cran: WGCNA | Projects | Ecosyste.ms: Papers

10.3389/fnins.2015.00176

Epigenetic modulation of brain gene networks for cocaine and alcohol abuse
Cited by: 47
Author(s): Sean P. Farris, R. Adron Harris, Igor Ponomarev
Software Mentions: 1
Published: over 9 years ago

The Predicted Key Molecules, Functions, and Pathways That Bridge Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD)
Cited by: 42
Author(s): Tao Ye, Yoo Min Han, Lujiao Yu, Qi Wang, Sean X. Leng, Haiyan Zhang
Software Mentions: 1
Published: over 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/fneur.2020.578972

Phenotypic Subtyping and Re-analyses of Existing Transcriptomic Data from Autistic Probands in Simplex Families Reveal Differentially Expressed and ASD Trait-Associated Genes
Cited by: 4
Author(s): Valerie W. Hu, Chongfeng Bi
Software Mentions: 1
Published: about 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/fnmol.2019.00197

Cross-Species Co-analysis of Prefrontal Cortex Chronic Ethanol Transcriptome Responses in Mice and Monkeys
Cited by: 21
Author(s): James W. Bogenpohl, Maren L. Smith, Sean P. Farris, Catherine I. Dumur, Marcelo F. López, Howard C. Becker, Kathleen A. Grant, Michael F. Miles
Software Mentions: 1
Published: over 5 years ago

10.3389/fnmol.2015.00042

Dynamical properties of gene regulatory networks involved in long-term potentiation
Cited by: 4
Author(s): Gonzalo S. Nido, Margaret M. Ryan, Ľubica Beňušková, Joanna M. Williams
Software Mentions: 1
Published: over 9 years ago

10.3389/fnmol.2017.00399

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington’s Disease
Cited by: 10
Author(s): Arlin Keo, N. Ahmad Aziz, Oleh Dzyubachyk, Jeroen van der Grond, Willeke M. C. van Roon‐Mom, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Mahfouz
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12920-021-01012-y

Multivariate transcriptome analysis identifies networks and key drivers of chronic lymphocytic leukemia relapse risk and patient survival
Cited by: 2
Author(s): Tiara Griffen, Eric B. Dammer, Courtney D. Dill, Kaylin Carey, Corey Young, Sha’Kayla Nunez, Adaugo Q. Ohandjo, Steven M. Kornblau, James W. Lillard
Software Mentions: 1
Published: over 3 years ago

10.3389/fnmol.2018.00102

Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses
Cited by: 10
Author(s): Jianxun Luo, Pei Xu, Peijian Cao, Hongjian Wan, Xiaonan Lv, Shengchun Xu, Gangjun Wang, Melloni N. Cook, Byron C. Jones, Lu Lu, Xusheng Wang
Software Mentions: 1
Published: over 6 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

10.1186/s12920-021-00890-6

Identification of monocyte-associated genes as predictive biomarkers of heart failure after acute myocardial infarction
Cited by: 11
Author(s): Qixin Chen, Qijin Yin, Junxian Song, Chuan‐Fen Liu, Chang Seop Hong, Sufang Li
Software Mentions: 1
Published: almost 4 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

10.3389/fnmol.2016.00139

mRNA Transcriptomics of Galectins Unveils Heterogeneous Organization in Mouse and Human Brain
Cited by: 9
Author(s): Sebastian John, Rashmi Mishra
Software Mentions: 1
Published: almost 8 years ago

10.3389/fmolb.2021.602227

Risk Signature Related to Immunotherapy Reaction of Hepatocellular Carcinoma Based on the Immune-Related Genes Associated With CD8+ T Cell Infiltration
Cited by: 3
Author(s): Yiping Zou, Zhihong Chen, Hongwei Han, Su Ruan, Lina Jin, Yuanpeng Zhang, Zhengrong Chen, Zuyi Ma, Qi Lou, Ning Shi, Haosheng Jin
Software Mentions: 1
Published: over 3 years ago

10.3389/fmolb.2019.00139

Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data
Cited by: 14
Author(s): Edgardo Galán-Vásquez, Ernesto Pérez‐Rueda
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12920-019-0608-2

A new method for mining information of co-expression network based on multi-cancers integrated data
Cited by: 4
Author(s): Mi-Xiao Hou, Ying-Lian Gao, Jin-Xing Liu, Junliang Shang, Rong Zhu, Shasha Yuan
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmolb.2021.625470

Exploration of a Robust and Prognostic Immune Related Gene Signature for Cervical Squamous Cell Carcinoma
Cited by: 7
Author(s): Zhihua Zuo, Junjun Xiong, Chuyi Zeng, Yao Jiang, Kang Xiong, Hualin Tao, Yongcan Guo
Software Mentions: 1
Published: over 3 years ago

10.1186/1755-8794-4-5

Incorporating higher-order representative features improves prediction in network-based cancer prognosis analysis
Cited by: 18
Author(s): Shuangge Ma, Michael R. Kosorok, Jian Huang, Ying Dai
Software Mentions: 1
Published: almost 14 years ago

10.3389/fmolb.2020.598599

Identification and Immunocorrelation of Prognosis-Related Genes Associated With Development of Muscle-Invasive Bladder Cancer
Cited by: 4
Author(s): Jingxian Li, Yantao Lou, Shuai Li, Fei Sheng, Shuaibing Liu, Eugenie Du, Zhihong Zhang
Software Mentions: 1
Published: almost 4 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/fmolb.2021.655361

Network-Based Expression Analyses and Experimental Verifications Reveal the Involvement of STUB1 in Acute Kidney Injury
Cited by: 7
Author(s): Yanting Shi, Genwen Chen, Jie Teng
Software Mentions: 1
Published: over 3 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/fmolb.2021.682471

Hub Long Noncoding RNAs with m6A Modification for Signatures and Prognostic Values in Kidney Renal Clear Cell Carcinoma
Cited by: 10
Author(s): Gaoteng Lin, Huadong Wang, Yuqi Wu, Keruo Wang, Gang Li
Software Mentions: 1
Published: over 3 years ago

10.1186/s12920-016-0171-z

Differential gene network analysis for the identification of asthma-associated therapeutic targets in allergen-specific T-helper memory responses
Cited by: 30
Author(s): Niamh M. Troy, Elysia M. Hollams, Patrick G. Holt, Anthony Bosco
Software Mentions: 1
Published: over 8 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/fmicb.2016.01155

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds
Cited by: 33
Author(s): Haifeng Geng, Mary Bao Tran-Gyamfi, Todd W. Lane, Kenneth L. Sale, Eizadora T. Yu
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2019.00352

Alterations of the Mice Gut Microbiome via Schistosoma japonicum Ova-Induced Granuloma
Cited by: 29
Author(s): Yanqing Zhao, Shuxu Yang, Bei Li, Wei Li, Jue Wang, Zongyun Chen, Jing Yang, Huabing Tan, Jian Li
Software Mentions: 1
Published: over 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

10.1128/mSystems.00499-20

Dietary Intervention Reverses Fatty Liver and Altered Gut Microbiota during Early-Life Undernutrition
Cited by: 3
Author(s): Kylynda C. Bauer, Kelsey E. Huus, Eric Brown, Tahereh Bozorgmehr, Charisse Petersen, Mihai Cirstea, Sarah E. Woodward, John J. McCoy, Jeong Ki Hun, Reinald Pamplona, Victòria Ayala, B. Brett Finlay
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

10.3389/fmicb.2015.00487

Identification of a transporter Slr0982 involved in ethanol tolerance in cyanobacterium Synechocystis sp. PCC 6803
Cited by: 25
Author(s): Yanan Zhang, Xiangfeng Niu, Mengliang Shi, Guangsheng Pei, Xiaoqing Zhang, Lei Chen, Weiwen Zhang
Software Mentions: 1
Published: over 9 years ago

10.3389/fmed.2020.584747

Integrating Tumor Stroma Biomarkers With Clinical Indicators for Colon Cancer Survival Stratification
Cited by: 4
Author(s): Yong Chen, Wenlong Wang, Bo Jiang, Lei Yao, Fada Xia, Xinying Li
Software Mentions: 1
Published: almost 4 years ago

10.3389/fimmu.2020.592084

Therapeutic Potential of Triptolide as an Anti-Inflammatory Agent in Dextran Sulfate Sodium-Induced Murine Experimental Colitis
Cited by: 31
Author(s): Bufu Tang, Jinyu Zhu, Baohui Zhang, Fazong Wu, Yajie Wang, Qiaoyou Weng, Shiji Fang, Zheng Lu, Yang Yang, Rongfang Qiu, Minjiang Chen, Min Xu, Zhongwei Zhao, Jiansong Ji
Software Mentions: 1
Published: about 4 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

10.3389/fimmu.2020.01070

Human Monocyte Subset Distinctions and Function: Insights From Gene Expression Analysis
Cited by: 48
Author(s): Sarah Cormican, Matthew D. Griffin
Software Mentions: 1
Published: over 4 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

10.3389/fimmu.2020.603337

Identifying Potential Candidate Hub Genes and Functionally Enriched Pathways in the Immune Responses to Quadrivalent Inactivated Influenza Vaccines in the Elderly Through Co-Expression Network Analysis
Cited by: 1
Author(s): Jing Yang, Jiayou Zhang, Renfeng Fan, Wei Zhao, Han Tian, Kai Duan, Xinguo Li, Peiyu Zeng, Jinglong Deng, Jikai Zhang, Xiaoming Yang
Software Mentions: 1
Published: almost 4 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

10.3389/fimmu.2020.01281

Identification of Immune-Related Genes Contributing to the Development of Glioblastoma Using Weighted Gene Co-expression Network Analysis
Cited by: 30
Author(s): Yahui Kong, Zichao Feng, Yulin Zhang, Xiaofei Liu, Yuan Ma, Zhimin Zhao, Bin Huang, An-Jing Chen, Di Zhang, Frits Thorsen, Jian Wang, Ning Yang, Xingang Li
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2021.730300

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

10.1186/s40246-021-00350-3

Identification of subgroups along the glycolysis-cholesterol synthesis axis and the development of an associated prognostic risk model
Cited by: 4
Author(s): Enchong Zhang, Yijing Chen, Shurui Bao, Xueying Hou, Jing Hu, Oscar Yong Nan Mu, Yi Song, Liping Shan
Software Mentions: 1
Published: over 3 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

10.3389/fimmu.2020.00616

A Signaling Pathway to Mediate the Combined Immunomodulation of Acetylcholine and Enkephalin in Oyster Crassostrea gigas
Cited by: 3
Author(s): Zhaoqun Liu, Zhi Zhou, Lingling Wang, Yukun Zhang, Yanan Zong, Yan Zheng, Meijia Li, Weilin Wang, Linsheng Song
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2020.01194

Expression of S100A Alarmins in Cord Blood Monocytes Is Highly Associated With Chorioamnionitis and Fetal Inflammation in Preterm Infants
Cited by: 12
Author(s): Veronika Golubinskaya, Henri Puttonen, Ing‐Marie Fyhr, Halfdan Rydbeck, Ann Hellström, Bo Jacobsson, Holger Nilsson, Carina Mallard, Karin Sävman
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2021.739514

Circulating Metabolomic Signature in Generalized Pustular Psoriasis Blunts Monocyte Hyperinflammation by Triggering Amino Acid Response
Cited by: 7
Author(s): Na Yu, Peng Chen, Wenjuan Chen, Zengqi Sun, Jianfeng Zheng, Shujie Zhang, Yangfeng Ding, Yujun Shi
Software Mentions: 1
Published: about 3 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

10.3389/fimmu.2019.00402

Transcriptional Analysis of the Human IgE-Expressing Plasma Cell Differentiation Pathway
Cited by: 10
Author(s): Faruk Ramadani, H. J. M. Bowen, Hannah Gould, David Fear
Software Mentions: 1
Published: over 5 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

10.3389/fimmu.2019.01459

A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis
Cited by: 22
Author(s): Adrià Aterido, Juan D. Cañete, Jesús Tornero, Francisco J. Blanco, Benjamín Fernández‐Gutiérrez, Carolina Pérez, Mercedes Alperi-López, A Olivé, Hèctor Corominas, Víctor M. Martínez‐Taboada, Inmaculada Fernández González, Antonio Fernández‐Nebro, Alba Erra, María López-Lasanta, Mireia López-Corbeto, Núria Palau, Sara Marsal, Antonio Julià
Software Mentions: 1
Published: over 5 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

10.3389/fimmu.2020.01795

Multiple Processes May Involve in the IgG4-RD Pathogenesis: An Integrative Study via Proteomic and Transcriptomic Analysis
Cited by: 8
Author(s): Shaozhe Cai, Yu Chen, Shaochong Lin, Cong Ye, Fang Zheng, Lingli Dong
Software Mentions: 1
Published: over 4 years ago

10.1186/s12920-018-0407-1

Identification of glioblastoma gene prognosis modules based on weighted gene co-expression network analysis
Cited by: 32
Author(s): Pengfei Xu, Jian Yang, Junhui Liu, Yang Xue, Jianming Liao, Fanen Yuan, Yang Xu, Baohui Liu
Software Mentions: 1
Published: about 6 years ago

10.1186/s40246-016-0071-5

Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia
Cited by: 33
Author(s): Garima Kushwaha, Mikhail G. Dozmorov, Jonathan D. Wren, Jing Qiu, Huidong Shi, Dong Xu
Software Mentions: 1
Published: over 8 years ago

10.1093/hmg/ddv166

Spatiotemporal dynamics of the postnatal developing primate brain transcriptome
Cited by: 32
Author(s): Trygve E. Bakken, Jeremy A. Miller, Rui Luo, Amy Bernard, Jeffrey Bennett, Chang Kyu Lee, Darren Bertagnolli, Neelroop N. Parikshak, Kimberly A. Smith, Susan M. Sunkin, David G. Amaral, Daniel H. Geschwind, Ed Lein
Software Mentions: 1
Published: over 9 years ago

10.3389/fimmu.2021.702733

Transcriptome Analysis of CCR9+ T Helper Cells From Primary Sjögren’s Syndrome Patients Identifies CCL5 as a Novel Effector Molecule
Cited by: 8
Author(s): Anneline C. Hinrichs, Sofie L M Blokland, Ana P Lopes, Catharina G K Wichers, Aike A. Kruize, Aridaman Pandit, Timothy R D J Radstake, Joël A G van Roon
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2021.624614

Predicted Disease-Specific Immune Infiltration Patterns Decode the Potential Mechanisms of Long Non-Coding RNAs in Primary Sjogren’s Syndrome
Cited by: 6
Author(s): Caiqi Cheng, Jun Zhou, Ruiying Chen, Yo Shibata, Ryouichi Tanaka, Jun Wang, Jiaming Zhang
Software Mentions: 1
Published: over 3 years ago

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 4 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

10.3389/fimmu.2021.659193

SDF4 Is a Prognostic Factor for 28-Days Mortality in Patients With Sepsis via Negatively Regulating ER Stress
Cited by: 10
Author(s): Tingting Zhu, Qun Su, Cuili Wang, Lingling Shen, Hongjun Chen, Shi Feng, Xing Peng, Siyu Chen, Yucheng Wang, Hong Jiang, Jianghua Chen
Software Mentions: 1
Published: over 3 years ago

10.1186/s12920-020-0702-5

Gene co-expression networks are associated with obesity-related traits in kidney transplant recipients
Cited by: 4
Author(s): Rosario B. Jaime-Lara, Abhrarup Roy, Yupeng Wang, Ansley Grimes Stanfill, Ann K. Cashion, Paule V. Joseph
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2020.00857

Identification of Gene Signatures for Diagnosis and Prognosis of Hepatocellular Carcinomas Patients at Early Stage
Cited by: 14
Author(s): Xiaoning Gan, Yue Luo, Guanqi Dai, Junhao Lin, Xinhui Liu, Zhang Xiang-qun, Aimin Li
Software Mentions: 1
Published: over 4 years ago

10.1093/hmg/ddaa132

Serum biomarkers associated with baseline clinical severity in young steroid-naïve Duchenne muscular dystrophy boys
Cited by: 14
Author(s): Utkarsh J. Dang, Michael Ziemba, Paula R. Clemens, Yetrib Hathout, Laurie S. Conklin, Cinrg Vamorolone, Investigators, Eric P. Hoffman
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2020.00981

Identification of KIAA0513 and Other Hub Genes Associated With Alzheimer Disease Using Weighted Gene Coexpression Network Analysis
Cited by: 20
Author(s): Min Zhu, Longfei Jia, Fangyu Li, Jianping Jia
Software Mentions: 1
Published: about 4 years ago

10.1186/s40478-015-0203-5

Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis
Cited by: 436
Author(s): Inge R. Holtman, Divya Raj, Jeremy A. Miller, W. Schaafsma, Zhuoran Yin, Nieske Brouwer, Paul D. Wes, Thomas Møller, Marie Orre, Willem Kamphuis, Elly M. Hol, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 1
Published: over 9 years ago

10.1161/HYPERTENSIONAHA.118.12409

<i>Camk2n1</i> Is a Negative Regulator of Blood Pressure, Left Ventricular Mass, Insulin Sensitivity, and Promotes Adiposity
Cited by: 13
Author(s): Neza Alfazema, Marjorie Barrier, Sophie Marion de Procé, Robert Menzies, Roderick Nicholas Carter, Kevin Stewart, Ana García Díaz, Ben Moyon, Zoë Webster, Christopher Bellamy, Mark J. Arends, Roland H Stimson, Nicholas M. Morton, Timothy J. Aitman, Philip Coan
Software Mentions: 1
Published: about 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: about 3 years ago

10.1186/s12920-015-0098-9

Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia
Cited by: 39
Author(s): Mariana Maschietto, Ana Carolina Tahira, Renato Puga, Leandro Lima, Daniel Mariani, Bruna Paulsen, Paulo Belmonte-de-Abreu, Henrique Cursino Vieira, Ana Cristina Victorino Krepischi, Dirce Maria Carraro, Joana Almeida Palha, Stevens K. Rehen, Helena Brentani
Software Mentions: 1
Published: over 9 years ago

10.1186/1755-8794-7-51

Genetic network identifies novel pathways contributing to atherosclerosis susceptibility in the innominate artery
Cited by: 9
Author(s): Jody Albright, Pamela M. Quizon, Aldons J. Lusis, Brian J. Bennett
Software Mentions: 1
Published: over 10 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: almost 5 years ago

10.3389/fgene.2018.00102

Identification and Functional Analysis of Long Intergenic Non-coding RNAs Underlying Intramuscular Fat Content in Pigs
Cited by: 25
Author(s): Cheng Zou, Li Long, Xiangdong Cheng, Cencen Li, Yuhua Fu, Fang Cui, Changchun Li
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2020.00378

Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
Cited by: 4
Author(s): Jiongliang Wang, Xuelian Ma, Jiaotong Yang, Yanan Hui, Jiajie She, Tian Tian, Zhongqiu Li, Wenying Xu, Zhimin Gao, Zhen Su, Hansheng Zhao
Software Mentions: 1
Published: over 4 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 4 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: over 3 years ago

10.1186/s12916-020-01741-4

Postpartum plasma metabolomic profile among women with preeclampsia and preterm delivery: implications for long-term health
Cited by: 10
Author(s): Xiumei Hong, Boyang Zhang, Liming Liang, Yan Zhang, Yuelong Ji, Guoying Wang, Hongkai Ji, Clary B. Clish, Irina Burd, Colleen Pearson, Barry Zuckerman, Frank B. Hu, Xiaobin Wang
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-018-4999-9

Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)
Cited by: 57
Author(s): Yuling Tai, Liu Chun, Shijie Yu, Hua Yang, Jun Sun, Chunxiao Guo, Bei Huang, Zhaoye Liu, Yuan Yang, Enhua Xia, Chaoling Wei, Xiaochun Wan
Software Mentions: 1
Published: over 6 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 3 years ago

10.3389/fgene.2020.00342

Identification of Crucial Genes Associated With Immune Cell Infiltration in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis
Cited by: 42
Author(s): Dengchuan Wang, Jun Li, Shengshuo Liu, Wenli Li
Software Mentions: 1
Published: over 4 years ago

10.1038/s41396-018-0342-3

Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis
Cited by: 43
Author(s): Ivan D. Mateus, Frédéric G. Masclaux, Consolée Aletti, Edward C. Rojas, Romain Savary, Cindy Dupuis, Ian R. Sanders
Software Mentions: 1
Published: almost 6 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 3 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: over 3 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: almost 11 years ago

10.3389/fgene.2019.01408

Identification of Prognostic Genes in Leiomyosarcoma by Gene Co-Expression Network Analysis
Cited by: 4
Author(s): Jun Yang, Cuili Li, Jianyi Zhou, Xiaoquan Liu, Shaohua Wang
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2021.695399

Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution
Cited by: 14
Author(s): Katie Ovens, B. Frank Eames, Ian McQuillan
Software Mentions: 1
Published: over 3 years ago

10.1038/s41396-019-0472-2

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection
Cited by: 54
Author(s): Bethany Kolody, John P. McCrow, Lisa Zeigler Allen, Frank O. Aylward, Kristina M. Fontanez, Ahmed Moustafa, Mohammad Moniruzzaman, Francisco P. Chávez, Christopher A. Scholin, Eric E. Allen, Alexandra Z. Worden, Edward F. DeLong, Andrew E. Allen
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07714-y

Transcriptomic insights into the effects of CytCo, a novel nematotoxic protein, on the pine wood nematode Bursaphelenchus xylophilus
Cited by: 4
Author(s): Ye Chen, Xiang Zhou, Kai Guo, Sha-Ni Chen, Xiu Su
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2020.00764

Comprehensive Construction of a Circular RNA-Associated Competing Endogenous RNA Network Identified Novel Circular RNAs in Hypertrophic Cardiomyopathy by Integrated Analysis
Cited by: 14
Author(s): Qi Guo, Junjie Wang, Rong Sun, Zhijian He, Qian Chen, Wenhao Liu, Maoxiong Wu, Jigang Bao, Zhaoyu Liu, Jingfeng Wang, Yuling Zhang
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2019.00874

Data Integration in Poplar: ‘Omics Layers and Integration Strategies
Cited by: 13
Author(s): Deborah Weighill, Timothy J. Tschaplinski, Gerald A. Tuskan, Daniel Jacobson
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-021-07368-w

De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress
Cited by: 22
Author(s): Pan Zhang, Tianqi Duo, Fengdan Wang, Xunzhong Zhang, Zouzhuan Yang, Guofu Hu
Software Mentions: 1
Published: almost 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 3 years ago

10.3389/fgene.2021.608017

Identification of Core Genes Related to Progression and Prognosis of Hepatocellular Carcinoma and Small-Molecule Drug Predication
Cited by: 5
Author(s): Nan Jiang, Xinzhuo Zhang, Da‐Lian Qin, Jing Yang, Anguo Wu, Long Wang, Yueshan Sun, Hong Li, Xianfeng Shen, Jing Lin, Fahsai Kantawong, Jianming Wu
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2018.00508

Weighted Gene Correlation Network Analysis (WGCNA) Reveals Novel Transcription Factors Associated With Bisphenol A Dose-Response
Cited by: 32
Author(s): Alexandra Maertens, Vy Tran, André Kleensang, Thomas Hartung
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2019.01398

Identification of the Key Factors Related to Bladder Cancer by lncRNA-miRNA-mRNA Three-Layer Network
Cited by: 13
Author(s): Xiaoxia Wang, Yanrui Ding, Jie Wang, Yanyan Wu
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2018.00406

De novo Mutations (DNMs) in Autism Spectrum Disorder (ASD): Pathway and Network Analysis
Cited by: 37
Author(s): Aitana Alonso-González, Cristina Rodríguez-Fontenla, Ángel Carracedo
Software Mentions: 1
Published: about 6 years ago

Projects: cran: WGCNA

Papers Mentioning WGCNA 3,479