cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1002/cam4.4022

A pharmacophore‐based classification better predicts the outcomes of HER2‐negative breast cancer patients receiving the anthracycline‐ and/or taxane‐based neoadjuvant chemotherapy
Cited by: 1
Author(s): Xuan Li, Hefen Sun, Qiqi Liu, Yang Liu, Yifeng Hou, Wei Jin
Software Mentions: 4
Published: over 5 years ago

10.1186/s12915-020-00862-9

Genome-enabled insights into the biology of thrips as crop pests
Cited by: 44
Author(s): Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G.C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis, Simon Snoeck, Clauvis Nji Tizi Taning, Dong Wei, Shirani M. K. Widana Gamage, Daniel Hughes, Shwetha C. Murali, Samuel T. Bailey, Nicolás Bejerman, Christopher J. Holmes, Emily C. Jennings, Andrew J. Rosendale, Andrew E. Rosselot, Kaylee Hervey, Brandi A. Schneweis, Sammy Cheng, Christopher P. Childers, Felipe A. Simão, Ralf G. Dietzgen, Hsu Chao, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Yi Han, Sandra L. Lee, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Joshua B. Benoit, Markus Friedrich, Jeffery W. Jones, Kristen A. Panfilio, Yoonseong Park, Hugh M. Robertson, Guy Smagghe, Diane E. Ullman, Maurijn van der Zee, Thomas Van Leeuwen, Jan A. Veenstra, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Anna E. Whitfield, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: almost 6 years ago

10.1002/cam4.3372

Identification of prognostic biomarkers associated with stromal cell infiltration in muscle‐invasive bladder cancer by bioinformatics analyses
Cited by: 10
Author(s): Pan Li, Jinlong Cao, Jianpeng Li, Zhiqiang Yao, Dali Han, Lijun Ying, Zhiping Wang, Junqiang Tian
Software Mentions: 4
Published: about 6 years ago

10.1002/cam4.2969

Identification of hub methylated‐CpG sites and associated genes in oral squamous cell carcinoma
Cited by: 14
Author(s): Yuxin Dai, Qiao‐Li Lv, Tingting Qi, Jian Qu, Hongli Ni, Yongkang Liao, Peng Liu, Qiang Qu
Software Mentions: 4
Published: over 6 years ago

10.3390/genes9010044

Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma
Cited by: 23
Author(s): Minjia Lu, Xingyu Xu, Baohang Xi, Qi Dai, Chenli Li, Li Su, Xiaobin Zhou, Min Tang, Yanwen Yao, Jialiang Yang
Software Mentions: 4
Published: over 8 years ago

10.3390/genes11050472

Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
Cited by: 7
Author(s): Mushtaque Ali, Hongyan Cheng, Mahtab Soomro, Shuyan Li, Muhammad Tufail, Mian Faisal Nazir, Feng Xu, Youping Zhang, Dongyun Zuo, Limin Lv, Qiaolian Wang, Guoli Song
Software Mentions: 4
Published: over 6 years ago

10.3389/fvets.2020.00251

Rumen Microbiota Distribution Analyzed by High-Throughput Sequencing After Oral Doxycycline Administration in Beef Cattle
Cited by: 5
Author(s): Fengmei Chen, Guangcun Cheng, Yan Xu, Yunzhou Wang, Qingxiang Xia, Shiqiang Hu
Software Mentions: 4
Published: over 6 years ago

10.1186/s12983-020-00366-w

Gut transcriptomic changes during hibernation in the greater horseshoe bat (Rhinolophus ferrumequinum)
Cited by: 4
Author(s): Haijian Sun, Jiaying Wang, Yanfeng Xing, Yi-Hsuan Pan, Xiuguang Mao
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2021.630243

Identification of Key Gene Networks Associated With Cell Wall Components Leading to Flesh Firmness in Watermelon
Cited by: 11
Author(s): Muhammad Anees, Lei Gao, Muhammad Umer, Pingli Yuan, Huiling Zhu, Xingrong Lu, Nan He, Chengsheng Gong, Mohamed Omar Kaseb, Shengjie Zhao, Wenge Liu
Software Mentions: 4
Published: about 5 years ago

10.3389/fpsyt.2019.00280

Transcriptome Changes in Relation to Manic Episode
Cited by: 15
Author(s): Ya Chin Lee, Yu Chao, Chiao-Erh Chang, Ming H. Hsieh, Kuan‐Ting Liu, Hsi‐Chung Chen, Mong Liang Lu, Wen Yin Chen, Chun Hsin Chen, Meng-Tsan Tsai, Tzu-Pin Lu, Ming Huang, Po-Hsiu Kuo
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2017.01430

Transcriptomic Analysis Reveals Candidate Genes for Female Sterility in Pomegranate Flowers
Cited by: 32
Author(s): Lina Chen, Jie Zhang, Haoxian Li, Juan Niu, Hui Xue, Beibei Liu, Qi Wang, Xiang Luo, Fuhong Zhang, Dan Zhao, Shangyin Cao
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2020.567249

Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon
Cited by: 7
Author(s): Kanae Masuda, Naoko Fujita, Ho Wen Yang, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Takashi Akagi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12935-020-01352-2

Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma
Cited by: 19
Author(s): Naiqiang Zhu, Jingyi Hou, Guiyun Ma, Shuai Guo, Chengliang Zhao, Bin Chen
Software Mentions: 4
Published: about 6 years ago

10.18632/aging.202634

Long non-coding RNAs ENST00000429730.1 and MSTRG.93125.4 are associated with metabolic activity in tuberculosis lesions of sputum-negative tuberculosis patients
Cited by: 5
Author(s): Lin Wang, Wen Zhu, Hui Ma, Liwei Wu, Hui Chen, Yijun Zhu, Liangfei Niu, Qihang Wu, Hongwei Li, Lei Shi, Leilei Li, Leiyi Wan, Jun Wang, Ka-Wing Wong, Yanzheng Song
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-13-S10-S7

A systematic comparison of genome-scale clustering algorithms
Cited by: 45
Author(s): Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, Michael A. Langston
Software Mentions: 4
Published: over 14 years ago

10.1534/g3.115.021550

Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response toFusarium graminearum
Cited by: 33
Author(s): Thomas Nußbaumer, Benedikt Warth, Sapna Sharma, Christian Ametz, Christoph Bueschl, Alexandra Parich, Matthias Pfeifer, Gerald Siegwart, Barbara Steiner, Marc Lemmens, Rainer Schuhmacher, Hermann Buerstmayr, Klaus Mayer, Karl G. Kugler, Wolfgang Schweiger
Software Mentions: 4
Published: almost 11 years ago

10.3389/fpls.2019.01098

Identification of Candidate Adaxial–Abaxial-Related Genes Regulating Petal Expansion During Flower Opening in Rosa chinensis “Old Blush”
Cited by: 10
Author(s): Yu Han, Yong Xue, Jiayao Yu, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.6694

Integrated analysis reveals five potential ceRNA biomarkers in human lung adenocarcinoma
Cited by: 14
Author(s): Yu Liu, Deyao Xie, Zuhua He, Liangcheng Zheng
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.4029

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii
Cited by: 44
Author(s): Wenya Zhang, Na Li, Xiaolong Tang, Naifa Liu, Zhao Wang
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2021.698602

Investigation Into Different Wood Formation Mechanisms Between Angiosperm and Gymnosperm Tree Species at the Transcriptional and Post-transcriptional Level
Cited by: 2
Author(s): Hui Li, Guanghui Chen, Hongying Pang, Qiao Wang, Xinren Dai
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.10594

Identification of hub genes and biological pathways in hepatocellular carcinoma by integrated bioinformatics analysis
Cited by: 6
Author(s): Qian Zhao, Yan Zhang, Shichun Shao, Yeqing Sun, Zhengkui Lin
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-6021-6

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)
Cited by: 17
Author(s): Liqing Zhou, Zhihong Liu, Yan Dong, Xiujun Sun, Biao Wu, Tao Yu, Yao Zheng, Aiguo Yang, Qing Zhao, Dan Zhao
Software Mentions: 4
Published: about 7 years ago

10.1002/ece3.6203

Caterpillars on a phytochemical landscape: The case of alfalfa and the Melissa blue butterfly
Cited by: 6
Author(s): Matthew L. Forister, Su’ad A. Yoon, Casey S. Philbin, Craig D. Dodson, Bret Hart, Joshua G. Harrison, Oren Shelef, James A. Fordyce, Zachary H. Marion, Chris C. Nice, Lora A. Richards, C. Alex Buerkle, Zachariah Gompert
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2021.666310

Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process
Cited by: 9
Author(s): Suyun Wei, Yingnan Chen, Jing Hou, Yonghua Yang, Tongming Yin
Software Mentions: 4
Published: over 5 years ago

10.15252/emmm.201708202

A proteomic network approach across the <scp>ALS</scp> ‐ <scp>FTD</scp> disease spectrum resolves clinical phenotypes and genetic vulnerability in human brain
Cited by: 115
Author(s): Mfon Umoh, Eric B. Dammer, Jingting Dai, Duc M. Duong, James J. Lah, Aĺlan I. Levey, Marla Gearing, Jonathan D. Glass, Nicholas T. Seyfried
Software Mentions: 4
Published: almost 9 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: about 7 years ago

10.1186/s13058-018-0933-y

HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors
Cited by: 44
Author(s): Anneleen Daemen, Gerard Manning
Software Mentions: 4
Published: over 8 years ago

10.1590/1414-431X2021e11363

Dysregulation of KIF14 regulates the cell cycle and predicts poor prognosis in cervical cancer: a study based on integrated approaches
Cited by: 4
Author(s): Xiao Li, Sisi Zhang, Qingyu Zheng, Shuirong Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2016.01431

Quantitative Resistance to Verticillium Wilt in Medicago truncatula Involves Eradication of the Fungus from Roots and Is Associated with Transcriptional Responses Related to Innate Immunity
Cited by: 13
Author(s): Maoulida Toueni, Cécile Ben, Aurélie Le Ru, Laurent Gentzbittel, Martina Rickauer
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2164-14-728

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12864-015-1522-4

Transcriptomic profiles of aging in purified human immune cells
Cited by: 57
Author(s): Lindsay M. Reynolds, Jingzhong Ding, Jeanette Taylor, Kurt Lohman, Nicola Soranzo, Alberto de la Fuente, Tie Fu Liu, Craig W. Johnson, R. Graham Barr, Thomas C. Register, Kathleen Donohue, Monica V. Talor, Daniela Čiháková, C. Charles Gu, Jasmin Divers, David S. Siscovick, Gregory L. Burke, Wendy S. Post, Steven Shea, David R. Jacobs, Ina Hoeschele, Charles E. McCall, Stephen B. Kritchevsky, David M. Herrington, Russell P. Tracy, Yongmei Liu
Software Mentions: 4
Published: over 11 years ago

10.18632/aging.202228

Identification of SCARA3 with potential roles in metabolic disorders
Cited by: 7
Author(s): Hui Peng, Qi Guo, Tian Su, Ye Xiao, Changjun Li, Yan Huang, Xiang‐Hang Luo
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9627

Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment
Cited by: 5
Author(s): Jiong Ma, Pu Cheng, Xuejun Chen, Chunxia Zhou, Zheng Wei
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2016.01924

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Setting in Triploid Loquat (Eriobotrya japonica)
Cited by: 25
Author(s): Shuang Jiang, Luo Jun, Fanjie Xu, Xueying Zhang
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-020-07118-4

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance
Cited by: 6
Author(s): Biruk A. Feyissa, Justin B. Renaud, Vida Nasrollahi, Susanne E. Kohalmi, Abdelali Hannoufa
Software Mentions: 4
Published: almost 6 years ago

10.1007/s00125-018-4612-4

Patterns of differential gene expression in a cellular model of human islet development, and relationship to type 2 diabetes predisposition
Cited by: 12
Author(s): Marta Perez-Alcantara, Christian Honoré, Agata Wesolowska-Andersen, Anna L. Gloyn, Mark I. McCarthy, Mattias Hansson, Nicola L. Beer, Martijn van de Bunt
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-018-2053-1

CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses
Cited by: 176
Author(s): Pedro Russo, Gustavo Rodrigues Ferreira, Lucas Esteves Cardozo, Matheus Carvalho Bürger, Raúl Arias‐Carrasco, Sandra Regina Maruyama, Thiago Dominguez Crespo Hirata, Diógenes Saulo de Lima, Fernando M. Passos, Kiyoshi F. Fukutani, Melissa Lever, João Silva, Vinicius Maracaja‐Coutinho, Hidehiko Nakaya
Software Mentions: 4
Published: over 8 years ago

10.3389/fphys.2021.601952

Weighted Gene Co-expression Network Analysis Identifies Crucial Genes Mediating Progression of Carotid Plaque
Cited by: 9
Author(s): Mengyin Chen, Siliang Chen, Dan Yang, Jiawei Zhou, Bao Liu, Yuexin Chen, Wei Ye, Hui Zhang, Lei Ji, Yuehong Zheng
Software Mentions: 4
Published: over 5 years ago

10.3389/fphys.2018.00399

Identification of Biomarkers Associated With Pathological Stage and Prognosis of Clear Cell Renal Cell Carcinoma by Co-expression Network Analysis
Cited by: 55
Author(s): Chen Liang, Lushun Yuan, Kaiyu Qian, Guofeng Qian, Yuan Zhu, Chin‐Lee Wu, Dong Han, Yu Xiao, Xinghuan Wang
Software Mentions: 4
Published: over 8 years ago

10.3389/fphar.2021.618773

Combination of Ginsenosides Rb2 and Rg3 Promotes Angiogenic Phenotype of Human Endothelial Cells via PI3K/Akt and MAPK/ERK Pathways
Cited by: 12
Author(s): Ran Joo Choi, Siti Zuraidah Mohamad Zobir, Benjamin Alexander-Dann, Naomi L. Sharma, Kenneth L. Marcella, Brian Lam, Giles S.H. Yeo, Guoqing Zhang, Tai-Ping Fan, Andreas Bender
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2021.678256

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells
Cited by: 5
Author(s): Yanwei Cheng, Xue Cao, Jiange Zhang, Dong Chen, Juan Zhu, Lijun Xu, Lijie Qin
Software Mentions: 4
Published: about 5 years ago

10.1155/2021/7331821

Identification of Neuropeptides as Potential Crosstalks Linking Down Syndrome and Periodontitis Revealed by Transcriptomic Analyses
Cited by: 6
Author(s): Yue Chen, Xiaofei Yu, Jia Kong
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.7696

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
Cited by: 4
Author(s): Shuaibin Lian, Liansheng Li, Yongjie Zhou, Zixiao Liu, Lei Wang
Software Mentions: 4
Published: almost 7 years ago

10.3389/fphys.2021.651690

Identification of VCAN as Hub Gene for Diabetic Kidney Disease Immune Injury Using Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Qiannan Xu, Binjue Li, Yucheng Wang, Cuili Wang, Shi Feng, Xue Lü, Jianghua Chen, Hong Jiang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-021-07731-x

Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice
Cited by: 16
Author(s): Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiaowei Chi, Tongzuo Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2021.685515

Regulatory Network Analysis of Mutated Genes Based on Multi-Omics Data Reveals the Exclusive Features in Tumor Immune Microenvironment Between Left-Sided and Right-Sided Colon Cancer
Cited by: 10
Author(s): Tianfei Yi, Yuwei Zhang, Derry Minyao Ng, Yang Xi, Meng Ye, Lvjun Cen, Jianjiong Li, Xiaoxiang Fan, Yanguo Li, Shiyun Hu, Hao Rong, Yangyang Xie, Guofang Zhao, Leyi Chen, Chen Chen, Shujing Ni, Jiaying Mi, Xiaoyu Dai, Qi Liao
Software Mentions: 4
Published: about 5 years ago

10.1042/BSR20203020

Network-based approach to identify prognosis-related genes in tamoxifen-treated patients with estrogen receptor-positive breast cancer
Cited by: 4
Author(s): Yanyan Wang, Xiaonan Gong, Yujie Zhang
Software Mentions: 4
Published: about 5 years ago

10.1042/BSR20200516

Association between SNAP25 and human glioblastoma multiform: a comprehensive bioinformatic analysis
Cited by: 5
Author(s): Changhong Yu, Jianxing Yin, Xiefeng Wang, Lijiu Chen, Yutian Wei, Chenfei Lu, Yongping You
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5850-7

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks
Cited by: 6
Author(s): Kevin B. Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, D Lambert, Stephen Brown, James R. Bradford
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1000642

A Systems Genetics Approach Implicates USF1, FADS3, and Other Causal Candidate Genes for Familial Combined Hyperlipidemia
Cited by: 144
Author(s): Christopher L. Plaisier, Steve Horvath, Adriana Huertas-Vázquez, Ivette Cruz-Bautista, Miguel F. Herrera, Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Päivi Pajukanta
Software Mentions: 4
Published: almost 17 years ago

10.3389/fonc.2020.00681

Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 50
Author(s): Chia‐Ying Li, Jia-Hua Cai, Jeffrey J. P. Tsai, Charles C.N. Wang
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.636451

Integrative Analysis of Histopathological Images and Genomic Data in Colon Adenocarcinoma
Cited by: 7
Author(s): Hui Li, Linyan Chen, Hao Zeng, Qimeng Liao, Jianrui Ji, Xuelei Ma
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2020.541401

Prognosis Analysis and Validation of m6A Signature and Tumor Immune Microenvironment in Glioma
Cited by: 46
Author(s): Sheng Lin, Houshi Xu, Anke Zhang, Yunjia Ni, Yuanzhi Xu, Tong Meng, Mingjie Wang, Meiqing Lou
Software Mentions: 4
Published: almost 6 years ago

10.1042/BSR20203235

Mining the key genes for ventilator-induced lung injury using co-expression network analysis
Cited by: 2
Author(s): Li Zhao, Yajun Xiao, Li Xu, Qingxiu Wang
Software Mentions: 4
Published: over 5 years ago

10.3389/fcell.2021.675438

Identification of Key Genes With Differential Correlations in Lung Adenocarcinoma
Cited by: 9
Author(s): You Zhou, Bin Xu, Yi Zhou, Jian Liu, Xiao Zheng, Yingting Liu, Hepu Deng, Ming Liu, Xiubao Ren, Jianchuan Xia, Xiangyin Kong, Tao Huang, Jingting Jiang
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.50462

Classification of Clear Cell Renal Cell Carcinoma based on Tumor Suppressor Genomic Profiling
Cited by: 2
Author(s): Weimin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-021-01959-9

Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast
Cited by: 31
Author(s): Satoi Nagasawa, Yuta Kuze, Ichiro Maeda, Yasuyuki Kojima, Ai Motoyoshi, Tatsuya Onishi, Tsuguo Iwatani, Takamichi Yokoe, Junki Koike, Motohiro Chosokabe, Manabu Kubota, Hibiki Seino, Ayako Suzuki, Masahide Seki, Katsuya Tsuchihara, Eisuke Inoue, Koichiro Tsugawa, Tomohiko Ohta, Yutaka Suzuki
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-019-0391-9

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation
Cited by: 25
Author(s): Alborz Mazloomian, Shinsuke Araki, Momoko Ohori, Amal M. El-Naggar, Damian Yap, Ali Bashashati, Shigetomi Nakao, Poul H. Sorensen, Atsushi Nakanishi, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 4
Published: over 7 years ago

10.1038/s42003-020-01152-4

Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs
Cited by: 23
Author(s): Maxwell J. Scott, Joshua B. Benoit, Rebecca J. Davis, Samuel T. Bailey, Virág Varga, Ellen O. Martinson, Paul V. Hickner, Zainulabeuddin Syed, Gisele Antoniazzi Cardoso, Tatiana Teixeira Torres, Matthew T. Weirauch, Elizabeth H. Scholl, Adam M. Phillippy, Agustin Sagel, Mario Vasquez, Gladys Quintero, S. Skoda
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2021.633899

High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma
Cited by: 7
Author(s): Xiaoqiang Du, Chen Zhang, Chuanzheng Yin, Wenjie Wang, Xueke Yan, Dawei Xie, Xichuan Zheng, Qi Zheng, Min Li, Zifang Song
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-06909-z

Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle
Cited by: 23
Author(s): Ze Yan, Hanyu Huang, Ellen Freebern, D. R. dos Santos, Dongmei Dai, Jingfang Si, Chengbin Ma, Jie Cao, Gang Guo, George E. Liu, Li Ma, Lingzhao Fang, Yi Zhang
Software Mentions: 4
Published: about 6 years ago

10.1038/s42003-020-01233-4

A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model
Cited by: 28
Author(s): Yuhua Fu, Jingya Xu, Zhenshuang Tang, Lu Wang, Yin Ding, Yu Fan, Dongdong Zhang, Fei Deng, Yanping Zhang, Haohao Zhang, Haiyan Wang, Wenhui Xing, Lilin Yin, Shilin Zhu, Mengjin Zhu, Mei Yu, Xinyun Li, Xiaolei Liu, Xiaohui Yuan, Zhao Song
Software Mentions: 4
Published: almost 6 years ago

10.1042/BSR20211280

Identification of hub genes in colorectal cancer based on weighted gene co-expression network analysis and clinical data from The Cancer Genome Atlas
Cited by: 23
Author(s): Yu Zhang, Jia Luo, Zhe Liu, Xudong Li, Ying Ma, Bohang Zhang, Yuxuan Chen, Xiaofeng Li, Zhi-Guo Feng, Ningning Yang, Dayun Feng, Lei Wang, Xiu–Peng Song
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2020.613333

Construction of Bone Metastasis-Specific Regulation Network Based on Prognostic Stemness-Related Signatures in Breast Invasive Carcinoma
Cited by: 2
Author(s): Runzhi Huang, Zhenyu Li, Jiayao Zhang, Zhiwei Zeng, Jiaqi Zhang, Mingxiao Li, Siqao Wang, Shuyuan Xian, Yuna Xue, Xi Chen, Jie Li, Wing Yan Elizabeth Cheng, Bin Wang, Penghui Yan, Daoke Yang, Zongqiang Huang
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-019-0382-x

Gene expression analysis delineates the potential roles of multiple interferons in systemic lupus erythematosus
Cited by: 62
Author(s): Michelle D. Catalina, Prathyusha Bachali, Nicholas S. Geraci, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2020.624752

Down-Regulation of Long Non-Coding RNA TINCR Induces Cell Dedifferentiation and Predicts Progression in Oral Squamous Cell Carcinoma
Cited by: 6
Author(s): Zerui Zhuang, Jing Huang, Weiwang Wang, Cheng Wang, Pei Yu, Jing Hu, Haichao Liu, Hanqi Yin, Jinsong Hou, Xiqiang Liu
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.102275

Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice
Cited by: 52
Author(s): Huimin Li, Xinhui Wang, Xinyue Lu, Hongxin Zhu, Sheng Li, Shiwei Duan, Xinzhi Zhao, Fuquan Zhang, Gil Alterovitz, Fudi Wang, Qiang Li, Xiao-Li Tian, Mingqing Xu
Software Mentions: 4
Published: almost 7 years ago

10.3390/biom10091230

The Transcriptomic Evidence on the Role of Abdominal Visceral vs. Subcutaneous Adipose Tissue in the Pathophysiology of Diabetes in Asian Indians Indicates the Involvement of Both
Cited by: 6
Author(s): Anshul Kumar, Prabhat Tiwari, Aditya Saxena, Naincy Purwar, Nitin Wahi, Balram Sharma, Sandeep Kumar Mathur
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-018-5115-x

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
Cited by: 19
Author(s): Bi Jun Li, Dan Jiang, Zhijun Meng, Yong Zhang, Zong Xian Zhu, Haoran Lin, Jun Xia
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.7705

The clinical significance of collagen family gene expression in esophageal squamous cell carcinoma
Cited by: 30
Author(s): Jieling Li, Wang Xiao, Kai Zheng, Ying Liu, Junjun Li, Shaoqi Wang, Kaisheng Liu, Xianrang Song, Nan Li, Shouqi Xie, Shaoxiang Wang
Software Mentions: 4
Published: almost 7 years ago

10.3390/biom10091207

Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder
Cited by: 24
Author(s): Dongmei Ai, Yuduo Wang, Xiaoxin Li, Hongfei Pan
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2019.01030

Novel Biomarkers Associated With Progression and Prognosis of Bladder Cancer Identified by Co-expression Analysis
Cited by: 42
Author(s): Yejinpeng Wang, Changhong Liang, Lingao Ju, Kaiyu Qian, Xuefeng Li, Xinghuan Wang, Yu Xiao
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: about 9 years ago

10.3389/fonc.2020.01374

Immunogenomic Profiling and Classification of Prostate Cancer Based on HIF-1 Signaling Pathway
Cited by: 8
Author(s): Jukun Song, Wei-Ming Chen, Guohua Zhu, Wei Wang, Fa Sun, Jianguo Zhu
Software Mentions: 4
Published: about 6 years ago

10.3390/biomedicines9010034

Shared Blood Transcriptomic Signatures between Alzheimer’s Disease and Diabetes Mellitus
Cited by: 14
Author(s): Taesic Lee, Hyunju Lee
Software Mentions: 4
Published: over 5 years ago

10.1186/s13058-020-01295-6

Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration
Cited by: 24
Author(s): Thilde Terkelsen, Francesco Russo, Pavel Gromov, Vilde Drageset Haakensen, Søren Brunak, Irina Gromova, Anders Krogh, Elena Papaleo
Software Mentions: 4
Published: about 6 years ago

10.1155/2020/4908427

Comprehensive Analysis of mRNA Expression Profiles in Head and Neck Cancer by Using Robust Rank Aggregation and Weighted Gene Coexpression Network Analysis
Cited by: 4
Author(s): Zijian Cao, Yin-Jie Ao, Yu Guo, Shui‐Hong Zhou
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/9921195

A Computational Framework to Identify Transcriptional and Network Differences between Hepatocellular Carcinoma and Normal Liver Tissue and Their Applications in Repositioning Drugs
Cited by: 0
Author(s): Aimin Hu, Wei Zheng, Zuxiang Zheng, Bichao Luo, Jieming Yi, Xinhong Zhou, Changjiang Zeng
Software Mentions: 4
Published: almost 5 years ago

10.1155/2021/9933136

Identification of Biomarkers for Predicting Allograft Rejection following Kidney Transplantation Based on the Weighted Gene Coexpression Network Analysis
Cited by: 2
Author(s): Lijun Wang, Xiao-Bo Ma, Hongying Xia, Xun Sun, Yu Lu, Qian Yang, Zongqiang Hu, Yi‐Fang Zhao, Wei Hu, Jianghua Ran
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-6161-8

Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat
Cited by: 17
Author(s): Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David Konkin, Ron Knox, Yuefeng Ruan, Pierre R. Fobert
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13148-021-01153-y

Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation
Cited by: 9
Author(s): Darina Czamara, Linda Dieckmann, Simone Röh, Sarah Kraemer, Rebecca C. Rancourt, Sara Sammallahti, Eero Kajantie, Hannele Laivuori, Johan G. Eriksson, Katri Räikkönen, Wolfgang Henrich, Andreas Plagemann, Elisabeth B. Binder, Thorsten Braun, Sonja Entringer
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-2596-9

Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
Cited by: 8
Author(s): André Voigt, Eivind Almaas
Software Mentions: 4
Published: over 7 years ago

10.1155/2020/3416807

Identification of Hub Genes as Biomarkers Correlated with the Proliferation and Prognosis in Lung Cancer: A Weighted Gene Co-Expression Network Analysis
Cited by: 2
Author(s): Xuting Xu, Limin Xu, Huilian Huang, Jing Li, Shunli Dong, Lili Jin, Zhiyong Ma, Liqin Li
Software Mentions: 4
Published: about 6 years ago

10.1155/2020/4348371

DHX36, BAX, and ARPC1B May Be Critical for the Diagnosis and Treatment of Tuberculosis
Cited by: 3
Author(s): Yunli Zhang, Yanming Liu, Hongling Li, Qingxia Liu, Wei Wang, Zijuan Jian, Wenen Liu
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.11045

Analysis of differences in the transcriptomic profiles of eutopic and ectopic endometriums in women with ovarian endometriosis
Cited by: 5
Author(s): Xiao Feng, Lingbin Qi, Xiaoyu Xu, Yun Feng, Xiaoming Gong, Aixingzi Aili, Yu Chen, Zhigang Xue, Jinfeng Xue, Xiaowen Tong
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/4612158

CCNB2, TOP2A, and ASPM Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis
Cited by: 9
Author(s): Yuping Zeng, He He, Yu Zhang, Xia Wang, Yang Lin-de, Zhenmei An
Software Mentions: 4
Published: about 6 years ago

10.3390/cells10071821

Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma
Cited by: 8
Author(s): Ujjwal Mukund Mahajan, Ahmed Alnatsha, Qi Li, Bettina Oehrle, Florian Weiß, Matthias Sendler, Marius Distler, Waldemar Uhl, Tim Fahlbusch, Elisabetta Goni, Georg Beyer, Ansgar M. Chromik, M. Bahra, Fritz Klein, Christian Pilarsky, Robert Grützmann, Markus M. Lerch, Kirsten Lauber, Nicole Christiansen, Beate Kamlage, Ivonne Regel, Julia Mayerle
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2021.634569

Sharp Downregulation of Hub Genes Associated With the Pathogenesis of Breast Cancer From Ductal Carcinoma In Situ to Invasive Ductal Carcinoma
Cited by: 4
Author(s): Yao Wang, Faqing Liang, Yuting Zhou, Juanjuan Qiu, Qing Lv, Zhenggui Du
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/2123787

Identification of lncRNA and mRNA Biomarkers in Osteoarthritic Degenerative Meniscus by Weighted Gene Coexpression Network and Competing Endogenous RNA Network Analysis
Cited by: 4
Author(s): Jun Zhao, Yu Su, Jianfei Jiao, Zhengchun Wang, Xiangchun Fang, Xuefeng He, Xiaofeng Zhang, Zhao Liu, Xilin Xu
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2020.01579

A Novel Immune-Related Competing Endogenous RNA Network Predicts Prognosis of Acute Myeloid Leukemia
Cited by: 8
Author(s): Shujuan Wang, Lu Yang, Yajun Liu, Yan Xu, Danfeng Zhang, Zhongxing Jiang, Chong Wang, Yanfang Liu
Software Mentions: 4
Published: about 6 years ago

10.3390/cells9081793

Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis
Cited by: 3
Author(s): Ho‐Su Lee, Maaike Vancamelbeke, Sare Verstockt, Tom Wilms, Bram Verstockt, João Sabino, Marc Ferrante, Séverine Vermeire, Isabelle Cleynen
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2021.620154

Bioinformatics-Based Identification of HDAC Inhibitors as Potential Drugs to Target EGFR Wild-Type Non-Small-Cell Lung Cancer
Cited by: 0
Author(s): Yizhe Wang, Chunlei Zheng, Wenqing Lü, Duo Wang, Cheng Yang, Yang Chen, Kezuo Hou, Jianfei Qi, Yunpeng Liu, Xiaofang Che, Xuejun Hu
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2019.07.091

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes
Cited by: 204
Author(s): Myles Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A. Hackney, Nandhini Ramamoorthi, Christopher R. John, David S. Watson, Sarah Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michèle Bombardieri, Nora Ng, Maria DiCicco, Désirée van der Heijde, Robert Landewé, Annette H M van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis
Software Mentions: 4
Published: about 7 years ago

10.1016/j.celrep.2019.12.034

Mouse Ovarian Cancer Models Recapitulate the Human Tumor Microenvironment and Patient Response to Treatment
Cited by: 56
Author(s): Eleni Maniati, Chiara Berlato, Ganga Gopinathan, Owen Heath, Panoraia Kotantaki, Anissa Lakhani, Jacqueline McDermott, Colin Pegrum, Robin Delaine-Smith, Oliver M.T. Pearce, Priyanka Hirani, Joash D. Joy, Ludmila Szabova, Ruth Perets, Owen J. Sansom, Ronny Drapkin, Peter J. Bailey, Frances R. Balkwill
Software Mentions: 4
Published: over 6 years ago

10.1016/j.celrep.2020.03.053

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex
Cited by: 82
Author(s): Donna M. Werling, Sirisha Pochareddy, Jinmyung Choi, Joon Yong An, Brooke Sheppard, Minshi Peng, Zhen Li, Claudia Dastmalchi, Gabriel Santpere, André M. M. Sousa, Andrew T.N. Tebbenkamp, Navjot Kaur, Forrest O. Gulden, Michael S. Breen, Lindsay Liang, Michael C. Gilson, Xuefang Zhao, Shan Dong, Lambertus Klei, A. Ercüment Çiçek, Joseph D. Buxbaum, Homa Adle‐Biassette, Jean Léon Thomas, Kimberly A. Aldinger, Diana R. O’Day, Ian A. Glass, Noah Zaitlen, Michael E. Talkowski, Kathryn Roeder, Matthew W. State, Bernie Devlin, Stephan J. Sanders, Nenad Šestan
Software Mentions: 4
Published: over 6 years ago

10.1016/j.celrep.2017.08.010

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
Cited by: 92
Author(s): Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalvès, Clara Alsinet, Martín Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michaël Schubert, Stacey Price, James C. Wright, Lu Yu, Meizhu Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrão, Alvis Brāzma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Sáez-Rodríguez, Ultan McDermott, Jyoti S. Choudhary
Software Mentions: 4
Published: about 9 years ago

10.1155/2021/6644827

Multiomics Analysis of Genetics and Epigenetics Reveals Pathogenesis and Therapeutic Targets for Atrial Fibrillation
Cited by: 2
Author(s): Li Liu, Jianjun Huang, Baomin Wei, Jianjiao Mo, Qinjiang Wei, Chengcai Chen, Yan Wang, Xian-Nan Huang, Fengzhen He, Lingling Qin, Hehua Huang, Xue Li, Xingshou Pan
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/8970340

Identification of Long Noncoding RNAs as Predictors of Survival in Triple-Negative Breast Cancer Based on Network Analysis
Cited by: 26
Author(s): Xiaoxiao Li, Limin Wang, Jie Hou, Hongyang Li, Rui Wang, Chao Wang, Wenhai Xie
Software Mentions: 4
Published: over 6 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479