10.1186/s12870-017-1165-5

Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)
Cited by: 27
Author(s): Haitao Li, Bo Wang, Qinghua Zhang, Jing Wang, Graham J. King, Kede Liu
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-015-1959-5

Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: about 11 years ago

10.1186/s12870-019-2196-x

Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.)
Cited by: 20
Author(s): Zihan Liu, Sha Li, Wei Li, Qi Liu, Lingli Zhang, Xiyue Song
Software Mentions: 3
Published: almost 7 years ago

10.1038/s42003-021-02559-3

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
Cited by: 63
Author(s): Caroline Belser, Franc-Christophe Baurens, Benjamin Noël, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hřibová, Jaroslav Doležel, Arnaud Lemainque, Patrick Wincker, Angélique D’Hont, Jean‐Marc Aury
Software Mentions: 3
Published: about 5 years ago

10.15252/embj.201489282

Aberrant methylation of t<scp>RNA</scp>s links cellular stress to neuro‐developmental disorders
Cited by: 426
Author(s): Sandra Blanco, Sabine Dietmann, Joana V. Flores, Shobbir Hussain, Claudia Kutter, Peter Humphreys, Margus Lukk, Patrick Lombard, Lucas Treps, Martyna Popis, Stefanie Kellner, Sabine M. Hölter, Lillian Garrett, Wolfgang Wurst, Lore Becker, Thomas Klopstock, Helmut Fuchs, Valérie Gailus‐Durner, Martin Hrabé de Angelis, Ragnhildur Thóra Káradóttir, Mark Helm, Jernej Ule, Joseph G. Gleeson, Duncan T. Odom, Michaela Frye
Software Mentions: 3
Published: over 12 years ago

10.3389/fgene.2021.671650

A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)
Cited by: 7
Author(s): Weidong Ding, Xinhui Zhang, Xiaomeng Zhao, Jing Wu, Zhen Cao, Jia Li, Yu Huang, Xinxin You, Min Wang, Qiong Shi, Xuwen Bing
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2014.00319

Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis
Cited by: 11
Author(s): Marianna Taffi, Nicola Paoletti, Claudio Angione, Sandra Pucciarelli, Mauro Marini, Píetro Lió
Software Mentions: 3
Published: about 12 years ago

10.3389/fgene.2019.00116

Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family in Gossypium
Cited by: 14
Author(s): Yupeng Cui, Jianjiang Ma, Guoyuan Liu, Nuohan Wang, Wenfeng Pei, Man Wu, Xingli Li, Jinfa Zhang, Jie-Ae Yu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-06877-4

Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max
Cited by: 4
Author(s): Kai Fan, Yunrui Chen, Zhijun Mao, Fang Yao, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jianping Liu, Jinwen Huang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-018-1386-2

High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time
Cited by: 23
Author(s): Gilad Gabay, Yardena Dahan, Yacov Izhaki, Adi Faigenboim, Giora Ben-Ari, Yonatan Elkind, Moshe A. Flaishman
Software Mentions: 3
Published: about 8 years ago

10.3390/cells8101253

Genome-Wide Mapping Defines a Role for C/EBPβ and c-Jun in Non-Canonical Cyclic AMP Signalling
Cited by: 5
Author(s): Jolanta Wiejak, Boy van Basten, Graham Hamilton, Stephen J. Yarwood
Software Mentions: 3
Published: about 7 years ago

10.1038/cr.2017.124

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
Cited by: 152
Author(s): Changsong Zou, A Chen, Li Xiao, H.-A. Müller, Peter Ache, Georg Haberer, M Zhang, Jia Wei, Ping Deng, Ru Huang, Daniel Lang, Li Feng, Dong Zhan, Xiaoyong Wu, H Zhang, Jennifer Böhm, Ruirui Liu, Lana Shabala, Rainer Hedrich, J-K Zhu
Software Mentions: 3
Published: about 9 years ago

10.3389/fimmu.2017.01063

Gut REG3γ-Associated Lactobacillus Induces Anti-inflammatory Macrophages to Maintain Adipose Tissue Homeostasis
Cited by: 16
Author(s): Yugang Huang, Houbao Qi, Zhiqian Zhang, Enlin Wang, Huan Yun, Hui Yan, Xiaomin Su, Yingquan Liu, Zenzen Tang, Yuan Gao, Wencong Shang, Zhou Jiang, Tianze Wang, Yongzhe Che, Yuan Zhang, Rongcun Yang
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-016-3336-4

The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance
Cited by: 53
Author(s): William T. Molin, Alice A. Wright, Amy Lawton‐Rauh, Christopher Saski
Software Mentions: 3
Published: almost 10 years ago

10.3389/fgene.2021.713224

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
Cited by: 18
Author(s): Ahmed H. El-Sappah, Rania G. Elbaiomy, Ahmed S. Elrys, Yu Wang, Yumin Zhu, Qiulan Huang, Yan Ke, Xingbo Zhao, Yun Li, Khaled A. El‐Tarabily, Jia Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s12866-020-01737-3

Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium
Cited by: 7
Author(s): Jiaokun Li, Tianyuan Gu, Liangzhi Li, Xueling Wu, Li Shen, Runlan Yu, Yuandong Liu, Guanzhou Qiu, Weimin Zeng
Software Mentions: 3
Published: over 6 years ago

10.1186/s13104-016-2069-4

Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus
Cited by: 4
Author(s): Matteo Buti, Daniel J. Sargent, Khethani Mhelembe, Pietro Delfino, K. R. Tobutt, Riccardo Velasco
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-019-2121-3

Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
Cited by: 14
Author(s): Juan Wang, Yuan Li, Chunjuan Li, Yan Cheng, Xiaobo Zhao, Cuiling Yuan, Quanxi Sun, Chengren Shi, Shiguang Shan
Software Mentions: 3
Published: almost 7 years ago

10.1007/s00401-013-1168-8

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
Cited by: 162
Author(s): Katja Kobow, Antony Kaspi, K N Harikrishnan, K. Kiese, Mark Ziemann, Ishant Khurana, Ina Fritzsche, Jan Hauke, Eric Hahnen, Roland Coras, Angelika Mühlebner, Assam El‐Osta, Ingmar Blümcke
Software Mentions: 3
Published: about 13 years ago

10.1186/s12920-017-0245-6

Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer
Cited by: 17
Author(s): Shirley Pepke, Greg Ver Steeg
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2016.00941

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field
Cited by: 23
Author(s): Donato Giovannelli, Giuseppe d’Errico, Federica Fiorentino, Daniele Fattorini, Francesco Regoli, Lorenzo Angeletti, Tatjana Bakran‐Petricioli, Costantino Vetriani, Mustafa Yücel, Marco Taviani, Elena Manini
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0185439

Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification
Cited by: 36
Author(s): Hailing Zhang, Yong Cao, Chaoqun Shang, Jikai Li, JianLi Wang, Zhenying Wu, Lichao Ma, Tianxiong Qi, Chunxiang Fu, Zetao Bai, HU Bao-zhong
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-016-2736-9

Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family
Cited by: 42
Author(s): Fengya Zheng, Haiyang Wu, Rongzhi Zhang, Shiming Li, Weiming He, Fuk‐Ling Wong, Genying Li, Shancen Zhao, Hon‐Ming Lam
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0249288

Characteristics and expression profiles of circRNAs during abdominal adipose tissue development in Chinese Gushi chickens
Cited by: 9
Author(s): Wenjiao Jin, Yaping Zhao, Bin Zhai, Yuanfang Li, Shengxin Fan, Pengtao Yuan, Guirong Sun, Ruirui Jiang, Yanbin Wang, Xiaojun Liu, Yadong Tian, Xiangtao Kang, Guoxi Li
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.00561

Genome-Wide Identification and Homoeologous Expression Analysis of PP2C Genes in Wheat (Triticum aestivum L.)
Cited by: 44
Author(s): Xiao‐Lan Yu, Jiapeng Han, Efan Wang, Jie Xiao, Rui Hu, Guangxiao Yang, Guoqing He
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.101461

The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese
Cited by: 20
Author(s): Xin Zhao, Xiaomin Liu, Aiping Zhang, Huashuai Chen, Qing Huo, Weiyang Li, Rui Ye, Zhihua Chen, Liping Liang, Alison Liu, Juan Shen, Xin Jin, Wenwen Li, Marianne Nygaard, Xiao Liu, Yong Hou, Ting Ni, Lars Bolund, William K. Gottschalk, Wei Tao, Jun Gu, Xiao-Li Tian, Huanming Yang, Jian Wang, Xun Xu, Michael W. Lutz, Junxia Min, Yi Zeng, Chao Nie
Software Mentions: 3
Published: over 8 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2019.01325

Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Cited by: 29
Author(s): Aniela B. Mundinger, Christopher E. Lawson, Mike S. M. Jetten, Hanna Koch, Sebastian Lücker
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0243270

The transcriptomic profiling of SARS-CoV-2 compared to SARS, MERS, EBOV, and H1N1
Cited by: 27
Author(s): Alsamman M. Alsamman, Hatem Zayed
Software Mentions: 3
Published: almost 6 years ago

10.3390/biology9090295

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing
Cited by: 33
Author(s): Girum Fitihamlak Ejigu, Jaehee Jung
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2019.00805

Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus
Cited by: 23
Author(s): Michał Bukowski, Rafał Piwowarczyk, Anna Mądry, Rafal Zagorski-Przybylo, Marcin Hydzik, Benedykt Władyka
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2020.01142

Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover
Cited by: 10
Author(s): Hongmiao Wu, Jinshen Xia, Xianjin Qin, Huiming Wu, Shengkai Zhang, Yanlin Zhao, Christopher Rensing, Wenxiong Lin
Software Mentions: 3
Published: over 6 years ago

10.1523/ENEURO.0205-16.2016

Graph Theoretic and Motif Analyses of the Hippocampal Neuron Type Potential Connectome
Cited by: 24
Author(s): Colin Rees, Diek W. Wheeler, D. R. Hamilton, Charise M. White, Alexander O. Komendantov, Giorgio A. Ascoli
Software Mentions: 3
Published: about 10 years ago

10.1155/2018/5206758

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in<i>Brassica rapa</i>
Cited by: 8
Author(s): Nadeem Khan, Chunmei Hu, Waleed Amjad Khan, Emal Naseri, Koeun Han, Hansong Dong, Xilin Hou
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-019-6416-4

Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line
Cited by: 10
Author(s): Shumin Zhou, Jinpeng Zhang, Hongyu Han, Jing Zhang, Huihui Ma, Zhi Zhang, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li, Lihui Li
Software Mentions: 3
Published: almost 7 years ago

10.1128/JVI.02083-19

Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain
Cited by: 11
Author(s): Syun suke Kadoya, Syun-ichi Urayama, Takuro Nunoura, Miho Hirai, Yoshihiro Takaki, Masaaki Kitajima, Toyoko Nakagomi, Osamu Nakagomi, Satoshi Okabe, Osamu Nishimura, Daisuke Sano
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-331

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells
Cited by: 40
Author(s): Suhn Kyong Rhie, Dennis J. Hazelett, Simon Coetzee, Chunli Yan, Houtan Noushmehr
Software Mentions: 3
Published: over 12 years ago

10.1155/2018/6023457

Genome-Wide Identification, Classification, and Expression Divergence of Glutathione-Transferase Family in<i> Brassica rapa</i> under Multiple Hormone Treatments
Cited by: 18
Author(s): Nadeem Khan, Chunmei Hu, Waleed Amjad Khan, Xilin Hou
Software Mentions: 3
Published: almost 9 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

10.18632/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

10.18632/oncotarget.26225

Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival
Cited by: 10
Author(s): Hanna Engqvist, Toshima Z. Parris, Elisabeth Werner Rönnerman, Elin Söderberg, Jana Biermann, Claudia Mateoiu, Karin Sundfeldt, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 3
Published: about 8 years ago

10.18632/oncotarget.13937

Conditionally reprogrammed normal and primary tumor prostate epithelial cells: a novel patient-derived cell model for studies of human prostate cancer
Cited by: 50
Author(s): Olga Timofeeva, Nancy Palechor-Ceron, Guanglei Li, Hang Yuan, Ewa Krawczyk, Xiaogang Zhong, Geng Li, Geeta Upadhyay, Aleksandra Dakić, Songtao Yu, Shuang Fang, Sujata Maiti Choudhury, Xueping Zhang, Andrew Ju, Myeong-Seon Lee, Dong Han, Youngmi Ji, Yong Hou, Yun‐Ling Zheng, Chris Albanese, Johng S. Rhim, Richard Schlegel, Anatoly Dritschilo, Xuefeng Li
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12859-017-1653-5

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
Cited by: 20
Author(s): Bertjan Broeksema, Magdalena Całusińska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem
Software Mentions: 3
Published: over 9 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: over 8 years ago

10.1002/path.4230

Distinct evolutionary trajectories of primary high‐grade serous ovarian cancers revealed through spatial mutational profiling
Cited by: 351
Author(s): Ali Bashashati, Gavin Ha, Alicia A. Tone, Jiarui Ding, Leah M Prentice, Andrew Roth, Jamie Rosner, Karey Shumansky, Steve E. Kalloger, Janine Senz, Winnie Yang, Melissa K. McConechy, Nataliya Melnyk, Michael S. Anglesio, Margaret Luk, Kane Tse, Thomas Zeng, Richard A. Moore, Yongjun Zhao, Marco A. Marra, Blake Gilks, Stephen Yip, David G. Huntsman, Jessica N. McAlpine, Sohrab P. Shah
Software Mentions: 3
Published: over 13 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

10.3390/ijms22094919

Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member
Cited by: 9
Author(s): Faiza Shafique Khan, Ren‐Fang Zeng, Zhi-Meng Gan, Jin‐Zhi Zhang, Chun-Gen Hu
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22169002

Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire
Cited by: 2
Author(s): Mojtaba Mohammadi, Eric A. Smith, M. E. Stanghellini, Rakesh Kaundal
Software Mentions: 3
Published: about 5 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

10.1371/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

10.1371/journal.pone.0189334

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
Cited by: 3
Author(s): Victor Renault, Jörg Tost, Fabien Pichon, Shu‐Fang Wang‐Renault, Éric Letouzé, Sandrine Imbeaud, Jessica Zucman‐Rossi, Jean‐François Deleuze, Alexandre How‐Kit
Software Mentions: 3
Published: almost 9 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

10.3390/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

10.1371/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/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/s20123362

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity
Cited by: 13
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
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

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn &amp; Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
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: almost 6 years ago

10.1038/s41598-021-89146-y

Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes
Cited by: 3
Author(s): Chris Smith
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-69389-x

A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics
Cited by: 22
Author(s): Honghao Lv, Yong Wang, Fengqing Han, Jialei Ji, Zhiyuan Fang, Mu Zhuang, Zhansheng Li, Yangyong Zhang, Limei Yang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-6404-8

EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis
Cited by: 0
Author(s): Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao‐Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung‐Yen Lin
Software Mentions: 3
Published: over 6 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

10.1038/s41598-019-54720-y

Statistical characteristics of amino acid covariance as possible descriptors of viral genomic complexity
Cited by: 7
Author(s): C. K. Sruthi, Meher K. Prakash
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-54446-x

High throughput barcoding method for genome-scale phasing
Cited by: 13
Author(s): David Redin, Tobias Frick, Hooman Aghelpasand, Max Käller, Erik Borgström, Remi‐André Olsen, Afshin Ahmadian
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-53802-1

Oral microbiome diversity in chimpanzees from Gombe National Park
Cited by: 14
Author(s): Andrew T. Ozga, Ian C. Gilby, Rebecca Nockerts, Michael L. Wilson, Anne E. Pusey, Anne C. Stone
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-017-4169-5

CGDV: a webtool for circular visualization of genomics and transcriptomics data
Cited by: 3
Author(s): Vineet Jha, Gulzar Singh, Sanjiv Kumar, Amol D. Sonawane, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: about 9 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

10.1038/s41598-019-53469-8

Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix)
Cited by: 6
Author(s): Xinhua Wang, Haiyang Liu, Maolin Pang, Bishi Fu, Xin Yu, Shunping He, Jingou Tong
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-39286-z

Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis)
Cited by: 41
Author(s): Dahe Qiao, Chun Yang, Juan Chen, Yan Guo, Yán Li, Suzhen Niu, Kemei Cao, Zhengwu Chen
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.3406

MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing
Cited by: 25
Author(s): Koji Ishiya, Shintaroh Ueda
Software Mentions: 3
Published: over 9 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

10.1038/s41598-018-36059-y

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: almost 12 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/s41598-018-37792-0

Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
Cited by: 20
Author(s): Girish Beedessee, Kanako Hisata, Michael C. Roy, Frances M. Van Dolah, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-50624-z

Diversity, Co-occurrence and Implications of Fungal Communities in Wastewater Treatment Plants
Cited by: 66
Author(s): Hailemariam Abrha Assress, Ramganesh Selvarajan, Hlengilizwe Nyoni, Khayalethu Ntushelo, Bhekie B. Mamba, Titus A.M. Msagati
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-23334-1

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
Cited by: 32
Author(s): Jinfang Zhang, Lijuan Wei, Jun Jiang, Annaliese S. Mason, Haojie Li, Cheng Cui, Linna Chai, Beibei Zheng, Yongqing Zhu, Qing Xia, Long Jiang, Donghui Fu
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-22237-5

Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity
Cited by: 13
Author(s): Álvaro Chiner‐Oms, Fernando Gónzález-Candelas, Iñaki Comas
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-17203-6

Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication
Cited by: 15
Author(s): Xinnian Xia, Lin Lin Luan, Gengsheng Qin, Yu Li, Zhi Wei Wang, Wan Chen Dong, Youjian Song, Yongli Qiao, Xian Sheng Zhang, Long Yang
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-018-2425-6

Tigmint: correcting assembly errors using linked reads from large molecules
Cited by: 86
Author(s): Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Ben Vandervalk, Sarah Yeo, Zhen‐Zhen Xue, Hamid Mohamadi, Jöerg Bohlmann, Steven J.M. Jones, İnanç Birol
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-20862-8

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions
Cited by: 79
Author(s): Nan Li, Yuezhu Wang, Chunping You, Jianke Ren, Chen Wan-yi, Huajun Zheng, Zhenmin Liu
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-018-30583-7

The landscape of the A-to-I RNA editome from 462 human genomes
Cited by: 14
Author(s): Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-017-10434-7

The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants
Cited by: 32
Author(s): Kamil Myszczyński, Alina Bączkiewicz, Katarzyna Buczkowska, Monika Ślipiko, Monika Szczecińska, Jakub Sawicki
Software Mentions: 3
Published: about 9 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

10.1038/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/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: about 9 years ago

10.1038/s41598-018-31770-2

Characterisation and functional predictions of canine long non-coding RNAs
Cited by: 24
Author(s): Céline Le Béguec, Valentin Wucher, Laëtitia Lagoutte, Édouard Cadieu, Nadine Botherel, Benoît. Hédan, Clotilde De Brito, Anne-Sophie Guillory, Catherine André, Thomas Derrien, Christophe Hitte
Software Mentions: 3
Published: about 8 years ago

10.3390/microorganisms8020182

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald
Cited by: 14
Author(s): Huili Zhang, Mbuya Sylvain Ntambo, Philippe Rott, Gongyou Chen, Lilan Chen, Mei-Ting Huang, San‐Ji Gao
Software Mentions: 3
Published: almost 7 years ago

10.3390/microorganisms8070981

Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves
Cited by: 15
Author(s): Yaoyue Wang, Qingmiao Shen, Shu Zhong, Yulin Chen, Yuxin Yang
Software Mentions: 3
Published: over 6 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

10.1038/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

10.1186/1471-2105-14-95

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes
Cited by: 34
Author(s): Jinkui Cheng, Zhiai Xu, Guomin Ren, Zhihua Liu
Software Mentions: 3
Published: over 13 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: about 13 years ago

10.1093/pcmedi/pbab012

Spaceflight decelerates the epigenetic clock orchestrated with a global alteration in DNA methylome and transcriptome in the mouse retina
Cited by: 7
Author(s): Zhong Chen, Seta Stanbouly, Nina C. Nishiyama, Xin Chen, Michael D. Delp, Hongyu Qiu, Xiao Wen Mao, Charles Wang
Software Mentions: 3
Published: over 5 years ago

10.1093/molbev/msaa109

Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study
Cited by: 12
Author(s): Bryan D. Clifton, Jamie Jimenez, Ashlyn Kimura, Zeinab Chahine, Pablo Librado, Alejandro Sánchez‐Gracia, Mashya Abbassi, Francisco Carranza, Carolus Chan, Marcella Marchetti, Wanting Zhang, Minjun Shi, Christine Hein Vu, Shu Dan Yeh, Laura Fanti, Xiao Qin Xia, Julio Rozas, José M. Ranz
Software Mentions: 3
Published: over 6 years ago

10.1186/s40168-019-0638-1

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms
Cited by: 52
Author(s): Matthew R. Olm, Patrick T. West, Brandon Brooks, Brian Firek, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 3
Published: over 7 years ago

10.1073/pnas.2005536117

Molecular causes of an evolutionary shift along the parasitism–mutualism continuum in a bacterial symbiont
Cited by: 12
Author(s): Paul Herrera, Lisa N Schuster, Cécilia Wentrup, Lena König, Thomas Kempinger, Hyunsoo Na, Jasmin Schwarz, Stephan Köstlbacher, Florian Wascher, Markus Zojer, Thomas Rattei, Matthias Horn
Software Mentions: 3
Published: about 6 years ago