cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1155/2021/1801873

Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma
Cited by: 2
Author(s): Dan Luo, Xiang Zhang, Xiaokai Li, Gang Chen
Software Mentions: 7
Published: about 5 years ago

10.3389/fonc.2020.553399

CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer
Cited by: 20
Author(s): Yutao Wang, Kexin Yan, Jiaxing Lin, Yang Liu, Jianfeng Wang, Xuejie Li, Xinxin Li, Zhixiong Hua, Zhenhua Zheng, Jianxiu Shi, Siqing Sun, Jianbin Bi
Software Mentions: 7
Published: almost 6 years ago

10.1136/jitc-2020-000778

M1<sup>hot</sup>tumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer
Cited by: 75
Author(s): Eva M. Garrido-Martín, Toby Mellows, James Clarke, Anusha-Preethi Ganesan, Oliver Wood, Angelica Cazaly, Grégory Seumois, Serena Chee, Aiman Alzetani, Emma V. King, Catherine C. Hedrick, Gareth J. Thomas, Peter S. Friedmann, Christian Ottensmeier, Pandurangan Vijayanand, Tilman Sánchez-Elsner
Software Mentions: 7
Published: about 6 years ago

10.3389/fonc.2021.626961

Identification of Stemness Characteristics Associated With the Immune Microenvironment and Prognosis in Gastric Cancer
Cited by: 15
Author(s): Deli Mao, Zhijun Zhou, Shenglei Song, Dongsheng Li, Yulong He, Zhewei Wei, Changhua Zhang
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers12082310

Systematic Analysis of Aberrant Biochemical Networks and Potential Drug Vulnerabilities Induced by Tumor Suppressor Loss in Malignant Pleural Mesothelioma
Cited by: 15
Author(s): Haitang Yang, Duo Xu, Yang Zhang, Feng Yao, Heng Zhao, Ralph A. Schmid, Ren‐Wang Peng
Software Mentions: 7
Published: about 6 years ago

10.1038/s41598-019-45989-0

Machine learning approaches to predict lupus disease activity from gene expression data
Cited by: 48
Author(s): Brian Kegerreis, Michelle D. Catalina, Prathyusha Bachali, Nicholas S. Geraci, Adam C. Labonte, Chen Zeng, Nathaniel Stearrett, Keith A. Crandall, Peter E. Lipsky, Amrie C. Grammer
Software Mentions: 7
Published: about 7 years ago

10.1038/s41598-019-53843-6

Monocytes affect bone mineral density in pre- and postmenopausal women through ribonucleoprotein complex biogenesis by integrative bioinformatics analysis
Cited by: 8
Author(s): Kang-Wen Xiao, Jiali Li, Zhao-Yi Zeng, Zhibo Liu, Zhiqiang Hou, Xin Yan, Lin Cai
Software Mentions: 7
Published: almost 7 years ago

10.3390/microorganisms9050996

Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions
Cited by: 1
Author(s): Karen Cristine Gonçalves dos Santos, G. Pelletier, Armand Séguin, François Guillemette, Jeffrey A. Hawkes, Isabel Desgagné‐Penix, Hugo Germain
Software Mentions: 7
Published: over 5 years ago

10.3389/fonc.2020.622251

Screening and Identification of Four Prognostic Genes Related to Immune Infiltration and G-Protein Coupled Receptors Pathway in Lung Adenocarcinoma
Cited by: 3
Author(s): Yan Wang, Longqing Qiu, Yu Chen, Xia Zhang, Yang Peng, Feng Xu
Software Mentions: 7
Published: over 5 years ago

10.3389/fcell.2021.665364

Hypoxia Constructing the Prognostic Model of Colorectal Adenocarcinoma and Related to the Immune Microenvironment
Cited by: 11
Author(s): Yuanyuan Zhang, Feng Yang, Xiaohong Peng, Xiaoyü Li, Na Luo, Wenjun Zhu, Min Fu, Qianxia Li, Guangyuan Hu
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-018-21161-y

Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
Cited by: 16
Author(s): Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masamitsu Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki
Software Mentions: 6
Published: over 8 years ago

10.1186/s40168-021-01150-6

Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants
Cited by: 40
Author(s): Qi Zhang, Zhenyan Zhang, Tao Lu, Yitian Yu, Josep Peñuelas, Yan Zhu, Haifeng Qian
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12920-021-00989-w

Identification of key genes in calcific aortic valve disease via weighted gene co-expression network analysis
Cited by: 7
Author(s): Jin-Yu Sun, Hua Yang, Hui Shen, Qiang Qu, Junyan Kan, Xiangqing Kong, Wei Sun, Yue-Yun Shen
Software Mentions: 6
Published: over 5 years ago

10.1007/s00018-020-03485-z

Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
Cited by: 17
Author(s): Tiziana Caputo, Van Du T. Tran, Nasim Bararpour, Carine Winkler, Gabriela Aguileta, Bao Khanh Trang, Greta Maria Paola Giordano Attianese, Anne Wilson, Aurélien Thomas, Marco Pagni, Nicolas Guex, Béatrice Desvergne, Federica Gilardi
Software Mentions: 6
Published: over 6 years ago

10.1111/jcmm.16414

Identification of hub genes associated with neutrophils infiltration in colorectal cancer
Cited by: 12
Author(s): Hao Su, Tianyi Cai, Sen Zhang, Xialin Yan, Leqi Zhou, Zengyou He, Peng Xue, Jianwen Li, Min Zheng, Xiao Yang, Bo Feng
Software Mentions: 6
Published: over 5 years ago

10.3389/fmolb.2021.628546

Identification of Molecular Subtypes and Key Genes of Atherosclerosis Through Gene Expression Profiles
Cited by: 3
Author(s): Yujia Yang, Yuchen Cai, Yuan Zhang, Yuanfu Xu, Zhiqiang Xu
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-018-31192-0

Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid
Cited by: 18
Author(s): Qing Liu, Kevin Van Bortle, Yue Zhang, Ming Zhao, Joe Z. Zhang, Benjamin Geller, Joshua J. Gruber, Chao Jiang, Joseph C. Wu, M Snyder
Software Mentions: 6
Published: about 8 years ago

10.3389/fmolb.2021.636991

Identifying Dendritic Cell–Related Genes Through a Co-Expression Network to Construct a 12-Gene Risk-Scoring Model for Predicting Hepatocellular Carcinoma Prognosis
Cited by: 7
Author(s): Chao-Yuan Huang, Xiaotao Jiang, Yuancheng Huang, Lina Zhao, Peiwu Li, Fengbin Liu
Software Mentions: 6
Published: over 5 years ago

10.1186/s12935-021-02049-w

Multi-omics analysis reveals prognostic value of tumor mutation burden in hepatocellular carcinoma
Cited by: 19
Author(s): Qianhui Xu, Hao Xu, Ruilong Deng, Zijie Wang, Nanjun Li, Zhixuan Qi, Jiaxin Zhao, Wen Huang
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2019.02491

Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection
Cited by: 30
Author(s): Liming Gu, Huixiong Deng, Zhihui Ren, Ying Zhao, Shun Yu, Yingzhu Guo, Jianping Dai, Xiaoxuan Chen, Kangsheng Li, Rui Li, Gefei Wang
Software Mentions: 6
Published: almost 7 years ago

10.3389/fcell.2021.724837

Integrative Analysis of m6A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in Lupus Nephritis
Cited by: 14
Author(s): Huanhuan Zhao, Shaokang Pan, Jiayu Duan, Fengxun Liu, Guangpu Li, Dongwei Li, Zhangsuo Liu
Software Mentions: 6
Published: almost 5 years ago

10.1111/jcmm.14721

Integrated analysis of co‐expression and ceRNA network identifies five lncRNAs as prognostic markers for breast cancer
Cited by: 41
Author(s): Yan Yao, Tingting Zhang, Ling‐Yu Qi, Chao Zhou, Junyu Wei, Fubin Feng, Ruijuan Liu, Changgang Sun
Software Mentions: 6
Published: almost 7 years ago

10.3389/fmicb.2020.01036

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants
Cited by: 29
Author(s): Qian Zhang, Jacquelinne J. Acuña, Nitza G. Inostroza, Paola Durán, Marı́a de la Luz Mora, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2020.00099

A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma
Cited by: 4
Author(s): J Chen, X Wang, Wei Li, Chao Shang, T Chen, Y Chen
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.701065

Identification of Tumor Antigens and Immune Landscape in Glioblastoma for mRNA Vaccine Development
Cited by: 12
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1008491

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-018-33498-5

Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer
Cited by: 28
Author(s): Raquel L. Costa, Mariana Boroni, Marcelo A. Soares
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12967-021-03078-9

Low CCL19 expression is associated with adverse clinical outcomes for follicular lymphoma patients treated with chemoimmunotherapy
Cited by: 1
Author(s): Yu Zhou, Shasha Wang, Yunxia Tao, Haizhu Chen, Yan Qin, Xiaohong He, Shengyu Zhou, Peng Liu, Jianliang Yang, Sheng Yang, Lin Gui, Ning Lou, Zhishang Zhang, Jiarui Yao, Xiaohong Han, Yuankai Shi
Software Mentions: 6
Published: almost 5 years ago

10.3390/metabo11060361

Opposing Effects of Ceanothus velutinus Phytochemistry on Herbivore Communities at Multiple Scales
Cited by: 2
Author(s): Casey S. Philbin, M. J. Paulsen, Lora A. Richards
Software Mentions: 6
Published: about 5 years ago

10.1534/g3.117.041624

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Cited by: 35
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando P Pardo Manuel De Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale
Software Mentions: 6
Published: over 9 years ago

10.1186/s12864-021-07443-2

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing
Cited by: 12
Author(s): Carolina P. Moraleda, Diego Robledo, Alejandro P. Gutiérrez, Jorge Del‐Pozo, José M. Yáñez, Ross D. Houston
Software Mentions: 6
Published: over 5 years ago

10.1172/jci.insight.140380

Patient ancestry significantly contributes to molecular heterogeneity of systemic lupus erythematosus
Cited by: 41
Author(s): Michelle D. Catalina, Prathyusha Bachali, Anthony E. T. Yeo, Nicholas S. Geraci, Michelle Petri, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 6
Published: about 6 years ago

10.3389/fphys.2019.01370

A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse Heart
Cited by: 1
Author(s): Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joël Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pgen.1009474

Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps
Cited by: 6
Author(s): Floria M. K. Uy, Christopher M. Jernigan, Natalie C. Zaba, Eshan Mehrotra, Sara Miller, Michael J. Sheehan
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-017-10930-w

Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis
Cited by: 69
Author(s): Maria Ryaboshapkina, Mårten Hammar
Software Mentions: 6
Published: almost 9 years ago

10.1002/cam4.3576

Establishment and validation of a prognostic nomogram based on a novel five‐DNA methylation signature for survival in endometrial cancer patients
Cited by: 6
Author(s): Xingchen Li, Fufen Yin, Fan Yuan, Yuan Cheng, Yangyang Dong, Jingyi Zhou, Zhiqi Wang, Jianliu Wang
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-017-09094-4

Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study
Cited by: 33
Author(s): Stephen P. Ficklin, Leland J. Dunwoodie, William L. Poehlman, Christopher Watson, Kimberly Roche, F. Alex Feltus
Software Mentions: 6
Published: about 9 years ago

10.1186/s12864-021-07720-0

Comparative neurotranscriptomics reveal widespread species differences associated with bonding
Cited by: 5
Author(s): Joel A. Tripp, Alejandro Berrío, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young, Steve Phelps
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2021.675208

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum
Cited by: 5
Author(s): Pragya Adhikari, Santiago X. Mideros, Tiffany M. Jamann
Software Mentions: 6
Published: over 5 years ago

10.3389/fcell.2021.724860

Integrative Analysis of Biomarkers Through Machine Learning Identifies Stemness Features in Colorectal Cancer
Cited by: 7
Author(s): Ran Wei, Jichuan Quan, Shuofeng Li, Hengchang Liu, Xu Guan, Zheng Jiang, Xishan Wang
Software Mentions: 6
Published: almost 5 years ago

10.3389/fcell.2021.641629

Dysregulation of miR-138-5p/RPS6KA1-AP2M1 Is Associated With Poor Prognosis in AML
Cited by: 10
Author(s): Donghu Yu, Chen Chen, Xiaoping Li, Jie Yao, Sheng Li, Xiaolan Ruan
Software Mentions: 6
Published: over 5 years ago

10.18632/oncotarget.16544

The integrative metabolomic-transcriptomic landscape of glioblastome multiforme
Cited by: 20
Author(s): Dieter Henrik Heiland, Jakob Wörner, Jan Gerrit Haaker, Daniel Delev, Nils Pompe, Bianca Mercas, Pamela Franco, Annette Gäbelein, Sabrina Heynckes, Dietmar Pfeifer, Stefan Weber, Irina Mader, Oliver Schnell
Software Mentions: 6
Published: over 9 years ago

10.3389/fphys.2018.01778

Identification of Crucial Genes and Pathways in Human Arrhythmogenic Right Ventricular Cardiomyopathy by Coexpression Analysis
Cited by: 11
Author(s): Peipei Chen, Bo Long, Yuanfu Xu, Wei Wu, Shuyang Zhang
Software Mentions: 6
Published: over 7 years ago

10.18632/oncotarget.28058

Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoids
Cited by: 4
Author(s): Matthew Devall, Christopher H. Dampier, Stephen Eaton, Mourad W. Ali, Virginia Díez-Obrero, Ferrán Moratalla-Navarro, Jennifer Bryant, Lucas T. Jennelle, Vı́ctor Moreno, Steven M. Powell, Ulrike Peters, Graham Casey
Software Mentions: 6
Published: almost 5 years ago

10.1155/2020/2319194

Immune-Related lncRNA Correlated with Transcription Factors Provide Strong Prognostic Prediction in Gliomas
Cited by: 4
Author(s): Yantao Tian, Yiquan Ke, Yanxia Ma
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12935-020-01179-x

Expression profile analysis identifies key genes as prognostic markers for metastasis of osteosarcoma
Cited by: 12
Author(s): Xiaoqing Guan, Zhiyuan Guan, Chunli Song
Software Mentions: 6
Published: over 6 years ago

10.3389/fcell.2021.646774

CRISPR-cas9 Screening Identified Lethal Genes Enriched in Cell Cycle Pathway and of Prognosis Significance in Breast Cancer
Cited by: 6
Author(s): Xi Sun, Zheng Wang, Xiaosong Chen, Kunwei Shen
Software Mentions: 6
Published: over 5 years ago

10.1186/s40104-019-0412-z

Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply
Cited by: 13
Author(s): Emilio Mármol-Sánchez, Yuliaxis Ramayo-Caldas, Raquel Quintanilla, Tainã Figueiredo Cardoso, Rayner González-Prendes, J. Tibau, Marcel Amills
Software Mentions: 6
Published: over 6 years ago

10.1038/s41422-020-0300-2

Embryonic endothelial evolution towards first hematopoietic stem cells revealed by single-cell transcriptomic and functional analyses
Cited by: 80
Author(s): Siyuan Hou, Zongcheng Li, Xiaona Zheng, Yun Gao, Ji Dong, Yanli Ni, Xiaobo Wang, Yunqiao Li, Xiaochen Ding, Zhilin Chang, Shuaili Li, Yuqiong Hu, Xiaoying Fan, Yu Hou, Lu Wen, Bing Liu, Fuchou Tang, Yu Lan
Software Mentions: 6
Published: over 6 years ago

10.3389/fonc.2021.587479

Identification of Mitochondrial-Related Prognostic Biomarkers Associated With Primary Bile Acid Biosynthesis and Tumor Microenvironment of Hepatocellular Carcinoma
Cited by: 21
Author(s): Tao Zhang, Yingli Nie, Jian Gu, Kailin Cai, Xiangdong Chen, Huili Li, Jiliang Wang
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22063028

Characterization of Biological Pathways Regulating Acute Cold Resistance of Zebrafish
Cited by: 19
Author(s): Jing Ren, Yong Long, Ran Liu, Guangliang Song, Qing Li, Zongbin Cui
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22126307

Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa
Cited by: 4
Author(s): Christina B. Bielmeier, Saskia Roth, Sabrina I. Schmitt, Stefaniya Boneva, Anja Schlecht, Mario Vallon, Ernst R. Tamm, Süleyman Ergün, Andreas Neueder, Barbara M. Braunger
Software Mentions: 6
Published: about 5 years ago

10.3390/brainsci9120381

A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder
Cited by: 6
Author(s): Laura B. Ferguson, Shruti Patil, Bailey A. Moskowitz, Igor Ponomarev, R. Adron Harris, R. Dayne Mayfield, Robert O. Messing
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0183517

Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study
Cited by: 7
Author(s): Han Wang, Zhenyu Zhang, Bangshun He, Yu Xu, Jun Zhang, Weijun Cao
Software Mentions: 6
Published: about 9 years ago

10.3389/fonc.2020.01001

Network-Based Approach to Identify the Antiproliferative Mechanisms of Bruceine D in Breast Cancer From the Cancer Genome Atlas
Cited by: 3
Author(s): Sai Tian, Rui Jiang, Weidong Zhang
Software Mentions: 6
Published: about 6 years ago

10.3389/fcvm.2020.580573

Comprehensive Identification of Key Genes Involved in Development of Diabetes Mellitus-Related Atherogenesis Using Weighted Gene Correlation Network Analysis
Cited by: 14
Author(s): Qi Huang, Guo-Xiong Deng, Rongguo Wei, Qiaoye Wang, Donghua Zou, Jinru Wei
Software Mentions: 6
Published: almost 6 years ago

10.3389/fnmol.2019.00316

Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis
Cited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.657658

Weighted Gene Co-expression Network Analysis Identified a Novel Thirteen-Gene Signature Associated With Progression, Prognosis, and Immune Microenvironment of Colon Adenocarcinoma Patients
Cited by: 2
Author(s): Cangang Zhang, Zhe Zhao, Haibo Li, Shukun Yao, Dongyan Zhao
Software Mentions: 6
Published: about 5 years ago

10.3389/fpsyt.2021.716722

Transcriptomics Analysis Reveals Shared Pathways in Peripheral Blood Mononuclear Cells and Brain Tissues of Patients With Schizophrenia
Cited by: 6
Author(s): Xuemian Song, Yiyun Liu, Juncai Pu, Siwen Gui, Xiaogang Zhong, Xiaopeng Chen, Weiyi Chen, Xiang Chen, Yue Chen, Haiyang Wang, Ke Cheng, Libo Zhao, Peng Xie
Software Mentions: 6
Published: almost 5 years ago

10.3389/fgene.2021.653474

Identifying ceRNA Networks Associated With the Susceptibility and Persistence of Atrial Fibrillation Through Weighted Gene Co-Expression Network Analysis
Cited by: 6
Author(s): Yaozhong Liu, Na Liu, Fan Bai, Qiming Liu
Software Mentions: 6
Published: about 5 years ago

10.3390/ijms20020263

Molecular Network-Based Drug Prediction in Thyroid Cancer
Cited by: 14
Author(s): Xingyu Xu, Hang Long, Baohang Xi, Binbin Ji, Zejun Li, Yunyue Dang, Cheng Jiang, Yao Yao, Jialiang Yang
Software Mentions: 6
Published: over 7 years ago

10.1186/s12920-021-01036-4

Multi-factor regulatory network and different clusters in hypertrophic obstructive cardiomyopathy
Cited by: 3
Author(s): Xianyu Qin, Lei Huang, Sicheng Chen, Shaoxian Chen, Pengju Wen, Yueheng Wu, Jian Zhuang
Software Mentions: 6
Published: about 5 years ago

10.1186/s13229-019-0287-z

A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood
Cited by: 12
Author(s): Charles E. Mordaunt, Bo Y. Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca Jean Schmidt, M. Daniele Fallin
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0109760

Copy Number Loss of the Interferon Gene Cluster in Melanomas Is Linked to Reduced T Cell Infiltrate and Poor Patient Prognosis
Cited by: 164
Author(s): Peter S. Linsley, Cate Speake, Elizabeth Whalen, Damien Chaussabel
Software Mentions: 6
Published: almost 12 years ago

10.7554/eLife.35368

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Cited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0254829

Tumor infiltrating lymphocytes associated competitive endogenous RNA networks as predictors of outcome in hepatic carcinoma based on WGCNA analysis
Cited by: 1
Author(s): Ying He, Xu Rui, Li Peng, Xiaoyu Hu
Software Mentions: 6
Published: about 5 years ago

10.1186/s13100-019-0180-5

Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements
Cited by: 20
Author(s): Nicky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Software Mentions: 6
Published: about 7 years ago

10.3389/fgene.2020.00011

Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance
Cited by: 6
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 6
Published: over 6 years ago

10.1038/s41398-021-01531-3

Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study
Cited by: 22
Author(s): Xiuxia Yuan, Yunpeng Wang, Xue Li, Jiajun Jiang, Yulin Kang, Lijuan Pang, Peifen Zhang, Ang Li, Luxian Lv, Ole A. Andreassen, Xiaoduo Fan, Shaohua Hu, Xueqin Song
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.10633

Gene signatures with predictive and prognostic survival values in human osteosarcoma
Cited by: 4
Author(s): Zhongpeng Qiu, Xuehui Du, Kai Chen, Yi Dai, Sibo Wang, Jun Xiao, Gang Li
Software Mentions: 6
Published: over 5 years ago

10.1038/s41398-021-01447-y

Essential genes from genome-wide screenings as a resource for neuropsychiatric disorders gene discovery
Cited by: 2
Author(s): Wei Zhang, Joao L De Quevedo, Gabriel R. Fries
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0233372

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs
Cited by: 20
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.8505

Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis
Cited by: 10
Author(s): Xuegang Hu, Genban Sun, Zhiqiang Shi, Hui Ni, Shan Jiang
Software Mentions: 6
Published: over 6 years ago

10.1186/s12885-017-3832-1

Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages
Cited by: 9
Author(s): Daifeng Wang, John D. Haley, Patricia Thompson
Software Mentions: 6
Published: almost 9 years ago

10.1186/s12885-018-4848-x

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Cited by: 53
Author(s): Kasey Jividen, Katarzyna Kedzierska, Chunsong Yang, Karol Szlachta, Aakrosh Ratan, Bryce M. Paschal
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12885-021-08052-8

Comprehensive analysis of immune-related prognostic genes in the tumour microenvironment of hepatocellular carcinoma
Cited by: 2
Author(s): Weike Gao, Luan Li, Xinyin Han, Siyao Liu, Chengzhen Li, Guanying Yu, Lei Zhang, Dongsheng Zhang, Caiyun Liu, Erhong Meng, Shuai Hong, Dongliang Wang, Peiming Guo, Guangjun Shi
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2020.634634

A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune Biomarkers
Cited by: 17
Author(s): Jin Ren, Yun Yang, Chuanyin Li, Lu Xie, Ronggui Hu, Qin Xiong, Menghuan Zhang
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2019.01056

Meta-Analysis of HTLV-1-Infected Patients Identifies CD40LG and GBP2 as Markers of ATLL and HAM/TSP Clinical Status: Two Genes Beat as One
Cited by: 5
Author(s): Eduardo R. Fukutani, Pablo Ivan Pereira Ramos, José Irahe Kasprzykowski, Lucas Gentil Azevedo, Moreno Magalhães de Souza Rodrigues, João Victor Lima, Helton Fábio Santos de Araújo, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: almost 7 years ago

10.3389/fgene.2020.00311

Weighted Gene Coexpression Network Analysis of Features That Control Cancer Stem Cells Reveals Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 57
Author(s): Yi Liao, Yulei Wang, Mengqing Cheng, Chengliang Huang, Xiaoxuan Fan
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-021-98059-9

Sex-dependent gene co-expression in the human body
Cited by: 9
Author(s): Robin Hartman, Michal Mokrý, Gérard Pasterkamp, Hester M. den Ruijter
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12918-018-0620-8

Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
Cited by: 11
Author(s): Theresia Conrad, Olaf Kniemeyer, Sebastian Henkel, Thomas Krüger, Derek J. Mattern, Vito Valiante, Reinhard Guthke, Ilse D. Jacobsen, Axel A. Brakhage, Sebastian Vlaic, Jörg Linde
Software Mentions: 6
Published: almost 8 years ago

10.1038/ismej.2017.165

Recurrent patterns of microdiversity in a temperate coastal marine environment
Cited by: 110
Author(s): Meghan Chafee, Antonio Fernández-Guerra, Pier Luigi Buttigieg, Gunnar Gerdts, A. Murat Eren, Hanno Teeling, Rudolf Amann
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0208132

Identification of alterations in macrophage activation associated with disease activity in systemic lupus erythematosus
Cited by: 67
Author(s): Adam C. Labonte, Brian Kegerreis, Nicholas S. Geraci, Prathyusha Bachali, Sushma Madamanchi, Robert Robl, Michelle D. Catalina, Peter E. Lipsky, Amrie C. Grammer
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-021-85848-5

Abnormal upregulation of cardiovascular disease biomarker PLA2G7 induced by proinflammatory macrophages in COVID-19 patients
Cited by: 18
Author(s): Yang Li, Yongzhong Jiang, Yi Zhang, Naizhe Li, Qiangling Yin, Linlin Liu, Xin Lv, Yan Liu, Aqian Li, Bin Fang, Jiajia Li, Hengping Ye, Gang Ye, Xiaoxian Cui, Yang Liu, Yuanyuan Qu, Chuan Li, Jiandong Li, Dexin Li, Zhongtao Gai, Shiwen Wang, Faxian Zhan, Mifang Liang
Software Mentions: 6
Published: over 5 years ago

10.18632/aging.203166

Identification and validation of inferior prognostic genes associated with immune signatures and chemotherapy outcome in acute myeloid leukemia
Cited by: 7
Author(s): Jie Wang, Hao Jian-ping, Nazim Uddin, Yun Wu, Rong Chen, Dongfeng Li, Dai-qin Xiong, Nan Ding, Jianhua Yang, Xiaowen Ding
Software Mentions: 6
Published: about 5 years ago

10.18632/aging.202638

Identification of key genes in coronary artery disease: an integrative approach based on weighted gene co-expression network analysis and their correlation with immune infiltration
Cited by: 10
Author(s): Yang Yang, Xiangshan Xu
Software Mentions: 6
Published: over 5 years ago

10.1186/s12885-021-08711-w

Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
Cited by: 12
Author(s): Rongjia Su, Chengjuan Jin, Lina Zhou, Yannan Cao, Menghua Kuang, Linxia Li, Jianbin Xiang
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-021-86048-x

A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients
Cited by: 9
Author(s): Yuzi Xu, Fengqin Xu, Yiming Lv, Siyuan Wang, Jia Li, Chuan Zhou, Jimin Jiang, Binbin Xie, Fuming He
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-91214-2

Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction
Cited by: 12
Author(s): Xin Luo, Jun Yin, Denise Dwyer, Tracy M. Yamawaki, Hong Zhou, Hongfei Ge, Chun-Ya Han, Artem Shkumatov, K. F. Snyder, Brandon Ason, Chi-Ming Li, Oliver Homann, Marina Stolina
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-019-2840-3

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network
Cited by: 30
Author(s): Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang, Jia Meng
Software Mentions: 6
Published: over 7 years ago

10.18632/aging.202474

Clinical and genomic characteristics of metabolic syndrome in colorectal cancer
Cited by: 2
Author(s): Yanyan Li, Jungang Zhao, Xiaoli Wu, Yini Zhang, Jia Yin, Weiyang Cai
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-65320-6

IRE1α and IGF signaling predict resistance to an endoplasmic reticulum stress-inducing drug in glioblastoma cells
Cited by: 10
Author(s): Jeffrey J. Rodvold, Xian Su, Julia K. Nussbacher, Brian Tsui, Thomas Waller, Stephen Searles, Alyssa Lew, Pengfei Jiang, Ivan Babić, Natsuko Nomura, Jonathan H. Lin, Santosh Kesari, Hannah Carter, Maurizio Zanetti
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-020-67842-5

Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis
Cited by: 18
Author(s): Jiangang Liu, Yong Beom Cho, Hye Kyung Hong, Song Wu, Philip J. Ebert, Steven M. Bray, Suei Nee Wong, Jason C. Ting, John N. Calley, Catherine F. Whittington, Shripad V. Bhagwat, Christoph Reinhard, Robert A. Wild, Do‐Hyun Nam, Amit Aggarwal, Woo Yong Lee, Sheng-Bin Peng
Software Mentions: 6
Published: about 6 years ago

10.1186/s12866-020-01739-1

Alter between gut bacteria and blood metabolites and the anti-tumor effects of Faecalibacterium prausnitzii in breast cancer
Cited by: 57
Author(s): Ji Ma, Lingqi Sun, Ying Liu, Hui Ren, Yali Shen, Feng Bi, Tao Zhang, Xin Wang
Software Mentions: 6
Published: over 6 years ago

10.1186/s12866-020-01913-5

Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau
Cited by: 11
Author(s): Mengjun Zhang, Liwei Chai, Muke Huang, Weiqian Jia, Jiabao Guo, Yi Huang
Software Mentions: 6
Published: about 6 years ago

10.1038/sdata.2018.185

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
Cited by: 284
Author(s): Minghui Wang, Noam D. Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chi Ming, Ryan Neff, Wanli Ma, John F. Fullard, Mads E. Hauberg, Jaroslav Bendl, Mette A. Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara M. Mangravite, Eric B. Dammer, Duc M. Duong, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Bin Zhang
Software Mentions: 6
Published: almost 8 years ago

10.18632/aging.103832

Prognostic model of patients with liver cancer based on tumor stem cell content and immune process
Cited by: 7
Author(s): Jie Zhu, Miaomiao Gao, Yuchen Jin, Weiran Huang, Zhuo Huang, Zhengwei Xie
Software Mentions: 6
Published: about 6 years ago

10.1186/s12920-018-0358-6

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability
Cited by: 5
Author(s): Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, André Reis, Rami Abou Jamra, Fulvia Ferrazzi
Software Mentions: 6
Published: over 8 years ago

10.12688/wellcomeopenres.14073.3

ANIMA: Association network integration for multiscale analysis
Cited by: 4
Author(s): Armin Deffur, Robert J. Wilkinson, Bongani M. Mayosi, Nicola Mulder
Software Mentions: 6
Published: almost 8 years ago

10.12688/wellcomeopenres.15115.1

Single-cell transcriptome analysis of CD8+ T-cell memory inflation
Cited by: 7
Author(s): Andrew J. Highton, Madeleine E Zinser, Lian Ni Lee, Claire Hutchings, Catherine de Lara, Chansavath Phetsouphanh, Christian Willberg, Claire L. Gordon, Paul Klenerman, Emanuele Marchi
Software Mentions: 6
Published: over 7 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Penalties:

Papers Mentioning WGCNA 3,479