cran: WGCNA | Projects | Ecosyste.ms: Papers

10.3389/fcell.2020.604627

Identification of a Gene Signature for Renal Cell Carcinoma–Associated Fibroblasts Mediating Cancer Progression and Affecting Prognosis
Cited by: 24
Author(s): Bitian Liu, Xiaonan Chen, Yunhong Zhan, Bin Wu, Pan Shen
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.22405

RNA-sequencing reveals genome-wide long non-coding RNAs profiling associated with early development of diabetic nephropathy
Cited by: 12
Author(s): Wanxin Tang, Dongmei Zhang, Xiaoke Ma
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-020-06854-x

Maternal dietary resistant starch does not improve piglet’s gut and liver metabolism when challenged with a high fat diet
Cited by: 2
Author(s): Martine Schroyen, Julie Leblois, Julie Uerlings, Bing Li, Ester Arévalo Sureda, Sébastien Massart, José Wavreille, Jérôme Bindelle, Nadia Everaert
Software Mentions: 2
Published: over 6 years ago

10.3389/pore.2021.1609968

Identification of Novel Diagnosis Biomarkers for Therapy-Related Neuroendocrine Prostate Cancer
Cited by: 5
Author(s): Cuijian Zhang, Jinqin Qian, Yucai Wu, Zhenpeng Zhu, Wei Yu, Yanqing Gong, Xuesong Li, Zhisong He, Liqun Zhou
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-018-19754-8

Transcriptome Analysis in Spleen Reveals Differential Regulation of Response to Newcastle Disease Virus in Two Chicken Lines
Cited by: 39
Author(s): J. Zhang, Michael G. Kaiser, Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 2
Published: almost 9 years ago

10.3389/fonc.2020.564733

MYCT1 Inhibits the Adhesion and Migration of Laryngeal Cancer Cells Potentially Through Repressing Collagen VI
Cited by: 10
Author(s): Pengpeng Wang, Siyu Ding, Yuanyuan Sun, Yunhui Li, Wei‐Neng Fu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-015-0078-0

Integrative network analysis reveals different pathophysiological mechanisms of insulin resistance among Caucasians and African Americans
Cited by: 15
Author(s): Swapan K. Das, Neeraj Kumar Sharma, Bin Zhang
Software Mentions: 2
Published: over 11 years ago

10.3389/fcell.2020.577032

The Landscape of Coronavirus Disease 2019 (COVID-19) and Integrated Analysis SARS-CoV-2 Receptors and Potential Inhibitors in Lung Adenocarcinoma Patients
Cited by: 6
Author(s): Bufu Tang, Jinyu Zhu, Ying Cong, Wenting Yang, Chunli Kong, Weiyue Chen, Yajie Wang, Yong Zeng, Jiansong Ji
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-016-3188-y

Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs
Cited by: 63
Author(s): Richard Ahn, Rashmi Gupta, Kevin Lai, Nitin Chopra, Sarah T. Arron, Wilson Liao
Software Mentions: 2
Published: about 10 years ago

10.3389/fcell.2021.607782

Hypermethylation and Downregulation of UTP6 Are Associated With Stemness Properties, Chemoradiotherapy Resistance, and Prognosis in Rectal Cancer: A Co-expression Network Analysis
Cited by: 1
Author(s): Yiyi Zhang, Qun Gao, Yong Wu, Yong Peng, Jinfu Zhuang, Yuanfeng Yang, Weizhong Jiang, Xing Liu, Guoxian Guan
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-017-12275-w

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies
Cited by: 35
Author(s): Zhangshuan Hou, Karen E. Nelson, James C. Stegen, Chris Murray, Evan Arntzen, Alex R. Crump, David W. Kennedy, M. C. Perkins, T. D. Scheibe, Jim K. Fredrickson, John M. Zachara
Software Mentions: 2
Published: about 9 years ago

10.1186/s12974-019-1433-4

Inflammatory, regulatory, and autophagy co-expression modules and hub genes underlie the peripheral immune response to human intracerebral hemorrhage
Cited by: 49
Author(s): Marc Durocher, Bradley P. Ander, Glen C. Jickling, Farah Hamade, Heather Hull, Bodie Knepp, Da Zhi Liu, Xinhua Zhan, Anh Tuấn Trần, Xiyuan Cheng, Kwan Ng, Alan Yee, Frank R. Sharp, Boryana Stamova
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-19147-x

Effluent and serum protein N-glycosylation is associated with inflammation and peritoneal membrane transport characteristics in peritoneal dialysis patients
Cited by: 11
Author(s): Evelina Ferrantelli, Karima Farhat, Agnes L. Hipgrave Ederveen, Karli R. Reiding, Robert H.J. Beelen, Frans J. van Ittersum, Manfred Wuhrer, Viktoria Dotz
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12920-021-00908-z

Identification of major depressive disorder disease-related genes and functional pathways based on system dynamic changes of network connectivity
Cited by: 6
Author(s): Ruijie Geng, Xiao Huang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-019-5433-7

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis
Cited by: 0
Author(s): Michael Fraser, Yuqi Long, Guoli Ji, Yangfeng Su, Pengchao Ye, Hongjuan Fu, Xiaohui Wu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12974-017-0937-z

Bioinformatics analysis of glial inflammatory responses to air pollution
Cited by: 0
Author(s): Chenyu Li, Wei Jiang, Nina Tang, Yan Xu
Software Mentions: 2
Published: about 9 years ago

10.1186/1752-0509-7-21

Cluster and propensity based approximation of a network
Cited by: 6
Author(s): John Michael O. Rañola, Peter Langfelder, Kenneth Lange, Steve Horvath
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12866-020-01853-0

Comparative transcriptome analysis of two Cercospora sojina strains reveals differences in virulence under nitrogen starvation stress
Cited by: 2
Author(s): Xiaorong Gu, Shuai Yang, Xiaoxue Yang, Liangliang Yao, Xuedong Gao, Maoming Zhang, Wei Liu, Haiming Zhao, Qingsheng Wang, Zengjie Li, Zhimin Li, Junjie Ding
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-37099-0

Associating transcriptional regulation for rapid germination of rapeseed (Brassica napus L.) under low temperature stress through weighted gene co-expression network analysis
Cited by: 18
Author(s): Tao Luo, Mengzhu Xian, Chen Zhang, Chenyu Zhang, Liyong Hu, Zhenghua Xu
Software Mentions: 2
Published: almost 8 years ago

10.3389/fonc.2020.01092

Identification of DGUOK-AS1 as a Prognostic Factor in Breast Cancer by Bioinformatics Analysis
Cited by: 11
Author(s): Yalun Li, Yiran Liang, Tingting Ma, Qifeng Yang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-021-02983-x

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize
Cited by: 13
Author(s): Huanhuan Liu, Haofeng Wu, Yan Wang, Huan Wang, Saihua Chen, Zhitong Yin
Software Mentions: 2
Published: over 5 years ago

10.1186/s12866-020-1701-6

Marine bacterial communities in the upper gulf of Thailand assessed by Illumina next-generation sequencing platform
Cited by: 26
Author(s): Pongrawee Nimnoi, Neelawan Pongsilp
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.10502

miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts
Cited by: 7
Author(s): Huan Guo, Xinke Zhao, Hongling Su, Chengxu Ma, Kai Li, Sue Kong, Kedan Liu, Haining Li, Juan Chang, Tao Wang, Hongyun Guo, Huiping Wei, Zhaoyuan Fu, Xinfang Lv, Yingdong Li
Software Mentions: 2
Published: almost 6 years ago

10.3389/fcell.2021.691540

Multi-Omics Integrative Bioinformatics Analyses Reveal Long Non-coding RNA Modulates Genomic Integrity via Competing Endogenous RNA Mechanism and Serves as Novel Biomarkers for Overall Survival in Lung Adenocarcinoma
Cited by: 4
Author(s): Zhong Lin Wang, Ziyuan Ren, Rui Li, Junpeng Ge, Guoming Zhang, Yaodong Xin, Yi-Qing Qu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12918-014-0139-6

Invariance and plasticity in the Drosophila melanogastermetabolomic network in response to temperature
Cited by: 19
Author(s): Ramkumar Hariharan, Jessica M. Hoffman, Ariel S Thomas, Quinlyn A. Soltow, Dean P. Jones, Daniel E. L. Promislow
Software Mentions: 2
Published: almost 12 years ago

10.3390/ijms221910785

Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival
Cited by: 3
Author(s): Nina Lukashina, Michael J. Williams, Elena Kartysheva, Elizaveta Virko, Błażej Kudłak, Robert Fredriksson, Ola Spjuth, Helgi B. Schiöth
Software Mentions: 2
Published: about 5 years ago

10.1186/s12870-020-02697-6

BrrICE1.1 is associated with putrescine synthesis through regulation of the arginine decarboxylase gene in freezing tolerance of turnip (Brassica rapa var. rapa)
Cited by: 12
Author(s): Xin Yin, Yunqiang Yang, Yanqiu Lv, Yan Li, Danni Yang, Yanling Yue, Yongping Yang
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms221910284

Behavioral and Physiological Plasticity Provides Insights into Molecular Based Adaptation Mechanism to Strain Shift in Spodoptera frugiperda
Cited by: 10
Author(s): Muhammad Hafeez, Xiaowei Li, Farman Ullah, Zhijun Zhang, Jinming Zhang, Jian‐Wen Huang, Muhammad Musa Khan, Limin Chen, Xiaoyun Ren, Shuxing Zhou, G. Mandela Fernández-Grandon, Myron P. Zalucki, Yitong Lu
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms221910443

Global Survey of the Full-Length Cabbage Transcriptome (Brassica oleracea Var. capitata L.) Reveals Key Alternative Splicing Events Involved in Growth and Disease Response
Cited by: 2
Author(s): Yong Wang, Jialei Ji, Li‐Tao Tong, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Honghao Lv
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2021.606106

Identification of Biomarkers Related to CD8+ T Cell Infiltration With Gene Co-expression Network in Lung Squamous Cell Carcinoma
Cited by: 10
Author(s): Min Tang, Yukun Li, Xianyu Luo, Jianru Xiao, Juan Wang, Xiaofeng Zeng, Qi-hao Hu, Xiaoyan Chen, Sijie Tan, Jun Hu
Software Mentions: 2
Published: over 5 years ago

10.1093/gigascience/gix093

Panax ginseng genome examination for ginsenoside biosynthesis
Cited by: 123
Author(s): Jiang Xu, Yang Chu, Baosheng Liao, Shaobo Xiao, Qinggang Yin, Rui Bai, He Su, Lixin Dong, Xiwen Li, Jun Qian, Jingjing Zhang, Yujun Zhang, Xiaoyan Zhang, Mingli Wu, Jie Zhang, Guozheng Li, Lei Zhang, Zhenzhan Chang, Yuebin Zhang, Zhengwei Jia, Zhixiang Liu, Daniel Ntiamoah Afreh, Ruth Nahurira, Lianjuan Zhang, Ruiyang Cheng, Yingjie Zhu, Guangwei Zhu, Wei Rao, Chao Zhou, Lin Qiao, Zhixing Huang, Yung Chi Cheng, Shilin Chen
Software Mentions: 2
Published: about 9 years ago

10.3390/genes11010106

Hormonal and Molecular Regulation of Phallus Differentiation in a Marsupial Tammar Wallaby
Cited by: 0
Author(s): Yu Chen, Marilyn B. Renfree
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-36231-4

lncRNA profile study reveals the mRNAs and lncRNAs associated with docetaxel resistance in breast cancer cells
Cited by: 43
Author(s): Peide Huang, Fengyu Li, Lin Li, Yuling You, Shizhi Luo, Dong Zhou, Qiang Gao, Song Wu, Nils Brünner, Jan Stenvang
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.12143

Construction of competing endogenous RNA interaction network as prognostic markers in metastatic melanoma
Cited by: 1
Author(s): Zan He, Zijuan Xin, Yongfei Peng, Hua Zhao, Xiangdong Fang
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22189704

Decapitation Experiments Combined with the Transcriptome Analysis Reveal the Mechanism of High Temperature on Chrysanthemum Axillary Bud Formation
Cited by: 1
Author(s): Yujie Yang, Sagheer Ahmad, Yang Qiu, Cunquan Yuan, Qixiang Zhang
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22189957

Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome P450 Genes in Medicago truncatula
Cited by: 8
Author(s): Xia Yin, Yang Jiao, Lin Ma, Yan Su, Yongzhen Pang
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.6028

Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for further study
Cited by: 6
Author(s): Qi Mao, Chengjie Chen, Tongxin Xie, Aiping Luan, Chaoyang Liu, Yehua He
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-015-1431-6

Pervasive and opposing effects of Unpredictable Chronic Mild Stress (UCMS) on hippocampal gene expression in BALB/cJ and C57BL/6J mouse strains
Cited by: 29
Author(s): Karim Malki, Yann S. Mineur, Maria Grazia Tosto, James Campbell, Priya Karia, Irfan Jumabhoy, Frans Sluyter, Wim E. Crusio, Leonard C. Schalkwyk
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms22179345

High Resolution Analysis of Proteome Dynamics during Bacillus subtilis Sporulation
Cited by: 5
Author(s): Zhiwei Tu, Henk Dekker, Winfried Roseboom, Bhagyashree N. Swarge, Peter Setlow, Stanley Brul, Gertjan Kramer
Software Mentions: 2
Published: about 5 years ago

10.1186/s12918-018-0531-8

KDiamend: a package for detecting key drivers in a molecular ecological network of disease
Cited by: 4
Author(s): Mengxuan Lyu, Jiaxing Chen, Yiqi Jiang, Wei Dong, Fang Zhou, Shuai Cheng Li
Software Mentions: 2
Published: over 8 years ago

10.3389/fcimb.2021.695515

Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy
Cited by: 9
Author(s): Shuang Li, Junping Zhu, Bin Su, Huimin Wei, Fei Chen, Hongshan Liu, Jiaqi Wei, Xiaodong Yang, Qiuyue Zhang, Wei Xia, Hao Wu, Qiushui He, Tong Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-019-2021-6

Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach
Cited by: 9
Author(s): Sebastián Moschen, Johanna Marino, Salvador Nicosia, Janet Higgins, Saleh Alseekh, Francisco Horacio Astigueta, Sofía A. Bengoa Luoni, Máximo Rivarola, Alisdair R. Fernie, Nicolas Blanchet, Nicolas B. Langlade, Norma Paniego, Paula Fernández, Ruth Amelia Heinz
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-021-02927-5

The mechanism of sesame resistance against Macrophomina phaseolina was revealed via a comparison of transcriptomes of resistant and susceptible sesame genotypes
Cited by: 11
Author(s): Wenqing Yan, Yunxia Ni, Xintao Liu, Hui Zhao, Yanhua Chen, Min Jiang, Mingming Liu, Hongyan Liu, Bin Tian
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2021.625838

Correlation Between APOBEC3B Expression and Clinical Characterization in Lower-Grade Gliomas
Cited by: 13
Author(s): Hao Zhang, Ziyang Chen, Zeyu Wang, Ziyu Dai, Zhengang Hu, Xun Zhang, Min Hu, Zhixiong Liu, Quan Cheng
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2021.560201

Chronic Intermittent Hypoxia Participates in the Pathogenesis of Atherosclerosis and Perturbs the Formation of Intestinal Microbiota
Cited by: 18
Author(s): Chaowei Hu, Pan Wang, Yunyun Yang, Juan Li, Xiaolu Jiao, Huahui Yu, Yongxiang Wei, Jing Li, Yanwen Qin
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22105291

Genome-Wide Analysis of nsLTP Gene Family and Identification of SiLTPs Contributing to High Oil Accumulation in Sesame (Sesamum indicum L.)
Cited by: 17
Author(s): Shengnan Song, Jun You, Lisong Shi, Sheng Chen, Wangyi Zhou, Senouwa Segla Koffi Dossou, Komivi Dossa, Linhai Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-019-1976-7

Gene co-expression network analysis reveals pathways associated with graft healing by asymmetric profiling in tomato
Cited by: 35
Author(s): Lulu Xie, C.Y. Dong, Qingmao Shang
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.9462

Expression profile analysis to predict potential biomarkers for glaucoma: BMP1, DMD and GEM
Cited by: 4
Author(s): Dao wei Zhang, Shenghai Zhang, Jihong Wu
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-019-6027-0

Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa
Cited by: 15
Author(s): Qi Wu, Xue Bai, Wei Zhao, Xiaodong Shi, Dabing Xiang, Yan Wan, Xiaoyong Wu, Yanxia Sun, Jianglin Zhao, Lianxin Peng, Gang Zhao
Software Mentions: 2
Published: about 7 years ago

10.3389/fphar.2019.00582

Prediction of VEGF-C as a Key Target of Pure Total Flavonoids From Citrus Against NAFLD in Mice via Network Pharmacology
Cited by: 17
Author(s): Hong Wang, Songsong Li, Liyan Wu, Beihui He, Jianping Jiang, Zhiyun Chen
Software Mentions: 2
Published: over 7 years ago

10.3389/fphar.2020.00387

NCAPG Is a Promising Therapeutic Target Across Different Tumor Types
Cited by: 30
Author(s): Cuicui Xiao, Jiao Gong, Yusheng Jie, Jing Cao, Zhongcheng Chen, Rong Li, Yutian Chong, Bo Hu, Qi Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.02123

Dramatic Remodeling of the Gut Microbiome Around Parturition and Its Relationship With Host Serum Metabolic Changes in Sows
Cited by: 20
Author(s): Xiaowan Huang, Jun Gao, Yuanzhang Zhao, Maozhang He, Shanlin Ke, Jinyuan Wu, Yunyan Zhou, Hao Fu, Hui Yang, Congying Chen, Lusheng Huang
Software Mentions: 2
Published: about 7 years ago

10.1111/jcmm.16647

PAICS is related to glioma grade and can promote glioma growth and migration
Cited by: 5
Author(s): Botao Du, Zheying Zhang, Wenyu Di, Wenzhong Xu, Lei Yang, Shitao Zhang, Guoyang He, Rui Yang, Maode Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-019-6180-5

The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination
Cited by: 2
Author(s): Chunpu Qu, Hongwei Zhao, Jinyuan Chen, Zhuang Zuo, Xue Sun, Jiahuan Huang, Chengjun Yang, Xiuli Zhang, Peng Zhang, Xiankui Quan, Xu Zhang, Guanjun Liu
Software Mentions: 2
Published: almost 7 years ago

10.3389/fphar.2021.658511

Uridine Diphosphate Promotes Rheumatoid Arthritis Through P2Y6 Activation
Cited by: 2
Author(s): Hongxing Wang, Hui Wu, Kehua Fang, Xiaotian Chang
Software Mentions: 2
Published: over 5 years ago

10.1002/jcp.29067

Identification of hub genes and construction of transcriptional regulatory network for the progression of colon adenocarcinoma hub genes and TF regulatory network of colon adenocarcinoma
Cited by: 23
Author(s): Shuxun Wei, Jinshui Chen, Yu Fang Huang, Qiang Sun, Haolu Wang, Xiaowen Liang, Zhiqian Hu, Xinxing Li
Software Mentions: 2
Published: about 7 years ago

10.3389/fphar.2021.732541

Distinctive Gut Microbiota in Patients with Overweight and Obesity with Dyslipidemia and its Responses to Long-term Orlistat and Ezetimibe Intervention: A Randomized Controlled Open-label Trial
Cited by: 17
Author(s): Jin Jin, Ruyue Cheng, Yan Ren, Xi Shi, Jiani Wang, Yigui Xue, Huimin Zhang, Xian Jia, Tingting Li, Fang He, Haoming Tian
Software Mentions: 2
Published: about 5 years ago

10.3390/jcm8081160

Identification of Prognostic Candidate Genes in Breast Cancer by Integrated Bioinformatic Analysis
Cited by: 56
Author(s): Charles C.N. Wang, Chia‐Ying Li, Jia-Hua Cai, Phillip C.-Y. Sheu, Jeffrey J. P. Tsai, Meng‐Yu Wu, Chia-Jung Li, Ming‐Feng Hou
Software Mentions: 2
Published: about 7 years ago

10.1038/s41416-019-0477-7

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation
Cited by: 32
Author(s): Theodosia Charitou, Sriganesh Srihari, Miriam A. Lynn, Mohamed Ali Jarboui, Erik Fasterius, Max Moldovan, Senji Shirasawa, Toshiyuki Tsunoda, Marius Ueffing, Jianling Xie, Xin Jin, Xuemin Wang, Christopher G. Proud, Karsten Boldt, Cristina Al‐Khalili Szigyarto, Walter Kölch, David J. Lynn
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-016-3435-2

Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types
Cited by: 29
Author(s): Bruno Giotti, Anagha Joshi, Tom C. Freeman
Software Mentions: 2
Published: almost 10 years ago

10.3390/jcm10163567

Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection
Cited by: 25
Author(s): Hassan Karami, Afshin Derakhshani, Mohammad GhasemiGol, Mohammad Fereidouni, Ebrahim Miri‐Moghaddam, Behzad Baradaran, Neda Jalili Tabrizi, Souzan Najafi, Antonio Giovanni Solimando, Leigh M. Marsh, Nicola Silvestris, Simona De Summa, Angelo Paradiso, Vito Racanelli, Hossein Safarpour
Software Mentions: 2
Published: about 5 years ago

10.3389/fphar.2020.575765

Regulatory Master Genes Identification and Drug Repositioning by Integrative mRNA-miRNA Network Analysis for Acute Type A Aortic Dissection
Cited by: 7
Author(s): Junjun Fang, Zongfu Pan, Hao Yu, Shuanying Yang, Xiaoping Hu, Xiaoyang Lu, Li Lü
Software Mentions: 2
Published: almost 6 years ago

10.1155/2020/4178639

Identification of Susceptibility Modules and Genes for Cardiovascular Disease in Diabetic Patients Using WGCNA Analysis
Cited by: 41
Author(s): Weiwei Liang, Fangfang Sun, Yingxin Zhao, Peng-Fei Shan, Han-Yu Lou
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-11-585

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse
Cited by: 56
Author(s): Ovidiu D. Iancu, Priscila Darakjian, Nicole A.R. Walter, Barry Malmanger, Denesa Oberbeck, John K. Belknap, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 2
Published: about 16 years ago

10.1093/jxb/erv118

Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis
Cited by: 33
Author(s): Rafael A. Cañas, Javier Canales, Carmen Muñoz-Hernández, José Manuel Granados, Concepción Ávila, Maria Luisa García-Martín, Francisco M. Cánovas
Software Mentions: 2
Published: over 11 years ago

10.1093/jxb/erv433

Transcriptome analysis of an apple (Malus×domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation
Cited by: 202
Author(s): Islam El‐Sharkawy, Dong Liang, Kenong Xu
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-019-5802-2

A single-cell transcriptomic atlas of the developing chicken limb
Cited by: 34
Author(s): Christian Feregrino, Fabio Sacher, Oren Parnas, Patrick Tschopp
Software Mentions: 2
Published: over 7 years ago

10.1093/jxb/erw460

Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis
Cited by: 64
Author(s): Juan Du, Shoudong Wang, Cunman He, Bin Zhou, Yong‐Ling Ruan, Huixia Shou
Software Mentions: 2
Published: almost 10 years ago

10.1186/s40478-019-0705-7

Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis
Cited by: 14
Author(s): Jeroen Melief, Marie Orre, Koen Bossers, C.G. van Eden, Karianne Schuurman, Matthew R. J. Mason, Joost Verhaagen, Jörg Hamann, Inge Huitinga
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-6002-9

Comparative transcriptomics of early petal development across four diverse species of Aquilegia reveal few genes consistently associated with nectar spur development
Cited by: 18
Author(s): Evangeline S. Ballerini, Elena M. Kramer, Scott A. Hodges
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.102397

Identifying hub genes of clear cell renal cell carcinoma associated with the proportion of regulatory T cells by weighted gene co-expression network analysis
Cited by: 11
Author(s): Ye‐Hui Chen, Shao‐Hao Chen, Jian Hou, Zhi‐Bin Ke, Yupeng Wu, Tingting Lin, Yong Wei, Xue-Yi Xue, Qing‐Shui Zheng, Jiaofeng Huang, Ning Xu
Software Mentions: 2
Published: almost 7 years ago

10.1093/jxb/ery291

Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans
Cited by: 30
Author(s): Huile Gao, Yan Wang, Wei Li, Ying Gu, Yongcai Lai, Ye Bi, Chaoying He
Software Mentions: 2
Published: about 8 years ago

10.1093/jxb/erz075

Identification of drought responsive proteins and related proteomic QTLs in barley
Cited by: 26
Author(s): Paweł Rodziewicz, Klaudia Chmielewska, Aneta Sawikowska, Łukasz Marczak, Magdalena Łuczak, Paweł Bednarek, Krzysztof Mikołajczak, Piotr Ogrodowicz, Anetta Kuczyńska, Paweł Krajewski, Maciej Stobiecki
Software Mentions: 2
Published: over 7 years ago

10.1093/jxb/erz564

The GATA transcription factor GNC plays an important role in photosynthesis and growth in poplar
Cited by: 59
Author(s): Yi An, Yangyan Zhou, Xiao Han, Chao Shen, Shu Wang, Chao Liu, Weilun Yin, Xinli Xia
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-018-4871-y

Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Cited by: 33
Author(s): Aline Silva Mello Cesar, Luciana Correia de Almeida Regitano, James M. Reecy, Mirele Daiana Poleti, P. S. N. Oliveira, Guilherme Bueno de Oliveira, Gabriel Costa Monteiro Moreira, Maurício A. Mudadu, P. C. Tizioto, James E. Koltes, Eric R. Fritz-Waters, Luke M. Kramer, Dorian J. Garrick, Hamid Beiki, Ludwig Geistlinger, Gérson Barreto Mourão, Adhemar Zerlotini
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-018-0441-4

Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction
Cited by: 167
Author(s): Xin Zhou, Jing Li, Junli Guo, Bin Geng, Wenjie Ji, Qian Zhao, Jinxin Li, Xinlin Liu, Junxiang Liu, Zhao-Zeng Guo, Wei Cai, Yun Ma, Dong Ren, Jun Miao, Shaobo Chen, Zhuoli Zhang, Junru Chen, Jiuchang Zhong, Wenbin Liu, Ming‐Hui Zou, Yuming Li, Jun Cai
Software Mentions: 2
Published: over 8 years ago

10.18632/aging.101005

Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels
Cited by: 174
Author(s): Steve Horvath, Peter Langfelder, Seung Kwak, Jeff Aaronson, Jim Rosinski, Thomas Vogt, M Eszes, Richard L.M. Faull, Maurice A. Curtis, Henry J. Waldvogel, Oi-Wa Choi, Steve Tung, Harry V. Vinters, Giovanni Coppola, X. William Yang
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms21228730

Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer
Cited by: 60
Author(s): Pamela Vernocchi, Tommaso Gili, Federica Conte, Federica Del Chierico, Giorgia Conta, Alfredo Miccheli, Andrea Botticelli, Paola Paci, Guido Caldarelli, Marianna Nuti, Paolo Marchetti, Lorenza Putignani
Software Mentions: 2
Published: almost 6 years ago

10.3389/fphar.2021.637253

IMCC: A Novel Quantitative Approach Revealing Variation of Global Modular Map and Local Inter-Module Coordination Among Differential Drug’s Targeted Cerebral Ischemic Networks
Cited by: 0
Author(s): Pengqian Wang, Yanan Yu, Jun Li, Bing Li, Yingying Zhang, Dongfeng Li, Wenjuan Xu, Qiong Liu, Zhong Wang
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.102483

Competing endogenous network analysis identifies lncRNA Meg3 activates inflammatory damage in UVB induced murine skin lesion by sponging miR-93-5p/epiregulin axis
Cited by: 10
Author(s): Nan Zhang, Zhong Zhang, Yujia Wang, Li Yang, Fengbo Wu, Cheng Peng, Wei Huang, Gu He
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2019.02365

Temporal Dynamics of the Soil Metabolome and Microbiome During Simulated Anaerobic Soil Disinfestation
Cited by: 44
Author(s): Shashika S. Hewavitharana, Emmi Klarer, Andrew J. Reed, Rachel Leisso, Brenton C. Poirier, Loren Honaas, David R. Rudell, Mark Mazzola
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.ppat.1005705

S100A12 Is Part of the Antimicrobial Network against Mycobacterium leprae in Human Macrophages
Cited by: 53
Author(s): Susan Realegeno, Kindra M. Kelly-Scumpia, Angeline T. Dang, Jing Lü, Rosane M. B. Teles, Philip T. Liu, Mirjam Schenk, Ernest Y. Lee, Nathan W. Schmidt, Gerard C. L. Wong, Euzenir Nunes Sarno, Thomas H. Rea, María Teresa Ochoa, Matteo Pellegrini, Robert L. Modlin
Software Mentions: 2
Published: over 10 years ago

10.1111/tpj.14020

Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploidBrassica napus
Cited by: 16
Author(s): D. Marc Jones, Rachel Wells, Nick Pullen, Martin Trick, Judith A. Irwin, Richard J. Morris
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.ppat.1006871

Liver macrophage-associated inflammation correlates with SIV burden and is substantially reduced following cART
Cited by: 18
Author(s): Bridget S. Fisher, Richard Green, Rachel Brown, Matthew P. Wood, Tiffany Hensley-McBain, Cole Fisher, Jean Chang, Andrew D. Miller, William J. Bosche, Jeffrey D. Lifson, Maud Mavigner, Charlene Miller, Michael Gale, Guido Silvestri, Ann Chahroudi, Nichole R. Klatt, Donald L. Sodora
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-15-644

Prediction of miRNA-mRNA associations in Alzheimer’s disease mice using network topology
Cited by: 24
Author(s): Hyun Ho Noh, Charny Park, Soojun Park, Young Seek Lee, Soo Young Cho, Hyemyung Seo
Software Mentions: 2
Published: about 12 years ago

10.3389/fimmu.2021.709164

Defining a Methylation Signature Associated With Operational Tolerance in Kidney Transplant Recipients
Cited by: 5
Author(s): Ramón María Alvargonzález Rodríguez, María P. Hernández-Fuentes, Viviana Corte-Iglesias, María Laura Sáiz, Juan José Lozano, Ana R. Cortázar, Isabel Mendizabal, María Luisa Suárez-Fernández, Eliécer Coto, Antonio López-Vázquez, Carmen Díaz‐Corte, Ana M. Aransay, Carlos López‐Larrea, Beatriz Suárez-Álvarez
Software Mentions: 2
Published: about 5 years ago

10.1186/s12934-014-0151-y

Metabolomic basis of laboratory evolution of butanol tolerance in photosynthetic Synechocystis sp. PCC 6803
Cited by: 54
Author(s): Yaxing Wang, Mengliang Shi, Xiangfeng Niu, Xiaoqing Zhang, Linfeng Gao, Lei Chen, Jiangxin Wang, Weiwen Zhang
Software Mentions: 2
Published: almost 12 years ago

10.3389/fphys.2018.00236

Arachidonic Acid Metabolism Pathway Is Not Only Dominant in Metabolic Modulation but Associated With Phenotypic Variation After Acute Hypoxia Exposure
Cited by: 8
Author(s): Chang Liu, Bao Liu, Lu Liu, Erlong Zhang, Bind-da Sun, Gang Xu, Jian Chen, Yuqi Gao
Software Mentions: 2
Published: over 8 years ago

10.1016/j.psj.2020.11.074

Effects of monobutyrin supplementation on egg production, biochemical indexes, and gut microbiota of broiler breeders
Cited by: 3
Author(s): Xin Feng, Fangang Kong, Liwei Zheng, Qien Qi, Lina Long, Li Gong, Weilong Huang, Huihua Zhang
Software Mentions: 2
Published: over 5 years ago

10.1098/rspb.2015.1746

Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum
Cited by: 16
Author(s): Jon Bråte, Marcin Adamski, Ralf Stefan Neumann, Kamran Shalchian-Tabrizi, Maja Adamska
Software Mentions: 2
Published: almost 11 years ago

10.1098/rspb.2019.0470

Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world
Cited by: 11
Author(s): Bradford A. Dimos, Siraje Arif Mahmud, Lauren E. Fuess, Laura D. Mydlarz, Mark W. Pellegrino
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-020-06853-y

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus
Cited by: 7
Author(s): Yue Zhang, Razgar Seyed Rahmani, Xingyu Yang, Jin‐Ming Chen, Tao Shi
Software Mentions: 2
Published: over 6 years ago

10.3389/fphys.2020.00106

An Overview of Embryogenesis: External Morphology and Transcriptome Profiling in the Hemipteran Insect Nilaparvata lugens
Cited by: 14
Author(s): Xiaolong Fan, Rui Pang, Wan‐Xue Li, Abhishek Ojha, Dan Li, Wenqing Zhang
Software Mentions: 2
Published: over 6 years ago

10.1007/s13238-017-0450-2

Single-cell transcriptomics reveals gene signatures and alterations associated with aging in distinct neural stem/progenitor cell subpopulations
Cited by: 29
Author(s): Zhanping Shi, Yanan Geng, Jiping Liu, Huina Zhang, Libing Zhou, Qing Lin, Juehua Yu, Kunshan Zhang, Jie Liu, Xinpei Gao, Chunxue Zhang, Yinan Yao, Chong Zhang, Yi Sun
Software Mentions: 2
Published: over 9 years ago

10.1186/s13068-020-01802-z

Gene coexpression network analysis reveals a novel metabolic mechanism of Clostridium acetobutylicum responding to phenolic inhibitors from lignocellulosic hydrolysates
Cited by: 14
Author(s): Huanhuan Liu, Jing Zhang, Jian Yuan, Xiaolong Jiang, Lingyan Jiang, Zhenjing Li, Zhiqiu Yin, Yuhui Du, Guang Zhao, Bin Liu, Di Huang
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-018-5072-4

Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize
Cited by: 23
Author(s): Yang Yu, Jianyang Shi, Xiyang Li, Jian Liu, Qi Geng, Shi Haichun, KE Yong-pei, Qun Sun
Software Mentions: 2
Published: about 8 years ago

10.18632/aging.102419

Characterization of long non-coding RNA and messenger RNA profiles in laryngeal cancer by weighted gene co-expression network analysis
Cited by: 26
Author(s): Huanhuan Liu, Yi Sun, Huan Tian, Xiaolian Xiao, Jiaqi Zhang, Yongzhen Wang, Fang Yu
Software Mentions: 2
Published: almost 7 years ago

10.3390/proteomes7030030

Network Analysis of a Membrane-Enriched Brain Proteome across Stages of Alzheimer’s Disease
Cited by: 16
Author(s): Lenora Higginbotham, Eric B. Dammer, Duc M. Duong, Erica Modeste, Thomas J. Montine, James J. Lah, Aĺlan I. Levey
Software Mentions: 2
Published: about 7 years ago

10.3389/fphys.2021.656649

Whitefly Network Analysis Reveals Gene Modules Involved in Host Plant Selection, Development and Evolution
Cited by: 6
Author(s): Jiahui Tian, Hao Zhan, Youssef Dewer, Biyun Zhang, Cheng Qu, Chen Luo, Fengqi Li, Shiyong Yang
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.581313

The Mosaic Architecture of NRPS-PKS in the Arbuscular Mycorrhizal Fungus Gigaspora margarita Shows a Domain With Bacterial Signature
Cited by: 7
Author(s): Francesco Venice, Alessandro Desirò, Gladstone Alves da Silva, Alessandra Salvioli, Paola Bonfante
Software Mentions: 2
Published: almost 6 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479