cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-24379-y

Pan-cancer analysis of somatic mutations and transcriptomes reveals common functional gene clusters shared by multiple cancer types
Cited by: 29
Author(s): Hyeongmin Kim, Yong Min Kim
Software Mentions: 2
Published: over 8 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

10.3389/fonc.2021.651622

Cancer Stemness Associated With Prognosis and the Efficacy of Immunotherapy in Adrenocortical Carcinoma
Cited by: 13
Author(s): Xiaoxi Shi, Yuanlin Liu, Shuai Cheng, Haidi Hu, Jian Zhang, Minjie Wei, Lin Zhao, Shijie Xin
Software Mentions: 2
Published: over 5 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/s41598-018-25826-6

Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
Cited by: 31
Author(s): Parul Goel, Nitesh Kumar Sharma, Monika Bhuria, Vishal Sharma, Rashi Chauhan, Shivalika Pathania, Mohit Kumar Swarnkar, Vandna Chawla, Vishal Acharya, Ravi Shankar, Anil Kumar Singh
Software Mentions: 2
Published: over 8 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

10.1371/journal.pone.0219013

Expression profiles of circRNAs and the potential diagnostic value of serum circMARK3 in human acute Stanford type A aortic dissection
Cited by: 19
Author(s): Chengming Tian, Xingming Tang, Xiyu Zhu, Qing Zhou, Yuting Guo, Rui Zhao, Dongjin Wang, Bing Gong
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0190933

Skin transcriptome reveals the dynamic changes in the Wnt pathway during integument morphogenesis of chick embryos
Cited by: 19
Author(s): Husile Gong, Hong Wang, YueXing Wang, Xue Bai, Bin Liu, Jinfeng He, Jianghong Wu, Wang-Mei Qi, Wenguang Zhang
Software Mentions: 2
Published: almost 9 years ago

10.3389/fphys.2018.00236

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

10.3389/fphys.2020.00106

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

10.1038/s41598-018-27530-x

Genome-wide transcriptional analysis of submerged lotus reveals cooperative regulation and gene responses
Cited by: 8
Author(s): Bei Wang, Qijiang Jin, Xiao Zhang, Neil S. Mattson, Huihui Ren, Jing Cao, Yanjie Wang, Dongrui Yao, Yingchun Xu
Software Mentions: 2
Published: over 8 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/s41598-018-29842-4

The coffee bean transcriptome explains the accumulation of the major bean components through ripening
Cited by: 21
Author(s): Bing Cheng, Agnelo Furtado, Robert J. Henry
Software Mentions: 2
Published: over 8 years ago

10.1038/s41438-019-0227-2

The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution
Cited by: 38
Author(s): Qingsen Zhu, Yang Xu, Yong Yang, Changfei Guan, Qiuyun Zhang, Jingwen Huang, Don Grierson, Kunsong Chen, Bangchu Gong, Yin X
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-29789-6

COPD is accompanied by co-ordinated transcriptional perturbation in the quadriceps affecting the mitochondria and extracellular matrix
Cited by: 27
Author(s): Saffron A.G. Willis‐Owen, Anna Thompson, Paul Kemp, Michael I. Polkey, Woc Cookson, Miriam F. Moffatt, Samantha A. Natanek
Software Mentions: 2
Published: about 8 years ago

10.1038/s41438-019-0212-9

Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
Cited by: 10
Author(s): Xiaoxue Sun, Ram Kumar Basnet, Zhichun Yan, Johan Bucher, Chengcheng Cai, Jianjun Zhao, Guusje Bonnema
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41416-019-0477-7

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

10.1038/s41598-018-31583-3

Minipuberty and Sexual Dimorphism in the Infant Human Thymus
Cited by: 17
Author(s): Carlos Alberto Moreira-Filho, Sílvia Yumi Bando, Fernanda Bernardi Bertonha, Leandro Ferreira, Christiana de Freitas Vinhas, Lucila Habib Bourguignon Oliveira, Maria Cláudia Nogueira Zerbini, Gláucio Furlanetto, Paulo Chaccur, Magda Carneiro‐Sampaio
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-31965-7

Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production
Cited by: 14
Author(s): Adriana M. Gallego, Luisa F. Rojas, O. Lorena Parra, Héctor Alejandro Céspedes Rodríguez, Juan C. Mazo Rivas, Aura I. Urrea, Lucía Atehortúa, Andrew S. Fister, Mark J. Guiltinan, Siela N. Maximova, Natalia Pabón‐Mora
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-33113-7

Gene coexpression network analysis combined with metabonomics reveals the resistance responses to powdery mildew in Tibetan hulless barley
Cited by: 35
Author(s): Hongjun Yuan, Xingquan Zeng, Qiaofeng Yang, Qijun Xu, Yulin Wang, Dunzhu Jabu, Zha Sang, Nyima Tashi
Software Mentions: 2
Published: about 8 years ago

10.1038/s41438-021-00627-7

Haplotype-resolved genome of diploid ginger (<i>Zingiber officinale</i>) and its unique gingerol biosynthetic pathway
Cited by: 46
Author(s): Honglei Li, Lin Wu, Zhaoming Dong, Yi Jiang, Sanjie Jiang, Haitao Xing, Qiang Li, Guocheng Liu, Shuming Tian, Zhangyan Wu, Bin Wu, Zhexin Li, Ping Zhao, Yan Zhang, Jianmin Tang, Jiabao Xu, Ke Huang, Xia Liu, Wenlin Zhang, Qinhong Liao, Yun Ren, Xianjin Huang, Qingzhi Li, Chengyong Li, Yi Wang, Baskaran Xavier-Ravi, Honghai Li, Yang Liu, Tao Wan, Qinhu Liu, Yong Zou, Jianbo Jian, Qingyou Xia, Yiqing Liu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0125718

Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study
Cited by: 51
Author(s): Christine Poitou, Claire Perret, François Mathieu, Vinh Truong, Yuna Blum, H Durand, Rohia Alili, Nadjim Chelghoum, Véronique Pelloux, Judith Aron‐Wisnewsky, Adriana Torcivia, Jean‐Luc Bouillot, Brian W. Parks, Ewa Ninio, Karine Clément, Laurence Tiret
Software Mentions: 2
Published: over 11 years ago

10.1186/s13040-020-00216-9

Identification of therapeutic targets from genetic association studies using hierarchical component analysis
Cited by: 3
Author(s): Hao-Chih Lee, Osamu Ichikawa, Benjamin S. Glicksberg, Aparna A. Divaraniya, Christine Becker, Pankaj Agarwal, Joel T. Dudley
Software Mentions: 2
Published: over 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

10.3389/fmicb.2019.02365

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

10.1186/s13040-020-00222-x

Deep learning-based ovarian cancer subtypes identification using multi-omics data
Cited by: 28
Author(s): Long-Yi Guo, Wu Ai, Yongxia Wang, Liping Zhang, Hua Chai, Xuefang Liang
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-020-00421-x

Integrated transcriptome and proteome analysis provides insight into chilling-induced dormancy breaking in Chimonanthus praecox
Cited by: 22
Author(s): Zhineng Li, Ning Liu, Wei Zhang, C. F. Wu, Yunbin Jiang, Jing Ma, Mingyang Li, Shunzhao Sui
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-36231-4

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

10.3390/ijms20051106

Transcriptome and Proteome-Based Network Analysis Reveals a Model of Gene Activation in Wheat Resistance to Stripe Rust
Cited by: 21
Author(s): Hong Zhang, Ying Fu, Huan Guo, Lu Zhang, Changyou Wang, Weining Song, Zhaogui Yan, Yajuan Wang, Wanquan Ji
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-37099-0

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

10.1038/s41598-018-35704-w

Blood Biochemistry Analysis to Detect Smoking Status and Quantify Accelerated Aging in Smokers
Cited by: 57
Author(s): Polina Mamoshina, Kirill Kochetov, Filomeno Cortese, Anna Kovalchuk, Alexander Aliper, Evgeny Putin, Morten Scheibye‐Knudsen, Charles R. Cantor, Neil M. Skjodt, Olga Kovalchuk, Alex Zhavoronkov
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41438-020-00381-2

Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers
Cited by: 43
Author(s): Binmei Sun, Xin Zhou, Changming Chen, Chengjie Chen, Kunhao Chen, Muxi Chen, Shaoqun Liu, Guoju Chen, Bihao Cao, Fanrong Cao, Jing Liu, Zhiwen Zhu
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-37413-w

RNA-Seq transcriptome analysis shows anti-tumor actions of melatonin in a breast cancer xenograft model
Cited by: 21
Author(s): Bruna V. Jardim‐Perassi, Pâmela Almeida Alexandre, Nathália Martins Sonehara, Rubens de Paula-Junior, Osvaldo Reis Júnior, Heidge Fukumasu, Roger Chammas, Luiz Lehmann Coutinho, Débora Aparecida Pires de Campos Zuccari
Software Mentions: 2
Published: over 7 years ago

10.1186/1756-0381-7-27

Combining functional genomics strategies identifies modular heterogeneity of breast cancer intrinsic subtypes
Cited by: 2
Author(s): Nima Pouladi, Richard Cowper-Sal·lari, Jason H. Moore
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12917-018-1711-x

Aspirin eugenol ester regulates cecal contents metabolomic profile and microbiota in an animal model of hyperlipidemia
Cited by: 19
Author(s): Ning Ma, Xi-Wang Liu, Xiaojun Kong, Shihong Li, Zeng-Hua Jiao, Zhe Qin, Yajun Yang, Jianyong Li
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12920-015-0078-0

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

10.1038/s41438-021-00635-7

The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases
Cited by: 4
Author(s): Alessandro Vannozzi, Fabio Palumbo, Gabriele Magon, Margherita Lucchin, Gianni Barcaccia
Software Mentions: 2
Published: about 5 years ago

10.1186/s12918-018-0644-0

Metabolomics of mammalian brain reveals regional differences
Cited by: 30
Author(s): William T. Choi, Mehmet Tosun, Hyun-Hwan Jeong, Cemal Karakas, Fatih Semerci, Zhandong Liu, Mirjana Maletić-Savatić
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-019-39298-9

Identification of key lncRNAs contributing to diabetic nephropathy by gene co-expression network analysis
Cited by: 18
Author(s): Jin Shang, Shuai Wang, Yumin Jiang, Yiqi Duan, Genyang Cheng, Dong Liu, Jing Xiao, Zhanzheng Zhao
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21124316

Comparative Transcriptome Analysis of Two Contrasting Soybean Varieties in Response to Aluminum Toxicity
Cited by: 16
Author(s): Lijuan Zhao, Jingjing Cui, Yuanyuan Cai, Songnan Yang, Juge Liu, Wei Wang, Junyi Gai, Zhubing Hu, Yan Li
Software Mentions: 2
Published: over 6 years ago

10.1186/1752-0509-7-21

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

10.1038/s41598-019-41428-2

Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp.chinensis)
Cited by: 66
Author(s): Aihua Wang, Jihong Hu, Changbin Gao, Guanglong Chen, Bingcai Wang, Chufa Lin, Liping Song, Yi Ding, Guolin Zhou
Software Mentions: 2
Published: over 7 years ago

10.3389/fonc.2019.00434

Integrating Clinical and Genetic Analysis of Perineural Invasion in Head and Neck Squamous Cell Carcinoma
Cited by: 40
Author(s): Ze Zhang, Ruoyan Liu, Rui Jin, Yonggang Fan, Tingting Li, Yanjie Shuai, Xingchen Li, Xudong Wang, Jingtao Luo
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21145095

Transcriptomic Profiling of Young Cotyledons Response to Chilling Stress in Two Contrasting Cotton (Gossypium hirsutum L.) Genotypes at the Seedling Stage
Cited by: 21
Author(s): Gongmin Cheng, Longyan Zhang, Hantao Wang, Jianhua Lü, Hengling Wei, Shuxun Yu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-021-00908-z

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

10.1038/s41598-019-42578-z

Single cell RNA-sequencing identified Dec2 as a suppressive factor for spermatogonial differentiation by inhibiting Sohlh1 expression
Cited by: 6
Author(s): Yoshinori Makino, Niels H. Jensen, Naoko Yokota, Moritz J. Rossner, Haruhiko Akiyama, Katsuhiko Shirahige, Yuki Okada
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-41252-8

Transcriptome Analyses of Heart and Liver Reveal Novel Pathways for Regulating Songbird Migration
Cited by: 13
Author(s): W. J. Horton, Matthew Jensen, Aswathy Sebastian, Craig A. Praul, István Albert, Paul A. Bartell
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-018-1529-5

Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat
Cited by: 56
Author(s): Kaifa Wei, Huiqin Chen
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41438-019-0128-4

Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla
Cited by: 25
Author(s): Lijun Bai, Qing Chen, Long Jiang, Yuanxiu Lin, Yuntian Ye, Peng Liu, Xiaorong Wang, Haoru Tang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41438-019-0215-6

The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis
Cited by: 84
Author(s): Feng-chao Jiang, Junhuan Zhang, Sen Wang, Yang Li, Yingfeng Luo, Shenghan Gao, Meiling Zhang, Shizhou Wu, Songnian Hu, Hui Sun, Yuzhu Wang
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2021.727104

The Role of graRS in Regulating Virulence and Antimicrobial Resistance in Methicillin-Resistant Staphylococcus aureus
Cited by: 4
Author(s): Le Chen, Zihui Wang, Tao Xu, Hongfei Ge, Fang Zhou, Xiaoyi Zhu, Xianhui Li, Di Qu, Cheng Zheng, Yang Wu, Keqing Zhao
Software Mentions: 2
Published: about 5 years ago

10.1186/s12918-014-0139-6

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

10.1038/s41598-019-44798-9

Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons
Cited by: 23
Author(s): Hope Kronman, Felix Richter, Benoît Labonté, Ramesh Chandra, Shan Zhao, Gabriel E. Hoffman, Mary Kay Lobo, Eric E. Schadt, Eric J. Nestler
Software Mentions: 2
Published: over 7 years ago

10.1186/s12918-018-0531-8

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

10.1038/s41598-019-45744-5

Genome wide identification and comparative analysis of glutathione transferases (GST) family genes in Brassica napus
Cited by: 31
Author(s): Lijuan Wei, Yan Zhu, Ruiying Liu, Aoxiang Zhang, Meicheng Zhu, Wen Xu, Lin Ai, Kun Lu, Jiana Li
Software Mentions: 2
Published: over 7 years ago

10.1038/s41438-021-00599-8

Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
Cited by: 27
Author(s): Shiping Cheng, Kai‐Hua Jia, Hui Liu, Rengang Zhang, Zhichao Li, Shanshan Zhou, Tian-Le Shi, Ai-Chu Ma, Congwen Yu, Chan Gao, Guanglei Cao, Zhao Wang, Shuai Nie, Jing‐Fang Guo, Si-Qian Jiao, Xue Tian, Xuemei Yan, Yu-Tao Bao, Quanzheng Yun, Xinzhu Wang, Ilga Porth, Yousry A. El‐Kassaby, Xiaoru Wang, Zhen Li, Yves Van de Peer, Jian‐Feng Mao
Software Mentions: 2
Published: about 5 years ago

10.1038/s41438-021-00610-2

Morphological, phenological, and transcriptional analyses provide insight into the diverse flowering traits of a mutant of the relic woody plant Liriodendron chinense
Cited by: 13
Author(s): Shanlin Yu, Zhaodong Hao, Peng Ye, Siqin Liu, Lingfeng Hu, Yongbao Shen, Jisen Shi, Jinhui Chen
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-47218-0

E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration
Cited by: 48
Author(s): Daniel P. Hollern, Matthew Swiatnicki, Jonathan Rennhack, Sean A. Misek, Brooke C. Matson, Andrew McAuliff, Kathleen A. Gallo, Kathleen M. Caron, Eran R. Andrechek
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0060213

Microarray Analyses of Glucocorticoid and Vitamin D3 Target Genes in Differentiating Cultured Human Podocytes
Cited by: 13
Author(s): Xiangguo Cheng, Xuan Zhao, Simran Khurana, Leslie A. Bruggeman, Hung Ying Kao
Software Mentions: 2
Published: over 13 years ago

10.3389/fonc.2019.00360

A Novel Set of WNT Pathway Effectors as a Predictive Marker of Uterine Corpus Endometrial Carcinoma–Study Based on Weighted Co-expression Matrices
Cited by: 3
Author(s): Katarzyna Kośla, Magdalena Orzechowska, Dorota Jędroszka, Izabela Baryła, Andrzej K. Bednarek, Elżbieta Płuciennik
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-48374-z

Dickkopf-related protein 1 is a progestomedin acting on the bovine embryo during the morula-to-blastocyst transition to program trophoblast elongation
Cited by: 14
Author(s): Paula Tríbulo, María Belén Rabaglino, Martin Bonet Bo, Luciano de Rezende Carvalheira, Jeanette V. Bishop, Thomas Hansen, Peter J. Hansen
Software Mentions: 2
Published: about 7 years ago

10.3389/fonc.2020.542492

Dysregulation of the Immune Microenvironment Contributes to Malignant Progression and Has Prognostic Value in Bladder Cancer
Cited by: 15
Author(s): Zongtai Zheng, Shun Mao, Wentao Zhang, Liu Ji, Cheng Li, Ruiliang Wang, Xudong Yao
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0233319

Brain regional gene expression network analysis identifies unique interactions between chronic ethanol exposure and consumption
Cited by: 7
Author(s): Maren L. Smith, Marcelo F. López, Aaron R. Wolen, Howard C. Becker, Michael F. Miles
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0106050

Tau Overexpression Impacts a Neuroinflammation Gene Expression Network Perturbed in Alzheimer’s Disease
Cited by: 87
Author(s): Paul D. Wes, Amy Easton, John P. Corradi, Donna M. Barten, Nino Devidze, Lynn B. DeCarr, Amy Truong, Aiqing He, Nestor X. Barrezueta, Craig Polson, Clotilde Bourin, Marianne E. Flynn, Stefanie Keenan, Regina Lidge, Jere E. Meredith, JoAnne E. Natale, Sethu Sankaranarayanan, Gregory Cadelina, Charlie Albright, Angela Cacace
Software Mentions: 2
Published: about 12 years ago

10.1038/s41438-021-00537-8

Comparative transcriptomic analysis highlights contrasting levels of resistance of Vitis vinifera and Vitis amurensis to Botrytis cinerea
Cited by: 10
Author(s): Ran Wan, Chunfang Guo, Xiaoqing Hou, Yanxun Zhu, Min Gao, Xiaoyan Hu, Songlin Zhang, Chen Jiao, Rongrong Guo, Zhi Li, Xiping Wang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-021-00513-2

Leaf nutrient content and transcriptomic analyses of endive (Cichorium endivia) stressed by downpour-induced waterlog reveal a gene network regulating kestose and inulin contents
Cited by: 7
Author(s): Giulio Testone, Anatoly P. Sobolev, Giovanni Mele, Chiara Nicolodi, Maria Gonnella, Giuseppe Arnesi, Tiziano Biancari, Donato Giannino
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-51626-7

Gene and lncRNA co-expression network analysis reveals novel ceRNA network for triple-negative breast cancer
Cited by: 27
Author(s): Kehao Le, Hui Guo, Qiulei Zhang, Xiaojuan Huang, Ming Xu, Ziwei Huang, Pengfei Yi
Software Mentions: 2
Published: about 7 years ago

10.3389/fonc.2020.00823

RNA Sequencing Revealed Signals of Evolution From Gallbladder Stone to Gallbladder Carcinoma
Cited by: 14
Author(s): Jinghan Wang, Chang Xu, Qiang Cheng, Jiangman Zhao, Shouxin Wu, Wushuang Li, Wenxue Ma, Chen Liu, Xiaoqing Jiang
Software Mentions: 2
Published: over 6 years ago

10.1155/2021/7182914

Integrative Network Analysis Revealed Genetic Impact of Pyruvate Kinase L/R on Hepatocyte Proliferation and Graft Survival after Liver Transplantation
Cited by: 2
Author(s): Zhengtao Liu, Junsheng Zhao, Qianqian Wang, Hai Zhu, Junjie Qian, Shuai Wang, Shuping Que, Feng Zhang, Shengyong Yin, Lin Zhou, Lei Geng, Shusen Zheng
Software Mentions: 2
Published: about 5 years ago

10.1155/2021/9957908

Citrate Synthase and OGDH as Potential Biomarkers of Atherosclerosis under Chronic Stress
Cited by: 5
Author(s): Ling‐Bing Meng, Gaifeng Hu, Mengjie Shan, Yuanmeng Zhang, Zemou Yu, Yun-Qing Liu, Hongxuan Xu, Li Wang, Tao Gong, Deping Liu
Software Mentions: 2
Published: about 5 years ago

10.1186/s12870-021-02889-8

Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour
Cited by: 9
Author(s): Elise Bizouerne, Julia Buitink, Benoît Ly Vu, Joseph Ly Vu, Eddi Esteban, Asher Pasha, Nicholas J. Provart, Jérôme Verdier, Olivier Leprince
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21228730

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

10.1002/iid3.373

Five immune‐gene‐signatures participate in the development and pathogenesis of Kawasaki disease
Cited by: 11
Author(s): Han Nie, Shizhi Wang, Qiong Wu, Danni Xue, Weimin Zhou
Software Mentions: 2
Published: almost 6 years ago

10.3389/fonc.2019.00678

The Expression and Effection of MicroRNA-499a in High-Tobacco Exposed Head and Neck Squamous Cell Carcinoma: A Bioinformatic Analysis
Cited by: 11
Author(s): Shi-Cai Gong, Meng Xu, Ming Xiang, Yijun Shan, Hao Zhang
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0216068

Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach
Cited by: 18
Author(s): Sanchari Sircar, Nita Parekh
Software Mentions: 2
Published: over 7 years ago

10.1186/s12918-019-0698-7

Anti-TNF- αtreatment-related pathways and biomarkers revealed by transcriptome analysis in Chinese psoriasis patients
Cited by: 6
Author(s): Lunfei Liu, Wenting Liu, Yuxin Zheng, Jisu Chen, Jiong Zhou, Huatuo Dai, Sheng Cai, Jianjun Li, Min Zheng, Yunqing Ren
Software Mentions: 2
Published: over 7 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

10.3390/microorganisms7070195

Dynamic Gene Network Analysis of Caco-2 Cell Response to Shiga Toxin-Producing Escherichia coli-Associated Hemolytic–Uremic Syndrome
Cited by: 6
Author(s): Sílvia Yumi Bando, Priscila Iamashita, Filipi Nascimento Silva, Luciano da Fontoura Costa, Cecília M. Abe, Fernanda Bernardi Bertonha, Beatriz Ernestina Cabílio Guth, André Fujita, Carlos Alberto Moreira-Filho
Software Mentions: 2
Published: over 7 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

10.1186/s40249-020-00722-2

Massive migration promotes the early spread of COVID-19 in China: a study based on a scale-free network
Cited by: 12
Author(s): Wenyu Song, Pan Zang, Zhongxing Ding, Xinyu Fang, Liguo Zhu, Yun Zhu, Changjun Bao, Feng Chen, Ming Wu, Zhihang Peng
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-55692-9

Characterization of cancer omics and drug perturbations in panels of lung cancer cells
Cited by: 13
Author(s): Ayako Suzuki, Keiichi Onodera, Kazuma Matsui, Masahide Seki, Hiroyasu Esumi, Tomoyoshi Soga, Sumio Sugano, Takashi Kohno, Yutaka Suzuki, Katsuya Tsuchihara
Software Mentions: 2
Published: almost 7 years ago

10.1128/IAI.00686-19

Cutaneous Immunoprofiles of Three Spotted Fever Group Rickettsia Cases
Cited by: 5
Author(s): Na Jia, Hongbo Liu, Yuan-Chun Zheng, Wenqiang Shi, Ran Wei, Yan-Li Chu, Nianzhi Ning, Bao-Gui Jiang, Rui-Ruo Jiang, Tao Li, Qiu-Bo Huo, Cai Bian, Xiong Liu, Yi Sun, Lian-Feng Li, Qian Wang, Wei Wei, Yawei Wang, Frans Jongejan, Jia-Fu Jiang, Jie Song, Hui Wang, Wu‐Chun Cao
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2019.00959

Profiling of tRNA Halves and YRNA Fragments in Serum and Tissue From Oral Squamous Cell Carcinoma Patients Identify Key Role of 5′ tRNA-Val-CAC-2-1 Half
Cited by: 17
Author(s): Joseph M. Dhahbi, Yury O. Nunez Lopez, Augusto Schneider, Berta Victoria, Tatiana D. Saccon, Krish Bharat, Thaddeus S. McClatchey, Hani Atamna, Wojciech Ścierski, Paweł Golusiński, Wojciech Golusiński, Michał M. Masternak
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-57182-4

Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs
Cited by: 23
Author(s): Victor Adriano Okstoft Carmelo, Priyanka Banerjee, Wellison J. S. Diniz, Haja N. Kadarmideen
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12890-015-0142-8

A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis
Cited by: 36
Author(s): Yong Huang, Shwu Fan, Rekha Vij, Justin M. Oldham, Jose D. Herazo‐Maya, Steven M. Broderick, Mary E. Strek, Steven R. White, D. Kyle Hogarth, Nathan Sandbo, Yves A. Lussier, Kevin F. Gibson, Naftali Kaminski, Joe G.N. Garcia, Imre Noth
Software Mentions: 2
Published: almost 11 years ago

10.3389/fonc.2021.583083

COL5A2 Promotes Proliferation and Invasion in Prostate Cancer and Is One of Seven Gleason-Related Genes That Predict Recurrence-Free Survival
Cited by: 26
Author(s): Xiaohan Ren, Xinglin Chen, Kai Fang, Xu Zhang, Xiao‐Hong Wei, Tong-Tong Zhang, Guangyao Li, Zhongwen Lü, Ninghong Song, Shangqian Wang, Chao Qin
Software Mentions: 2
Published: over 5 years ago

10.3390/insects12080704

Transcriptional Profiles of Diploid Mutant Apis mellifera Embryos after Knockout of csd by CRISPR/Cas9
Cited by: 4
Author(s): Xiuxiu Wang, Yan Lin, Liqiang Liang, Haiyang Geng, Meng Zhang, Hongyi Nie, Songkun Su
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0035796

mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection
Cited by: 53
Author(s): Elizabeth A. Savory, Bishwo N. Adhikari, John Hamilton, Brieanne Vaillancourt, C. Robin Buell, Brad Day
Software Mentions: 2
Published: over 14 years ago

10.1186/s40168-018-0441-4

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

10.3390/ijms20163930

Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.)
Cited by: 45
Author(s): Komivi Dossa, Marie Ali Mmadi, Rong Zhou, Tianyuan Zhang, Ruqi Su, Yujuan Zhang, Linhai Wang, Jun You
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-61016-z

Gene regulatory network analysis with drug sensitivity reveals synergistic effects of combinatory chemotherapy in gastric cancer
Cited by: 6
Author(s): Jeong Hoon Lee, Yu Rang Park, Min-A Jung, Sun Gyo Lim
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2019.01474

Comprehensive Analysis of Competitive Endogenous RNAs Network, Being Associated With Esophageal Squamous Cell Carcinoma and Its Emerging Role in Head and Neck Squamous Cell Carcinoma
Cited by: 11
Author(s): Donghu Yu, Xiaolan Ruan, Jingyu Huang, Weidong Hu, Chen Chen, Yu Xu, Jian Hou, Sheng Li
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-60231-y

Shared transcriptional responses to con- and heterospecific behavioral antagonists in a wild songbird
Cited by: 10
Author(s): Matthew I. M. Louder, Michael Lafayette, Amber A. Louder, Floria M. K. Uy, Christopher N. Balakrishnan, Ken Yasukawa, Márk E. Hauber
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61162-4

Identification of the key genes and pathways involved in the tumorigenesis and prognosis of kidney renal clear cell carcinoma
Cited by: 36
Author(s): Hao Cui, Hong‐Wei Shan, Michael Z. Miao, Zhiguo Jiang, Yuanyuan Meng, Ran Chen, Longzhen Zhang, Yong Liu
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20164030

Dynamic Changes in Metabolite Accumulation and the Transcriptome during Leaf Growth and Development in Eucommia ulmoides
Cited by: 21
Author(s): Long Li, Minhao Liu, Kun Shi, Zhiying Yu, Ying Zhou, Ruishen Fan, Qianqian Shi
Software Mentions: 2
Published: about 7 years ago

10.3389/fonc.2019.01019

Multi-omics Analysis of Microenvironment Characteristics and Immune Escape Mechanisms of Hepatocellular Carcinoma
Cited by: 51
Author(s): Wenli Li, Huimei Wang, Zhu Ma, Jian Zhang, Wen Ouyang, Qi Yan, Jun Li
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-61942-y

Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome
Cited by: 13
Author(s): Leila Ghanbari Maman, Fahimeh Palizban, Fereshteh Fallah Atanaki, Naser Elmi, Shohreh Ariaeenejad, Mohammad Reza Ghaffari, Kaveh Kavousi
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2019.00291

Identification of RE1-Silencing Transcription Factor as a Promoter of Metastasis in Pancreatic Cancer
Cited by: 6
Author(s): Haoyi Jin, Peng Liu, Lingming Kong, Xiang Fei, Yang Gao, Tianyu Wu, Defeng Sun
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-019-2069-3

Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas
Cited by: 10
Author(s): Maosheng Chen, Miaomiao Zhao, Guijuan Wang, Hua He, Xue Bai, Bang-Zhen Pan, Qi Fu, Yongfu Tao, Mingyong Tang, Jorge Martínez‐Herrera, Zeng-Fu Xu
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-62853-8

Network-based metabolic characterization of renal cell carcinoma
Cited by: 48
Author(s): Nishtha Pandey, Vinay Lanke, P. K. Vinod
Software Mentions: 2
Published: over 6 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479