cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1038/s41438-020-0279-3

Transcriptome profiles reveal that gibberellin-related genes regulate weeping traits in crape myrtle
Cited by: 14
Author(s): Suzhen Li, Tangchun Zheng, Xiaokang Zhuo, Zhuojiao Li, Lulu Li, Ping Li, Like Qiu, Huitang Pan, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-021-00653-5

Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation
Cited by: 8
Author(s): Guizhi Feng, Xiu Ai, Hualin Yi, Wen‐Wu Guo, Juxun Wu
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41438-019-0225-4

Tea plant genomics: achievements, challenges and perspectives
Cited by: 90
Author(s): Enhua Xia, Wei Tong, Qiong Wu, Wei Shu, Jian Zhao, Zhengzhu Zhang, Chaoling Wei, Xiaochun Wan
Software Mentions: 1
Published: over 5 years ago

10.1093/jnci/djx121

Targeting the Myofibroblastic Cancer-Associated Fibroblast Phenotype Through Inhibition of NOX4
Cited by: 125
Author(s): Christopher J. Hanley, Massimiliano Mellone, Kirsty Ford, Steve Thirdborough, Toby Mellows, Steven J. Frampton, David M. Smith, Elena L. Harden, Cédric Szyndralewiez, Marc D. Bullock, Fergus Noble, Karwan A. Moutasim, Emma V. King, Pandurangan Vijayanand, Alex H. Mirnezami, Tim Underwood, Christian Ottensmeier, Gareth J. Thomas
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41438-020-0245-0

A temporal gene expression map of Chrysanthemum leaves infected with Alternaria alternata reveals different stages of defense mechanisms
Cited by: 21
Author(s): Ye Liu, Jingjing Xin, Lina Liu, Aiping Song, Zhiyong Guan, Weimin Fang, Fadi Chen
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-021-00591-2

Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera
Cited by: 28
Author(s): Zhouchen Ye, Jing Yu, Wuping Yan, Junfeng Zhang, Dongmei Yang, Guanglong Yao, Zijin Liu, Yougen Wu, Xilin Hou
Software Mentions: 1
Published: about 4 years ago

10.1038/s41438-021-00490-6

The chromosome-based lavender genome provides new insights into Lamiaceae evolution and terpenoid biosynthesis
Cited by: 33
Author(s): Jingrui Li, Yiming Wang, Yanmei Dong, Wenying Zhang, Di Wang, Hongtong Bai, Kui Li, Hui Li, Lei Shi
Software Mentions: 1
Published: over 4 years ago

10.1002/iid3.414

Bioinformatics analysis of the prognosis and biological significance of VCAN in gastric cancer
Cited by: 11
Author(s): Xiaoyan Huang, Jinjian Liu, Xiong Liu, Yao‐hui Wang, Wei Xiang
Software Mentions: 1
Published: over 4 years ago

10.1002/iid3.436

Genomic analysis of host gene responses to cerebral <i>Plasmodium falciparum</i> malaria
Cited by: 4
Author(s): Ke Li, Wei Han, Hongfeng Zhang, Xiaoxiao Zhao, Yongji Lai, Fangfang Liu
Software Mentions: 1
Published: about 4 years ago

10.1016/j.immuni.2014.01.006

Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation
Cited by: 1,570
Author(s): Jia Xue, Susanne V. Schmidt, Jil Sander, Astrid M. Draffehn, Wolfgang Krebs, Inga Quester, Dominic De Nardo, Trupti D. Gohel, Martina Emde, Lisa Schmidleithner, Hariharasudan Ganesan, Andrea Niño‐Castro, Michael R. Mallmann, Larisa I. Labzin, Heidi Theis, Michael Kraut, Marc Beyer, Eicke Latz, Tom C. Freeman, Thomas Ulas, Joachim L. Schultze
Software Mentions: 1
Published: over 11 years ago

10.1186/s12974-016-0603-x

Pathways and gene networks mediating the regulatory effects of cannabidiol, a nonpsychoactive cannabinoid, in autoimmune T cells
Cited by: 51
Author(s): Ewa Kozela, Ana Juknat, Fuying Gao, Nathali Kaushansky, Giovanni Coppola, Zvi Vogel
Software Mentions: 1
Published: about 9 years ago

10.18632/aging.202996

Circular RNA circitga7 accelerates glioma progression via miR-34a-5p/VEGFA axis
Cited by: 10
Author(s): Ling Qi, Weiyao Wang, Guifang Zhao, Hong Jiang, Yu Zhang, Donghai Zhao, Hong Jin, Haojun Yu, Haidong Xu
Software Mentions: 1
Published: about 4 years ago

10.1001/jamaneurol.2020.5257

Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets
Cited by: 74
Author(s): Demis A. Kia, David Zhang, Sebastian Guelfi, Claudia Manzoni, Leon Hubbard, Regina H. Reynolds, Juan A. Botía, Mina Ryten, Raffaele Ferrari, Patrick A. Lewis, Nigel Williams, Daniah Trabzuni, John Hardy, Nicholas W. Wood, Alastair Noyce, Rauan Kaiyrzhanov, Ben Middlehurst, Manuela Tan, Henry Houlden, Huw Morris, Hélène Plun‐Favreau, Peter Holmans, José Brás, John P. Quinn, Kin Y. Mok, Kerri J. Kinghorn, Kimberley Billingsley, Patrick A. Lewis, Sebastian R Schreglmann, Rita Guerreiro, Ruth C. Lovering, Lea R’Bibo, Mie Rizig, Valentina Escott‐Price, Viorica Chelban, Thomas Foltynie, Alexis Brice, Fabrice Danjou, Suzanne Lesage, Jean‐Christophe Corvol, María Teresa González Martínez, Claudia Schulte, Kathrin Brockmann, Javier Simón‐Sánchez, Peter Heutink, Patrizia Rizzu, Manu Sharma, Thomas Gasser, Aude Nicolas, Mark Cookson, Sara Bandrés‐Ciga, Cornelis Blauwendraat, David W. Craig, Faraz Faghri, J. Raphael Gibbs, Dena G. Hernandez, Kendall Van Keuren‐Jensen, Zhandong Liu, Hampton Leonard, Mike A. Nalls, Laurie Robak, Steven Lubbe, Steven Finkbeiner, Niccolò E. Mencacci, Codrin Lungu, Andrew B. Singleton, Sonja W. Scholz, Xylena Reed, Roy N. Alcalay, Ziv Gan‐Or, Guy A. Rouleau, Lynne Krohn, Jacobus J. van Hilten, Johan Marinus, Astrid Adarmes‐Gómez, Miquel Aguilar, Victoria Álvarez, Victoria Álvarez, Francisco Javier Barrero, Jesús Alberto Bergareche Yarza, Inmaculada Bernal‐Bernal, Marta Blázquez, Marta Bonilla‐Toribio, Juan A. Botía, María Teresa Boungiorno, Dolores Buiza‐Rueda, Ana Cámara, Fátima Carrillo, Mario Carrión‐Claro, Debora Cerdan, Jordi Clarimón, Yaroslau Compta, Mónica Díez-Fairén, Oriol Dols‐Icardo, Jacinto Duarte, Raquel Durán, Francisco Escamilla‐Sevilla, Mario Ezquerra, Cici Feliz, Manel Fernández, Rubén Fernández‐Santiago, Ciara García, Pedro J. García‐Ruiz, Pilar Gómez-Garré, Maria Jose Gómez Heredia, Isabel González Aramburu, Ana Gorostidi Pagola, Janet Hoenicka, Jon Infante, Adriano Jiménez‐Escrig, Jaime Kulisevsky, Miguel A. Labrador‐Espinosa, José López‐Sendón, Adolfo López de Munaín Arregui, Daniel Macías, Irene Martínez Torres, Juan Marín, Marı́a José Martı́, Juan Carlos Martínez‐Castrillo, Carlota Méndez‐del‐Barrio, Manuel Menéndez González, Marina Mata Adolfo Mínguez, Pablo Mir, Elisabet Mondragón Rezola, Esteban Muñoz, Javier Pagonabarraga, Pau Pástor, Francisco Errázquin, María Teresa Periñán, Javier Rúiz-Martínez, Clara Ruz, A Rodríguez, María Sierra, Esther Suárez-Sanmartín, C Tabernero, Juan Pablo Tartari, Cristina Tejera‐Parrado, Eduard Tolosa, Francesc Valldeoriola, Laura Vargas‐González, Lydia Vela, Francisco Vives, Alexander Zimprich, Lasse Pihlstrøm, Mathias Toft, Sulev Kõks, Pille Taba, Sharon Hassin‐Baer, Michael E. Weale, Adaikalavan Ramasamy, Colin Smith, Manuel Sebastian Guelfi, Karishma D’Sa, Paola Forabosco
Software Mentions: 1
Published: over 4 years ago

10.1186/s12974-020-02030-w

Immunological classification of gliomas based on immunogenomic profiling
Cited by: 15
Author(s): Qiushi Feng, Lin Li, Mengyuan Li, Xiaosheng Wang
Software Mentions: 1
Published: over 4 years ago

10.1172/jci.insight.141420

Role of MIF in coordinated expression of hepatic chemokines in patients with alcohol-associated hepatitis
Cited by: 5
Author(s): Kyle L. Poulsen, Xiude Fan, Christopher Kibler, Emily Huang, Xiaoqin Wu, Megan R. McMullen, Lin Leng, Richard Bucala, Meritxell Ventura-Cots, Josepmaria Argemí, R. Bataller, Laura E. Nagy
Software Mentions: 1
Published: about 4 years ago

10.1016/j.jaci.2017.04.005

Phenotypic and genetic aspects of epithelial barrier function in asthmatic patients
Cited by: 66
Author(s): Matthew Loxham, Donna E. Davies
Software Mentions: 1
Published: about 8 years ago

10.1093/jas/skab193

The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies
Cited by: 7
Author(s): Victoria Asselstine, Stephanie Lam, F. Miglior, Luiz F. Brito, Hannah Sweett, Leluo Guan, Sinéad M. Waters, Graham Plastow, Ángela Cánovas
Software Mentions: 1
Published: almost 4 years ago

10.1186/s40104-021-00556-4

Transcriptomic analysis reveals the molecular mechanisms of rumen wall morphological and functional development induced by different solid diet introduction in a lamb model
Cited by: 15
Author(s): Dongdong Sun, Yi Yin, Chang Guo, Lixiang Liu, Shengyong Mao, Weiyun Zhu, Junhua Liu
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-019-6035-0

MiR-190a potentially ameliorates postoperative cognitive dysfunction by regulating Tiam1
Cited by: 18
Author(s): Qiang Liu, Aisheng Hou, Yongyi Zhang, Ying Guo, Jingjing Li, Yinghao Yao, Kaimeng Niu, Hao Li, Yunlong Ma, Jiangbei Cao
Software Mentions: 1
Published: almost 6 years ago

10.1002/jbmr.271

Systems genetics analysis of mouse chondrocyte differentiation
Cited by: 15
Author(s): Jaijam Suwanwela, Charles R. Farber, Bau-lin Haung, Buer Song, Calvin Pan, Karen M. Lyons, Aldons J. Lusis
Software Mentions: 1
Published: over 14 years ago

10.1002/jcsm.12597

Metabolic profiling shows pre‐existing mitochondrial dysfunction contributes to muscle loss in a model of ICU‐acquired weakness
Cited by: 19
Author(s): Paul R. Kemp, Richard Paúl, Aaron C. Hinken, David Neil, Alan J. Russell, Mark Griffiths
Software Mentions: 1
Published: about 5 years ago

10.7150/jca.31234

Expression profile analysis of prognostic long non-coding RNA in adult acute myeloid leukemia by weighted gene co-expression network analysis (WGCNA)
Cited by: 23
Author(s): Cunte Chen, Peipei Wang, Wenjian Mo, Yuping Zhang, Zhou Wei, Tingfen Deng, Ming Zhou, Xiaowei Chen, Shunqing Wang, Caixia Wang
Software Mentions: 1
Published: over 6 years ago

10.7150/jca.38211

Bioinformatics analysis and identification of potential genes related to pathogenesis of cervical intraepithelial neoplasia
Cited by: 9
Author(s): Xue Zhang, Jian Bai, Cheng Yuan, Long Long, Zhewen Zheng, Qingqing Wang, Fengxia Chen, Youwen Zhou
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5978-5

Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development
Cited by: 16
Author(s): Haron Salih, Wenfang Gong, Shoupu He, Xia Wang, Magwanga Richard Odongo, Xinying Du
Software Mentions: 1
Published: almost 6 years ago

10.7150/jca.39645

Identification of Key Gene and Pathways for the Prediction of Peritoneal Metastasis of Gastric Cancer by Co-expression Analysis
Cited by: 11
Author(s): Simeng Zhang, Dan Zang, Changhong Yu, Zhi Li, Bowen Yang, Tianshu Guo, Yunpeng Liu, Xiujuan Qu, Xiaofang Che
Software Mentions: 1
Published: over 5 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: over 8 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 4 years ago

10.1186/s12864-015-1238-5

Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle
Cited by: 10
Author(s): Xiao Ling Zhao, Zhaoyang Liu, Qingxin Liu
Software Mentions: 1
Published: over 10 years ago

10.7150/jca.52156

Identification of Prognosis-related Hub RNA Binding Proteins Function through Regulating Metabolic Processes in Tongue Cancer
Cited by: 6
Author(s): Tao Shen, Meiting Wang, Xiangting Wang
Software Mentions: 1
Published: over 4 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: about 4 years ago

10.18632/aging.202596

Integrative analysis of exosomal microRNA-149-5p in lung adenocarcinoma
Cited by: 7
Author(s): Wen Tian, Yang He, Baosen Zhou
Software Mentions: 1
Published: over 4 years ago

10.7150/jca.51059

A Novel Set of Immune-associated Gene Signature predicts Biochemical Recurrence in Localized Prostate Cancer Patients after Radical Prostatectomy
Cited by: 8
Author(s): Jiaochen Luan, Qijie Zhang, Kai Zhao, Xiang Zhou, Liangyu Yao, Tongtong Zhang, Taidui Zeng, Jun Xia, Ninghong Song
Software Mentions: 1
Published: over 4 years ago

10.18632/aging.202432

Identification of hub genes and key pathways in the emphysema phenotype of COPD
Cited by: 6
Author(s): Qiunan Zuo, Youyu Wang, Deqing Yang, Shujin Guo, Xiaohui Li, Jiajia Dong, Chun Wan, Yongchun Shen, Fuqiang Wen
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-020-07106-8

Transcriptional landscape of the embryonic chicken Müllerian duct
Cited by: 8
Author(s): Zahida Yesmin Roly, Rasoul Godini, Martín Estermann, Andrew T. Major, Roger Pocock, Craig A. Smith
Software Mentions: 1
Published: almost 5 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 4 years ago

10.1186/s12864-018-4756-0

Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis
Cited by: 49
Author(s): Wenjing Tao, Jinlin Chen, Dejie Tan, Jing Yang, Lina Sun, Jing Wei, Matthew A. Conte, Thomas D. Kocher, Deshou Wang
Software Mentions: 1
Published: about 7 years ago

10.1111/jcmm.12447

Pathway mapping and development of disease‐specific biomarkers: protein‐based network biomarkers
Cited by: 23
Author(s): Hao Chen, Zhou Zhu, Ying–Hui Zhu, Jian Wang, Yunqing Mei, Yunfeng Cheng
Software Mentions: 1
Published: over 10 years ago

10.1111/jcmm.14300

Temporal expression and functional analysis of long non‐coding <scp>RNA</scp> s in colorectal cancer initiation
Cited by: 19
Author(s): Lei Dai, Junshu Li, Zhexu Dong, Y Liu, Ye Chen, Na Chen, Lin Cheng, Chao Fang, Huiling Wang, Yanhong Ji, Shuang Chen, Xiaolan Su, Gang Shi, Yi Lin, Shuang Zhang, Yang Yang, Qingcai Meng, Dechao Yu, Wei Huang, Zong‐Guang Zhou, Yuquan Wei, Hongxin Deng
Software Mentions: 1
Published: over 6 years ago

10.1111/jcmm.14422

Long non‐coding RNAs in the spinal cord injury: Novel spotlight
Cited by: 18
Author(s): Zheng Li, Idy H. T. Ho, Xingye Li, Derong Xu, William Ka Kei Wu, Matthew T. V. Chan, Shugang Li, Xiao Dong Liu
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-019-6366-x

Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis
Cited by: 26
Author(s): Zhanru Shao, Pengyan Zhang, Chao Lu, Shaoxuan Li, Zhihang Chen, Xiuliang Wang, Delin Duan
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.14746

Pan‐cancer RNA‐seq data stratifies tumours by some hallmarks of cancer
Cited by: 26
Author(s): Frederick G. Frost, Praveen F. Cherukuri, Samuel Milanovich, Cornelius F. Boerkoel
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.14676

Expression and functional analysis of lncRNAs in the hippocampus of immature rats with status epilepticus
Cited by: 6
Author(s): Jing Gan, Lingyi Huang, Yi Qu, Rong Luo, Qianyun Cai, Fengyan Zhao, Dezhi Mu
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.14828

The CCN1 (CYR61) protein promotes skin growth by enhancing epithelial‐mesenchymal transition during skin expansion
Cited by: 9
Author(s): Yiwen Zhou, Haizhou Li, Xiao Liang, Hengyu Du, Yingjun Suo, Hao Chen, Wenhui Liu, Ran Duan, Xiaolu Huang, Qingfeng Li
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.14852

Identification of dynamic signatures associated with smoking‐related squamous cell lung cancer and chronic obstructive pulmonary disease
Cited by: 10
Author(s): Xiaoru Sun, Jingzhe Shang, Aiping Wu, Jingyan Xia, Feng Xu
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.14976

Transcriptome analyses reveal molecular mechanisms underlying phenotypic differences among transcriptional subtypes of glioblastoma
Cited by: 20
Author(s): Yuan‐Bo Pan, Siqi Wang, Biao Yang, Zhenqi Jiang, Cameron Lenahan, Jianhua Wang, Jianmin Zhang, Anwen Shao
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.15145

Gene signatures based on therapy responsiveness provide guidance for combined radiotherapy and chemotherapy for lower grade glioma
Cited by: 10
Author(s): Guangqi Li, Yufei Jiang, Xintong Lyu, Yiru Cai, Miao Zhang, Qiao Qiao
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-730

Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides
Cited by: 18
Author(s): Lourdes Peña‐Castillo, Ryan G. Mercer, Anastasia Gurinovich, Stephen Callister, Aaron Wright, Alexander B. Westbye, J. Thomas Beatty, Andrew S. Lang
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-020-07352-w

Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
Cited by: 8
Author(s): Rongfa Chen, Yanting Fan, Huiwen Zhou, Shanping Mo, Zhongfeng Zhou, Haifeng Yan, Ting Luo, Xing Huang, Mengling Weng, Prakash Lakshmanan, Yang‐Rui Li, Lihang Qiu, Jianming Wu
Software Mentions: 1
Published: over 4 years ago

10.1111/jcmm.15561

Systematic analysis on multiple Gene Expression Omnibus data sets reveals fierce immune response in hepatitis B virus‐related acute liver failure
Cited by: 3
Author(s): Huadi Chen, Wenting Zhao, Yixi Zhang, Yiwen Guo, Weixin Luo, Xiaobo Wang, Yu Nie, Maodong Ye, Changjun Huang, Dongping Wang, Maogen Chen, Xiaoshun He, Qiang Zhao
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-15-33

Sex differences in the human peripheral blood transcriptome
Cited by: 124
Author(s): Ritsert C. Jansen, Sandra Batista, Andrew I. Brooks, Jay A. Tischfield, Gonneke Willemsen, Gerard van Grootheest, Jouke Jan Hottenga, Yuri Milaneschi, Hamdi Mbarek, Vered Madar, Wouter J. Peyrot, Jacqueline M. Vink, C. L. Verweij, Eco J. C. de Geus, Johannes H. Smit, Fred A. Wright, Patrick F. Sullivan, Dorret I. Boomsma, Brenda W. J. H. Penninx
Software Mentions: 1
Published: over 11 years ago

10.1111/jcmm.15690

Landscape of associations between long non‐coding RNAs and infiltrating immune cells in liver hepatocellular carcinoma
Cited by: 7
Author(s): Li Li, Xiaowei Song, Yanju Lv, Qi Jiang, Chengjuan Fan, Dayong Huang
Software Mentions: 1
Published: almost 5 years ago

10.1111/jcmm.15923

GNG5 is an unfavourable independent prognostic indicator of gliomas
Cited by: 11
Author(s): Biao Yang, Zhaolong Han, Wen‐Juan Wang, Yupo Ma, Sheng‐Hua Chu
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-021-07839-0

Trehalose in pine wood nematode participates in DJ3 formation and confers resistance to low-temperature stress
Cited by: 5
Author(s): Qiaoli Chen, Ruizhi Zhang, Danlei Li, Feng Wang, Shengwei Jiang, Jianan Wang
Software Mentions: 1
Published: about 4 years ago

10.1177/1759091419854627

Identification of the Molecular Events Involved in the Development of Prefrontal Cortex Through the Analysis of RNA-Seq Data From BrainSpan
Cited by: 2
Author(s): Hadi Najafi, Mohadeseh Naseri, Javad Zahiri, Mehdi Totonchi, Shahana Majid
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-5549-9

A modular analysis of microglia gene expression, insights into the aged phenotype
Cited by: 22
Author(s): Christine E. Cho, Sagar S. Damle, Edward V. Wancewicz, Swagatam Mukhopadhyay, Christopher E. Hart, Curt Mazur, Eric E. Swayze, Fredrik Kamme
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-1535-z

Poplar trees reconfigure the transcriptome and metabolome in response to drought in a genotype- and time-of-day-dependent manner
Cited by: 52
Author(s): Erin T. Hamanishi, Genoa L H Barchet, Rébecca Dauwe, Shawn D. Mansfield, Malcolm M. Campbell
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-021-07585-3

Aging features of the migratory locust at physiological and transcriptional levels
Cited by: 5
Author(s): Siyuan Guo, Pengcheng Yang, Bo Liang, Feng Zhou, Hou Li, Le Kang, Xianhui Wang
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-019-5708-z

Developmental transcriptomics of Chinese cordyceps reveals gene regulatory network and expression profiles of sexual development-related genes
Cited by: 19
Author(s): Xiao Li, Fen Wang, Qing Liu, Quanping Li, Zhengming Qian, Xiaoling Zhang, Kuan Li, Wenjia Li, Caihong Dong
Software Mentions: 1
Published: about 6 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: about 4 years ago

10.1186/s12864-020-07193-7

Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance
Cited by: 8
Author(s): Hui Xia, Xiaoyan Ma, Kai Xu, Lei Wang, Hongyan Liu, Liang Chen, Lijun Luo
Software Mentions: 1
Published: over 4 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: over 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: almost 6 years ago

10.1186/s12864-016-3176-2

Large-scale gene co-expression network as a source of functional annotation for cattle genes
Cited by: 16
Author(s): Hamid Beiki, A. Nejati‐Javaremi, A. Pakdel, Ali Masoudi‐Nejad, Zhi-Liang Hu, James M. Reecy
Software Mentions: 1
Published: over 8 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: over 7 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: about 5 years ago

10.18632/aging.102971

Prognostic values of immune scores and immune microenvironment-related genes for hepatocellular carcinoma
Cited by: 22
Author(s): Penglei Ge, Shifang Li, Weiwei Wang, Chunbo Li, Yu-Bin Fu, Zhengkai Feng, Lin Li, Gong Zhang, Zhiqiang Gao, Xiaowei Dang, Yang Wu
Software Mentions: 1
Published: over 5 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 12 years ago

10.1186/1471-2164-12-S3-S3

Liverome: a curated database of liver cancer-related gene signatures with self-contained context information
Cited by: 40
Author(s): Langho Lee, Kai Wang, Gang Li, Zhi Xie, Yuli Wang, Jiangchun Xu, Shaoxian Sun, David Pocalyko, Jong Bhak, Chulhong Kim, Kee-Ho Lee, Ye Jin Jang, Young Il Yeom, Hyang Sook Yoo, Seungwoo Hwang
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-018-5104-0

Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.)
Cited by: 13
Author(s): Guangyan Feng, Lei Xu, Jianping Wang, Gang Nie, B. Shaun Bushman, Wengang Xie, Haidong Yan, Zhongfu Yang, Hao Guan, Linkai Huang, Xinquan Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-020-07250-1

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line
Cited by: 5
Author(s): Meng Zhang, Ji Liu, Qiang Ma, Yuan Qin, Hantao Wang, Pengyun Chen, Liang Ma, Xiaokang Fu, Longfu Zhu, Hengling Wei, Shuang Yu
Software Mentions: 1
Published: over 4 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 4 years ago

10.1186/s12864-019-5424-8

Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening
Cited by: 36
Author(s): Qiuyun Zhang, Chao Feng, Wenhui Li, Zehui Qu, Ming Zeng, Wanpeng Xi
Software Mentions: 1
Published: over 6 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: over 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: about 7 years ago

10.1186/s12864-019-5773-3

A deficiency in SUMOylation activity disrupts multiple pathways leading to neural tube and heart defects in Xenopus embryos
Cited by: 11
Author(s): Michelle M. Bertke, Kyle M. Dubiak, Laura Cronin, Erliang Zeng, Paul W. Huber
Software Mentions: 1
Published: about 6 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: about 9 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: about 7 years ago

10.1186/s12864-016-3201-5

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass
Cited by: 14
Author(s): Taylor P. Frazier, Nathan A. Palmer, Fuliang Xie, Christian M. Tobias, Teresa Donze-Reiner, Aureliano Bombarely, Kevin L. Childs, Shengqiang Shu, Jerry Jenkins, Jeremy Schmutz, Baohong Zhang, Gautam Sarath, Bingyu Zhao
Software Mentions: 1
Published: over 8 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: about 4 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: about 4 years ago

10.1186/1471-2164-11-589

Is human blood a good surrogate for brain tissue in transcriptional studies?
Cited by: 101
Author(s): Chaochao Cai, Peter Langfelder, Tova Fuller, Michael C. Oldham, Rui Luo, Leonard H van den Berg, Roel A. Ophoff, Steve Horvath
Software Mentions: 1
Published: almost 15 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 8 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: over 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: about 6 years ago

10.1186/1471-2164-10-327

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells
Cited by: 189
Author(s): Mike J. Mason, Guoping Fan, Kathrin Plath, Qing Zhou, Steve Horvath
Software Mentions: 1
Published: about 16 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: over 4 years ago

10.1186/s12284-020-00439-8

Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice
Cited by: 2
Author(s): Dagang Tian, Zaijie Chen, Yan Lin, Ziqiang Chen, Zonghua Wang, Wang Feng
Software Mentions: 1
Published: over 4 years ago

10.1186/s12863-015-0311-z

Gene expression in large pedigrees: analytic approaches
Cited by: 5
Author(s): Rita M. Cantor, Heather J. Cordell
Software Mentions: 1
Published: over 9 years ago

10.1186/s12863-018-0648-1

Epigenetics, heritability and longitudinal analysis
Cited by: 5
Author(s): Haakon E. Nustad, Marcio Almeida, Angelo J. Canty, Marissa LeBlanc, Christian M. Page, Phillip E. Melton
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12876-017-0637-2

miR-363-5p as potential prognostic marker for hepatocellular carcinoma indicated by weighted co-expression network analysis of miRNAs and mRNA
Cited by: 18
Author(s): Jun Zhang, Jia Fan, Chongming Zhou, Yanyu Qi
Software Mentions: 1
Published: about 8 years ago

10.1186/s12862-017-1036-6

Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication
Cited by: 12
Author(s): Yun-Mei Wang, Haibo Xu, Mingshan Wang, Newton O. Otecko, Lingqun Ye, Dongdong Wu, Yaping Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41597-021-00828-8

Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera
Cited by: 22
Author(s): Hui Li, Xingyu Yang, Yue Zhang, Zhiyan Gao, Yuting Liang, Jin‐Ming Chen, Tao Shi
Software Mentions: 1
Published: over 4 years ago

10.1038/srep12298

Network analysis of immunotherapy-induced regressing tumours identifies novel synergistic drug combinations
Cited by: 55
Author(s): W. Joost Lesterhuis, Catherine Rinaldi, Anya C. Jones, Esdy N. Rozali, Ian M. Dick, Andrea Khong, Louis Boon, Bruce Robinson, Anna K. Nowak, Anthony Bosco, Richard Lake
Software Mentions: 1
Published: about 10 years ago

10.1038/srep13248

Derivation of a fifteen gene prognostic panel for six cancers
Cited by: 22
Author(s): Mamata F. Khirade, Girdhari Lal, Sharmila A. Bapat
Software Mentions: 1
Published: almost 10 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: almost 5 years ago

10.1038/srep17494

Honey bee microRNAs respond to infection by the microsporidian parasite Nosema ceranae
Cited by: 15
Author(s): Qiang Huang, Yanping Chen, Rui Wu Wang, Ryan S. Schwarz, Jay D. Evans
Software Mentions: 1
Published: over 9 years ago

10.1038/srep18045

Proteome Analysis of Renoprotection Mediated by a Novel Cyclic Helix B Peptide in Acute Kidney Injury
Cited by: 18
Author(s): Cheng Yang, Junjun Liu, Li Long, Man Hu, Ya‐Qiu Long, Xiaohui Liu, Tongyu Zhu, Xiao Huang, Shouliang Zhao, Shangfeng Liu, Ruiming Rong
Software Mentions: 1
Published: over 9 years ago

10.1038/srep19430

DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders
Cited by: 66
Author(s): Fan Wang, Hao Xu, Hongyu Zhao, Joel Gelernter, Huiping Zhang
Software Mentions: 1
Published: over 9 years ago

10.1038/srep25261

Elucidation of molecular and functional heterogeneity through differential expression network analyses of discrete tumor subsets
Cited by: 6
Author(s): Rutika R. Naik, Nilesh Gardi, Sharmila A. Bapat
Software Mentions: 1
Published: about 9 years ago

10.1038/srep26396

The simple neuroendocrine-immune regulatory network in oyster Crassostrea gigas mediates complex functions
Cited by: 38
Author(s): Zhaoqun Liu, Lingling Wang, Zhi Zhou, Ying Sun, Mengqiang Wang, Hao Wang, Zujun Hou, Dahai Gao, Qiang Gao, Linsheng Song
Software Mentions: 1
Published: about 9 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479