/mBio.01399-18

<i>Leishmania</i> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification
Cited by: 76
Author(s): Giovanni Bussotti, Evi Gouzelou, Mariana Côrtes Boité, Ihcene Kherachi Djenad, Zoubir Harrat, Naouel Eddaikra, Jeremy C. Mottram, Μαρία Αντωνίου, Vasiliki Christodoulou, Aymen Bali, Fatma Z. Guerfali, Dhafer Laouini, M. Shahid Mukhtar, Franck Dumetz, Jean‐Claude Dujardin, Despina Smirlis, Pierre Lechat, Pascale Pescher, Adil El Hamouchi, Meryem Lemrani, Carmen Chicharro, Ivonne Pamela Llanes-Acevedo, Laura Botana, Israel Cruz, Javier Moreno, Fakhri Jeddi, Abdul Karim, A. Bouratbine, Elisa Cupolillo, Gérald F. Späth
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1008646

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages
Cited by: 26
Author(s): Yufeng Fang, Marco A. Coelho, Haidong Shu, Klaas Schotanus, Bhagya C. Thimmappa, Vikas Yadav, H Chen, Ewa Malc, Jeremy Wang, Piotr A. Mieczkowski, Brent Kronmiller, Brett M. Tyler, Kaustuv Sanyal, Suomeng Dong, Minou Nowrousian, Joseph Heitman
Software Mentions: 3
Published: over 6 years ago

10.3390/jof6010007

Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1
Cited by: 5
Author(s): Ling Peng, Liangwei Li, Xiaochuan Liu, Jianwei Chen, Chengcheng Shi, Wenjie Guo, Qiwu Xu, Guangyi Fan, Xin Liu, Dehai Li
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.22152

Mapping the function of neuronal ion channels in model and experiment
Cited by: 32
Author(s): William F Podlaski, Alexander Seeholzer, Lukas N. Groschner, Gero Miesenböck, Rajnish Ranjan, Tim P. Vogels
Software Mentions: 3
Published: over 9 years ago

10.1007/s00122-019-03517-8

Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot
Cited by: 22
Author(s): Beatrice Corsi, Lawrence Percival‐Alwyn, Rowena Downie, Luca Venturini, Elyce M. Iagallo, Camila Campos Mantello, Charlie McCormick-Barnes, Pao Theen See, Richard P. Oliver, Caroline S. Moffat, James Cockram
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-014-0422-y

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
Cited by: 9
Author(s): Shi Tan, Avirup Dutta, Nicholas S. Jakubovics, Mia Yang Ang, Cheuk Chuen Siow, Naresh V.R. Mutha, Hamed Heydari, Wei Yee Wee, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: over 11 years ago

10.1007/s00122-016-2762-7

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat
Cited by: 51
Author(s): Huihuang Yan, Wubishet A. Bekele, Charlene P. Wight, Yuanying Peng, Tim Langdon, Robert G. Latta, Yong‐Bi Fu, Axel Diederichsen, Catherine Howarth, Eric N. Jellen, Brian Boyle, Yuming Wei, Nicholas A. Tinker
Software Mentions: 3
Published: about 10 years ago

10.7150/thno.53737

Intratumor heterogeneity of breast cancer detected by epialleles shows association with hypoxic microenvironment
Cited by: 5
Author(s): Yihan Wang, Yan Zhang, Yan Huang, Chuangeng Chen, Xingda Zhang, Ying Xing, Yue Gu, Mengyan Zhang, Li Cai, Shouping Xu, Baoqing Sun
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1008980

VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
Cited by: 1
Author(s): Wojciech Wesołowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-09680-6

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
Cited by: 10
Author(s): Qi You, Xin Yi, Kang Zhang, Chunchao Wang, Xuelian Ma, Xueyan Zhang, Wenying Xu, Fuguang Li, Zhen Su
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-03528-9

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations
Cited by: 8
Author(s): Yufang Guo, Wei Kuang Lin, Qiuxia Chen, Verónica Vallejo, Ryan M. Warner
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-14-617

Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent
Cited by: 99
Author(s): Janja Zajc, Yongfeng Liu, Wenkui Dai, Zhenyu Yang, Jingzhi Hu, Cene Gostinčar, Nina Gunde‐Cimerman
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pgen.1006628

Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA
Cited by: 55
Author(s): Anders Berglund, Clara Navarrete, Martin K. M. Engqvist, Eike Hoberg, Zsolt Szilágyi, Robert W. Taylor, Claes M. Gustafsson, Maria Falkenberg, Anders R. Clausen
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-15363-z

LPPtiger software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets
Cited by: 45
Author(s): Zhixu Ni, Georgia Angelidou, Ralf Hoffmann, Maria Fedorova
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep32417

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 20
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 3
Published: about 10 years ago

10.1038/srep25107

Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns
Cited by: 27
Author(s): Weike Duan, Zhinan Huang, Xiaoming Song, Tongkun Liu, Hailong Liu, Xilin Hou, Ying Liu
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.1310

Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Cited by: 25
Author(s): Rakesh Kumar Majhi, S. K. Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush P. Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-13-S8-S8

An eQTL biological data visualization challenge and approaches from the visualization community
Cited by: 10
Author(s): Christopher W. Bartlett, Soo Yeon Cheong, Liping Hou, Jesse Paquette, Pek Yee Lum, Günter Jäger, Florian Battke, Corinna Vehlow, Julian Heinrich, Kay Nieselt, Ryo Sakai, Jan Aerts, William C. Ray
Software Mentions: 3
Published: over 14 years ago

10.1038/srep20957

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
Cited by: 9
Author(s): Sandra Steyaert, Jolien Diddens, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Antje Bakker, Nina Sohnius-Wilhelmi, Carolina Frankl-Vilches, Annemie Van der Linden, Wim Van Criekinge, Wim Vanden Berghe, Tim De Meyer
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-017-4110-y

Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes (Vitis vinifera L.)
Cited by: 45
Author(s): Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
Software Mentions: 3
Published: about 9 years ago

10.1038/s41597-019-0291-3

A de novo genome assembly of the dwarfing pear rootstock Zhongai 1
Cited by: 23
Author(s): C. Ou, Fei Wang, Jiahong Wang, Li Song, Yanjie Zhang, Ming Fang, Li Ma, Yanan Zhao, Shuling Jiang
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41597-019-0014-9

Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells
Cited by: 14
Author(s): Xiaoyong Li, Geng Tian, Yue Zhao, Ji Wu
Software Mentions: 3
Published: over 7 years ago

10.1038/srep02962

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Cited by: 17
Author(s): Jianliang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher M. Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera
Software Mentions: 3
Published: almost 13 years ago

10.3390/plants10091874

Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)
Cited by: 3
Author(s): Zhihua Xie, Weikang Rui, Yazhou Yuan, Xiaofei Song, Xing Liu, Xin Gong, Jianping Bao, Shaoling Zhang, Khanizadeh Shahrokh, Shutian Tao
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1006508

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
Cited by: 88
Author(s): Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Yingying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell, Jukka Corander
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0240916

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors
Cited by: 5
Author(s): Luisa M. Arias-Giraldo, Marina Muñoz, Carolina Hernández, Giovanny Herrera, Natalia Velásquez-Ortiz, Omar Cantillo-Barraza, Plutarco Urbano, Juan David Ramírez
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.53944

Loss of centromere function drives karyotype evolution in closely related Malassezia species
Cited by: 37
Author(s): Sundar Ram Sankaranarayanan, Giuseppe Ianiri, Marco A. Coelho, Hashim Reza, Bhagya C. Thimmappa, Promit Ganguly, Rakesh Netha Vadnala, Sheng Sun, Rahul Siddharthan, Christian Tellgren-Roth, Thomas L. Dawson, Joseph Heitman, Kaustuv Sanyal
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.6698

The synergistic effect of concatenation in phylogenomics: the case in Pantoea
Cited by: 11
Author(s): Marike Palmer, Stephanus N. Venter, Alistair R. McTaggart, Martin Petrus Albertus Coetzee, Stephanie van Wyk, Juanita R. Avontuur, Chrizelle W. Beukes, Gerda Fourie, Quentin C. Santana, Magriet A. van der Nest, Jochen Blom, Emma Theodora Steenkamp
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.10616

Transcriptome analysis reveals the mechanism of improving erect-plant-type peanut yield by single-seeding precision sowing
Cited by: 1
Author(s): Sha Yang, Jialei Zhang, Yi Geng, Zhongwei Tang, Wang Jian-guo, Feng Guo, Jingjing Meng, Quan Wang, Shubo Wan, Xinguo Li
Software Mentions: 2
Published: over 5 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

10.7717/peerj.9936

Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in <i>Gossypium hirsutum</i> L.
Cited by: 7
Author(s): Jingjing Wang, Zhaohai Du, Xuehan Huo, Juan Zhou, Chunmei Yu, Jingxia Zhang, Ao Pan, Xiaoyang Wang, Furong Wang, Jun Zhang
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.11647

Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in <i>Solanum tuberosum</i>
Cited by: 10
Author(s): Nida Mushtaq, Faiza Munir, Alvina Gul, Rabia Amir, Rehan Zafar Paracha
Software Mentions: 2
Published: over 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

10.1371/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

10.1128/AEM.01911-20

Critical Role of MetR/MetB/MetC/MetX in Cysteine and Methionine Metabolism, Fungal Development, and Virulence of Alternaria alternata
Cited by: 13
Author(s): Yunpeng Gai, Lei Li, Hongshen Ma, Brendan K. Riely, Bing Liu, Hongye Li
Software Mentions: 2
Published: over 5 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

10.1093/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

10.1155/2019/5604843

Microarray Analysis For Expression Profiles of lncRNAs and circRNAs in Rat Liver after Brain-Dead Donor Liver Transplantation
Cited by: 12
Author(s): Sanyang Chen, Hongbo Fang, Jie Li, Jihua Shi, Jiakai Zhang, Peihao Wen, Zhihui Wang, Yang Han, Shengli Cao, Huapeng Zhang, Hongwei Tang, Wenzhi Guo, Shuijun Zhang
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-021-07958-8

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues
Cited by: 10
Author(s): Jiecuo Duo, Huan Xiong, Xiongxiong Wu, Yuan Li, Jianping Si, Chao Zhang, Ran Duan
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-019-6133-z

Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya
Cited by: 15
Author(s): Gang Wang, Jingxian Lin, Yang Shi, Xiaoguang Chang, Yuanyuan Wang, Lin Guo, Wenhui Wang, Meijie Dou, Youjin Deng, Ray Ming, Jisen Zhang
Software Mentions: 2
Published: almost 7 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/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: over 17 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

10.1093/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

10.3390/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

10.3390/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

10.1186/s12864-018-4511-6

Evolutionary and expression analyses of soybean basic Leucine zipper transcription factor family
Cited by: 65
Author(s): Man Zhang, Qing Liu, Hongbo Shi, Mingliang Guo, Mengnan Chai, Qing-Yu He, Mei Yan, Du Cao, Lihua Zhao, Hanyang Cai, Yuan Qin
Software Mentions: 2
Published: over 8 years ago

10.1093/bioinformatics/btv433

ClicO FS: an interactive web-based service of Circos
Cited by: 78
Author(s): Wei-Hien Cheong, Yung-Chie Tan, Soon-Joo Yap, Kee-Peng Ng
Software Mentions: 2
Published: about 11 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

10.1590/1678-4685-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

10.1186/1471-2164-14-573

Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis)
Cited by: 160
Author(s): Xiaoming Song, Ying Liu, Xilin Hou
Software Mentions: 2
Published: about 13 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/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

10.3390/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/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/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/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

10.3390/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/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

10.3390/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

10.1186/s12864-018-4558-4

Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines
Cited by: 31
Author(s): Tanya Copley, Marc‐Olivier Duceppe, Louise S. O’Donoughue
Software Mentions: 2
Published: over 8 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

10.1093/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

10.3390/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

10.3390/genes11101134

Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance
Cited by: 16
Author(s): Shichao Liu, Ruibin Sun, Xiaojian Zhang, Zili Feng, Feng Wei, Lihong Zhao, Yalin Zhang, Longfu Zhu, Hongjie Feng, Heqin Zhu
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-14-397

Web-based visual analysis for high-throughput genomics
Cited by: 44
Author(s): Jeremy Goecks, Carl Eberhard, Tomithy Too, Anton Nekrutenko, James Taylor
Software Mentions: 2
Published: over 13 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

10.1186/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