Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: WGCNA

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/WGCNA

Weighted Correlation Network Analysis
52 versions
Latest release: almost 2 years ago
20 dependent packages
9,120 downloads last month

Papers Mentioning WGCNA 3,479

10.3389/fpls.2021.624319
Grafting Delays Watermel on Fruit Ripening by Altering Gene Expression of ABA Centric Phytohormone Signaling
Cited by: 5
Author(s): Sheng Guo, Honghe Sun, Jiaxing Tian, Guoyu Zhang, Guoyi Gong, Yi Ren, Jie Zhang, Maoying Li, Haiying Zhang, Haizhen Li, Yong Xu
Software Mentions: 1
Published: over 3 years ago
10.3389/fpls.2020.616338
Interspecific Variation in the Unsaturation Level of Seed Oils Were Associated With the Expression Pattern Shifts of Duplicated Desaturase Genes and the Potential Role of Other Regulatory Genes
Cited by: 3
Author(s): Mengli Wang, Lexuan Gao, Gengyun Li, Chengchuan Zhou, Jinjing Jian, Zhen Xing, Yuguo Wang, Wenju Zhang, Song Zhang, Yonghong Hu, Ji Hyun Yang
Software Mentions: 1
Published: almost 4 years ago
10.3389/fpls.2020.528108
Comparative Genomics of Spatholobus suberectus and Insight Into Flavonoid Biosynthesis
Cited by: 5
Author(s): Shuangshuang Qin, Kunhua Wei, Zhan-Hu Cui, Ying Liang, Mingjie Li, Li Gu, Chuyun Yang, Xiaolei Zhou, Linxuan Li, Wei Xü, Can Liu, Miao Jin, Zhongyi Zhang
Software Mentions: 1
Published: about 4 years ago
10.3389/fpls.2015.00829
Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach
Cited by: 16
Author(s): Wenchuan Xie, Junfeng Huang, Yang Liu, Rao Jianan, Da Luo, Miao He
Software Mentions: 1
Published: about 9 years ago
10.1155/2017/4535710
Metabolic Differences between Dogs of Different Body Sizes
Cited by: 26
Author(s): Rondo Middleton, Sébastien Lacroix, Marie‐Pier Scott‐Boyer, N. Ðorđević, Adam D. Kennedy, Amanda R. Slusky, Jérôme Carayol, Christina Petzinger-Germain, Alison N. Beloshapka, Jim Kaput
Software Mentions: 1
Published: almost 8 years ago
10.1186/s12885-017-3413-3
Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration
Cited by: 24
Author(s): Princy Parsana, Sarah R. Amend, James R. Hernandez, Kenneth J. Pienta, Alexis Battle
Software Mentions: 1
Published: over 7 years ago
10.1155/2021/5531736
Identification of MiR-93-5p Targeted Pathogenic Markers in Acute Myeloid Leukemia through Integrative Bioinformatics Analysis and Clinical Validation
Cited by: 2
Author(s): Jie Wang, Yun Wu, Nazim Uddin, Hao Jian-ping, Rong Chen, Dai-qin Xiong, Nan Ding, Jianhua Yang, Jianhua Wang, Xiaowen Ding
Software Mentions: 1
Published: over 3 years ago
10.3389/fpls.2020.604849
Network Analysis Combining Proteomics and Metabolomics Reveals New Insights Into Early Responses of Eucalyptus grandis During Rust Infection
Cited by: 11
Author(s): Alline Sekiya, Felipe Garbelini Marques, Thiago Falda Leite, Thaís Regiani Cataldi, Fabrício Edgar de Moraes, Ana Lúcia Mendes Pinheiro, Mônica Teresa Veneziano Labate, Carlos Alberto Labate
Software Mentions: 1
Published: almost 4 years ago
10.3389/fpls.2021.705321
A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense
Cited by: 9
Author(s): Zhonghua Tu, Yu-Fang Shen, Shaoying Wen, Huanhuan Liu, Lingmin Wei, Huogen Li
Software Mentions: 1
Published: over 3 years ago
10.3389/fpls.2017.00092
De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissues
Cited by: 19
Author(s): Shi-Fang Wu, Jing Liu, Guoju Chen, Hancai Chen, Bihao Cao, Changming Chen
Software Mentions: 1
Published: almost 8 years ago
10.3389/fpls.2017.01371
Phenotypic and Comparative Transcriptome Analysis of Different Ploidy Plants in Dendrocalamus latiflorus Munro
Cited by: 11
Author(s): Guirong Qiao, Mingying Liu, Kunlin Song, Haiying Li, Haiming Yang, Yafang Yin, Renying Zhuo
Software Mentions: 1
Published: over 7 years ago
10.3389/fpls.2021.668736
Comparison of Transcriptional Response of C3 and C4 Plants to Drought Stress Using Meta-Analysis and Systems Biology Approach
Cited by: 7
Author(s): Ahmad Tahmasebi, Ali Niazi‎
Software Mentions: 1
Published: over 3 years ago
10.3389/fpls.2018.01139
The Galling Truth: Limited Knowledge of Gall-Associated Volatiles in Multitrophic Interactions
Cited by: 13
Author(s): Renée M. Borges
Software Mentions: 1
Published: over 6 years ago
10.1155/2021/4836292
The Heterogeneity of Infiltrating Macrophages in Metastatic Osteosarcoma and Its Correlation with Immunotherapy
Cited by: 7
Author(s): Zhanchao Wang, Huiqiao Wu, Yu Chen, Huajiang Chen, Wen Yuan, Xinwei Wang
Software Mentions: 1
Published: over 3 years ago
10.1186/s12885-021-07817-5
Comprehensive analysis of ceRNA network related to lincRNA in glioblastoma and prediction of clinical prognosis
Cited by: 3
Author(s): Guangdong Liu, Danian Liu, Jingjing Huang, Jianxin Li, Chuang Wang, Shiqiang Ge, Haidong Gong
Software Mentions: 1
Published: almost 4 years ago
10.3389/fpls.2020.00224
Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses
Cited by: 11
Author(s): Lauriane Hennet, Angélique Berger, Noemí Trabanco, Emeline Ricciuti, Jean François Dufayard, Stéphanie Bocs, Denis Bastianelli, Laurent Bonnal, Sandrine Roques, Laura Rossini, Delphine Luquet, Nancy Terrier, David Pot
Software Mentions: 1
Published: over 4 years ago
10.3389/fpls.2020.01256
Transcriptome and Flavonoids Metabolomic Analysis Identifies Regulatory Networks and Hub Genes in Black and White Fruits of Lycium ruthenicum Murray
Cited by: 16
Author(s): Tingting Li, Yunfang Fan, Huan Qin, Guoli Dai, Guo‐Xiu Li, Yanlong Li, Jingjin Wang, Yue Yin, Fang Chen, Xiaoya Qin, Yang Cao, Lin Tang
Software Mentions: 1
Published: over 4 years ago
10.3389/fpls.2016.00497
Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System
Cited by: 67
Author(s): Collin M. Timm, Dale A. Pelletier, Sara Jawdy, Lee E. Gunter, Jeremiah A. Henning, Nancy L. Engle, Jayde A. Aufrecht, Emily Gee, Intawat Nookaew, Zamin K. Yang, Tse Yuan S Lu, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, David J. Weston
Software Mentions: 1
Published: over 8 years ago
10.3389/fpls.2021.679629
Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)
Cited by: 6
Author(s): Yuan‐Jen Chang, Feifei Sun, Shufeng Sun, Lanfen Wang, Jing Wu, Zhendong Zhu
Software Mentions: 1
Published: over 3 years ago
10.1155/2021/5533923
CD8+ T Lymphocyte Coexpression Genes Correlate with Immune Microenvironment and Overall Survival in Breast Cancer
Cited by: 0
Author(s): Jialing Jiang, Yi Zhao
Software Mentions: 1
Published: over 3 years ago
10.3389/fpls.2018.01155
Shedding Light on Chemically Mediated Tri-Trophic Interactions: A 1H-NMR Network Approach to Identify Compound Structural Features and Associated Biological Activity
Cited by: 10
Author(s): Lora A. Richards, Celso José Bruno de Oliveira, Lee A. Dyer, Arran Rumbaugh, Federico Urbano-Muñoz, Ian S. Wallace, Craig D. Dodson, Christopher S. Jeffrey
Software Mentions: 1
Published: over 6 years ago
10.3389/fpls.2017.00398
Spatiotemporal Transcriptome Analysis Provides Insights into Bicolor Tepal Development in Lilium “Tiny Padhye”
Cited by: 39
Author(s): Liang Xu, Panpan Yang, Yue Feng, Hua Xu, Yuwei Cao, Yuchao Tang, Suxia Yuan, Xinyan Li, Jun Ming
Software Mentions: 1
Published: over 7 years ago
10.3389/fpsyt.2019.00706
Integrated Analysis of Brain Transcriptome Reveals Convergent Molecular Pathways in Autism Spectrum Disorder
Cited by: 12
Author(s): Xiaodan Li, Yuncong Zhang, Luxi Wang, Yunqing Lin, Zhaomin Gao, Xiaolei Zhan, Yan Huang, Chongde Sun, Dong Wang, Shuang Liang, Lijie Wu
Software Mentions: 1
Published: about 5 years ago
10.3389/fpsyt.2020.543893
Non-Coding RNAs in Psychiatric Disorders and Suicidal Behavior
Cited by: 38
Author(s): Yuta Yoshino, Yogesh K. Dwivedi
Software Mentions: 1
Published: about 4 years ago
10.3389/fpsyt.2020.580307
A Weighted Gene Co-expression Network Analysis Reveals lncRNA Abnormalities in the Peripheral Blood Associated With Ultra-High-Risk for Psychosis
Cited by: 2
Author(s): Yan Ren, Wei Li, Sha Li, Zhi Li, Jiaying Wang, Hong Yang, Yong Xu
Software Mentions: 1
Published: almost 4 years ago
10.3389/fpsyt.2021.581093
Gene Expression Differences Between Young Adults Based on Trauma History and Post-traumatic Stress Disorder
Cited by: 0
Author(s): Kaitlin Bountress, Vladimir I. Vladimirov, Gowon O. McMichael, Zachary N. Taylor, Gary Hardiman, Dongjun Chung, Zachary W. Adams, Carla Kmett Danielson, Ananda B. Amstadter
Software Mentions: 1
Published: over 3 years ago
10.1186/s12983-019-0336-7
Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes
Cited by: 12
Author(s): Hanbo Zhao, Hui Wang, Tong Liu, Sen Liu, Longru Jin, Xiaobin Huang, Wentao Dai, Keping Sun, Jiang Feng
Software Mentions: 1
Published: about 5 years ago
10.1007/s10142-018-0607-y
Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection
Cited by: 15
Author(s): Jinfeng Zhang, Wenjuan Zhao, Rong Fu, Chunyan Fu, Lingxia Wang, Huainian Liu, Shuangcheng Li, Qi Deng, Shiquan Wang, Jun Zhu, Yueyang Liang, Ping Li, Aiping Zheng
Software Mentions: 1
Published: over 6 years ago
10.1007/s10142-019-00678-z
Global transcriptome analysis uncovers the gene co-expression regulation network and key genes involved in grain development of wheat (Triticum aestivum L.)
Cited by: 12
Author(s): Qing Chi, Lijian Guo, Meng Ma, Lijian Zhang, Hude Mao, Baowei Wu, Xiangli Liu, Ricardo H. Ramírez-González, Cristóbal Uauy, R. Appels, Huixian Zhao
Software Mentions: 1
Published: over 5 years ago
10.1534/g3.112.004788
Systems-Level Analysis of Genome-Wide Association Data
Cited by: 43
Author(s): Charles R. Farber
Software Mentions: 1
Published: almost 12 years ago
10.1534/g3.116.033894
Preservation Analysis of Macrophage Gene Coexpression Between Human and Mouse Identifies PARK2 as a Genetically Controlled Master Regulator of Oxidative Phosphorylation in Humans
Cited by: 12
Author(s): Veronica Codoni, Yuna Blum, Mete Civelek, Carole Proust, Oscar Franzén, Johan Björkegren, Wilfried Le Goff, François Cambien, Aldons J. Lusis, David‐Alexandre Trégouët
Software Mentions: 1
Published: about 8 years ago
10.1186/s12885-021-08066-2
A novel tp53-associated nomogram to predict the overall survival in patients with pancreatic cancer
Cited by: 15
Author(s): Xun Liu, Bobo Chen, Jiahui Chen, Shung Shung Sun
Software Mentions: 1
Published: over 3 years ago
10.1534/g3.117.042408
A Systemic Analysis of Transcriptomic and Epigenomic Data To Reveal Regulation Patterns for Complex Disease
Cited by: 6
Author(s): Chao Xu, Jigang Zhang, Dongdong Lin, Lan Zhang, Hui Shen, Hong‐Wen Deng
Software Mentions: 1
Published: over 7 years ago
10.1534/g3.117.043679
Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat
Cited by: 52
Author(s): Philippa Borrill, Sophie A Harrington, Cristóbal Uauy
Software Mentions: 1
Published: about 7 years ago
10.1534/g3.120.401275
Dissecting the Genetic Architecture of Cystatin C in Diversity Outbred Mice
Cited by: 9
Author(s): Md. Nazmul Huda, Melissa VerHague, Jody Albright, Tangi Smallwood, Timothy A. Bell, Excel Que, Darla R. Miller, Baback Roshanravan, Hooman Allayee, Fernando P Pardo Manuel De Villena, Brian J. Bennett
Software Mentions: 1
Published: over 4 years ago
10.1534/g3.120.401067
NetExtractor: Extracting a Cerebellar Tissue Gene Regulatory Network Using Differentially Expressed High Mutual Information Binary RNA Profiles
Cited by: 2
Author(s): Benafsh Husain, Allison R Hickman, Yuqing Hang, Benjamin T. Shealy, Karan Sapra, Frank Alexander Feltus
Software Mentions: 1
Published: about 4 years ago
10.1007/s10120-018-00911-x
Prognostic and clinicopathological significance of long noncoding RNA CTD-2510F5.4 in gastric cancer
Cited by: 30
Author(s): Zhe Wang, Baoli Qin
Software Mentions: 1
Published: almost 6 years ago
10.1053/j.gastro.2021.01.221
Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction
Cited by: 34
Author(s): Yael Haberman, Najeeha Talat Iqbal, Sudhir Ghandikota, Indika Mallawaarachchi, Tzipi Braun, Phillip Dexheimer, Najeeb Rahman, Rotem Hadar, Kamran Sadiq, Zubair Ahmad, Romana Idress, Junaid Iqbal, Sheraz Ahmed, Aneeta Hotwani, Fayyaz Umrani, Lubaina Ehsan, Greg Medlock, Sana Syed, Chris Moskaluk, Z. Jennie, Anil G. Jegga, Sean R. Moore, Syed Asad Ali, Lee A. Denson
Software Mentions: 1
Published: over 3 years ago
10.3390/genes9070325
Weighted Gene Co-Expression Network Analysis Reveals Dysregulation of Mitochondrial Oxidative Phosphorylation in Eating Disorders
Cited by: 4
Author(s): Liulin Yang, Yun Li, Turki Turki, Huizi Tan, Zhi Wei, Xiao Chang
Software Mentions: 1
Published: over 6 years ago
10.3390/genes9070336
Transcriptome Analysis of Adipose Tissue Indicates That the cAMP Signaling Pathway Affects the Feed Efficiency of Pigs
Cited by: 23
Author(s): Yongming Xu, Xiaolong Qi, Mingyang Hu, Ruiyi Lin, Ye Hou, Zhangxu Wang, Huanhuan Zhou, Yi‐Fang Zhao, Yu Luan, Shuhong Zhao, Xinyun Li
Software Mentions: 1
Published: over 6 years ago
10.3390/genes10040296
Brassica napus Infected with Leptosphaeria maculans
Cited by: 8
Author(s): Jinqi Ma, Lijuan Wei, Lin Ai, Chao Zhang, Wei Sun, Bo Yang, Kun Lu, Jiana Li
Software Mentions: 1
Published: over 5 years ago
10.1186/1471-2105-14-365
Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma
Cited by: 22
Author(s): Chao Wu, Jun Zhu, Xuegong Zhang
Software Mentions: 1
Published: almost 11 years ago
10.1155/2018/8726456
“Omics” Signatures in Peripheral Monocytes from Women with Low BMD Condition
Cited by: 2
Author(s): Bhavna Daswani, M. Ikram Khatkhatay
Software Mentions: 1
Published: almost 7 years ago
10.3390/genes10100798
Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis
Cited by: 17
Author(s): Gabriel Chew, Enrico Petretto
Software Mentions: 1
Published: about 5 years ago
10.3390/genes10110920
RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure
Cited by: 6
Author(s): Weina Zhang, Cunwu Zuo, Zhongjian Chen, Yichen Kang, Shuhao Qin
Software Mentions: 1
Published: about 5 years ago
10.3390/genes11030315
Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets
Cited by: 11
Author(s): Yi Wang, Rui Zhang, Zhenchang Liang, Shaohua Li
Software Mentions: 1
Published: over 4 years ago
10.1186/s12859-017-1590-3
Preservation affinity in consensus modules among stages of HIV-1 progression
Cited by: 14
Author(s): Sk Md Mosaddek Hossain, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 1
Published: over 7 years ago
10.1186/s12859-016-1319-8
SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations
Cited by: 14
Author(s): Casey P. Shannon, Virginia Chen, Mandeep Takhar, Zsuzsanna Hollander, Robert Balshaw, Bruce M. McManus, Scott J. Tebbutt, Don D. Sin, Raymond T. Ng
Software Mentions: 1
Published: about 8 years ago
10.3390/genes11080927
Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica
Cited by: 10
Author(s): Xifang Zong, Yan Qi, Fan Wu, Qian Ma, Jiyu Zhang
Software Mentions: 1
Published: over 4 years ago
10.3390/genes11080942
Advances in Genomics for Drug Development
Cited by: 18
Author(s): Roberto Spreafico, Leah Soriaga, Johannes Grosse, Herbert W. Virgin, Amalio Telenti
Software Mentions: 1
Published: over 4 years ago
10.1186/s12859-018-2433-6
A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
Cited by: 41
Author(s): Gualter Silva Pereira, Antônio Augusto Franco Garcia, Gabriel Rodrigues Alves Margarido
Software Mentions: 1
Published: about 6 years ago
10.3390/genes12010087
K-Module Algorithm: An Additional Step to Improve the Clustering Results of WGCNA Co-Expression Networks
Cited by: 15
Author(s): Jie Hou, Xiufen Ye, Chuanlong Li, Yixing Wang
Software Mentions: 1
Published: almost 4 years ago
10.3390/genes12030449
Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses
Cited by: 7
Author(s): Hansen Fu, Tuo Zeng, Yangyang Zhao, Tingting Luo, Huijie Deng, Chenwei Meng, Luo Jia, Caiyun Wang
Software Mentions: 1
Published: over 3 years ago
10.3390/genes12081254
Pseudogene Transcripts in Head and Neck Cancer: Literature Review and In Silico Analysis
Cited by: 4
Author(s): Juliana Carron, Rafael Della Coletta, Gustavo Jacob Lourenço
Software Mentions: 1
Published: over 3 years ago
10.1186/s12263-019-0639-5
Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile
Cited by: 9
Author(s): Bénédicte L. Tremblay, Frédéric Guénard, Benoı̂t Lamarche, Louis Pérusse, Marie‐Claude Vohl
Software Mentions: 1
Published: over 5 years ago
10.1186/s12263-021-00697-1
Vegetarian diet duration’s influence on women’s gut environment
Cited by: 3
Author(s): Xinqi Deng, Jiangtao Si, Yonglong Qu, Jie Li, Yingkun He, Chun-Guo Wang, Yuping Zhang
Software Mentions: 1
Published: about 3 years ago
10.1186/s12711-016-0217-x
Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare
Cited by: 125
Author(s): Prashanth Suravajhala, Lisette J. A. Kogelman, Haja N. Kadarmideen
Software Mentions: 1
Published: over 8 years ago
10.1186/s12859-016-0952-6
A NMF based approach for integrating multiple data sources to predict HIV-1–human PPIs
Cited by: 17
Author(s): Sumanta Ray, Sanghamitra Bandyopadhyay
Software Mentions: 1
Published: over 8 years ago
10.1016/j.isci.2021.102265
Temporal metabolic and transcriptomic characteristics crossing islets and liver reveal dynamic pathophysiology in diet-induced diabetes
Cited by: 8
Author(s): Rui Gao, Qi Fu, Hemin Jiang, Min Shen, Ruipeng Zhao, Yu Q, Yunqiang He, Kuanfeng Xu, Xinyu Xu, Heng Chen, Quan Zhang, Tao Yang
Software Mentions: 1
Published: over 3 years ago
10.1186/gb-2012-13-10-r97
Aging effects on DNA methylation modules in human brain and blood tissue
Cited by: 527
Author(s): Steve Horvath, Yafeng Zhang, Peter Langfelder, René S. Kahn, Marco P. Boks, Kristel R. van Eijk, Leonard H. van den Berg, Roel A. Ophoff
Software Mentions: 1
Published: almost 13 years ago
10.1186/1471-2105-15-S15-S3
Gene differential coexpression analysis based on biweight correlation and maximum clique
Cited by: 35
Author(s): Chun-Hou Zheng, Yandan Lin, Shengjun Wen, Zhan-Li Sun
Software Mentions: 1
Published: almost 10 years ago
10.1186/s13059-014-0457-4
The small RNA diversity from Medicago truncatularoots under biotic interactions evidences the environmental plasticity of the miRNAome
Cited by: 69
Author(s): Damien Formey, Erika Sallet, Christine Lelandais‐Brière, Cécile Ben, Pilar Bustos-Sanmamed, Andréas Niebel, Florian Frugier, Jean Combier, Frederic Debellé, Caroline Hartmann, Julie Poulain, Fréderick Gavory, Patrick Wincker, Christophe Roux, Laurent Gentzbittel, Jérôme Gouzy, Martín Crespi
Software Mentions: 1
Published: about 10 years ago
10.1186/s13059-014-0525-9
Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis
Cited by: 58
Author(s): Assieh Saadatpour, Guoji Guo, Stuart H. Orkin, Guo Cheng Yuan
Software Mentions: 1
Published: almost 10 years ago
10.1186/s13059-014-0475-2
Big effects of small RNAs on legume root biotic interactions
Cited by: 2
Author(s): Huan Wang, Nam‐Hai Chua
Software Mentions: 1
Published: about 10 years ago
10.1186/s12859-017-1946-8
A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer’s disease progression
Cited by: 19
Author(s): Sumanta Ray, Sk Md Mosaddek Hossain, Lutfunnesa Khatun, Anirban Mukhopadhyay
Software Mentions: 1
Published: almost 7 years ago
10.1186/s13048-020-00710-y
Identification of WTAP-related genes by weighted gene co-expression network analysis in ovarian cancer
Cited by: 11
Author(s): Jing Wang, Jing Xu, Ke Li, Yunke Huang, Yilin Dai, Congjian Xu, Yu Kang
Software Mentions: 1
Published: about 4 years ago
10.1186/s12859-020-03861-3
LC-N2G: a local consistency approach for nutrigenomics data analysis
Cited by: 1
Author(s): Xiangnan Xu, Samantha M. Solon-Biet, Alistair M. Senior, David Raubenheimer, Stephen J. Simpson, Luigi Fontana, Samuel Mueller, Jean Yee Hwa Yang
Software Mentions: 1
Published: about 4 years ago
10.18632/oncotarget.8496
Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs
Cited by: 8
Author(s): Weian Wang, Liang‐Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang
Software Mentions: 1
Published: over 8 years ago
10.1186/gm452
Genes and pathways underlying regional and cell type changes in Alzheimer's disease
Cited by: 209
Author(s): Jeremy A. Miller, Randall L. Woltjer, Jeff M Goodenbour, Steve Horvath, Daniel H. Geschwind
Software Mentions: 1
Published: almost 12 years ago
10.1186/s12859-020-3418-9
Combining feature selection and shape analysis uncovers precise rules for miRNA regulation in Huntington’s disease mice
Cited by: 5
Author(s): Lucile Mégret, Satish S. Nair, Julia Dancourt, Jeff Aaronson, Jim Rosinski, Christian Néri
Software Mentions: 1
Published: over 4 years ago
10.1186/s13073-017-0444-y
brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets
Cited by: 11
Author(s): Saskia Freytag, Rosemary Burgess, Karen Oliver, Melanie Bahlo
Software Mentions: 1
Published: over 7 years ago
10.1186/s13073-017-0466-5
Parkinson’s disease is associated with DNA methylation levels in human blood and saliva
Cited by: 111
Author(s): Yen Chuang, Kimberly C. Paul, Jeff M. Bronstein, Yvette Bordelon, Steve Horvath, Beate Ritz
Software Mentions: 1
Published: about 7 years ago
10.1186/s13073-021-00845-7
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer
Cited by: 36
Author(s): Hryhorii Chereda, Annalen Bleckmann, Kerstin Menck, Júlia Perera-Bel, Philip Stegmaier, Florian Auer, Frank Krämer, Andreas Leha, Tim Beißbarth
Software Mentions: 1
Published: over 3 years ago
10.1186/s12859-019-3089-6
A robustness metric for biological data clustering algorithms
Cited by: 6
Author(s): Yuping Lu, Charles Phillips, Michael A. Langston
Software Mentions: 1
Published: almost 5 years ago
10.1093/gigascience/gix059
The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization
Cited by: 145
Author(s): Xiaodong Du, Guangyi Fan, Yu Jiao, He Zhang, Ximing Guo, Ronglian Huang, Zhe Zheng, Chao Bian, Yuewen Deng, Qingheng Wang, Zhongduo Wang, Xinming Liang, Haiying Liang, Chengcheng Shi, Xiyang Zhao, Fengming Sun, Ruijuan Hao, Jie Bai, Liu Jialiang, Wenbin Chen, Jinlian Liang, Weiqing Liu, Zhe Xu, Qiong Shi, Xun Xu, Guofan Zhang, Xin Liu
Software Mentions: 1
Published: over 7 years ago
10.1186/s12859-018-2193-3
Identification of common coexpression modules based on quantitative network comparison
Cited by: 4
Author(s): Yousang Jo, Sang-Hyun Kim, Doheon Lee
Software Mentions: 1
Published: over 6 years ago
10.1186/s41065-019-0089-5
Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis
Cited by: 10
Author(s): Ying Zhang, Jia‐Long Yao, Hui Feng, Jianfu Jiang, Xiucai Fan, Yunfei Jia, Ran Wang, Chonghuai Liu
Software Mentions: 1
Published: over 5 years ago
10.1186/s41065-019-0083-y
Bladder cancer stage-associated hub genes revealed by WGCNA co-expression network analysis
Cited by: 63
Author(s): Yu Di, Dongshan Chen, Wenxia Yu, Lei Yan
Software Mentions: 1
Published: almost 6 years ago
10.18632/oncotarget.10680
Aberrant transcriptional networks in step-wise neurogenesis of paroxysmal kinesigenic dyskinesia-induced pluripotent stem cells
Cited by: 4
Author(s): Chun Li, Yu Ma, Kunshan Zhang, Junjie Gu, Fan Tang, Shengdi Chen, Li Cao, Siguang Li, Ying Jin
Software Mentions: 1
Published: over 8 years ago
10.18632/oncotarget.11304
Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data
Cited by: 27
Author(s): Jiajun Qiu, Zhaorui Ren, Jingbin Yan
Software Mentions: 1
Published: over 8 years ago
10.1186/s13075-020-02248-2
Identification of novel genes associated with dysregulation of B cells in patients with primary Sjögren’s syndrome
Cited by: 22
Author(s): Jun Inamo, Katsuya Suzuki, Masaru Takeshita, Yoshiaki Kassai, Maiko Takiguchi, Rina Kurisu, Yuumi Okuzono, Shinya Tasaki, Akihiko Yoshimura, Tsutomu Takeuchi
Software Mentions: 1
Published: over 4 years ago
10.1111/jcmm.16703
Transcriptome wide analysis of long non‐coding RNA‐associated ceRNA regulatory circuits in psoriasis
Cited by: 12
Author(s): Jingxia Lin, Xuefei Li, Fangfei Zhang, Lei Zhu, Yongfeng Chen
Software Mentions: 1
Published: over 3 years ago
10.1002/jcla.23680
Constructing a 10‐core genes panel for diagnosis of pediatric sepsis
Cited by: 4
Author(s): Xiaojie Zhou, Yumin Wang, Jie Chen, Jingye Pan
Software Mentions: 1
Published: almost 4 years ago
10.3390/jcm8101719
Reformulating Pro-Oxidant Microglia in Neurodegeneration
Cited by: 45
Author(s): Juan García-Revilla, Isabel María Alonso-Bellido, Miguel Ángel Burguillos, Antonio J. Herrera, Ana M. Espinosa-Oliva, Rocío Ruiz, Luis Cruz-Hernández, Irene García-Domínguez, María Angustias Roca-Ceballos, Marti Santiago, José A. Rodríguez‐Gómez, Manuel Sarmiento Soto, Rocío M. de Pablos, José L. Venero
Software Mentions: 1
Published: about 5 years ago
10.3390/antiox10091385
Characterization of Heat Shock Protein 60 as an Interacting Partner of Superoxide Dismutase 2 in the Silkworm, Bombyx mori, and Its Response to the Molting Hormone, 20-Hydroxyecdysone
Cited by: 2
Author(s): Yosui Nojima
Software Mentions: 1
Published: about 3 years ago
10.1093/jxb/eraa206
Low temperature modulates natural peel degreening in lemon fruit independently of endogenous ethylene
Cited by: 24
Author(s): Oscar W. Mitalo, Takumi Otsuki, Rui Okada, Saeka Obitsu, Kanae Masuda, Yuko Hojo, Takakazu Matsuura, Izumi C. Mori, Daigo Abe, William Olubero Asiche, Takashi Akagi, Yasutaka Kubo, Koichiro Ushijima
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.ppat.1003196
Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross
Cited by: 179
Author(s): Martin T. Ferris, David L. Aylor, Daniel Bottomly, Alan C. Whitmore, Lauri Aicher, Timothy A. Bell, Birgit Bradel-Tretheway, Janine T. Bryan, Ryan J. Buus, Lisa E. Gralinski, Bart L. Haagmans, Leonard McMillan, Darla R. Miller, Elizabeth Rosenzweig, William Valdar, Jeremy Wang, Gary A. Churchill, David W. Threadgill, Shannon K. McWeeney, Michael G. Katze, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise
Software Mentions: 1
Published: over 11 years ago
10.3390/antibiotics10070861
Crosstalks between NOD1 and Histone H2A Contribute to Host Defense against Streptococcus agalactiae Infection in Zebrafish
Cited by: 2
Author(s): Xiaoyu Wu, Fan Xiong, Hong Fang, Jie Zhang, Ming Chang
Software Mentions: 1
Published: over 3 years ago
10.1007/s13238-016-0247-8
Coupled electrophysiological recording and single cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation
Cited by: 34
Author(s): Xiaoying Chen, Kunshan Zhang, Libing Zhou, Xinpei Gao, Junbang Wang, Yinan Yao, Fei He, Yuan Luo, Yongchun Yu, Siguang Li, Liming Cheng, Yi Sun
Software Mentions: 1
Published: almost 9 years ago
10.1007/s13238-018-0559-y
Unbiased transcriptomic analyses reveal distinct effects of immune deficiency in CNS function with and without injury
Cited by: 9
Author(s): Dandan Luo, Weihong Ge, Xiao Hu, Chen Li, Chia Ming Lee, Libing Zhou, Zhourui Wu, Juehua Yu, Shaochong Lin, Jing Yu, Wei Xu, Lei Chen, Chong Zhang, Kun Jiang, Xuding Zhu, Haotian Li, Xinpei Gao, Yanan Geng, Bo Jing, Zhen Wang, Changhong Zheng, Rongrong Zhu, Yan Qiao, Qing Lin, Keqiang Ye, Yi Sun, Liming Cheng
Software Mentions: 1
Published: over 6 years ago
10.3390/ani11061745
Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences
Cited by: 10
Author(s): Ben‐Ben Miao, Su‐Fang Niu, Renxie Wu, Zhen‐Bang Liang, Tang Baogui, Yun Zhai, Xue-Qi Xu
Software Mentions: 1
Published: over 3 years ago
10.1136/rmdopen-2015-000183
Leucocyte subset-specific type 1 interferon signatures in SLE and other immune-mediated diseases
Cited by: 25
Author(s): Shaun Flint, Vojislav Jovanović, Boon Wee Teo, Anselm Mak, Julian Thumboo, Eoín McKinney, James C. Lee, Paul A. MacAry, David M. Kemeny, David Jayne, Kok Yong Fong, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 1
Published: over 8 years ago
10.1098/rsos.172062
Transcriptional analyses provide new insight into the late-stage immune response of a diseased Caribbean coral
Cited by: 28
Author(s): Lauren E. Fuess, Whitney T. Mann, Lea R. Jinks, Vanessa Brinkhuis, Laura D. Mydlarz
Software Mentions: 1
Published: over 6 years ago
10.3390/ani11020314
Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)
Cited by: 8
Author(s): Yongliang Fan, Abdelaziz Adam Idriss Arbab, Huimin Zhang, Yi Yang, Mudasir Nazar, Ziyin Han, Zhangping Yang
Software Mentions: 1
Published: almost 4 years ago
10.1016/j.redox.2021.101933
Network analysis of nitrate-sensitive oral microbiome reveals interactions with cognitive function and cardiovascular health across dietary interventions
Cited by: 20
Author(s): Anni Vanhatalo, Joanna E. L’Heureux, James Kelly, Jamie R. Blackwell, Lee J. Wylie, Jonathan Fulford, Paul G. Winyard, David Wynne Williams, Mark van der Giezen, Andrew M. Jones
Software Mentions: 1
Published: over 3 years ago
10.1186/s12958-021-00785-2
Abnormally increased DNA methylation in chorionic tissue might play an important role in development of ectopic pregnancy
Cited by: 1
Author(s): Chen Wen, Yang Liu, Ruiqing Zhang, Yang Yao, Shuangdi Li, Jiarong Zhang
Software Mentions: 1
Published: over 3 years ago
10.1186/s12931-017-0558-1
Network-based analysis reveals novel gene signatures in peripheral blood of patients with chronic obstructive pulmonary disease
Cited by: 31
Author(s): Ma’en Obeidat, Yunlong Nie, Virginia Chen, Casey P. Shannon, Anand Kumar Andiappan, Bernett Lee, Olaf Rötzschke, Peter J. Castaldi, Craig P. Hersh, Nick Fishbane, Raymond T. Ng, Bruce M. McManus, Bruce E. Miller, Stephen I. Rennard, Peter D. Paré, Don D. Sin
Software Mentions: 1
Published: over 7 years ago
10.1186/s12931-018-0965-y
Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
Cited by: 8
Author(s): Rosa Faner, Jarrett Morrow, Sandra Casas-Recasens, Suzanne M. Cloonan, Guillaume Noell, Alejandra López-Giraldo, Ruth Tal‐Singer, Bruce E. Miller, Edwin K. Silverman, Àlvar Agustí, Craig P. Hersh
Software Mentions: 1
Published: almost 6 years ago
10.1186/s12931-019-1105-z
Multi-level immune response network in mild-moderate Chronic Obstructive Pulmonary Disease (COPD)
Cited by: 33
Author(s): Tamara Cruz, Alejandra López-Giraldo, Guillaume Noell, Sandra Casas-Recasens, Tamara García, Laureano Molins, Manel Juan, Marco A. Fernández, Àlvar Agustí, Rosa Faner
Software Mentions: 1
Published: over 5 years ago
10.1186/s12284-020-00437-w
Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice
Cited by: 16
Author(s): Lanlan Wang, Jingjing Jin, Lihua Li, Shaohong Qu
Software Mentions: 1
Published: about 4 years ago