bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1155/2021/5597135

A New Lectin from Auricularia auricula Inhibited the Proliferation of Lung Cancer Cells and Improved Pulmonary Flora
Cited by: 2
Author(s): Zhendong Liu, Liang Li, Bei Xue, Dandan Zhao, Yanlong Zhang, Xiufeng Yan
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-017-3251-3

Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients
Cited by: 16
Author(s): Thomas Urup, Line Mærsk Staunstrup, Signe Regner Michaelsen, Kristoffer Vitting-Seerup, Marc Bennedbæk, Anders Toft, Lars Rønn Olsen, Lars Jønson, Shohreh Issazadeh‐Navikas, Helle Broholm, Petra Hamerlik, Hans Skovgaard Poulsen, Ulrik Lassen
Software Mentions: 1
Published: over 9 years ago

10.1186/s12915-017-0354-x

MicroRNA miR-29 controls a compensatory response to limit neuronal iron accumulation during adult life and aging
Cited by: 70
Author(s): Roberto Ripa, Adam Antebi, Marco Terrigno, Luca Pandolfini, Aurora Savino, Valeria Arcucci, Marco Groth, Eva Terzibasi Tozzini, Mario Baumgart, Alessandro Cellerino
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-21371-4

Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy
Cited by: 28
Author(s): María Carolina Gallego Iradi, Judy C. Triplett, James Thomas, Rachel Davila, Anthony M Crown, Hilda Brown, Jada Lewis, Maurice S. Swanson, Guilian Xu, Edgardo Rodríguez-Lebrón, David R. Borchelt
Software Mentions: 1
Published: over 8 years ago

10.1155/2021/8875971

High FAM189B Expression and Its Prognostic Value in Patients with Gastric Cancer
Cited by: 3
Author(s): Changliang Wu, Quan-Xiao Tan, Dan Liŭ, Jun-E Jiang, Ting Lu, Zu-Mei Huang, Yingjie Su
Software Mentions: 1
Published: over 5 years ago

10.1155/2017/2503847

Fish Oil Feeding Modulates the Expression of Hepatic MicroRNAs in a Western-Style Diet-Induced Nonalcoholic Fatty Liver Disease Rat Model
Cited by: 11
Author(s): Hualin Wang, Yang Shao, Fahu Yuan, Na Li, Hongyu Zhang, Chaodong Wu, Zhiguo Liu
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms22063156

Megalocytivirus Induces Complicated Fish Immune Response at Multiple RNA Levels Involving mRNA, miRNA, and circRNA
Cited by: 11
Author(s): Qian Wu, Xianhui Ning, Li Sun
Software Mentions: 1
Published: over 5 years ago

10.1155/2020/7340312

Pediococcus acidilactici P25 Protected Caenorhabditis elegans against Enterotoxigenic Escherichia coli K88 Infection and Transcriptomic Analysis of Its Potential Mechanisms
Cited by: 9
Author(s): Keqin Tan, Dun Deng, Xianyong Ma, Yiyan Cui, Zhonghuan Tian
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-23714-7

Vitamin C promotes apoptosis in breast cancer cells by increasing TRAIL expression
Cited by: 61
Author(s): David W. Sant, Sushmita Mustafi, Christopher B. Gustafson, Joshua Chen, Joyce M. Slingerland, Gaofeng Wang
Software Mentions: 1
Published: over 8 years ago

10.1155/2020/9426204

Effects of Cardiac Sympathetic Neurodegeneration and PPARγ Activation on Rhesus Macaque Whole Blood miRNA and mRNA Expression Profiles
Cited by: 1
Author(s): Jeanette M. Metzger, Mary S. Lopez, Jenna Kropp Schmidt, Megan E. Murphy, Raghu Vemuganti, Marina E. Emborg
Software Mentions: 1
Published: over 6 years ago

10.1155/2019/6763596

Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer
Cited by: 8
Author(s): Anna Pačínková, Vlad Popovici
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-019-3247-x

A protocol to evaluate RNA sequencing normalization methods
Cited by: 64
Author(s): Zachary B. Abrams, Travis Johnson, Kun Huang, Philip R. O. Payne, Kevin R. Coombes
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-24284-4

Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice (Glycyrrhiza uralensis) plants under UV-B irradiation
Cited by: 33
Author(s): Xiao Zhang, Xiaoli Ding, Yaxi Ji, Shouchuang Wang, Yingying Chen, Jie Luo, Yingbai Shen, Peng Li
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-016-0926-8

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack
Cited by: 2
Author(s): Renée X. de Menezes, Leila Mohammadi, Jelle J. Goeman, Judith M. Boer
Software Mentions: 1
Published: over 10 years ago

10.1155/2020/3801748

Four Autophagy-Related lncRNAs Predict the Prognosis of HCC through Coexpression and ceRNA Mechanism
Cited by: 23
Author(s): Hao Wu, Tiantian Liu, Jianni Qi, Chengyong Qin, Qing Zhu
Software Mentions: 1
Published: about 6 years ago

10.1155/2019/7505260

RNA-Sequencing and Bioinformatics Analysis of Long Noncoding RNAs and mRNAs in the Prefrontal Cortex of Mice Following Repeated Social Defeat Stress
Cited by: 4
Author(s): Xian Wang, Shaolei Ma, Mao Mao, Caijuan Li, Xiaofeng Shen, Shunqing Xu, Jianjun Yang
Software Mentions: 1
Published: over 7 years ago

10.1155/2020/2671281

Identification and Analysis of Novel Biomarkers Involved in Chromophobe Renal Cell Carcinoma by Integrated Bioinformatics Analyses
Cited by: 2
Author(s): Wei Zhang, Yin Xu, Jinghan Zhang, Jun Wu
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-15-116

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs
Cited by: 36
Author(s): Mark A. van de Wiel, Maarten Neerincx, Tineke E. Buffart, Daoud Sie, Henk M.W. Verheul
Software Mentions: 1
Published: over 12 years ago

10.1186/s13048-021-00814-z

Plasma-derived exosomal miR-4732-5p is a promising noninvasive diagnostic biomarker for epithelial ovarian cancer
Cited by: 28
Author(s): Jingjing Liu, Ji Geun Yoo, Jung Ho, Yoon Young Jung, Sanha Lee, Soo Young Hur, Youn Jin Choi
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-64288-7

Transcriptome profile analysis of two Vicia faba cultivars with contrasting salinity tolerance during seed germination
Cited by: 19
Author(s): Fangwen Yang, Hongwei Chen, Changyan Liu, Li Li, Liangjun Liu, Xuesong Han, Zhengjie Wan, Aihua Sha
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-018-1307-4

Parallel evolution of storage roots in morning glories (Convolvulaceae)
Cited by: 14
Author(s): Lauren A. Eserman, Robert L. Jarret, James H. Leebens‐Mack
Software Mentions: 1
Published: over 8 years ago

10.1186/s12870-018-1237-1

Resistance to Plum Pox Virus (PPV) in apricot (Prunus armeniaca L.) is associated with down-regulation of two MATHd genes
Cited by: 30
Author(s): Elena Zuriaga, Carlos Romero, José Blanca, M. L. Badenes
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-020-64022-3

Transcriptome profiling reveals insertional mutagenesis suppressed the expression of candidate pathogenicity genes in honeybee fungal pathogen, Ascosphaera apis
Cited by: 3
Author(s): Awraris Getachew, Tessema Aynalem Abejew, Jiangli Wu, Jin Xu, Yu Hou, Jian Tan, Peng-Jie Wu, Yan Tu, Weipeng Kang, Zheng Wang, Shufa Xu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-64890-9

Transcriptomic evidence that insulin signalling pathway regulates the ageing of subterranean termite castes
Cited by: 13
Author(s): Haroon, Xiaoming Ma, Yuxin Li, Hongxin Zhang, Qing Liu, Xiaoqing Su, Lianxi Xing
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-018-1356-8

Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata)
Cited by: 11
Author(s): Jiaoying Huang, Xuehong Hao, Ye Jin, Xiaohuan Guo, Qing Shao, Krishna B. Kumar, Yogesh Ahlawat, David E. Harry, Chandrashekhar P. Joshi, Youliang Zheng
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.6638

Sorafenib treatment during partial hepatectomy reduces tumorgenesis in an inflammation-associated liver cancer model
Cited by: 16
Author(s): Tamar Zahavi, Tali Lanton, Mali Salmon‐Divon, Asher Salmon, Tamar Peretz, Eithan Galun, Jonathan H. Axelrod, Amir Sonnenblick
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-14-110

Differential expression analysis for paired RNA-seq data
Cited by: 18
Author(s): Lisa Chung, John Ferguson, Wei Zheng, Feng Qian, Vincent M. Bruno, Ruth R. Montgomery, Hongyu Zhao
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-020-65536-6

Opposite Roles of the JMJD1A Interaction Partners MDFI and MDFIC in Colorectal Cancer
Cited by: 16
Author(s): Shushan Yuan, Yongming Li, Sangphil Oh, Bin Zhang, Willard M. Freeman, Sook Shin, Ralf Janknecht
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-2244-6

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum
Cited by: 22
Author(s): Donghong Chen, Han-Lin Qiu, Yong Huang, Lei Zhang, Jinping Si
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-66469-w

Transcriptomic study in women with trisomy 21 identifies a possible role of the GTPases of the immunity-associated proteins (GIMAP) in the protection of breast cancer
Cited by: 13
Author(s): André Mégarbané, David Piquemal, Anne-Sophie Rebillat, Samantha Stora, Fabien Pierrat, Roman Bruno, Florian Noguier, Clotilde Mircher, Aimé Ravel, Marie Vilaire-Meunier, Sophie Durand, Gérard Lefranc
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-66500-0

Transcriptome analyses suggest that changes in fungal endophyte lifestyle could be involved in grapevine bud necrosis
Cited by: 13
Author(s): Thales Henrique Cherubino Ribeiro, Christiane Noronha Fernandes-Brum, C. R. de Souza, Frédérico Alcântara Novelli Dias, Osmar de Almeida-Junior, Murilo de Albuquerque Regina, Kellen Kauanne Pimenta de Oliveira, Gabriel Lasmar dos Reis, Larissa Maia de Oliveira, Fernanda de Paula Fernandes, Laurent Torregrosa, Jorge Teodoro de Souza, Antônio Chalfun-Júnior
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-66675-6

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)
Cited by: 23
Author(s): Jing Hu, Yuping Liu, Xiaohui Tang, Huajing Rao, Chaoxiang Ren, Chen Jiang, Qinghua Wu, Yi Jiang, Fuchang Geng, Jin Pei
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-66021-w

Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology
Cited by: 11
Author(s): Akito Ishikawa, Keisuke Shimizu, Yukinobu Isowa, Takeshi Takeuchi, Rongjun Zhao, Keiji Kito, Manabu Fujie, Noriyuki Satoh, Kazuhiko Endo
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-02375-7

High post-anthesis temperature effects on bread wheat (Triticum aestivum L.) grain transcriptome during early grain-filling
Cited by: 10
Author(s): Richard Ian Kino, Till K. Pellny, Rachel Mitchell, Asier Gonzalez-Uriarte, Paola Tosi
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-64257-0

Core Binding Factors are essential for ovulation, luteinization, and female fertility in mice
Cited by: 10
Author(s): Somang Lee-Thacker, Hayce Jeon, Yohan Choi, Ichiro Taniuchi, Takeshi Takarada, Yukio Yoneda, Che Myong Ko, Misung Jo
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-021-03172-6

De novo transcriptome analysis provides insights into formation of in vitro adventitious root from leaf explants of Arnebia euchroma
Cited by: 6
Author(s): Jyoti Devi, Ekjot Kaur, Mohit Kumar Swarnkar, Vishal Acharya, Shashi Bhushan
Software Mentions: 1
Published: about 5 years ago

10.1186/s12870-019-1742-x

Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)
Cited by: 25
Author(s): Yuanyuan Cui, Ziran Wang, Shangwu Chen, Alexander Vainstein, Huiqin Ma
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-020-02330-6

Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud
Cited by: 16
Author(s): Jingjing Wang, Chunlei An, Hailin Guo, Xiangyang Yang, Jingbo Chen, Jingfeng Zong, Li Jianjian, Jianxiu Liu
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms22083882

Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus
Cited by: 2
Author(s): Roberto Martín‐Hernández, Rossanna Rodríguez-Canul, Nuvia Kantún-Moreno, Miguel A. Olvera‐Novoa, Óscar Medina-Contreras, Cristobal Garikoitz-Legarda, Juan Carlos Triviño, Jesús Alejandro Zamora‐Briseño, Víctor May-Solis, Alicia Poot-Salazar, Juan Antonio Pérez-Vega, Judit Gil-Zamorano, George Grant, Alberto Dávalos, Leticia Olivera‐Castillo
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-019-2067-5

Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng
Cited by: 22
Author(s): Xuejiao Li, Jianli Yang, Bin Hao, Yingchun Lu, Zhi-Long Qian, Ying Liu, Shuang Ye, Junrong Tang, Mo Chen, Guangqiang Long, Yan Zhao, Guanghui Zhang, Junwen Chen, Wei Fan, Shengchao Yang
Software Mentions: 1
Published: about 7 years ago

10.1186/s12870-019-1824-9

Analysis of metabolic pathways related to fertility restoration and identification of fertility candidate genes associated with Aegilops kotschyi cytoplasm in wheat (Triticum aestivum L.)
Cited by: 7
Author(s): Sha Li, Zihan Liu, Yulin Jia, Jiali Ye, Xiaohong R. Yang, Lingli Zhang, Xiyue Song
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-021-02827-8

Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers
Cited by: 5
Author(s): Yu Qiao, Qiming Cheng, Yutong Zhang, Yan Wang, Fengyan Yi, Fengling Shi
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-67476-7

Co-expression based cancer staging and application
Cited by: 7
Author(s): Xiangchun Yu, Sha Cao, Yi Zhou, Zhezhou Yu, Ying Xu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-67635-w

Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
Cited by: 7
Author(s): Jaya Gupta, Sagar Thapa, Madhulika Verma, Ritu Som, Kakali Mukherjee
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-018-1336-z

Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications
Cited by: 51
Author(s): Hangxiao Zhang, Huihui Wang, Qiang Zhu, Yanfeng Gao, Huiyuan Wang, Liangzhen Zhao, Yongsheng Wang, Feihu Xi, Wenfei Wang, Yanqiu Yang, Chentao Lin, Lianfeng Gu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-020-66387-x

Combined PLT and NE to predict the prognosis of patients with locally advanced cervical cancer
Cited by: 5
Author(s): Han Wang, Wen-Ming Chen, Yong-Heng Zhou, Jianping Shi, Yongzhen Huang, Wenjie Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-02638-3

Comparative transcriptome analysis suggests convergent evolution of desiccation tolerance in Selaginella species
Cited by: 8
Author(s): Gerardo Alejo‐Jacuinde, Sandra Isabel González-Morales, Araceli Oropeza-Aburto, June Simpson, Luis Herrera-Estrella
Software Mentions: 1
Published: about 6 years ago

10.1186/s40478-019-0739-x

c-MYC overexpression induces choroid plexus papillomas through a T-cell mediated inflammatory mechanism
Cited by: 5
Author(s): Ashirwad Merve, Xinyu Zhang, Nicola Pomella, Serena Acquati, Joerg D. Hoeck, Anaëlle Dumas, Gabriel Rosser, Yichen Li, Jennie N. Jeyapalan, Silvia Vicenzi, Qianhai Fan, Zeng Jie Yang, Arianna Sabò, Denise Sheer, Axel Behrens, Silvia Marino
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-68339-x

Transcriptional and in silico analyses of MIF cytokine and TLR signalling interplay in the LPS inflammatory response of Ciona robusta
Cited by: 9
Author(s): Vincenzo Arizza, Angela Bonura, Laura La Paglia, Alfonso Urso, Annalisa Pinsino, Aiti Vizzini
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-021-03119-x

The core autophagy machinery is not required for chloroplast singlet oxygen-mediated cell death in the Arabidopsis thaliana plastid ferrochelatase two mutant
Cited by: 16
Author(s): Matthew D. Lemke, Karen E. Fisher, Marta A. Kozlowska, David W. Tano, Jesse D. Woodson
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.6859

Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs
Cited by: 92
Author(s): Chunjie Jiang, Yongsheng Li, Zheng Zhao, Jianping Lu, Hong Chen, Na Ding, Guangjuan Wang, Juan Xu, Xia Li
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2229-11-177

Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
Cited by: 38
Author(s): Li Xiao, Hui Wang, Wan Park, Tingyun Kuang, Yulong He
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12870-018-1564-2

Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos
Cited by: 17
Author(s): Andreia S. Rodrigues, Jose J De Vega, Celia María Gonzalo Miguel
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-018-1428-9

Comprehensive transcriptome analysis reveals genes in response to water deficit in the leaves of Saccharum narenga (Nees ex Steud.) hack
Cited by: 33
Author(s): Xihui Liu, Ronghua Zhang, Hesheng Ou, Yiyun Gui, Jizhen Wei, Hui Zhou, Huachun Tan, Yang–Rui Li
Software Mentions: 1
Published: about 8 years ago

10.1186/s12870-020-02745-1

Under fire-simultaneous volatilome and transcriptome analysis unravels fine-scale responses of tansy chemotypes to dual herbivore attack
Cited by: 11
Author(s): Mary V. Clancy, Georg Haberer, Werner Jud, Bishu Niederbacher, Simon Niederbacher, Matthias Senft, Sharon E. Zytynska, Wolfgang W. Weisser, Jörg‐Peter Schnitzler
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-015-0694-z

Physiological and transcriptional analyses of developmental stages along sugarcane leaf
Cited by: 48
Author(s): Lúcia Mattiello, Diego Mauricio Riaño-Pachón, Marina C. M. Martins, Larissa Prado da Cruz, D. Bassi, Paulo Eduardo Ribeiro Marchiori, Rafael Vasconcelos Ribeiro, Mônica Teresa Veneziano Labate, Carlos Alberto Labate, Marcelo Menossi
Software Mentions: 1
Published: almost 11 years ago

10.18632/oncotarget.7963

Comparative analysis of human and mouse transcriptomes of Th17 cell priming
Cited by: 39
Author(s): Soile Tuomela, Sini Rautio, Helena Ahlfors, Viveka Öling, Verna Salo, Ubaid Ullah, Zhi Chen, Saara Hämälistö, Subhash Tripathi, Tarmo Äijö, Omid Rasool, Hayssam Soueidan, Lodewyk Wessels, Brigitta Stockinger, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 1
Published: over 10 years ago

10.1186/s12870-020-2265-1

Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress
Cited by: 26
Author(s): Lei Wang, Bo Zheng, Yahong Yuan, Quanxi Xu, Peng Chen
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-69434-9

Comparative transcriptome analysis of Sclerotinia sclerotiorum revealed its response mechanisms to the biological control agent, Bacillus amyloliquefaciens
Cited by: 18
Author(s): Xiaoxiang Yang, Lei Zhang, Yunjia Xiang, Lei Du, Xiaoqin Huang, Yong Liu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-67760-6

A cluster of metabolism-related genes predict prognosis and progression of clear cell renal cell carcinoma
Cited by: 21
Author(s): Mei Liu, Qiufeng Pan, Ruihai Xiao, Yi Yu, Wenbao Lu, Longwang Wang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-68637-4

Cellular, mitochondrial and molecular alterations associate with early left ventricular diastolic dysfunction in a porcine model of diabetic metabolic derangement
Cited by: 14
Author(s): Ilkka Heinonen, Oana Sorop, Bas M. van Dalen, Rob C I Wüst, Jens van de Wouw, Vincent J. de Beer, Yanti Octavia, Richard van Duin, Youri Hoogstrate, Lau Blonden, Milla Alkio, Katja Anttila, Andrew Stubbs, Jolanda van der Velden, Daphne Merkus, Dirk J. Duncker
Software Mentions: 1
Published: about 6 years ago

10.3390/nu12123762

Sasa quelpaertensis Leaf Extract Ameliorates Dyslipidemia, Insulin Resistance, and Hepatic Lipid Accumulation in High-Fructose-Diet-Fed Rats
Cited by: 2
Author(s): Jeong Yong Park, Mi Jang, Jung Min Oh, Hee-Chul Ko, Sung‐Pyo Hur, Jae-Won Kim, Songyee Baek, Se-Jae Kim
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-020-02486-1

Comparative transcriptome analysis of mulberry reveals anthocyanin biosynthesis mechanisms in black (Morus atropurpurea Roxb.) and white (Morus alba L.) fruit genotypes
Cited by: 27
Author(s): Gaiqun Huang, Yichun Zeng, Wei Ling, Yongquan Yao, Jie Dai, Gang Liu, Zhongzheng Gui
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-70484-2

Construct a circRNA/miRNA/mRNA regulatory network to explore potential pathogenesis and therapy options of clear cell renal cell carcinoma
Cited by: 50
Author(s): Shengjie Bai, Yinying Wu, Yanli Yan, Shuai Shao, Jiangzhou Zhang, Jiaxin Liu, Baojun Hui, Rui Li, Hailin Ma, Xiaozhi Zhang, Juan Ren
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-15-S17-S2

Identification of genes and pathways involved in kidney renal clear cell carcinoma
Cited by: 45
Author(s): William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen, Liangjiang Wang, Dong Xu, Hamid R. Arabnia, Weida Tong, Mary Qu Yang
Software Mentions: 1
Published: almost 12 years ago

10.3390/ijms22094910

Extracellular Vesicles in Synovial Fluid from Rheumatoid Arthritis Patients Contain miRNAs with Capacity to Modulate Inflammation
Cited by: 15
Author(s): Andrew D Foers, Alexandra L. Garnham, Simon Chatfield, Gordon K. Smyth, Lesley Cheng, Andrew F. Hill, Ian P. Wicks, Ken C Pang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-70932-z

Elucidation of resistance signaling and identification of powdery mildew resistant mapping loci (ClaPMR2) during watermelon-Podosphaera xanthii interaction using RNA-Seq and whole-genome resequencing approach
Cited by: 6
Author(s): Mihir Mandal, Haktan Suren, Chandrasekar S. Kousik
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-71050-6

RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva
Cited by: 3
Author(s): Qing Liu, Nan Chen, Huabo Chen, Yusen Huang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-014-0400-6

Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing
Cited by: 45
Author(s): Yue Luo, Xiaona Zhang, Zhitian Luo, Qinglin Zhang, Jihong Liu
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12870-019-2138-7

Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues
Cited by: 12
Author(s): Yingdan Yuan, Jinchi Zhang, Justin Kallman, Xin Liu, Miaojing Meng, Jie Lin
Software Mentions: 1
Published: almost 7 years ago

10.3390/nu7085297

Dietary Selenium Levels Affect Selenoprotein Expression and Support the Interferon-γ and IL-6 Immune Response Pathways in Mice
Cited by: 63
Author(s): Petra A. Tsuji, Bradley A. Carlson, Christine B. Anderson, Harold E. Seifried, Dolph L. Hatfield, Michael Howard
Software Mentions: 1
Published: about 11 years ago

10.1186/s12870-019-1940-6

RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes
Cited by: 32
Author(s): Mummadireddy Ramya, Pue Hee Park, Yu Chen Chuang, Oh Keun Kwon, Hye Ryun An, Pil Man Park, Yun Su Baek, Byoung Chorl Kang, Wen Chieh Tsai, Hong Hwa Chen
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-72117-0

A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Cited by: 9
Author(s): James A. Budnick, Lauren M. Sheehan, Miranda. J. Ginder, Kevin C. Failor, Julia. M. Perkowski, John. F. Pinto, Kirsten A. Kohl, Lin Kang, Pawel Michalak, Li Luo, Jason E. Heindl, Clayton C. Caswell
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-017-1135-y

Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers
Cited by: 13
Author(s): Kaidong Liu, Haili Li, Weijin Li, Jun Zhong, Chen Yan, Chenjia Shen, Changchun Yuan
Software Mentions: 1
Published: about 9 years ago

10.1186/s12870-019-1641-1

Flax (Linum usitatissimum L.) response to non-optimal soil acidity and zinc deficiency
Cited by: 18
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Alexander V. Zyablitsin, Anastasiya V. Snezhkina, Maria S. Fedorova, Elena N. Pushkova, Parfait Kezimana, Roman O. Novakovskiy, Liubov V. Povkhova, М. И. Смирнова, О. В. Муравенко, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-72448-y

Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion
Cited by: 6
Author(s): Katsuya Sakai, Takumi Nishiuchi, Shoichiro Tange, Yoshinori Suzuki, Seiji Yano, Minoru Terashima, Takeshi Suzuki, Kunio Matsumoto
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-019-2134-y

Wheat straw increases the defense response and resistance of watermelon monoculture to Fusarium wilt
Cited by: 14
Author(s): Lili Tang, Shaorui Nie, Wenhui Li, Chao Fan, Siqi Wang, Fengzhi Wu, Kaiwen Pan
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-015-0537-y

The effect of red light and far-red light conditions on secondary metabolism in Agarwood
Cited by: 31
Author(s): Tony Kuo, Chuan-Hung Chen, Shu-Hwa Chen, I-Hsuan Lu, Mei-Ju Chu, Li-Chun Huang, Chung‐Yen Lin, Chien‐Yu Chen, Hsiao-Feng Lo, Shih‐Tong Jeng, Long‐Fang O. Chen
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-020-74049-1

De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites
Cited by: 8
Author(s): Nisha Dhiman, Anil Kumar, Dinesh Kumar, Amita Bhattacharya
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-11-564

Empirical bayes analysis of sequencing-based transcriptional profiling without replicates
Cited by: 45
Author(s): Zhijin Wu, Bethany D. Jenkins, Tatiana A. Rynearson, Sonya T. Dyhrman, Mak A. Saito, Melissa L. Mercier, LeAnn P. Whitney
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12870-019-2037-y

Water-deficit responsive microRNAs in the primary root growth zone of maize
Cited by: 17
Author(s): Candace M. Seeve, Ramanjulu Sunkar, Yun Zheng, Li Liu, Zhijie Liu, Michael D. McMullen, Sven K. Nelson, Robert E. Sharp, Melvin J. Oliver
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-74789-0

Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale
Cited by: 23
Author(s): Xinqiao Zhan, Jufeng Qi, Bin Zhou, Bizeng Mao
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-019-2001-x

Comparative analysis of proso millet (Panicum miliaceum L.) leaf transcriptomes for insight into drought tolerance mechanisms
Cited by: 25
Author(s): Yuyu Zhang, Xiaoli Gao, Jing Li, Xiangwei Gong, Pu Yang, Jinfeng Gao, Pengke Wang, Baili Feng
Software Mentions: 1
Published: about 7 years ago

10.1186/s12870-018-1479-y

OsWRKY67 positively regulates blast and bacteria blight resistance by direct activation of PR genes in rice
Cited by: 42
Author(s): Qing Liu, Xia Li, Shijuan Yan, Ting Yu, Yang Jiao, Jingfang Dong, Shaohong Zhang, Junliang Zhao, Ting Yang, Xingxue Mao, Xiaoyuan Zhu, Bin Liu
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms22105088

Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination
Cited by: 5
Author(s): Yu Wu, Lamei Zheng, Bing Jie, Huimin Liu, Genfa Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-73164-3

Assessing the prognostic value of stemness-related genes in breast cancer patients
Cited by: 5
Author(s): Wenjie Wang, Han Wang, Meng-Sen Wang, Yongzhen Huang, Yuan Ma, Jie Qi, Jianping Shi, Wei Li
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-75537-0

Enhanced FGFR3 activity in postmitotic principal neurons during brain development results in cortical dysplasia and axonal tract abnormality
Cited by: 5
Author(s): Jui-Yen Huang, Bruna Baumgarten Krebs, Marisha Lynn Miskus, May Lin Russell, Eamonn Patrick Duffy, Jason Michael Graf, Hui-Chen Lu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-021-03108-0

Transcriptomic analysis to reveal the differentially expressed miRNA targets and their miRNAs in response to Ralstonia solanacearum in ginger species
Cited by: 9
Author(s): Mohandas Snigdha, D. Prasath
Software Mentions: 1
Published: about 5 years ago

10.1186/s12886-020-01348-6

Different transcriptome profiles between human retinoblastoma Y79 cells and an etoposide-resistant subline reveal a chemoresistance mechanism
Cited by: 13
Author(s): Wei Song, S. Q. Zheng, Hong Yao, Xiao Zhou, Rui Li, Cheng Yue Zhang, Jun Zhao, Lie Wei Wang, Rong Shao, Liang Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12868-018-0443-y

Blue light induces a neuroprotective gene expression program in Drosophila photoreceptors
Cited by: 29
Author(s): Hana Hall, Junwei Ma, Sudhanshu Shekhar, Walter D. Leon-Salas, Vikki M. Weake
Software Mentions: 1
Published: over 8 years ago

10.1186/s12867-017-0080-5

Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae)
Cited by: 21
Author(s): Kangsheng Ma, Fen Li, Ying Liu, Pingzhuo Liang, Xuewei Chen, Xiwu Gao
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-76171-6

Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments
Cited by: 6
Author(s): Sera Jung, Jong Hee Lee
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-021-04201-9

Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development
Cited by: 0
Author(s): Thomas E. Bartlett
Software Mentions: 1
Published: over 5 years ago

10.1186/s12866-021-02132-2

Interactional mechanisms of Paenibacillus polymyxa SC2 and pepper (Capsicum annuum L.) suggested by transcriptomics
Cited by: 16
Author(s): Hu Liu, Yufei Li, Ke Ge, Binghai Du, Kai Liu, Chengqiang Wang, Yuqiang Ding
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-019-3144-3

ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data
Cited by: 7
Author(s): Matúš Medo, Daniel M. Aebersold, Michaela Medová
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12866-016-0695-6

In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study
Cited by: 36
Author(s): Yijuan Xu, Raluca Maltesen, Lone Heimann Larsen, Henrik Carl Schønheyder, Vang Quy Le, Jeppe Lund Nielsen, Per Halkjær Nielsen, Trine Rolighed Thomsen, Kåre Lehmann Nielsen
Software Mentions: 1
Published: over 10 years ago

10.1186/s12866-016-0739-y

Identification of the crp gene in avian Pasteurella multocida and evaluation of the effects of crp deletion on its phenotype, virulence and immunogenicity
Cited by: 17
Author(s): Xinxin Zhao, Qing Liu, Kangpeng Xiao, Yunlong Hu, Xueyan Liu, Yanyan Li, Qingke Kong
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2180-14-31

Hyperexpression of α-hemolysin explains enhanced virulence of sequence type 93 community-associated methicillin-resistant Staphylococcus aureus
Cited by: 46
Author(s): Kyra Chua, Ian R. Monk, Ya-Hsun Lin, Torsten Seemann, Kellie L. Tuck, Jessica L. Porter, Justin Stepnell, Geoffrey W. Coombs, John K. Davies, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-020-74594-9

Involvement of neutrophils in machineries underlying the rupture of intracranial aneurysms in rats
Cited by: 19
Author(s): Mika Kushamae, Haruka Miyata, Makoto Shirai, Kampei Shimizu, Mieko Oka, Hirokazu Koseki, Yu Abekura, Isao Ono, Kazuhiko Nozaki, Tohru Mizutani, Tomohiro Aoki
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2180-11-45

Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense
Cited by: 160
Author(s): Ann Hess, Abhishek N. Prasad, Andrey A. Ptitsyn, Gregory D. Ebel, Ken E. Olson, Cátálin Bárbácioru, Cinna K. Monighetti, Corey L. Campbell
Software Mentions: 1
Published: over 15 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568