cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1186/s12864-021-07595-1

Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
Cited by: 15
Author(s): Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, Yu Jiang
Software Mentions: 7
Published: over 5 years ago

10.1053/j.gastro.2017.10.007

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
Cited by: 199
Author(s): Kate J. Howell, Judith Kraiczy, Komal Nayak, Marco Gasparetto, Alex Ross, Claire Lee, Tim N. Mak, Bon–Kyoung Koo, Nitin Kumar, Trevor D. Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Software Mentions: 7
Published: over 8 years ago

10.3389/fgene.2021.639642

Immune-Related Genes Are Prognostic Markers for Prostate Cancer Recurrence
Cited by: 10
Author(s): Min Fu, Qiang Wang, Hanbo Wang, Ying Dai, Jin Wang, Weiting Kang, Zilian Cui, Xunbo Jin
Software Mentions: 7
Published: about 5 years ago

10.3389/fgene.2020.00895

Identification of Hub Genes Associated With Hepatocellular Carcinoma Using Robust Rank Aggregation Combined With Weighted Gene Co-expression Network Analysis
Cited by: 10
Author(s): Hongjiang Song, Na Ding, Shang Li, Jianlong Liao, Aimin Xie, Youtao Yu, Chunlong Zhang, Caifang Ni
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13195-020-00733-z

Exploring the role of RALYL in Alzheimer’s disease reserve by network-based approaches
Cited by: 4
Author(s): Yixuan Zhang, Jiali Wang, Xiaoquan Liu, Haochen Liu
Software Mentions: 7
Published: almost 6 years ago

10.3389/fgene.2020.595757

Periostin Contributes to Immunoglobulin a Nephropathy by Promoting the Proliferation of Mesangial Cells: A Weighted Gene Correlation Network Analysis
Cited by: 4
Author(s): Jinlong Wu, Qisheng Lin, Shu Li, Xinghua Shao, Xuying Zhu, Minfang Zhang, Wenyan Zhou, Zhaohui Ni
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2017.00413

Identification of Circular RNAs in Kiwifruit and Their Species-Specific Response to Bacterial Canker Pathogen Invasion
Cited by: 54
Author(s): Zupeng Wang, Yifei Liu, Dawei Li, Li Li, Qiong Zhang, Shuaibin Wang, Hongwen Huang
Software Mentions: 7
Published: over 9 years ago

10.3389/fpls.2020.619404

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I
Cited by: 18
Author(s): Abdellah Barakate, Jamie Orr, Miriam Schreiber, Isabelle Colas, Dominika Lewandowska, Nicola McCallum, Malcolm Macaulay, Jenny Morris, Mikel Arrieta, Pete E. Hedley, Luke Ramsay, Robbie Waugh
Software Mentions: 7
Published: over 5 years ago

10.1111/jcmm.15805

Identification of purity and prognosis‐related gene signature by network analysis and survival analysis in brain lower grade glioma
Cited by: 15
Author(s): Zujian Xiong, Yi Xiong, Hongwei Liu, L. Chang, Xuejun Li
Software Mentions: 7
Published: about 6 years ago

10.1002/ece3.4756

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata
Cited by: 9
Author(s): Martin Helmkampf, M. Renee Bellinger, Monika Frazier, Misaki Takabayashi
Software Mentions: 7
Published: over 7 years ago

10.3390/brainsci9120381

A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder
Cited by: 6
Author(s): Laura B. Ferguson, Shruti Patil, Bailey A. Moskowitz, Igor Ponomarev, R. Adron Harris, R. Dayne Mayfield, Robert O. Messing
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0233372

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs
Cited by: 20
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 6
Published: over 6 years ago

10.3389/fphys.2018.01778

Identification of Crucial Genes and Pathways in Human Arrhythmogenic Right Ventricular Cardiomyopathy by Coexpression Analysis
Cited by: 11
Author(s): Peipei Chen, Bo Long, Yuanfu Xu, Wei Wu, Shuyang Zhang
Software Mentions: 6
Published: over 7 years ago

10.3389/fphys.2019.01370

A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse Heart
Cited by: 1
Author(s): Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joël Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
Software Mentions: 6
Published: almost 7 years ago

10.3389/fphar.2016.00142

Comparative Transcriptome Analysis Identifies CCDC80 as a Novel Gene Associated with Pulmonary Arterial Hypertension
Cited by: 22
Author(s): Shota Sasagawa, Yuhei Nishimura, Hirofumi Sawada, Eric Erquan Zhang, Shiko Okabe, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Koki Kawaguchi, Reiko Kawase, Yoshihide Mitani, Kazuo Maruyama, Toshio Tanaka
Software Mentions: 6
Published: about 10 years ago

10.3389/fphar.2020.593247

Identification of FPR3 as a Unique Biomarker for Targeted Therapy in the Immune Microenvironment of Breast Cancer
Cited by: 7
Author(s): Jian Qi, Yu Liu, Jiliang Hu, Li Lu, Zhen Dou, Haiming Dai, Hongzhi Wang, Wulin Yang
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2021.614531

Identification and Validation of Hub Genes Associated With Hepatocellular Carcinoma Via Integrated Bioinformatics Analysis
Cited by: 8
Author(s): Sumei Wang, Zuoli Song, Bing Teng, Jinjuan Zhang, Jiandong Zhang, Shuye Liu
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-021-07443-2

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing
Cited by: 12
Author(s): Carolina P. Moraleda, Diego Robledo, Alejandro P. Gutiérrez, Jorge Del‐Pozo, José M. Yáñez, Ross D. Houston
Software Mentions: 6
Published: over 5 years ago

10.1186/s12885-017-3832-1

Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages
Cited by: 9
Author(s): Daifeng Wang, John D. Haley, Patricia Thompson
Software Mentions: 6
Published: almost 9 years ago

10.1186/s12885-018-4848-x

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Cited by: 53
Author(s): Kasey Jividen, Katarzyna Kedzierska, Chunsong Yang, Karol Szlachta, Aakrosh Ratan, Bryce M. Paschal
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12885-021-08052-8

Comprehensive analysis of immune-related prognostic genes in the tumour microenvironment of hepatocellular carcinoma
Cited by: 2
Author(s): Weike Gao, Luan Li, Xinyin Han, Siyao Liu, Chengzhen Li, Guanying Yu, Lei Zhang, Dongsheng Zhang, Caiyun Liu, Erhong Meng, Shuai Hong, Dongliang Wang, Peiming Guo, Guangjun Shi
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0109760

Copy Number Loss of the Interferon Gene Cluster in Melanomas Is Linked to Reduced T Cell Infiltrate and Poor Patient Prognosis
Cited by: 164
Author(s): Peter S. Linsley, Cate Speake, Elizabeth Whalen, Damien Chaussabel
Software Mentions: 6
Published: almost 12 years ago

10.18632/aging.103743

Identification of subtype-specific genes signature by WGCNA for prognostic prediction in diffuse type gastric cancer
Cited by: 6
Author(s): Qi Zhou, Liqun Zhou, Shihao Li, Yi‐Wu Yuan, Li Liu, Jinliang Wang, Deng-Zhong Wu, You Wu, Lin Xin
Software Mentions: 6
Published: almost 6 years ago

10.18632/aging.203166

Identification and validation of inferior prognostic genes associated with immune signatures and chemotherapy outcome in acute myeloid leukemia
Cited by: 7
Author(s): Jie Wang, Hao Jian-ping, Nazim Uddin, Yun Wu, Rong Chen, Dongfeng Li, Dai-qin Xiong, Nan Ding, Jianhua Yang, Xiaowen Ding
Software Mentions: 6
Published: about 5 years ago

10.18632/aging.202638

Identification of key genes in coronary artery disease: an integrative approach based on weighted gene co-expression network analysis and their correlation with immune infiltration
Cited by: 10
Author(s): Yang Yang, Xiangshan Xu
Software Mentions: 6
Published: over 5 years ago

10.1186/s12885-021-08711-w

Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
Cited by: 12
Author(s): Rongjia Su, Chengjuan Jin, Lina Zhou, Yannan Cao, Menghua Kuang, Linxia Li, Jianbin Xiang
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-021-07720-0

Comparative neurotranscriptomics reveal widespread species differences associated with bonding
Cited by: 5
Author(s): Joel A. Tripp, Alejandro Berrío, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young, Steve Phelps
Software Mentions: 6
Published: over 5 years ago

10.3390/biom9010012

Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in Poplar
Cited by: 63
Author(s): Jie Luo, Wenxiu Xia, Pei Cao, Zheng’ang Xiao, Yan Zhang, Meifeng Liu, Chengjun Zhan, Nian Wang
Software Mentions: 6
Published: over 7 years ago

10.3390/biomedicines9091120

Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth
Cited by: 3
Author(s): Letizia Messa, Bianca Barzaghini, Federica Rey, Cecilia Pandini, Gian Vincenzo Zuccotti, Cristina Cereda, Stephana Carelli, Manuela Teresa Raimondi
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0205406

Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: A prospective observational study
Cited by: 10
Author(s): Andrew P Zammit, Rohit Anthony Sinha, Caroline Cooper, Christopher Perry, Ian H. Frazer, Zewen Kelvin Tuong
Software Mentions: 6
Published: almost 8 years ago

10.3389/fonc.2021.636479

An Immune Cell-Based Signature Associating With EMT Phenotype Predicts Postoperative Overall Survival of ESCC
Cited by: 4
Author(s): Hongliang Yu, Dayong Gu, Chao Yang, Jianhua Xu, Feng Yan, Xu He
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0183517

Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study
Cited by: 7
Author(s): Han Wang, Zhenyu Zhang, Bangshun He, Yu Xu, Jun Zhang, Weijun Cao
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0254829

Tumor infiltrating lymphocytes associated competitive endogenous RNA networks as predictors of outcome in hepatic carcinoma based on WGCNA analysis
Cited by: 1
Author(s): Ying He, Xu Rui, Li Peng, Xiaoyu Hu
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.629633

GMFG Has Potential to Be a Novel Prognostic Marker and Related to Immune Infiltrates in Breast Cancer
Cited by: 5
Author(s): Yan Yang, Xin He, Qianqian Tang, You-Cheng Shao, Wenjing Song, Peng Gong, Yifan Zeng, Shu‐Chun Huang, Jiang-Yao Zhou, Huifang Wan, Lei Wei, Jingwei Zhang
Software Mentions: 6
Published: about 5 years ago

10.1186/s12859-019-2840-3

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network
Cited by: 30
Author(s): Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang, Jia Meng
Software Mentions: 6
Published: over 7 years ago

10.18632/aging.202474

Clinical and genomic characteristics of metabolic syndrome in colorectal cancer
Cited by: 2
Author(s): Yanyan Li, Jungang Zhao, Xiaoli Wu, Yini Zhang, Jia Yin, Weiyang Cai
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2021.639600

Identification of VWF as a Novel Biomarker in Lung Adenocarcinoma by Comprehensive Analysis
Cited by: 8
Author(s): Yi He, Ruijie Liu, Minghui Yang, Wu Bi, Liuyin Zhou, Sai Zhang, Jin Jin, Xujun Liang, Pengfei Zhang
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2021.666558

The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest
Cited by: 6
Author(s): Priyanka Chowdhury, Stefan Golas, Lauren Alteio, Joshua T. E. Stevens, Andrew F. Billings, Jeffrey L. Blanchard, Jerry M. Melillo, Kristen M. DeAngelis
Software Mentions: 6
Published: about 5 years ago

10.18632/aging.103832

Prognostic model of patients with liver cancer based on tumor stem cell content and immune process
Cited by: 7
Author(s): Jie Zhu, Miaomiao Gao, Yuchen Jin, Weiran Huang, Zhuo Huang, Zhengwei Xie
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0236186

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat
Cited by: 16
Author(s): Liangjie Lv, Wenying Zhang, Lijing Sun, Aiju Zhao, Yingjun Zhang, Limei Wang, Yuping Liu, Ziqian Li, Xiyong Chen
Software Mentions: 6
Published: about 6 years ago

10.3389/fimmu.2021.632798

Comprehensive Transcriptomic Analysis Identifies Novel Antiviral Factors Against Influenza A Virus Infection
Cited by: 11
Author(s): Ao Zhou, Dong Xia, Mengyun Liu, Bin Tang
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.670218

KIF11 Serves as an Independent Prognostic Factor and Therapeutic Target for Patients With Lung Adenocarcinoma
Cited by: 13
Author(s): Zhaodong Li, Bin Yu, Fanghua Qi, Fan Li
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0208132

Identification of alterations in macrophage activation associated with disease activity in systemic lupus erythematosus
Cited by: 67
Author(s): Adam C. Labonte, Brian Kegerreis, Nicholas S. Geraci, Prathyusha Bachali, Sushma Madamanchi, Robert Robl, Michelle D. Catalina, Peter E. Lipsky, Amrie C. Grammer
Software Mentions: 6
Published: over 7 years ago

10.18632/aging.103994

Molecular identification of protein kinase C beta in Alzheimer's disease
Cited by: 6
Author(s): Zhike Zhou, Fenqin Chen, Shanshan Zhong, Yi Zhou, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Mei Zhao, Chuansheng Zhao
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12967-020-02616-1

Immune landscape of periodontitis unveils alterations of infiltrating immunocytes and molecular networks-aggregating into an interactive web-tool for periodontitis related immune analysis and visualization
Cited by: 7
Author(s): Xiaoqi Zhang, Qingxuan Wang, Xinyu Yan, Yue Shan, Xing Lü, Minqi Li, Hu Long, Wenli Lai
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0227258

Accelerated brain aging towards transcriptional inversion in a zebrafish model of the K115fs mutation of human PSEN2
Cited by: 29
Author(s): Nhi Hin, Morgan Newman, Jan Kaslin, Alon M. Douek, Amanda L. Lumsden, Seyyed Hani Moussavi Nik, Yang Dong, Xin Zhou, Noralyn B. Mañucat-Tan, Alastair J. Ludington, David L. Adelson, Stephen Pederson, Michael Lardelli
Software Mentions: 6
Published: over 6 years ago

10.3390/ijms20020263

Molecular Network-Based Drug Prediction in Thyroid Cancer
Cited by: 14
Author(s): Xingyu Xu, Hang Long, Baohang Xi, Binbin Ji, Zejun Li, Yunyue Dang, Cheng Jiang, Yao Yao, Jialiang Yang
Software Mentions: 6
Published: over 7 years ago

10.3389/fimmu.2021.645839

Multi-Omics Profiling Identifies Risk Hypoxia-Related Signatures for Ovarian Cancer Prognosis
Cited by: 11
Author(s): Xingyu Chen, Hua Lan, Dong He, Runshi Xu, Yao Zhang, Ying Cheng, Haotian Chen, Songshu Xiao, Ke Cao
Software Mentions: 6
Published: about 5 years ago

10.18632/aging.202603

Functional analysis of brain derived neurotrophic factor (BDNF) in Huntington’s disease
Cited by: 6
Author(s): Zhike Zhou, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 6
Published: over 5 years ago

10.1186/s12967-020-02260-9

Identification of key genes controlling breast cancer stem cell characteristics via stemness indices analysis
Cited by: 42
Author(s): Jianying Pei, Yanxia Wang, Yan Li
Software Mentions: 6
Published: over 6 years ago

10.1155/2021/5552623

Integrative Functional Genomic Analysis of Molecular Signatures and Mechanistic Pathways in the Cell Cycle Underlying Alzheimer’s Disease
Cited by: 5
Author(s): Zhike Zhou, Jun Bai, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 6
Published: about 5 years ago

10.1155/2018/4246703

Candidate Biomarkers and Molecular Mechanism Investigation for Glioblastoma Multiforme Utilizing WGCNA
Cited by: 64
Author(s): Qi Yang, Rui Wang, Bo Wei, Chuangang Peng, Le Wang, Guozhang Hu, Daliang Kong, Chao Du
Software Mentions: 6
Published: almost 8 years ago

10.3389/fgene.2020.634634

A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune Biomarkers
Cited by: 17
Author(s): Jin Ren, Yun Yang, Chuanyin Li, Lu Xie, Ronggui Hu, Qin Xiong, Menghuan Zhang
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0241128

Kin recognition: Neurogenomic response to mate choice and sib mating avoidance in a parasitic wasp
Cited by: 0
Author(s): Aurore Gallot, Sandrine Sauzet, Emmanuel Desouhant
Software Mentions: 6
Published: almost 6 years ago

10.3389/fgene.2020.00011

Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance
Cited by: 6
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-019-6375-9

Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics
Cited by: 27
Author(s): Yanchao Xu, Richard Odongo Magwanga, Xiaomin Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Kunbo Wang, Fang Liu
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.10633

Gene signatures with predictive and prognostic survival values in human osteosarcoma
Cited by: 4
Author(s): Zhongpeng Qiu, Xuehui Du, Kai Chen, Yi Dai, Sibo Wang, Jun Xiao, Gang Li
Software Mentions: 6
Published: over 5 years ago

10.1038/ismej.2017.165

Recurrent patterns of microdiversity in a temperate coastal marine environment
Cited by: 110
Author(s): Meghan Chafee, Antonio Fernández-Guerra, Pier Luigi Buttigieg, Gunnar Gerdts, A. Murat Eren, Hanno Teeling, Rudolf Amann
Software Mentions: 6
Published: almost 9 years ago

10.7554/eLife.35368

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Cited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: over 8 years ago

10.3389/fgene.2020.00311

Weighted Gene Coexpression Network Analysis of Features That Control Cancer Stem Cells Reveals Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 57
Author(s): Yi Liao, Yulei Wang, Mengqing Cheng, Chengliang Huang, Xiaoxuan Fan
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2019.01056

Meta-Analysis of HTLV-1-Infected Patients Identifies CD40LG and GBP2 as Markers of ATLL and HAM/TSP Clinical Status: Two Genes Beat as One
Cited by: 5
Author(s): Eduardo R. Fukutani, Pablo Ivan Pereira Ramos, José Irahe Kasprzykowski, Lucas Gentil Azevedo, Moreno Magalhães de Souza Rodrigues, João Victor Lima, Helton Fábio Santos de Araújo, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41398-021-01447-y

Essential genes from genome-wide screenings as a resource for neuropsychiatric disorders gene discovery
Cited by: 2
Author(s): Wei Zhang, Joao L De Quevedo, Gabriel R. Fries
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.8505

Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis
Cited by: 10
Author(s): Xuegang Hu, Genban Sun, Zhiqiang Shi, Hui Ni, Shan Jiang
Software Mentions: 6
Published: over 6 years ago

10.1038/s41398-021-01531-3

Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study
Cited by: 22
Author(s): Xiuxia Yuan, Yunpeng Wang, Xue Li, Jiajun Jiang, Yulin Kang, Lijuan Pang, Peifen Zhang, Ang Li, Luxian Lv, Ole A. Andreassen, Xiaoduo Fan, Shaohua Hu, Xueqin Song
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2019.00209

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data
Cited by: 23
Author(s): Shenhe Liu, Tingzhu Ye, Zipeng Li, Jun Li, Muhammad Jamil Ahmad, Yang Zhou, Guohua Hua, Aixin Liang, Tingxian Deng, Liguo Yang
Software Mentions: 6
Published: over 7 years ago

10.3389/fgene.2019.01120

Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets
Cited by: 12
Author(s): Pablo Ivan Pereira Ramos, Luis Willian Pacheco Arge, Nicholas Costa Barroso Lima, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: almost 7 years ago

10.3389/fgene.2021.723519

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken
Cited by: 8
Author(s): Siyuan Xing, Ranran Liu, Guiping Zhao, M.A.M. Groenen, Ole Madsen, Lu Liu, Maiqing Zheng, Qiao Wang, Zhou Wu, R.P.M.A. Crooijmans, Jie Wen
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12864-016-3020-8

RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Cited by: 27
Author(s): Jeanine S. Morey, Marion G. Neely, Denise Lunardi, Paul E. Anderson, Lori H. Schwacke, Michelle R. Campbell, Frances M. Van Dolah
Software Mentions: 6
Published: almost 10 years ago

10.1186/s12864-020-6767-x

Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats
Cited by: 11
Author(s): Dongdong Bo, Xunping Jiang, Guiqiong Liu, Feng Xu, Ronggui Hu, Teketay Wassie, Yuqing Chong, S. Sohail Ahmed, Chenhui Liu, Shishay Girmay
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2019.00823

Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages
Cited by: 19
Author(s): Lucas F. Maciel, David A. Morales-Vicente, Gilbert O. Silveira, Raphael O. Ribeiro, Giovanna G. O. Olberg, David S. Pires, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: almost 7 years ago

10.3389/fgene.2020.566159

Identifying 8-mRNAsi Based Signature for Predicting Survival in Patients With Head and Neck Squamous Cell Carcinoma via Machine Learning
Cited by: 10
Author(s): Yanhua Tian, Juncheng Wang, Chao Qin, Guanghao Zhu, Xuan Chen, Zhixiang Chen, Yuexiang Qin, Ming Wei, Zhexuan Li, Xin Zhang, Yunxia Lv, Gengming Cai
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-86048-x

A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients
Cited by: 9
Author(s): Yuzi Xu, Fengqin Xu, Yiming Lv, Siyuan Wang, Jia Li, Chuan Zhou, Jimin Jiang, Binbin Xie, Fuming He
Software Mentions: 6
Published: over 5 years ago

10.12688/wellcomeopenres.15115.1

Single-cell transcriptome analysis of CD8+ T-cell memory inflation
Cited by: 7
Author(s): Andrew J. Highton, Madeleine E Zinser, Lian Ni Lee, Claire Hutchings, Catherine de Lara, Chansavath Phetsouphanh, Christian Willberg, Claire L. Gordon, Paul Klenerman, Emanuele Marchi
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-021-85848-5

Abnormal upregulation of cardiovascular disease biomarker PLA2G7 induced by proinflammatory macrophages in COVID-19 patients
Cited by: 18
Author(s): Yang Li, Yongzhong Jiang, Yi Zhang, Naizhe Li, Qiangling Yin, Linlin Liu, Xin Lv, Yan Liu, Aqian Li, Bin Fang, Jiajia Li, Hengping Ye, Gang Ye, Xiaoxian Cui, Yang Liu, Yuanyuan Qu, Chuan Li, Jiandong Li, Dexin Li, Zhongtao Gai, Shiwen Wang, Faxian Zhan, Mifang Liang
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-91214-2

Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction
Cited by: 12
Author(s): Xin Luo, Jun Yin, Denise Dwyer, Tracy M. Yamawaki, Hong Zhou, Hongfei Ge, Chun-Ya Han, Artem Shkumatov, K. F. Snyder, Brandon Ason, Chi-Ming Li, Oliver Homann, Marina Stolina
Software Mentions: 6
Published: about 5 years ago

10.1186/s12918-018-0620-8

Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
Cited by: 11
Author(s): Theresia Conrad, Olaf Kniemeyer, Sebastian Henkel, Thomas Krüger, Derek J. Mattern, Vito Valiante, Reinhard Guthke, Ilse D. Jacobsen, Axel A. Brakhage, Sebastian Vlaic, Jörg Linde
Software Mentions: 6
Published: almost 8 years ago

10.3389/fimmu.2018.00056

The Immune and Non-Immune Pathways That Drive Chronic Gastrointestinal Helminth Burdens in the Wild
Cited by: 20
Author(s): Simon A. Babayan, Wei Liu, Graham Hamilton, Elizabeth Kilbride, Evelyn C. Rynkiewicz, Melanie Clerc, Amy B. Pedersen
Software Mentions: 6
Published: over 8 years ago

10.15252/msb.20209684

Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis
Cited by: 14
Author(s): Frode Norheim, Karthickeyan Chella Krishnan, Thomas Bjellaas, Laurent Vergnes, Calvin Pan, Brian W. Parks, Yan Meng, Jennifer M. Lang, James A. Ward, Karen Reue, Margarete Mehrabian, Thomas E. Gundersen, Miklós Péterfy, Knut Tomas Dalen, Christian A. Drevon, Simon T. Hui, Aldons J. Lusis, Marcus M. Seldin
Software Mentions: 6
Published: over 5 years ago

10.1080/21623945.2019.1595269

Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians
Cited by: 17
Author(s): Aditya Saxena, Prabhat Tiwari, Nitin Wahi, Arpana Soni, Ram Chandra Bansiwal, Anshul Kumar, Balram Sharma, Prakash P Punjabi, Nidhi Gupta, Babita Malik, Krishna Mohan Medicherla, Prashanth Suravajhala, Sandeep Kumar Mathur
Software Mentions: 6
Published: over 7 years ago

10.1080/22221751.2021.1942228

Single-cell immune checkpoint landscape of PBMCs stimulated with Candida albicans
Cited by: 8
Author(s): Wei‐Wei Deng, Zhen Su, Panpan Liang, Yubo Ma, Yufang Liu, Kai Zhang, Yi Zhang, Ting Liang, Jinyan Shao, X. Liu, Wenling Han, Ruoyu Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s13024-017-0219-3

Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer’s disease
Cited by: 92
Author(s): Andrew McKenzie, Sarah Moyon, Minghui Wang, Igor Katsyv, Won Min Song, Xianxiao Zhou, Eric B. Dammer, Duc M. Duong, Joshua D. Aaker, Yang Zhao, Noam D. Beckmann, Pei Wang, Jun Zhu, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Brian Popko, Patrizia Casaccia, Bin Zhang
Software Mentions: 6
Published: almost 9 years ago

10.1002/ece3.7861

Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco (Nicotiana tabacum L.)
Cited by: 9
Author(s): Lei Xing, Jianlei Yang, Yuping Jia, Xiaobing Hu, Yi Liu, Heng Xu, Huaqun Yin, Juan Li, Zhenxie Yi
Software Mentions: 6
Published: about 5 years ago

10.1038/sdata.2018.185

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
Cited by: 284
Author(s): Minghui Wang, Noam D. Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chi Ming, Ryan Neff, Wanli Ma, John F. Fullard, Mads E. Hauberg, Jaroslav Bendl, Mette A. Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara M. Mangravite, Eric B. Dammer, Duc M. Duong, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Bin Zhang
Software Mentions: 6
Published: almost 8 years ago

10.1126/sciadv.abj1132

Plasma lipids and growth faltering: A longitudinal cohort study in rural Gambian children
Cited by: 2
Author(s): Gerard Bryan Gonzales, Daniëlla Brals, Bakary Sonko, Fatou Sosseh, Andrew M. Prentice, Sophie E. Moore, Albert Koulman
Software Mentions: 6
Published: almost 5 years ago

10.1111/mec.15743

The strength and form of natural selection on transcript abundance in the wild
Cited by: 9
Author(s): Freed Ahmad, Paul V. Debes, Ilkka Nousiainen, Siim Kahar, Lilian Pukk, Riho Gross, Mikhail Ozerov, Anti Vasemägi
Software Mentions: 6
Published: over 5 years ago

10.1073/pnas.2008890118

OCT4 induces embryonic pluripotency via STAT3 signaling and metabolic mechanisms
Cited by: 23
Author(s): Giuliano Giuseppe Stirparo, Agata Kurowski, Akira Yanagida, Lawrence E. Bates, Stanley E. Strawbridge, Siarhei Hladkou, Hannah Stuart, Thorsten Boroviak, José C.R. Silva, Jennifer Nichols
Software Mentions: 6
Published: over 5 years ago

10.1186/s13229-019-0287-z

A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood
Cited by: 12
Author(s): Charles E. Mordaunt, Bo Y. Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca Jean Schmidt, M. Daniele Fallin
Software Mentions: 6
Published: almost 7 years ago

10.1186/s10020-021-00322-2

High expression of LAMA3/AC245041.2 gene pair associated with KRAS mutation and poor survival in pancreatic adenocarcinoma: a comprehensive TCGA analysis
Cited by: 11
Author(s): Chengming Tian, Xiyao Li, Chunlin Ge
Software Mentions: 6
Published: about 5 years ago

10.1186/s12931-016-0459-8

Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations
Cited by: 47
Author(s): Robert S. Busch, Weiliang Qiu, Jessica Lasky‐Su, Jarrett Morrow, Gerard J. Criner, Dawn L. DeMeo
Software Mentions: 6
Published: almost 10 years ago

10.1038/s41598-020-65320-6

IRE1α and IGF signaling predict resistance to an endoplasmic reticulum stress-inducing drug in glioblastoma cells
Cited by: 10
Author(s): Jeffrey J. Rodvold, Xian Su, Julia K. Nussbacher, Brian Tsui, Thomas Waller, Stephen Searles, Alyssa Lew, Pengfei Jiang, Ivan Babić, Natsuko Nomura, Jonathan H. Lin, Santosh Kesari, Hannah Carter, Maurizio Zanetti
Software Mentions: 6
Published: over 6 years ago

10.1242/dmm.047225

Hearing impairment due to Mir183/96/182 mutations suggests both loss-of-function and gain-of-function effects
Cited by: 10
Author(s): Morag A. Lewis, Francesca Di Domenico, Neil J. Ingham, Haydn M. Prosser, Karen P. Steel
Software Mentions: 6
Published: over 5 years ago

10.18632/aging.102714

ISG20 serves as a potential biomarker and drives tumor progression in clear cell renal cell carcinoma
Cited by: 22
Author(s): Tianbo Xu, Hailong Ruan, Su Gao, Jingchong Liu, Yuenan Liu, Zhengshuai Song, Qi Cao, Keshan Wang, Lin Bao, Di Liu, Junwei Tong, Jian Shi, Huageng Liang, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 6
Published: over 6 years ago

10.1186/s13100-019-0180-5

Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements
Cited by: 20
Author(s): Nicky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Software Mentions: 6
Published: almost 7 years ago

10.1111/jcmm.16414

Identification of hub genes associated with neutrophils infiltration in colorectal cancer
Cited by: 12
Author(s): Hao Su, Tianyi Cai, Sen Zhang, Xialin Yan, Leqi Zhou, Zengyou He, Peng Xue, Jianwen Li, Min Zheng, Xiao Yang, Bo Feng
Software Mentions: 6
Published: over 5 years ago

10.15252/embj.2019101695

Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma
Cited by: 61
Author(s): María D. Giraldez, Ryan M Spengler, Alton Etheridge, Annika Jane Goicochea, Missy Tuck, Sung Won Choi, David J. Galas, Muneesh Tewari
Software Mentions: 6
Published: over 7 years ago

10.1186/s40168-021-01150-6

Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants
Cited by: 40
Author(s): Qi Zhang, Zhenyan Zhang, Tao Lu, Yitian Yu, Josep Peñuelas, Yan Zhu, Haifeng Qian
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12864-019-6061-y

Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks
Cited by: 12
Author(s): Jim A. Mossman, Leann M. Biancani, David M. Rand
Software Mentions: 6
Published: about 7 years ago

10.12688/wellcomeopenres.14073.3

ANIMA: Association network integration for multiscale analysis
Cited by: 4
Author(s): Armin Deffur, Robert J. Wilkinson, Bongani M. Mayosi, Nicola Mulder
Software Mentions: 6
Published: almost 8 years ago

10.18632/aging.202718

TMBIM6, a potential virus target protein identified by integrated multiomics data analysis in SARS-CoV-2-infected host cells
Cited by: 4
Author(s): Qizheng Han, Junhao Wang, Haihua Luo, Lei Li, Xinya Lu, Aihua Liu, Yongqiang Deng, Yong Jiang
Software Mentions: 6
Published: over 5 years ago

10.3390/metabo11060361

Opposing Effects of Ceanothus velutinus Phytochemistry on Herbivore Communities at Multiple Scales
Cited by: 2
Author(s): Casey S. Philbin, M. J. Paulsen, Lora A. Richards
Software Mentions: 6
Published: about 5 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479