cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1186/s40170-016-0143-y

Integration of omics: more than the sum of its parts
Cited by: 84
Author(s): Joerg M. Buescher, Edward M. Driggers
Software Mentions: 1
Published: over 10 years ago

The Regulatory Network of CMPG1-V in Wheat–Blumeria graminis f. sp. tritici Interaction Revealed by Temporal Profiling Using RNA-Seq
Cited by: 5
Author(s): Jia Liu, Li Sun, Yiming Chen, Luyang Wei, Yongli Hao, Zhongyu Yu, Zongkuan Wang, Heng Zhang, Xu Zhang, Mengli Li, Haiyan Wang, Jin Xiao, Xiue Wang
Software Mentions: 1
Published: about 6 years ago

10.1002/cam4.3369

Microarray profiling of differentially expressed lncRNAs and mRNAs in lung adenocarcinomas and bioinformatics analysis
Cited by: 12
Author(s): Fei He, Liping Huang, Qiuping Xu, Weimin Xiong, Shuang Liu, Huimin Yang, Wenzhou Lu, Rendong Xiao, Zhijian Hu, Lin Cai
Software Mentions: 1
Published: about 6 years ago

10.1002/cam4.3240

Development and validation of an immune‐related prognostic signature in lung adenocarcinoma
Cited by: 69
Author(s): Sijin Sun, Wei Guo, Zhen Wang, Xin Wang, Guochao Zhang, Hao Zhang, Renda Li, Yibo Gao, Bin Qiu, Fengwei Tan, Yushun Gao, Qi Xue, Shugeng Gao, Jie He
Software Mentions: 1
Published: about 6 years ago

10.3389/fimmu.2021.739514

Circulating Metabolomic Signature in Generalized Pustular Psoriasis Blunts Monocyte Hyperinflammation by Triggering Amino Acid Response
Cited by: 7
Author(s): Na Yu, Peng Chen, Wenjuan Chen, Zengqi Sun, Jianfeng Zheng, Shujie Zhang, Yangfeng Ding, Yujun Shi
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms21196994

Transcriptome Sequencing Revealed an Inhibitory Mechanism of Aspergillus flavus Asexual Development and Aflatoxin Metabolism by Soy-Fermenting Non-Aflatoxigenic Aspergillus
Cited by: 9
Author(s): Ke Yang, Qingru Geng, Fengqin Song, Xiaona He, Tianran Hu, Shihua Wang, Jun Tian
Software Mentions: 1
Published: almost 6 years ago

10.1001/jamaneurol.2020.5257

Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets
Cited by: 74
Author(s): Demis A. Kia, David Zhang, Sebastian Guelfi, Claudia Manzoni, Leon Hubbard, Regina H. Reynolds, Juan A. Botía, Mina Ryten, Raffaele Ferrari, Patrick A. Lewis, Nigel Williams, Daniah Trabzuni, John Hardy, Nicholas W. Wood, Alastair Noyce, Rauan Kaiyrzhanov, Ben Middlehurst, Manuela Tan, Henry Houlden, Huw Morris, Hélène Plun‐Favreau, Peter Holmans, José Brás, John P. Quinn, Kin Y. Mok, Kerri J. Kinghorn, Kimberley Billingsley, Patrick A. Lewis, Sebastian R Schreglmann, Rita Guerreiro, Ruth C. Lovering, Lea R’Bibo, Mie Rizig, Valentina Escott‐Price, Viorica Chelban, Thomas Foltynie, Alexis Brice, Fabrice Danjou, Suzanne Lesage, Jean‐Christophe Corvol, María Teresa González Martínez, Claudia Schulte, Kathrin Brockmann, Javier Simón‐Sánchez, Peter Heutink, Patrizia Rizzu, Manu Sharma, Thomas Gasser, Aude Nicolas, Mark Cookson, Sara Bandrés‐Ciga, Cornelis Blauwendraat, David W. Craig, Faraz Faghri, J. Raphael Gibbs, Dena G. Hernandez, Kendall Van Keuren‐Jensen, Zhandong Liu, Hampton Leonard, Mike A. Nalls, Laurie Robak, Steven Lubbe, Steven Finkbeiner, Niccolò E. Mencacci, Codrin Lungu, Andrew B. Singleton, Sonja W. Scholz, Xylena Reed, Roy N. Alcalay, Ziv Gan‐Or, Guy A. Rouleau, Lynne Krohn, Jacobus J. van Hilten, Johan Marinus, Astrid Adarmes‐Gómez, Miquel Aguilar, Victoria Álvarez, Victoria Álvarez, Francisco Javier Barrero, Jesús Alberto Bergareche Yarza, Inmaculada Bernal‐Bernal, Marta Blázquez, Marta Bonilla‐Toribio, Juan A. Botía, María Teresa Boungiorno, Dolores Buiza‐Rueda, Ana Cámara, Fátima Carrillo, Mario Carrión‐Claro, Debora Cerdan, Jordi Clarimón, Yaroslau Compta, Mónica Díez-Fairén, Oriol Dols‐Icardo, Jacinto Duarte, Raquel Durán, Francisco Escamilla‐Sevilla, Mario Ezquerra, Cici Feliz, Manel Fernández, Rubén Fernández‐Santiago, Ciara García, Pedro J. García‐Ruiz, Pilar Gómez-Garré, Maria Jose Gómez Heredia, Isabel González Aramburu, Ana Gorostidi Pagola, Janet Hoenicka, Jon Infante, Adriano Jiménez‐Escrig, Jaime Kulisevsky, Miguel A. Labrador‐Espinosa, José López‐Sendón, Adolfo López de Munaín Arregui, Daniel Macías, Irene Martínez Torres, Juan Marín, Marı́a José Martı́, Juan Carlos Martínez‐Castrillo, Carlota Méndez‐del‐Barrio, Manuel Menéndez González, Marina Mata Adolfo Mínguez, Pablo Mir, Elisabet Mondragón Rezola, Esteban Muñoz, Javier Pagonabarraga, Pau Pástor, Francisco Errázquin, María Teresa Periñán, Javier Rúiz-Martínez, Clara Ruz, A Rodríguez, María Sierra, Esther Suárez-Sanmartín, C Tabernero, Juan Pablo Tartari, Cristina Tejera‐Parrado, Eduard Tolosa, Francesc Valldeoriola, Laura Vargas‐González, Lydia Vela, Francisco Vives, Alexander Zimprich, Lasse Pihlstrøm, Mathias Toft, Sulev Kõks, Pille Taba, Sharon Hassin‐Baer, Michael E. Weale, Adaikalavan Ramasamy, Colin Smith, Manuel Sebastian Guelfi, Karishma D’Sa, Paola Forabosco
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21207695

Multiple-Purpose Connectivity Map Analysis Reveals the Benefits of Esculetin to Hyperuricemia and Renal Fibrosis
Cited by: 9
Author(s): Yiming Wang, Jie Zhu, Liang Wang, Tianyu Zhang, Baoxin Huang, Jia Meng, Baoxue Yang, Zhengwei Xie, Hong Zhou
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms20163846

Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass
Cited by: 7
Author(s): Most. Humaira Sultana, FangJie Liu, Md. Alamin, Limin Mao, Jia Lu, Hongyu Chen, Dongya Wu, Yingying Wang, Fei Fu, Sanling Wu, Weidi Wang, Chu-Yu Ye, Qian Zhu, Jie Qiu, Longjiang Fan
Software Mentions: 1
Published: about 7 years ago

10.3389/fcvm.2019.00100

Isoproterenol-Induced Cardiac Diastolic Dysfunction in Mice: A Systems Genetics Analysis
Cited by: 14
Author(s): Jessica Wang, Adriana Huertas-Vázquez, Yibin Wang, Aldons J. Lusis
Software Mentions: 1
Published: about 7 years ago

10.1186/2049-2618-1-17

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships
Cited by: 230
Author(s): Ian Howard Mchardy, Maryam Goudarzi, Man‐Li Tong, Paul Ruegger, Emma Schwager, John R. Weger, Thomas G. Graeber, Justin L. Sonnenburg, Steve Horvath, Curtis Huttenhower, Dermot P. McGovern, Albert J. Fornace, James Borneman, Jonathan Braun
Software Mentions: 1
Published: over 13 years ago

10.3389/fmicb.2016.01155

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds
Cited by: 33
Author(s): Haifeng Geng, Mary Bao Tran-Gyamfi, Todd W. Lane, Kenneth L. Sale, Eizadora T. Yu
Software Mentions: 1
Published: about 10 years ago

10.3389/fbioe.2020.00177

Investigation of miRNA and mRNA Co-expression Network in Ependymoma
Cited by: 12
Author(s): Feili Liu, Hang Dong, Zi Mei, Tao Huang
Software Mentions: 1
Published: over 6 years ago

10.1172/jci.insight.141420

Role of MIF in coordinated expression of hepatic chemokines in patients with alcohol-associated hepatitis
Cited by: 5
Author(s): Kyle L. Poulsen, Xiude Fan, Christopher Kibler, Emily Huang, Xiaoqin Wu, Megan R. McMullen, Lin Leng, Richard Bucala, Meritxell Ventura-Cots, Josepmaria Argemí, R. Bataller, Laura E. Nagy
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21228618

Identification and Characterization of the Intra-Articular Microbiome in the Osteoarthritic Knee
Cited by: 11
Author(s): Joseph C. Tsai, Grant Casteneda, Abby Lee, Kypros Dereschuk, Wei Tse Li, Jaideep Chakladar, Alecio F. Lombardi, Weg M. Ongkeko, Eric Y. Chang
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms20184358

Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
Cited by: 5
Author(s): Xiaoxiang Zhang, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Junpeng Wang, Chang Liu, Yin Su, Juan Zhou, Ning Xiao, Cunhong Pan, Yabin Xu, Guichun Dong, Zefeng Yang, Aihong Li, Jianye Huang, Yulong Wang, Youli Yao
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-50909-3

Proteomic analysis of eleven tissues in the Chinese giant salamander (Andrias davidianus)
Cited by: 5
Author(s): Xiaofang Geng, Jiuxin Guo, Xiayan Zang, Cuifang Chang, Haitao Shang, Hong Wei, Chi Xu
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.jaci.2017.04.005

Phenotypic and genetic aspects of epithelial barrier function in asthmatic patients
Cited by: 66
Author(s): Matthew Loxham, Donna E. Davies
Software Mentions: 1
Published: over 9 years ago

10.3389/fbioe.2021.651895

Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System
Cited by: 8
Author(s): Lina Mattsson, Eva Sörenson, Eric Capo, Hanna Farnelid, Maurice Hirwa, Martin Olofsson, Fredrik Svensson, Elin Lindehoff, Catherine Legrand
Software Mentions: 1
Published: over 5 years ago

10.1093/jas/skab193

The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies
Cited by: 7
Author(s): Victoria Asselstine, Stephanie Lam, F. Miglior, Luiz F. Brito, Hannah Sweett, Leluo Guan, Sinéad M. Waters, Graham Plastow, Ángela Cánovas
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-53052-1

Products of Chemoenzymatic Synthesis Representing MUC1 Tandem Repeat Unit with T-, ST- or STn-antigen Revealed Distinct Specificities of Anti-MUC1 Antibodies
Cited by: 23
Author(s): Yayoi Yoshimura, Kaori Denda-Nagai, Yoshie Takahashi, Izuru Nagashima, H. Shimizu, Toshimitsu Kishimoto, Miki Noji, Shigeyuki Shichino, Yasunori Chiba, Tatsuro Irimura
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-019-52883-2

Comprehensive Analysis of the Expression Profiles of Long Non-Coding RNAs with Associated ceRNA Network Involved in the Colon Cancer Staging and Progression
Cited by: 14
Author(s): Man‐Li C. Wu, Wenliang Li, Fengchang Huang, Jing Sun, Kang ping Li, Jiandong Shi, Jingyu Yang, Jianfang Li, Yanhan Li, Ningzhu Hu, Yunzhang Hu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s40104-021-00556-4

Transcriptomic analysis reveals the molecular mechanisms of rumen wall morphological and functional development induced by different solid diet introduction in a lamb model
Cited by: 15
Author(s): Dongdong Sun, Yi Yin, Chang Guo, Lixiang Liu, Shengyong Mao, Weiyun Zhu, Junhua Liu
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2020.01194

Expression of S100A Alarmins in Cord Blood Monocytes Is Highly Associated With Chorioamnionitis and Fetal Inflammation in Preterm Infants
Cited by: 12
Author(s): Veronika Golubinskaya, Henri Puttonen, Ing‐Marie Fyhr, Halfdan Rydbeck, Ann Hellström, Bo Jacobsson, Holger Nilsson, Carina Mallard, Karin Sävman
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2021.695625

Translational Proteomics Analysis of Anthracycline-Induced Cardiotoxicity From Cardiac Microtissues to Human Heart Biopsies
Cited by: 11
Author(s): Nhan Nguyen, Tancredo Augusto Feitosa de Souza, Marcha Verheijen, Hans Gmuender, Nathalie Selevsek, Ralph Schlapbach, Jos Kleinjans, Danyel Jennen
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0170870

Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development
Cited by: 7
Author(s): Zachary T. Neeb, Daniel J. Hogan, Sol Katzman, Alan M. Zahler
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-019-54943-z

Water-soluble phosphorus contributes significantly to shaping the community structure of rhizospheric bacteria in rocky desertification areas
Cited by: 9
Author(s): Jinge Xie, Wei Xue, Cong Liu, Zongqiang Yan, Dong Li, Guoqiang Li, Xiwen Chen, Defu Chen
Software Mentions: 1
Published: almost 7 years ago

10.1002/jbmr.271

Systems genetics analysis of mouse chondrocyte differentiation
Cited by: 15
Author(s): Jaijam Suwanwela, Charles R. Farber, Bau-lin Haung, Buer Song, Calvin Pan, Karen M. Lyons, Aldons J. Lusis
Software Mentions: 1
Published: over 15 years ago

10.1002/jcsm.12597

Metabolic profiling shows pre‐existing mitochondrial dysfunction contributes to muscle loss in a model of ICU‐acquired weakness
Cited by: 19
Author(s): Paul R. Kemp, Richard Paúl, Aaron C. Hinken, David Neil, Alan J. Russell, Mark Griffiths
Software Mentions: 1
Published: about 6 years ago

10.7150/jca.31234

Expression profile analysis of prognostic long non-coding RNA in adult acute myeloid leukemia by weighted gene co-expression network analysis (WGCNA)
Cited by: 23
Author(s): Cunte Chen, Peipei Wang, Wenjian Mo, Yuping Zhang, Zhou Wei, Tingfen Deng, Ming Zhou, Xiaowei Chen, Shunqing Wang, Caixia Wang
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms20194781

The Need for Multi-Omics Biomarker Signatures in Precision Medicine
Cited by: 242
Author(s): Michael Olivier, Reto Asmis, Gregory A. Hawkins, Timothy D. Howard, Laura A. Cox
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-019-54995-1

Morpho-physiological and proteomic responses to water stress in two contrasting tobacco varieties
Cited by: 17
Author(s): Zheng Chen, Jianing Xu, Fazhan Wang, Lin Wang, Zicheng Xu
Software Mentions: 1
Published: almost 7 years ago

10.3389/fonc.2021.679851

CD86 Molecule Might Be a Novel Immune-Related Prognostic Biomarker for Patients With Bladder Cancer by Bioinformatics and Experimental Assays
Cited by: 4
Author(s): Xin Yan, Guo-Wei Du, Zhao Chun-hua, Tong-Zu Liu, Sheng Li
Software Mentions: 1
Published: about 5 years ago

10.1186/s12934-020-01349-6

Repeated fed-batch strategy and metabolomic analysis to achieve high docosahexaenoic acid productivity in Crypthecodinium cohnii
Cited by: 9
Author(s): Liangsen Liu, Fangzhong Wang, Guangsheng Pei, Jinyu Cui, Jinjin Diao, Mingming Lv, Lei Chen, Weiwen Zhang
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2020.00857

Identification of Gene Signatures for Diagnosis and Prognosis of Hepatocellular Carcinomas Patients at Early Stage
Cited by: 14
Author(s): Xiaoning Gan, Yue Luo, Guanqi Dai, Junhao Lin, Xinhui Liu, Zhang Xiang-qun, Aimin Li
Software Mentions: 1
Published: about 6 years ago

10.3389/fimmu.2020.00616

A Signaling Pathway to Mediate the Combined Immunomodulation of Acetylcholine and Enkephalin in Oyster Crassostrea gigas
Cited by: 3
Author(s): Zhaoqun Liu, Zhi Zhou, Lingling Wang, Yukun Zhang, Yanan Zong, Yan Zheng, Meijia Li, Weilin Wang, Linsheng Song
Software Mentions: 1
Published: over 6 years ago

10.7150/jca.38211

Bioinformatics analysis and identification of potential genes related to pathogenesis of cervical intraepithelial neoplasia
Cited by: 9
Author(s): Xue Zhang, Jian Bai, Cheng Yuan, Long Long, Zhewen Zheng, Qingqing Wang, Fengxia Chen, Youwen Zhou
Software Mentions: 1
Published: over 6 years ago

10.3389/fonc.2021.688545

The Identification of Stemness-Related Genes in the Risk of Head and Neck Squamous Cell Carcinoma
Cited by: 2
Author(s): Guanying Feng, Feifei Xue, Yingzheng He, Tianxiao Wang, Hua Yuan
Software Mentions: 1
Published: over 5 years ago

10.7150/jca.39645

Identification of Key Gene and Pathways for the Prediction of Peritoneal Metastasis of Gastric Cancer by Co-expression Analysis
Cited by: 11
Author(s): Simeng Zhang, Dan Zang, Changhong Yu, Zhi Li, Bowen Yang, Tianshu Guo, Yunpeng Liu, Xiujuan Qu, Xiaofang Che
Software Mentions: 1
Published: over 6 years ago

10.1155/2019/9567641

Weighted Gene Coexpression Network Analysis Identified MicroRNA Coexpression Modules and Related Pathways in Type 2 Diabetes Mellitus
Cited by: 26
Author(s): Tianyu Feng, Kexin Li, Pingping Zheng, Yanjun Wang, Yaogai Lv, Ли Шен, Chen Yang, Zhiqiang Xue, Bo Li, Lina Jin, Yan Yao
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2018.00508

Weighted Gene Correlation Network Analysis (WGCNA) Reveals Novel Transcription Factors Associated With Bisphenol A Dose-Response
Cited by: 32
Author(s): Alexandra Maertens, Vy Tran, André Kleensang, Thomas Hartung
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-020-58179-0

Depicting the genetic architecture of pediatric cancers through an integrative gene network approach
Cited by: 15
Author(s): Clara Savary, Artem Kim, Alexandra Lespagnol, Virginie Gandemer, Isabelle Pellier, Catherine Andrieu, Gilles Pagès, Marie‐Dominique Galibert, Yuna Blum, Marie de Tayrac
Software Mentions: 1
Published: over 6 years ago

10.1186/s13058-018-1043-6

Foxf2 plays a dual role during transforming growth factor beta-induced epithelial to mesenchymal transition by promoting apoptosis yet enabling cell junction dissolution and migration
Cited by: 19
Author(s): Nathalie Meyer-Schaller, Chantal Heck, Stefanie Tiede, M. Deniz Yilmaz, Gerhard Christofori
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0014821

Epigenetic Predictor of Age
Cited by: 737
Author(s): Sven Bocklandt, Wen Lin, Mary E. Sehl, Francisco J. Sánchez, Janet S. Sinsheimer, Steve Horvath, Éric Vilain
Software Mentions: 1
Published: about 15 years ago

10.3390/ijms21249417

Activation of the Ion Channel TRPV4 Induces Epithelial to Mesenchymal Transition in Breast Cancer Cells
Cited by: 20
Author(s): Iman Azimi, Mélanie Robitaille, Kaela Armitage, Choon Leng So, Michael J. G. Milevskiy, Korinne Northwood, Huai Fang Lim, Erik W. Thompson, Sarah J. Roberts‐Thomson, Gregory R. Monteith
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0094868

Rat Hepatocytes Weighted Gene Co-Expression Network Analysis Identifies Specific Modules and Hub Genes Related to Liver Regeneration after Partial Hepatectomy
Cited by: 20
Author(s): Yun Zhou, Jiucheng Xu, Yunqing Liu, Juntao Li, Cuifang Chang, Chi Xu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0183359

Titanium biomaterials with complex surfaces induced aberrant peripheral circadian rhythms in bone marrow mesenchymal stromal cells
Cited by: 18
Author(s): Nathaniel Hassan, Kirstin McCarville, Kenzo Morinaga, Cristiane Machado Mengatto, Peter Langfelder, Akishige Hokugo, Yu Tahara, Christopher S. Colwell, Ichiro Nishimura
Software Mentions: 1
Published: about 9 years ago

10.7150/jca.52156

Identification of Prognosis-related Hub RNA Binding Proteins Function through Regulating Metabolic Processes in Tongue Cancer
Cited by: 6
Author(s): Tao Shen, Meiting Wang, Xiangting Wang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0100204

Whole Brain Expression of Bipolar Disorder Associated Genes: Structural and Genetic Analyses
Cited by: 23
Author(s): Michael J. McCarthy, Sheng-Fu Liang, Andrea D. Spadoni, John R. Kelsoe, Alan N. Simmons
Software Mentions: 1
Published: about 12 years ago

10.3389/fgene.2020.00981

Identification of KIAA0513 and Other Hub Genes Associated With Alzheimer Disease Using Weighted Gene Coexpression Network Analysis
Cited by: 20
Author(s): Min Zhu, Longfei Jia, Fangyu Li, Jianping Jia
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-60456-x

Functionally Enigmatic Genes in Cancer: Using TCGA Data to Map the Limitations of Annotations
Cited by: 14
Author(s): Alexandra Maertens, Vy Tran, Mikhail Maertens, André Kleensang, Thomas Luechtefeld, Thomas Hartung, Channing J. Paller
Software Mentions: 1
Published: over 6 years ago

10.7150/jca.51059

A Novel Set of Immune-associated Gene Signature predicts Biochemical Recurrence in Localized Prostate Cancer Patients after Radical Prostatectomy
Cited by: 8
Author(s): Jiaochen Luan, Qijie Zhang, Kai Zhao, Xiang Zhou, Liangyu Yao, Tongtong Zhang, Taidui Zeng, Jun Xia, Ninghong Song
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2021.693034

The Key Gene Expression Patterns and Prognostic Factors in Malignant Transformation from Enchondroma to Chondrosarcoma
Cited by: 5
Author(s): Jinliang Wu, Yanfang Huang, Chengxuan Yu, Xia Li, Limengmeng Wang, Jundong Hong, Daochao Lin, Xiaoping Han, Guoji Guo, Tianye Hu, He Huang
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2018.00102

Identification and Functional Analysis of Long Intergenic Non-coding RNAs Underlying Intramuscular Fat Content in Pigs
Cited by: 25
Author(s): Cheng Zou, Li Long, Xiangdong Cheng, Cencen Li, Yuhua Fu, Fang Cui, Changchun Li
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-020-59953-w

Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response
Cited by: 25
Author(s): Xin He, Li Liao, Sai Xie, Yang Gi Min, Ping Xie, Wei Liu, Yu Kang, Luyao Huang, Mei Wang, Lunwen Qian, Zhongsong Liu, Chunyun Guan, Mei Guan, Wei Hua
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0077629

Serum Metabolomics of Slow vs. Rapid Motor Progression Parkinson’s Disease: a Pilot Study
Cited by: 101
Author(s): James R. Roede, Karan Uppal, Youngja Park, Kichun Lee, ViLinh Tran, Douglas I. Walker, Frederick H. Strobel, Shannon Rhodes, Beate Ritz, Dean P. Jones
Software Mentions: 1
Published: almost 13 years ago

10.1007/s00429-016-1338-2

Brain transcriptome atlases: a computational perspective
Cited by: 17
Author(s): Ahmed Mahfouz, Sjoerd M. H. Huisman, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders
Software Mentions: 1
Published: almost 10 years ago

10.3389/fimmu.2021.730300

Integration of Molecular Inflammatory Interactome Analyses Reveals Dynamics of Circulating Cytokines and Extracellular Vesicle Long Non-Coding RNAs and mRNAs in Heroin Addicts During Acute and Protracted Withdrawal
Cited by: 7
Author(s): Zunyue Zhang, Hongjin Wu, Qingyan Peng, Zhenrong Xie, Fengrong Chen, Yuru Ma, Yizhi Zhang, Yong Zhou, Jun Yang, Cheng Chen, Shaoyou Li, Yongjin Zhang, Wen Tian, Yuan Wang, Yu Xu, Huayou Luo, Mei Zhu, Yi‐Qun Kuang, Juehua Yu, Kunhua Wang
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0219837

A comprehensive expression analysis of the expansin gene family in potato (Solanum tuberosum) discloses stress-responsive expansin-like B genes for drought and heat tolerances
Cited by: 29
Author(s): Yongkun Chen, Bo Zhang, Canhui Li, Chunxia Lei, Chunyan Kong, Yang Yu, Ming Gong
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-59605-z

Identification of Key Components in Colon Adenocarcinoma Using Transcriptome to Interactome Multilayer Framework
Cited by: 8
Author(s): Ehsan Pournoor, Zaynab Mousavian, Abbas Nowzari Dalini, Ali Masoudi‐Nejad
Software Mentions: 1
Published: over 6 years ago

10.1111/jcmm.12447

Pathway mapping and development of disease‐specific biomarkers: protein‐based network biomarkers
Cited by: 23
Author(s): Hao Chen, Zhou Zhu, Ying–Hui Zhu, Jian Wang, Yunqing Mei, Yunfeng Cheng
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0163812

Alcohol-Induced Molecular Dysregulation in Human Embryonic Stem Cell-Derived Neural Precursor Cells
Cited by: 12
Author(s): Yi Young Kim, Ivan Roubal, Youn Soo Lee, Jin Seok Kim, Michael Hoang, Nathan Mathiyakom, Yong Kim
Software Mentions: 1
Published: almost 10 years ago

10.1111/jcmm.14300

Temporal expression and functional analysis of long non‐coding <scp>RNA</scp> s in colorectal cancer initiation
Cited by: 19
Author(s): Lei Dai, Junshu Li, Zhexu Dong, Y Liu, Ye Chen, Na Chen, Lin Cheng, Chao Fang, Huiling Wang, Yanhong Ji, Shuang Chen, Xiaolan Su, Gang Shi, Yi Lin, Shuang Zhang, Yang Yang, Qingcai Meng, Dechao Yu, Wei Huang, Zong‐Guang Zhou, Yuquan Wei, Hongxin Deng
Software Mentions: 1
Published: over 7 years ago

10.1111/jcmm.14422

Long non‐coding RNAs in the spinal cord injury: Novel spotlight
Cited by: 18
Author(s): Zheng Li, Idy H. T. Ho, Xingye Li, Derong Xu, William Ka Kei Wu, Matthew T. V. Chan, Shugang Li, Xiao Dong Liu
Software Mentions: 1
Published: over 7 years ago

10.3389/fgene.2019.01398

Identification of the Key Factors Related to Bladder Cancer by lncRNA-miRNA-mRNA Three-Layer Network
Cited by: 13
Author(s): Xiaoxia Wang, Yanrui Ding, Jie Wang, Yanyan Wu
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0061505

When Is Hub Gene Selection Better than Standard Meta-Analysis?
Cited by: 229
Author(s): Peter Langfelder, Paul S. Mischel, Steve Horvath
Software Mentions: 1
Published: over 13 years ago

10.1111/jcmm.14746

Pan‐cancer RNA‐seq data stratifies tumours by some hallmarks of cancer
Cited by: 26
Author(s): Frederick G. Frost, Praveen F. Cherukuri, Samuel Milanovich, Cornelius F. Boerkoel
Software Mentions: 1
Published: almost 7 years ago

10.1111/jcmm.14676

Expression and functional analysis of lncRNAs in the hippocampus of immature rats with status epilepticus
Cited by: 6
Author(s): Jing Gan, Lingyi Huang, Yi Qu, Rong Luo, Qianyun Cai, Fengyan Zhao, Dezhi Mu
Software Mentions: 1
Published: almost 7 years ago

10.1111/jcmm.14828

The CCN1 (CYR61) protein promotes skin growth by enhancing epithelial‐mesenchymal transition during skin expansion
Cited by: 9
Author(s): Yiwen Zhou, Haizhou Li, Xiao Liang, Hengyu Du, Yingjun Suo, Hao Chen, Wenhui Liu, Ran Duan, Xiaolu Huang, Qingfeng Li
Software Mentions: 1
Published: almost 7 years ago

10.1111/jcmm.14852

Identification of dynamic signatures associated with smoking‐related squamous cell lung cancer and chronic obstructive pulmonary disease
Cited by: 10
Author(s): Xiaoru Sun, Jingzhe Shang, Aiping Wu, Jingyan Xia, Feng Xu
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2018.00406

De novo Mutations (DNMs) in Autism Spectrum Disorder (ASD): Pathway and Network Analysis
Cited by: 37
Author(s): Aitana Alonso-González, Cristina Rodríguez-Fontenla, Ángel Carracedo
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0167543

The rs3957357C>T SNP in GSTA1 Is Associated with a Higher Risk of Occurrence of Hepatocellular Carcinoma in European Individuals
Cited by: 19
Author(s): Hanane Akhdar, Said El Shamieh, Orlando Musso, Romain Désert, Wissam H. Joumaa, Dominique Guyader, Caroline Aninat, Anne Corlu, Franck Morel
Software Mentions: 1
Published: almost 10 years ago

10.1111/jcmm.14976

Transcriptome analyses reveal molecular mechanisms underlying phenotypic differences among transcriptional subtypes of glioblastoma
Cited by: 20
Author(s): Yuan‐Bo Pan, Siqi Wang, Biao Yang, Zhenqi Jiang, Cameron Lenahan, Jianhua Wang, Jianmin Zhang, Anwen Shao
Software Mentions: 1
Published: over 6 years ago

10.1186/s12935-021-02047-y

LRRK2 is a candidate prognostic biomarker for clear cell renal cell carcinoma
Cited by: 3
Author(s): Chunxiu Yang, Jingjing Pang, Jian Xu, He Pan, Yueying Li, Huainian Zhang, Huan Liu, Shu‐Yuan Xiao
Software Mentions: 1
Published: about 5 years ago

10.1111/jcmm.15145

Gene signatures based on therapy responsiveness provide guidance for combined radiotherapy and chemotherapy for lower grade glioma
Cited by: 10
Author(s): Guangqi Li, Yufei Jiang, Xintong Lyu, Yiru Cai, Miao Zhang, Qiao Qiao
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.01281

Identification of Immune-Related Genes Contributing to the Development of Glioblastoma Using Weighted Gene Co-expression Network Analysis
Cited by: 30
Author(s): Yahui Kong, Zichao Feng, Yulin Zhang, Xiaofei Liu, Yuan Ma, Zhimin Zhao, Bin Huang, An-Jing Chen, Di Zhang, Frits Thorsen, Jian Wang, Ning Yang, Xingang Li
Software Mentions: 1
Published: about 6 years ago

10.3389/fimmu.2020.603337

Identifying Potential Candidate Hub Genes and Functionally Enriched Pathways in the Immune Responses to Quadrivalent Inactivated Influenza Vaccines in the Elderly Through Co-Expression Network Analysis
Cited by: 1
Author(s): Jing Yang, Jiayou Zhang, Renfeng Fan, Wei Zhao, Han Tian, Kai Duan, Xinguo Li, Peiyu Zeng, Jinglong Deng, Jikai Zhang, Xiaoming Yang
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12935-021-01880-5

Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation
Cited by: 12
Author(s): Yan Liao, Fang Wang, Yadong Zhang, Hao Cai, Song Fan, Jinsong Hou
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0218528

Distinct leaf transcriptomic response of water deficient Eucalyptus grandis submitted to potassium and sodium fertilization
Cited by: 13
Author(s): Bénédicte Favreau, Marie Denis, Raphaël Ployet, Fabien Mounet, Hana Peireira da Silva, Lívia Maria Franceschini, Jean‐Paul Laclau, Carlos Alberto Labate, Helaine Carrer
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0116644

Glioma-Associated Microglia/Macrophages Display an Expression Profile Different from M1 and M2 Polarization and Highly Express Gpnmb and Spp1
Cited by: 295
Author(s): Frank Szulzewsky, Andreas Pelz, Xi Feng, Michael Synowitz, Darko Marković, Thomas Langmann, Inge R. Holtman, Xi Wang, Bart J. L. Eggen, Hendrikus Boddeke, Dolores Hambardzumyan, Susanne Wolf, Helmut Kettenmann
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0150850

Immune-Mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I
Cited by: 16
Author(s): Omar Khalid, Moin Vera, Philip L.S.M. Gordts, N. Matthew Ellinwood, Philip H. Schwartz, Patricia Dickson, Jeffrey D. Esko, Raymond Wang
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms22010454

RNA-Seq Provides New Insights into the Molecular Events Involved in “Ball-Skin versus Bladder Effect” on Fruit Cracking in Litchi
Cited by: 10
Author(s): Jun Wang, Xuehong Wu, Yong Tang, Jian Guo Li, Ming Zhao
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.51309

CDH1 is Identified as A Therapeutic Target for Skin Regeneration after Mechanical Loading
Cited by: 9
Author(s): Xiaolu Huang, Xiao Liang, Yiwen Zhou, Haizhou Li, Hengyu Du, Yinjun Suo, Wenhui Liu, Rui Jin, Bangda Chai, Ran Duan, Qingfeng Li
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.15561

Systematic analysis on multiple Gene Expression Omnibus data sets reveals fierce immune response in hepatitis B virus‐related acute liver failure
Cited by: 3
Author(s): Huadi Chen, Wenting Zhao, Yixi Zhang, Yiwen Guo, Weixin Luo, Xiaobo Wang, Yu Nie, Maodong Ye, Changjun Huang, Dongping Wang, Maogen Chen, Xiaoshun He, Qiang Zhao
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0178006

Disease-related gene module detection based on a multi-label propagation clustering algorithm
Cited by: 7
Author(s): Xue Jiang, Han Zhang, Xiongwen Quan, Zhandong Liu, Yanbin Yin
Software Mentions: 1
Published: over 9 years ago

10.7150/ijbs.59559

Upregulation of ATP Binding Cassette Subfamily C Member 5 facilitates Prostate Cancer progression and Enzalutamide resistance via the CDK1-mediated AR Ser81 Phosphorylation Pathway
Cited by: 7
Author(s): Guangjie Ji, Shiming He, Cong Huang, Yanqing Gong, Xuesong Li, Liqun Zhou
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2021.604315

Identification of Hub Genes Associated With Sensitivity of 5-Fluorouracil Based Chemotherapy for Colorectal Cancer by Integrated Bioinformatics Analysis
Cited by: 3
Author(s): Ya Wang, Qunhui Wei, Yuqiao Chen, Shichao Long, Yuanbing Yao, Kai Fu
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.15690

Landscape of associations between long non‐coding RNAs and infiltrating immune cells in liver hepatocellular carcinoma
Cited by: 7
Author(s): Li Li, Xiaowei Song, Yanju Lv, Qi Jiang, Chengjuan Fan, Dayong Huang
Software Mentions: 1
Published: about 6 years ago

10.1111/jcmm.15923

GNG5 is an unfavourable independent prognostic indicator of gliomas
Cited by: 11
Author(s): Biao Yang, Zhaolong Han, Wen‐Juan Wang, Yupo Ma, Sheng‐Hua Chu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0213501

Distinct transcriptional modules in the peripheral blood mononuclear cells response to human respiratory syncytial virus or to human rhinovirus in hospitalized infants with bronchiolitis
Cited by: 9
Author(s): Sandra Elisabete Vieira, Sílvia Yumi Bando, Milena de Paulis, Danielle Bruna Leal Oliveira, Luciano Matsumiya Thomazelli, Edison Luiz Durigon, Marina Baquerizo Martinez, Carlos Alberto Moreira-Filho
Software Mentions: 1
Published: over 7 years ago

10.1186/s13046-018-1002-1

Classification of triple-negative breast cancers based on Immunogenomic profiling
Cited by: 274
Author(s): Hanlin Yin, Zhongshan Jiang, Chen Cai, Xiaosheng Wang
Software Mentions: 1
Published: almost 8 years ago

10.3389/fimmu.2020.01070

Human Monocyte Subset Distinctions and Function: Insights From Gene Expression Analysis
Cited by: 48
Author(s): Sarah Cormican, Matthew D. Griffin
Software Mentions: 1
Published: over 6 years ago

10.1002/brb3.2309

Coexpression of the discoidin domain receptor 1 gene with oligodendrocyte‐related and schizophrenia risk genes in the developing and adult human brain
Cited by: 6
Author(s): Gerard Muntané, Marc Chillida, Selena Aranda, Arcadi Navarro, Elisabet Vilella
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0082656

Neurobiological Signatures of Alcohol Dependence Revealed by Protein Profiling
Cited by: 29
Author(s): Giorgio Gorini, Amanda J. Roberts, R. Dayne Mayfield
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0092395

Cancer-Risk Module Identification and Module-Based Disease Risk Evaluation: A Case Study on Lung Cancer
Cited by: 7
Author(s): Jian Xu, Zhengqiang Miao, Li Wan, Liangcai Zhang, Chenchen Feng, Yuehan He, Xiaoman Bi, Liqiang Wang, Ye Du, Min Hou, Dapeng Hao, Yun Xiao, Lina Chen, Kongning Li
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms21030699

Review—Current Concepts in Inflammatory Skin Diseases Evolved by Transcriptome Analysis: In-Depth Analysis of Atopic Dermatitis and Psoriasis
Cited by: 36
Author(s): Julius Schwingen, Mustafa Kaplan, Florian C. Kurschus
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0134706

Interleukin 21 Controls mRNA and MicroRNA Expression in CD40-Activated Chronic Lymphocytic Leukemia Cells
Cited by: 15
Author(s): Loris De Cecco, Matteo Capaia, Simona Zupo, Giovanna Cutrona, Serena Matis, Antonella Brizzolara, Anna Maria Orengo, Michela Croce, Edoardo Marchesi, Manlio Ferrarini, Silvana Canevari, Silvano Ferrini
Software Mentions: 1
Published: about 11 years ago

10.1186/s13046-020-01803-8

Hepatitis B virus P protein initiates glycolytic bypass in HBV-related hepatocellular carcinoma via a FOXO3/miRNA-30b-5p/MINPP1 axis
Cited by: 47
Author(s): Wenbiao Chen, Jingjing Jiang, Lan Gong, Zheyue Shu, Da‐Xiong Xiang, Xujun Zhang, Kefan Bi, Hongyan Diao
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0190110

A complex network approach reveals a pivotal substructure of genes linked to schizophrenia
Cited by: 22
Author(s): A. Monaco, Anna Monda, Nicola Amoroso, Alessandro Bertolino, Giuseppe Blasi, Pasquale Di Carlo, Marco Papalino, Giulio Pergola, Sabina Tangaro, R. Bellotti
Software Mentions: 1
Published: over 8 years ago

10.1186/s13046-020-01782-w

Alcoholic fatty liver disease inhibited the co-expression of Fmo5 and PPARα to activate the NF-κB signaling pathway, thereby reducing liver injury via inducing gut microbiota disturbance
Cited by: 27
Author(s): Ling Kong, Jing Chen, Xiao li Ji, Qian Qin, Hui Yang, Dan Liú, De liang Li, Mei ling Sun
Software Mentions: 1
Published: over 5 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479