10.1186/s12870-021-02983-x

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

10.1186/s12859-017-1890-7

Identification and characterization of conserved lncRNAs in human and rat brain
Cited by: 20
Author(s): Dan Li, Mary Qu Yang
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-020-73654-4

Extensive fragmentation and re-organization of transcription in Systemic Lupus Erythematosus
Cited by: 8
Author(s): Vasilis F. Ntasis, Nikolaos Panousis, Maria G Tektonidou, Emmanouil T. Dermitzakis, Dimitrios T. Boumpas, George Βertsias, Christoforos Nikolaou
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-72986-5

Inoculation of Ensifer fredii strain LP2/20 immobilized in agar results in growth promotion and alteration of bacterial community structure of Chinese kale planted soil
Cited by: 15
Author(s): Neelawan Pongsilp, Pongrawee Nimnoi
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2105-12-322

Strategies for aggregating gene expression data: The collapseRows R function
Cited by: 257
Author(s): Jeremy A. Miller, Chaochao Cai, Peter Langfelder, Daniel H. Geschwind, Sunil M. Kurian, Daniel R. Salomon, Steve Horvath
Software Mentions: 2
Published: about 15 years ago

10.1038/s41598-020-72197-y

Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the gastrointestinal tract
Cited by: 32
Author(s): David M. Johanson, Jennifer E. Goertz, Ioana Marin, John Costello, Christopher C. Overall, Alban Gaultier
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2021.615859

Integrated Transcriptome Profiling Revealed That Elevated Long Non-Coding RNA-AC007278.2 Expression Repressed CCR7 Transcription in Systemic Lupus Erythematosus
Cited by: 14
Author(s): Yi You, Xingwang Zhao, WU Yu-hua, Jiangming Mao, Lan Ge, Junkai Guo, Chunrong Zhao, Dong Chen, Zhiqiang Song
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-016-3385-8

Functional changes in mRNA expression and alternative pre-mRNA splicing associated with the effects of nutrition on apoptosis and spermatogenesis in the adult testis
Cited by: 20
Author(s): Yongjuan Guan, Guanxiang Liang, Graeme B. Martin, Le Luo Guan
Software Mentions: 2
Published: almost 10 years ago

10.3390/antibiotics10020097

Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages
Cited by: 7
Author(s): Lu Lu, Ranlei Wei, Sanjib Bhakta, Simon J. Waddell, Ester Boix
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-020-02705-9

Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice
Cited by: 15
Author(s): Baiyang Yu, Jianbin Liu, Di Wu, Ying Liu, Weijian Cen, Shaokui Wang, Rongbai Li, Jijing Luo
Software Mentions: 2
Published: about 6 years ago

10.1186/s12920-020-0672-7

Pathway mapping of leukocyte transcriptome in influenza patients reveals distinct pathogenic mechanisms associated with progression to severe infection
Cited by: 12
Author(s): Yoann Zerbib, Emily Jenkins, Maryam Shojaei, Adrienne F. A. Meyers, John Ho, T. Blake Ball, Yoav Keynan, Amarnath Pisipati, Aseem Kumar, Anand Kumar, Marek Nalos, Benjamin Tang, Klaus Schughart, Anthony S. McLean
Software Mentions: 2
Published: over 6 years ago

10.1042/BSR20202219

Novel insights into plasma biomarker candidates in patients with chronic mountain sickness based on proteomics
Cited by: 7
Author(s): Peili Zhang, Zhanquan Li, Faman Yang, Linhua Ji, Yingzhong Yang, Chuan-Chuan Liu, Huihui Liu, Jie Ma, Jie Liu, Zhancui Dang, Shengyan Wang, Ri-Li Ge, Sen Cui
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-68093-0

Mechanism of Astragalus membranaceus in the treatment of laryngeal cancer based on gene co-expression network and molecular docking
Cited by: 8
Author(s): Kai Dong, Meng Qi Huo, Heng Sun, Tian Ke Li, Dan Li
Software Mentions: 2
Published: over 6 years ago

10.3390/genes10030225

Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice
Cited by: 13
Author(s): Katya L. Mack, Megan Phifer‐Rixey, Bettina Harr, Michael W. Nachman
Software Mentions: 2
Published: over 7 years ago

10.1042/BSR20204293

High expression of COL5A2, a member of COL5 family, indicates the poor survival and facilitates cell migration in gastric cancer
Cited by: 20
Author(s): Yongjun Tan, Qingchuan Chen, Xing Yao, Chao Zhang, Siwei Pan, Wei An, Hui Xu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-020-2322-9

Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis
Cited by: 21
Author(s): Huirong Duan, Lirong Wang, Guangxin Cui, Xingyue Zhou, Xiaorong Duan, Hongshan Yang
Software Mentions: 2
Published: over 6 years ago

10.3390/genes10020119

Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis
Cited by: 27
Author(s): Xianyan Zou, Àiyīng Liú, Zhen Zhang, Qún Gě, Senmiao Fan, Wànkuí Gǒng, Jùnwén Lǐ, Jǔwǔ Gōng, Yùzhēn Shí, Bin Tian, Yanling Wang, Ruixian Liu, Kang Lei, Qi Zhang, Xiao Jiang, Yulong Feng, Shuya Zhang, Tingting Jia, Lipeng Zhang, Yǒulù Yuán, Hǎihóng Shāng
Software Mentions: 2
Published: over 7 years ago

10.3390/genes9100478

An Improved Method for Prediction of Cancer Prognosis by Network Learning
Cited by: 32
Author(s): Min‐Seon Kim, Ilhwan Oh, Jaegyoon Ahn
Software Mentions: 2
Published: about 8 years ago

10.1186/s12870-021-02965-z

Transcriptome regulation of carotenoids in five flesh-colored watermelons (Citrullus lanatus)
Cited by: 13
Author(s): Pingli Yuan, Muhammad Umer, Nan He, Shanjiang Zhao, Xingrong Lu, Huiling Zhu, Chengsheng Gong, Weinan Diao, Haileslassie Gebremeskel, Hanhui Kuang, Wenge Liu
Software Mentions: 2
Published: over 5 years ago

10.1186/s13068-020-01802-z

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

10.1002/2211-5463.12964

LMTK3 promotes tumorigenesis in bladder cancer via the ERK/MAPK pathway
Cited by: 15
Author(s): Tao Jiang, Xia Lu, Feiya Yang, Mingshuai Wang, Hua Yang, Nianzeng Xing
Software Mentions: 2
Published: about 6 years ago

10.1155/2018/5862571

Neuronal Signal Transduction-Involved Genes in Pig Hypothalamus Affect Feed Efficiency as Revealed by Transcriptome Analysis
Cited by: 17
Author(s): Ye Hou, Mingyang Hu, Huanhuan Zhou, Changchun Li, Xinyun Li, Xiangdong Liu, Yi‐Fang Zhao, Zhao Song
Software Mentions: 2
Published: almost 8 years ago

10.1002/fsn3.2283

Chain length‐dependent inulin alleviates diet‐induced obesity and metabolic disorders in mice
Cited by: 9
Author(s): Liangkui Li, Lu Zhang, Linkang Zhou, Meijun Jin, Li Xu
Software Mentions: 2
Published: over 5 years ago

10.3389/fphys.2019.01081

Identification of Hub Genes and Key Pathways Associated With Bipolar Disorder Based on Weighted Gene Co-expression Network Analysis
Cited by: 70
Author(s): Yang Liu, Hao Gu, Jie Zhu, Yu‐Ming Niu, Zhang Chao, Guangling Guo
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-66132-4

Identification of key genes and modules in response to Cadmium stress in different rice varieties and stem nodes by weighted gene co-expression network analysis
Cited by: 27
Author(s): Qi Wang, Xianmin Zeng, Qiulai Song, Yu Sun, Yang Feng, Yongcai Lai
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-021-03987-y

ComHub: Community predictions of hubs in gene regulatory networks
Cited by: 9
Author(s): Julia Åkesson, Zelmina Lubovac-Pilav, Rasmus Magnusson, Mika Gustafsson
Software Mentions: 2
Published: over 5 years ago

10.1038/s41416-019-0477-7

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

10.1093/brain/awaa217

Dystonia genes functionally converge in specific neurons and share neurobiology with psychiatric disorders
Cited by: 45
Author(s): Niccolò E. Mencacci, Regina H Reynolds, Sonia García-Ruiz, Jana Vandrovcová, Paola Forabosco, Álvaro Sánchez‐Ferrer, Viola Volpato, Juan A. Botía, Karishma D’Sa, Paola Forabosco, Sebastian Guelfi, John Hardy, Jana Vandrovcová, Chris-Ann Mackenzie, Adaikalavan Ramasamy, Mina Ryten, Colin Smith, Daniah Trabzuni, Michael E. Weale, Alastair Noyce, Rauan Kaiyrzhanov, Ben Middlehurst, Demis A. Kia, Manuela Tan, Henry Houlden, Huw R. Morris, Hélène Plun‐Favreau, Peter Holmans, John Hardy, Daniah Trabzuni, José Brás, John P. Quinn, Kin Y. Mok, Kerri J. Kinghorn, Kimberley Billingsley, Nicholas W. Wood, Patrick A. Lewis, Rita Guerreiro, Ruth C. Lovering, Lea R’Bibo, Claudia Manzoni, Mie Rizig, Mina Ryten, Sebastian Guelfi, Valentina Escott‐Price, Viorica Chelban, Thomas Foltynie, Nigel Williams, Chingiz Shashakin, Nazira Zharkinbekova, Elena Zholdybayeva, Akbota Aitkulova, Kirsten Harvey, Michael E. Weale, Kailash P. Bhatia, Caleb Webber, John Hardy, Juan A. Botía, Mina Ryten
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-65479-y

Identification of prognostic signature of non–small cell lung cancer based on TCGA methylation data
Cited by: 17
Author(s): Yifan Wang, Ying Wang, Yongjun Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-15-S10-I1

Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014
Cited by: 0
Author(s): Eric C. Rouchka, Julia H. Chariker
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-017-06145-8

Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment
Cited by: 42
Author(s): James D. Mills, Anand M. Iyer, Jackelien van Scheppingen, Anika Bongaarts, Jasper J. Anink, Bart Janssen, Till S. Zimmer, Wim G.M. Spliet, Peter C. van Rijen, Floor E. Jansen, Martha Feucht, Johannes A. Hainfellner, Pavel Kršek, Josef Zámečnı́k, Katarzyna Kotulska, Sergiusz Jóźwiak, Anna Jansen, Lieven Lagae, Paolo Curatolo, David J. Kwiatkowski, R. Jeroen Pasterkamp, Ketharini Senthilkumar, Lars von Oerthel, Marco F.M. Hoekman, Jan A. Gorter, Peter B. Crino, Angelika Mühlebner, Brendon P. Scicluna, Eleonora Aronica
Software Mentions: 2
Published: about 9 years ago

10.1186/s12859-018-2553-z

Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency
Cited by: 38
Author(s): Suraya Mohamad Salleh, Gianluca Mazzoni, Peter Løvendahl, Haja N. Kadarmideen
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.bbi.2018.05.016

Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes
Cited by: 20
Author(s): Michael S. Breen, Aliza P. Wingo, Nastassja Koen, Kirsten A. Donald, Mark P. Nicol, Heather J. Zar, Kerry J. Ressler, Joseph D. Buxbaum, Dan J. Stein
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-017-07029-7

Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes
Cited by: 12
Author(s): Surbhi Chamaria, Kipp W. Johnson, Yuliya Vengrenyuk, Usman Baber, Khader Shameer, Aparna A. Divaraniya, Benjamin S. Glicksberg, Li Li, Samit Bhatheja, Pedro R. Moreno, Akiko Maehara, Roxana Mehran, Joel T. Dudley, Jagat Narula, Samin K. Sharma, Annapoorna Kini
Software Mentions: 2
Published: about 9 years ago

10.1186/s12920-014-0060-2

A common gene expression signature in Huntington’s disease patient brain regions
Cited by: 46
Author(s): Andreas Neueder, Gillian P. Bates
Software Mentions: 2
Published: about 12 years ago

10.3389/fphys.2018.00215

Mechanistic Role of Reactive Oxygen Species and Therapeutic Potential of Antioxidants in Denervation- or Fasting-Induced Skeletal Muscle Atrophy
Cited by: 62
Author(s): Jiaying Qiu, Qian Fang, Tongtong Xu, Changyue Wu, Lai Xu, Lingbin Wang, Xiaoming Yang, Shu Yu, Qi Zhang, Fei Ding, Hualin Sun
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-6144-9

Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley
Cited by: 42
Author(s): Licao Cui, Guang Yang, Jiali Yan, Yan Pan, Xiaojun Nie
Software Mentions: 2
Published: about 7 years ago

10.1590/1414-431X20176685

Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA
Cited by: 9
Author(s): Zhonghua Song, Wenhua Zhao, Dong-Yuan Cao, Jinqing Zhang, Shouhua Chen
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-017-4257-6

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI
Cited by: 38
Author(s): Weijing Wang, Wenjie Jiang, Lin Hou, Haiping Duan, Yili Wu, Chunsheng Xu, Qihua Tan, Shuxia Li, Dongfeng Zhang
Software Mentions: 2
Published: almost 9 years ago

10.3389/fnagi.2018.00153

Integrative Analysis of Hippocampus Gene Expression Profiles Identifies Network Alterations in Aging and Alzheimer’s Disease
Cited by: 53
Author(s): Vinay Lanke, S.T.R. Moolamalla, Dipanjan Roy, P. Vinod
Software Mentions: 2
Published: over 8 years ago

10.3389/fnagi.2020.605961

Co-expression Network Analysis Reveals Novel Genes Underlying Alzheimer’s Disease Pathogenesis
Cited by: 16
Author(s): Ruiting Hu, Qian Yu, Shao-Dan Zhou, Yuqing Yin, Rui-guang Hu, Hai-peng Lu, Bang-li Hu
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-020-2245-5

Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato
Cited by: 16
Author(s): Dongye Zhang, Yufang Bao, Yaoguang Sun, Huanhuan Yang, Tingting Zhao, Hui-Jia Li, Chong Du, Jingbin Jiang, Jin-Fu Li, Libo Xie, Xiangyang Xu
Software Mentions: 2
Published: almost 7 years ago

10.1155/2020/1371632

Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma
Cited by: 1
Author(s): Jianguo Li, Jin Zhang, Shuangshuang Kai, Can Wang, Daijun Wang, Jiying Jiang
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-017-05044-2

Characterization of transcriptional modules related to fibrosing-NAFLD progression
Cited by: 43
Author(s): Yi Liu, Guoyan Tian, Yu Song, Yinlan Liu, Yidan Chen, Junping Shi, Jin Yang
Software Mentions: 2
Published: over 9 years ago

10.1186/s12870-019-2021-6

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

10.1186/s12864-019-6228-6

Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle
Cited by: 17
Author(s): Shuli Liu, Lingzhao Fang, Yang Zhou, D. R. dos Santos, Ruidong Xiang, Hans D. Daetwyler, Amanda J. Chamberlain, John B. Cole, Congjun Li, Ying Yu, Li Ma, Shengli Zhang, George E. Liu
Software Mentions: 2
Published: almost 7 years ago

10.1093/bib/bbt034

Supervised, semi-supervised and unsupervised inference of gene regulatory networks
Cited by: 129
Author(s): Stefan Maetschke, Piyush B. Madhamshettiwar, Melissa J. Davis, Mark A. Ragan
Software Mentions: 2
Published: over 13 years ago

10.3389/frai.2021.674370

Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues
Cited by: 6
Author(s): Vy Tran, Robert Kim, Mikhail Maertens, Thomas Hartung, Alexandra Maertens
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-015-0496-3

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping
Cited by: 24
Author(s): Niklas Körber, Anja Bus, Jinquan Li, Janet Higgins, Ian Bancroft, Erin E. Higgins, Isobel A. P. Parkin, Bertha M. Salazar-Colqui, Rod J. Snowdon, Benjamin Stich
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-017-01517-6

A Systems Genetics Approach Identified GPD1L and its Molecular Mechanism for Obesity in Human Adipose Tissue
Cited by: 12
Author(s): Hao He, Dianjianyi Sun, Yong Zeng, Ruifeng Wang, Wei Zhu, Shaolong Cao, George A. Bray, Wei Chen, Hui Shen, Frank M. Sacks, Lü Qi, Hong Wen Deng
Software Mentions: 2
Published: over 9 years ago

10.1155/2017/3035481

Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns
Cited by: 6
Author(s): Zhi Han, Travis Johnson, Jie Zhang, Xuan Zhang, Kun Huang
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12870-018-1526-8

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress
Cited by: 31
Author(s): Lingling Wang, Zhaoen Yang, Bin Zhang, Daoqian Yu, Ji Liu, Qian Gong, Ghulam Qanmber, Yi Li, Lili Lu, Yongjun Lin, Zuoren Yang, Fuguang Li
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12935-020-01180-4

Identification of novel biomarkers affecting the metastasis of colorectal cancer through bioinformatics analysis and validation through qRT-PCR
Cited by: 10
Author(s): Wenping Lian, Jin Huang, Jingjing Cao, Xinyu Zhang, Tao Zhu, Shuai Zhao, Sujuan Wu, Kailu Zou, Xinyun Zhang, Mingliang Zhang, Xiaoli Zheng, Mengle Peng
Software Mentions: 2
Published: over 6 years ago

10.3390/genes9020092

Identification of Key Pathways and Genes in the Dynamic Progression of HCC Based on WGCNA
Cited by: 115
Author(s): Yin Li, Zhihui Cai, Baoan Zhu, Chi Xu
Software Mentions: 2
Published: over 8 years ago

10.3389/fbioe.2014.00048

Protein Network Signatures Associated with Exogenous Biofuels Treatments in Cyanobacterium Synechocystis sp. PCC 6803
Cited by: 11
Author(s): Guangsheng Pei, Lei Chen, Jiangxin Wang, Jianjun Qiao, Weiwen Zhang
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12935-021-01854-7

Pentraxin 3 is a diagnostic and prognostic marker for ovarian epithelial cancer patients based on comprehensive bioinformatics and experiments
Cited by: 9
Author(s): Xiaolin Chang, Dan Li, Chang Liu, Zhe Zhang, Tao Wang
Software Mentions: 2
Published: over 5 years ago

10.3389/fbioe.2020.00729

OASL as a Diagnostic Marker for Influenza Infection Revealed by Integrative Bioinformatics Analysis With XGBoost
Cited by: 7
Author(s): Yang Li, Hongjie Liu, Quan Xu, Rui Wu, Yi Zhang, Naizhe Li, Xiaozhou He, Mengjie Yang, Mifang Liang, Xuejun Ma
Software Mentions: 2
Published: over 6 years ago

10.3389/fbioe.2020.00031

Transcriptomic Analyses for Identification and Prioritization of Genes Associated With Alzheimer’s Disease in Humans
Cited by: 17
Author(s): Yuchen Shi, Hui Liu, Changbo Yang, Kang Xu, Yangyang Cai, Zhao Wang, Zheng Zhao, Tingting Shao, Yixue Li
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-01280-8

Metabolomic and Proteomic Analysis of Maize Embryonic Callus induced from immature embryo
Cited by: 32
Author(s): Fei Ge, Hongmei Hu, Xing Huang, Yanling Zhang, Yanli Wang, Zhaoling Li, Chaoying Zou, Huanwei Peng, Lujiang Li, Shibin Gao, Guangtang Pan, Yaou Shen
Software Mentions: 2
Published: over 9 years ago

10.1186/s12935-020-01488-1

Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme
Cited by: 18
Author(s): Xiaolong Zhu, Lan Jiang, Hui Yang, Tianbing Chen, Xiang Wu, Kun Lv
Software Mentions: 2
Published: about 6 years ago

10.3390/genes8120359

Transcriptional and Hormonal Regulation of Weeping Trait in Salix matsudana
Cited by: 12
Author(s): Juanjuan Liu, Yan‐Fei Zeng, Peiyao Yan, Caiyun He, Jianguo Zhang
Software Mentions: 2
Published: almost 9 years ago

10.3389/fbioe.2018.00151

Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30
Cited by: 19
Author(s): Gustavo Pagotto Borin, Marcelo Falsarella Carazzolle, Renato Augusto Corrêa dos Santos, Diego Mauricio Riaño‐Pachón, Juliana Velasco de Castro Oliveira
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-019-6329-2

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks
Cited by: 22
Author(s): Nam D. Nguyen, Ian K. Blaby, Daifeng Wang
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-016-2492-x

A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration
Cited by: 16
Author(s): Lakshmi Kuttippurathu, Egle Juskeviciute, Rachael P. Dippold, Jan B. Hoek, Rajanikanth Vadigepalli
Software Mentions: 2
Published: over 10 years ago

10.1186/s12935-020-01361-1

Identification of four hub genes as promising biomarkers to evaluate the prognosis of ovarian cancer in silico
Cited by: 16
Author(s): Jingxuan Chen, Yun Cai, Rui Xu, Jiadong Pan, Jie Zhou, Jie Mei
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.102231

TPM2 as a potential predictive biomarker for atherosclerosis
Cited by: 39
Author(s): Ling‐Bing Meng, Mengjie Shan, Yong Qiu, Ruomei Qi, Zemou Yu, Peng Guo, Chen-Yi Di, Tao Gong
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-021-85000-3

Multi-factor mediated functional modules identify novel classification of ulcerative colitis and functional gene panel
Cited by: 6
Author(s): Lijie Lai, Li Hanyang, Qi Feng, Jun Shen, Zhihua Ran
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.685136

Unraveling the Regulatory Mechanism of Color Diversity in Camellia japonica Petals by Integrative Transcriptome and Metabolome Analysis
Cited by: 44
Author(s): Mingyue Fu, Yongsheng Xu, Jiarui Zheng, Ling Wang, Xiaoyan Yang, Yi Fang Tu, Jiabao Ye, Weiwei Zhang, Yongling Liao, Shuiyuan Cheng, Feng Xu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-00171-2

Exploring the microbial community (microflora) associated with ovine Haemonchus contortus (macroflora) field strains
Cited by: 22
Author(s): Saeed El‐Ashram, Xun Suo
Software Mentions: 2
Published: over 9 years ago

10.3389/fcvm.2021.647953

The Integrative Analysis of Competitive Endogenous RNA Regulatory Networks in Coronary Artery Disease
Cited by: 3
Author(s): Yuyao Ji, Tao Yan, Shijie Zhu, Runda Wu, Miao Zhu, Yangyang Zhang, Changfa Guo, Kang Yao
Software Mentions: 2
Published: about 5 years ago

10.3389/fcvm.2020.631775

Integrative Identification of Hub Genes Associated With Immune Cells in Atrial Fibrillation Using Weighted Gene Correlation Network Analysis
Cited by: 9
Author(s): Tao Yan, Shijie Zhu, Miao Zhu, Chunsheng Wang, Changfa Guo
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12935-019-0928-5

A nomogram based on 9-lncRNAs signature for improving prognostic prediction of clear cell renal cell carcinoma
Cited by: 24
Author(s): Wen Jiang, Qing Guo, Chenghe Wang, Yu Zhu
Software Mentions: 2
Published: about 7 years ago

10.1186/s12935-018-0703-z

Identification of biomarkers of chromophobe renal cell carcinoma by weighted gene co-expression network analysis
Cited by: 17
Author(s): Xiaomao Yin, Jianfeng Wang, Jin Zhang
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2013.00028

Maximal information component analysis: a novel non-linear network analysis method
Cited by: 20
Author(s): Christoph Rau, N. Wisniewski, Luz D. Orozco, Brian J. Bennett, James N. Weiss, Aldons J. Lusis
Software Mentions: 2
Published: almost 14 years ago

10.3390/antibiotics10070792

Correction: Lu et al. Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages. Antibiotics 2021, 10, 97
Cited by: 1
Author(s): Lu Lu, Ranlei Wei, Sanjib Bhakta, Simon J. Waddell, Ester Boix
Software Mentions: 2
Published: over 5 years ago

10.1155/2019/5742608

Identification of Candidate Genes and MicroRNAs for Acute Myocardial Infarction by Weighted Gene Coexpression Network Analysis
Cited by: 18
Author(s): Yan Li, Xiao Nan He, Chao Li, Ling Gong, Min Liu
Software Mentions: 2
Published: over 7 years ago

10.3390/genes7120109

Divergent Expression Patterns in Two Vernicia Species Revealed the Potential Role of the Hub Gene VmAP2/ERF036 in Resistance to Fusarium oxysporum in Vernicia montana
Cited by: 7
Author(s): Qiyan Zhang, Ming Gao, Liwen Wu, Yangdong Wang, Yicun Chen
Software Mentions: 2
Published: almost 10 years ago

10.18632/aging.102168

Copy number variations primed lncRNAs deregulation contribute to poor prognosis in colorectal cancer
Cited by: 22
Author(s): Huimin Liu, Xiaoyu Gu, Guihua Wang, Ying Huang, Shaoqing Ju, Jianfei Huang, Xudong Wang
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-019-6027-0

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

10.1038/srep42593

Chilling Affects Phytohormone and Post-Embryonic Development Pathways during Bud Break and Fruit Set in Apple (Malus domestica Borkh.)
Cited by: 19
Author(s): Gulshan Kumar, Khushboo Gupta, Shivalika Pathania, Mohit Kumar Swarnkar, Usha Kumari Rattan, Gagandeep Singh, Ram Kumar Sharma, Anil Kumar Singh
Software Mentions: 2
Published: over 9 years ago

10.3389/fcvm.2021.712061

Association of Circulating, Inflammatory-Response Exosomal mRNAs With Acute Myocardial Infarction
Cited by: 7
Author(s): Guangbin He, Yu-Qing Huang, Lin Liu, Jiayi Huang, Kenneth Lo, Yu-Ling Yu, Chaolei Chen, Bin Zhang, Yingqing Feng
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2020.617020

Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming
Cited by: 7
Author(s): Marcella Siqueira Simões, Sávio Siqueira Ferreira, Adriana Grandis, Jorge Rencoret, Staffan Persson, Eny Iochevet Segal Floh, André Ferraz, José C. del Rı́o, Marcos Silveira Buckeridge, Igor Cesarino
Software Mentions: 2
Published: almost 6 years ago

10.18632/aging.101592

Sirtuin 3 attenuates amyloid-β induced neuronal hypometabolism
Cited by: 18
Author(s): Jun Yin, Shiping Li, Megan Nielsen, Tanner Carcione, Winnie S. Liang, Jiong Shi
Software Mentions: 2
Published: about 8 years ago

10.3389/fcell.2021.742421

An Advanced Systems Pharmacology Strategy Reveals AKR1B1, MMP2, PTGER3 as Key Genes in the Competing Endogenous RNA Network of Compound Kushen Injection Treating Gastric Carcinoma by Integrated Bioinformatics and Experimental Verification
Cited by: 3
Author(s): Wei Zhou, Chao Wu, Chao Zhao, Zhihong Huang, Shan Lu, Xiaotian Fan, Yingying Tan, Antony Stalin, Rongli You, Xinkui Liu, Jingyuan Zhang, Zhishan Wu, Jiarui Wu
Software Mentions: 2
Published: about 5 years ago

10.1186/s12920-014-0072-y

Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods
Cited by: 49
Author(s): Jarrett Morrow, Weiliang Qiu, Divya Chhabra, Stephen I. Rennard, Paula Belloni, Anton Belousov, Sreekumar Pillai, Craig P. Hersh
Software Mentions: 2
Published: almost 12 years ago

10.1038/srep39398

Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries
Cited by: 60
Author(s): Xiangyang Miao, Qingmiao Luo, Haiping Zhao, Xiaoqiong Qin
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep39240

Gene expression in local stroma reflects breast tumor states and predicts patient outcome
Cited by: 11
Author(s): Russell Bainer, Casey Frankenberger, Daniel C. Rabe, Gary An, Yoav Gilad, Marsha Rich Rosner
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12881-019-0791-1

Weighted correlation network and differential expression analyses identify candidate genes associated with BRAF gene in melanoma
Cited by: 9
Author(s): Bin Zhao, Yanqiu You, Weiping Zheng, Yunhan Ma, Yani Huo, Hongyi Liu, Yuanyuan Zhou, Wei Quan, Weibin Chen, Xiaohong Zhang, Fujun Li, Yilin Zhao
Software Mentions: 2
Published: over 7 years ago

10.1155/2021/5512624

Identifying Mitochondrial-Related Genes NDUFA10 and NDUFV2 as Prognostic Markers for Prostate Cancer through Biclustering
Cited by: 2
Author(s): Haokun Zhang, Yuanhua Shao, Weijun Chen, Xin Chen
Software Mentions: 2
Published: over 5 years ago

10.1007/s00204-016-1824-6

Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity
Cited by: 20
Author(s): Salil N. Pendse, Alexandra Maertens, Michael Rosenberg, Dipanwita Roy, Rick A. Fasani, Marguerite M. Vantangoli, Samantha J. Madnick, Kim Boekelheide, Albert J. Fornace, Shelly Odwin, James D. Yager, Thomas Hartung, Melvin E. Andersen, Patrick D. McMullen
Software Mentions: 2
Published: about 10 years ago

10.1002/cam4.3453

A four‐gene signature associated with clinical features can better predict prognosis in prostate cancer
Cited by: 7
Author(s): Peipei Yuan, Le Ling, Qing Fan, Xintao Gao, Taotao Sun, Jianping Miao, Xianglin Yuan, Jihong Liu, Bo Liu
Software Mentions: 2
Published: about 6 years ago

10.1002/cam4.3965

Histopathological image and gene expression pattern analysis for predicting molecular features and prognosis of head and neck squamous cell carcinoma
Cited by: 8
Author(s): Linyan Chen, Hao Zeng, Mingxuan Zhang, Yuling Luo, Xuelei Ma
Software Mentions: 2
Published: over 5 years ago

10.1038/srep38333

Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development
Cited by: 18
Author(s): Jingyu Li, Zheng-ling Gao, Xinyu Wang, Hongbo Liu, Yan Zhang, Liu Z
Software Mentions: 2
Published: almost 10 years ago

10.1002/cam4.3047

Identification of cancer stem cell characteristics in liver hepatocellular carcinoma by WGCNA analysis of transcriptome stemness index
Cited by: 69
Author(s): Kunhao Bai, Siyuan He, Lingling Shu, Weida Wang, Sensen Lin, Qian-Yi Zhang, Liang Li, Lei Cheng, Yong Dai
Software Mentions: 2
Published: over 6 years ago

10.1111/acel.13229

Underlying features of epigenetic aging clocks in vivo and in vitro
Cited by: 84
Author(s): Zuyun Liu, Diana Leung, Kyra Thrush, Wei Zhao, Scott Ratliff, Toshiko Tanaka, Lauren Schmitz, Jennifer A. Smith, Luigi Ferrucci, Morgan E. Levine
Software Mentions: 2
Published: about 6 years ago

10.3389/fphys.2017.00947

Identification of Biomarkers Correlated with the TNM Staging and Overall Survival of Patients with Bladder Cancer
Cited by: 78
Author(s): Sheng Li, Xiaoping Li, Tongzu Liu, Xiangyu Meng, Xiaohong Yin, Cheng Fang, Di Huang, Yue Cao, Hong Weng, Xian‐Tao Zeng, Xinghuan Wang
Software Mentions: 2
Published: almost 9 years ago

10.1002/cam4.4132

Identification of a competing endogenous RNA axis “SVIL‐AS1/miR‐103a/ICE1” associated with chemoresistance in lung adenocarcinoma by comprehensive bioinformatics analysis
Cited by: 5
Author(s): Lili Guo, Ling Ding, Jiaguang Tang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-019-2733-5

Generalized gene co-expression analysis via subspace clustering using low-rank representation
Cited by: 5
Author(s): Tongxin Wang, Jie Zhang, Kun Huang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-018-2536-0

MicroRNA dysregulational synergistic network: discovering microRNA dysregulatory modules across subtypes in non-small cell lung cancers
Cited by: 9
Author(s): Nhat Tran, Vinay V. Abhyankar, Kytai T. Nguyen, Jon A. Weidanz, Jean Gao
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12882-021-02447-2

Comprehensive analysis of diabetic nephropathy expression profile based on weighted gene co-expression network analysis algorithm
Cited by: 17
Author(s): Alieh Gholaminejad, Mohammad Fathalipour, Amir Roointan
Software Mentions: 2
Published: over 5 years ago