Ecosyste.ms: Papers

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

Projects: cran: WGCNA

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

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

Papers Mentioning WGCNA 3,479

10.3389/fonc.2020.566183
Comprehensive Analysis of CDCAs Methylation and Immune Infiltrates in Hepatocellular Carcinoma
Cited by: 8
Author(s): Yongkang Wang, Yinfeng Yang, Honglei Gao, Ting Ouyang, Luyao Zhang, Jili Hu, Hu Sheng, Hongxing Kan
Software Mentions: 5
Published: almost 4 years ago
10.1186/s12864-020-6545-9
Trait differentiation and modular toxin expression in palm-pitvipers
Cited by: 16
Author(s): Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Darin R. Rokyta, Mahmood Sasa, Christopher L. Parkinson
Software Mentions: 5
Published: almost 5 years ago
10.3389/fonc.2020.00444
Multi-Omics Integration Reveals a Competitive Endogenous RNAs Network for the Identification of Progression Biomarkers and the Stratification of Patients Diagnosed With Nephroblastoma
Cited by: 2
Author(s): Jingbo Wang, Yuan Wang, Han Liang, Mohamed Shahen, Chaofeng Hu, Furong Li
Software Mentions: 5
Published: over 4 years ago
10.1038/srep46156
Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens
Cited by: 18
Author(s): Xi Lan, Yan Wang, Kai Tian, Fei Ye, Huadong Yin, Xiaoling Zhao, Hengyong Xu, Yong Huang, Haibo Li, John Hsieh, Susan J. Lamont, Qing Zhu
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0143128
RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize
Cited by: 30
Author(s): Liu Ya, Miaoyi Zhou, Zhaoxu Gao, Wen Ren, Fan Yang, Hang He, Jiuran Zhao
Software Mentions: 5
Published: almost 9 years ago
10.3389/fonc.2021.615234
Combined Analysis of RNA Sequence and Microarray Data Reveals a Competing Endogenous RNA Network as Novel Prognostic Markers in Malignant Pleural Mesothelioma
Cited by: 5
Author(s): Weicheng Duan, Kang Wang, Yijie Duan, Xiuyi Chen, Xufeng Chu, Ping Hu, Bo Xiong
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0257343
Analysis of potential genetic biomarkers and molecular mechanism of smoking-related postmenopausal osteoporosis using weighted gene co-expression network analysis and machine learning
Cited by: 7
Author(s): Shaoshuo Li, Baixing Chen, Hao Chen, Zhen Hua, Yang Shao, Heng Yin, Jianwei Wang
Software Mentions: 5
Published: about 3 years ago
10.1371/journal.pone.0044736
Brain Transcriptional and Epigenetic Associations with Autism
Cited by: 131
Author(s): Matthew R. Ginsberg, Robert A. Rubin, Tatiana Falcone, Angela H. Ting, Marvin R. Natowicz
Software Mentions: 5
Published: about 12 years ago
10.1186/1471-2164-14-725
Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence
Cited by: 113
Author(s): Yury O. Nunez, Jay Truitt, Giorgio Gorini, Olga N. Ponomareva, Yuri A. Blednov, R. Adron Harris
Software Mentions: 5
Published: about 11 years ago
10.1371/journal.pone.0129610
Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach
Cited by: 4
Author(s): Nilotpal Chowdhury, Shantanu Sapru
Software Mentions: 5
Published: over 9 years ago
10.3389/fcell.2020.560766
Transcriptome Reveals Multi Pigmentation Genes Affecting Dorsoventral Pattern in Avian Body
Cited by: 6
Author(s): Xi Yang, Hehe Liu, Li Liang, Qian Xu, Yisi Liu, Lei Wang, Shengchao Ma, Jianmei Wang, Lili Bai, Rongping Zhang, Chunchun Han
Software Mentions: 5
Published: about 4 years ago
10.3389/fcell.2021.652408
Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
Cited by: 21
Author(s): Xianliang Hou, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Ruilian Zhe, Xinqiong Liu, Donge Tang, Minglin Ou, Yong Dai
Software Mentions: 5
Published: over 3 years ago
10.1186/s13567-021-00972-4
Transcriptomic analysis of equine chorioallantois reveals immune networks and molecular mechanisms involved in nocardioform placentitis
Cited by: 8
Author(s): Hesham A. Ali, Shavahn C. Loux, Laura Kennedy, Kirsten E. Scoggin, Pouya Dini, Carleigh E. Fedorka, Theodore S. Kalbfleisch, A. Esteller-Vico, David W. Horohov, Erdal Erol, Craig N. Carter, Jon J. Smith, Barry A. Ball
Software Mentions: 5
Published: over 3 years ago
10.3389/fcell.2021.719192
PARP1 Inhibitor Combined With Oxaliplatin Efficiently Suppresses Oxaliplatin Resistance in Gastric Cancer-Derived Organoids via Homologous Recombination and the Base Excision Repair Pathway
Cited by: 1
Author(s): Huafu Li, Chunming Wang, Linxiang Lan, Wenhui Wu, Ian M. Evans, E Josue Ruiz, Le-Ping Yan, Zhijun Zhou, Joaquím M. Oliveira, Rui L. Reis, Zhenran Hu, Wei Chen, Axel Behrens, Yulong He, Changhua Zhang
Software Mentions: 5
Published: about 3 years ago
10.1186/s12903-021-01587-z
A four-hypoxia-genes-based prognostic signature for oral squamous cell carcinoma
Cited by: 10
Author(s): Chenguang Zhao, Yingrui Zhou, Hongwei Ma, Jinhui Wang, Hongxu Guo, Hao Líu
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2021.621430
Identification of Hub Genes Associated With Melanoma Development by Comprehensive Bioinformatics Analysis
Cited by: 8
Author(s): Jie Jiang, Chong Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Xinli Zhan
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0243857
Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in NAc and PFC
Cited by: 7
Author(s): Eric Vornholt, John W. Drake, Mohammed Mamdani, Gowon O. McMichael, Zachary N. Taylor, Silviu‐Alin Bacanu, Michael F. Miles, Vladimir I. Vladimirov
Software Mentions: 5
Published: almost 4 years ago
10.3389/fmicb.2016.01335
Visual Comparative Omics of Fungi for Plant Biomass Deconstruction
Cited by: 31
Author(s): Shingo Miyauchi, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean‐Guy Berrin, Bernard Henrissat, Marie‐Noëlle Rosso
Software Mentions: 5
Published: about 8 years ago
10.3389/fcell.2021.700607
Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 23
Author(s): Haihui Zhong, Jie Wang, Yaru Zhu, Yefeng Shen
Software Mentions: 5
Published: about 3 years ago
10.1371/journal.pntd.0004992
Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: about 8 years ago
10.1371/journal.pone.0118731
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
Cited by: 77
Author(s): Katherine C. H. Amrine, Bárbara Blanco-Ulate, Dario Cantu
Software Mentions: 5
Published: over 9 years ago
10.3389/fmicb.2016.01637
Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats
Cited by: 60
Author(s): Mathilde Jeanbille, Jérôme Gury, Robert Duran, Jacek Tronczyński, Hélène Agogué, Olfa Ben Saïd, Jean-François Ghiglione, Jean‐Christophe Auguet
Software Mentions: 5
Published: about 8 years ago
10.1038/s41598-021-85061-4
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Cited by: 12
Author(s): Jerry C. Wang, Gokul Ramaswami, Daniel H. Geschwind
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1008367
Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development
Cited by: 15
Author(s): Robert L. Baker, Wen Fung Leong, Marcus T. Brock, Matthew J. Rubin, R. J. Cody Markelz, Stephen M. Welch, Julin Maloof, Cynthia Weinig
Software Mentions: 5
Published: about 5 years ago
10.1042/BSR20191547
Transcriptome profiling of digital flexor tendons after injury in a chicken model
Cited by: 1
Author(s): Wenfei Mao, Yancun Yu, Chen Chen, Ya Fang Wu
Software Mentions: 5
Published: over 4 years ago
10.1186/s12863-020-00852-4
Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs
Cited by: 9
Author(s): Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto, W. L. Flowers
Software Mentions: 5
Published: over 4 years ago
10.3389/fonc.2019.00898
Genome-Wide Identification of a Novel Eight-lncRNA Signature to Improve Prognostic Prediction in Head and Neck Squamous Cell Carcinoma
Cited by: 26
Author(s): Bowen Yang, Jiming Shen, Xu Lu, Ying Chen, Xiaofang Che, Xiujuan Qu, Yunpeng Liu, Yuee Teng, Zhi Li
Software Mentions: 5
Published: about 5 years ago
10.1186/s13024-018-0282-4
Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease
Cited by: 147
Author(s): Erik C. B. Johnson, Eric B. Dammer, Duc M. Duong, Luming Yin, Madhav Thambisetty, Juan C. Troncoso, James J. Lah, Aĺlan I. Levey, Nicholas T. Seyfried
Software Mentions: 5
Published: about 6 years ago
10.3389/fmicb.2020.00571
Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile
Cited by: 17
Author(s): Marcia Astorga-Eló, Qian Zhang, Giovanni Larama, Alexandra Stoll, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 5
Published: over 4 years ago
10.1098/rsos.200792
Tissue-specific developmental regulation and isoform usage underlie the role of<i>doublesex</i>in sex differentiation and mimicry in<i>Papilio</i>swallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: about 4 years ago
10.3389/fcimb.2019.00225
Cepharanthine Hydrochloride Improves Cisplatin Chemotherapy and Enhances Immunity by Regulating Intestinal Microbes in Mice
Cited by: 25
Author(s): Pengjun Zhou, Ziyao Li, Dandan Xu, Ying Wang, Qi Bai, Yulin Feng, Guifeng Su, Pengxiao Chen, Yao Wang, Huizhong Liu, Xiaogang Wang, Zhang Rong, Yifei Wang
Software Mentions: 4
Published: over 5 years ago
10.1186/s12862-021-01762-4
Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume
Cited by: 10
Author(s): Man Zhang, Ping Li, Xiao-lan Yan, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pgen.1008518
Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis
Cited by: 10
Author(s): Alfredo Rago, John H. Werren, John K. Colbourne
Software Mentions: 4
Published: almost 5 years ago
10.1186/s12967-020-02327-7
Identification of hub genes in papillary thyroid carcinoma: robust rank aggregation and weighted gene co-expression network analysis
Cited by: 15
Author(s): Yang Liu, Ting‐Yu Chen, Zhi-Yan Yang, Wei Bin Fang, Qian Wu, Zhang Chao
Software Mentions: 4
Published: over 4 years ago
10.1186/s12967-020-02698-x
Identification of key biomarkers and immune infiltration in systemic lupus erythematosus by integrated bioinformatics analysis
Cited by: 78
Author(s): Xingwang Zhao, Longlong Zhang, Juan Wang, Min Zhang, Zhiqiang Song, Bing Ni, Yi You
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pgen.1000642
A Systems Genetics Approach Implicates USF1, FADS3, and Other Causal Candidate Genes for Familial Combined Hyperlipidemia
Cited by: 144
Author(s): Christopher L. Plaisier, Steve Horvath, Adriana Huertas-Vázquez, Ivette Cruz-Bautista, Miguel F. Herrera, Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Päivi Pajukanta
Software Mentions: 4
Published: about 15 years ago
10.1186/s12967-020-02491-w
Analyzing and validating the prognostic value and mechanism of colon cancer immune microenvironment
Cited by: 46
Author(s): Xinyi Wang, Jinzhong Duanmu, Xiaorui Fu, Taiyuan Li, Qunguang Jiang
Software Mentions: 4
Published: about 4 years ago
10.1186/1755-8794-6-51
Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia
Cited by: 26
Author(s): Eduardo Tejera, João Bernardes, Irene Rebelo
Software Mentions: 4
Published: about 11 years ago
10.18632/oncotarget.27935
Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability
Cited by: 5
Author(s): Matthew Devall, Graham Casey
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1007851
LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer
Cited by: 16
Author(s): Junpeng Zhang, Taosheng Xu, Lin Liu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le
Software Mentions: 4
Published: over 4 years ago
10.1186/s12872-020-01838-x
Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Cited by: 4
Author(s): Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu
Software Mentions: 4
Published: almost 4 years ago
10.3389/fimmu.2021.644350
Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple Cancers
Cited by: 5
Author(s): Lei Liu, Qiuchen Zhao, Chao Cheng, Jingwen Yi, Hongyan Sun, Qi Wang, Weili Quan, Yaqiang Xue, Luguo Sun, Xianling Cong, Yi Zhang
Software Mentions: 4
Published: over 3 years ago
10.18632/oncotarget.24898
Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets
Cited by: 17
Author(s): Rosemarie Weikard, Frieder Hadlich, H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Christa Kühn
Software Mentions: 4
Published: over 6 years ago
10.1186/s12920-015-0133-x
Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways
Cited by: 115
Author(s): David Adrian Ewald, Dana Malajian, James G. Krueger, Christopher T. Workman, Tianjiao Wang, Suyan Tian, Thomas Litman, Emma Guttman‐Yassky, Mayte Suárez‐Fariñas
Software Mentions: 4
Published: about 9 years ago
10.1186/s12920-019-0518-3
Integrative genomic and transcriptomic analysis of genetic markers in Dupuytren’s disease
Cited by: 9
Author(s): Junghyun Jung, Go Woon Kim, Byungjo Lee, Jong Wha J. Joo, Wonhee Jang
Software Mentions: 4
Published: over 5 years ago
10.3389/fimmu.2021.677730
Dual-Organ Transcriptomic Analysis of Rainbow Trout Infected With Ichthyophthirius multifiliis Through Co-Expression and Machine Learning
Cited by: 9
Author(s): HyeongJin Roh, Nameun Kim, Yoonhang Lee, Jiyeon Park, Bo Seong Kim, Mu Kun Lee, Chan-Il Park, Do-Hyung Kim
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pgen.1005474
Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
Cited by: 16
Author(s): Christian Kappel, Gerda Trost, Hjördis Czesnick, Anna Ramming, Benjamin Kolbe, Son Lang, Cláudia Bispo, Jörg Becker, Cornelia H. de Moor, Michael Lenhard
Software Mentions: 4
Published: about 9 years ago
10.18632/oncotarget.22475
Organotypic three-dimensional cancer cell cultures mirror drug responses<i>in vivo</i>: lessons learned from the inhibition of EGFR signaling
Cited by: 35
Author(s): Nico Jacobi, Rita Seeboeck, Elisabeth Hofmann, Helmut Schweiger, Veronika Smolinská, Thomas Mohr, Alexandra Boyer, Wolfgang Sommergruber, P. Lechner, Corina Pichler-Huebschmann, Kamil Önder, Harald Hundsberger, Christoph Wiesner, Andreas Eger
Software Mentions: 4
Published: about 7 years ago
10.1371/journal.pcbi.1004755
FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks
Cited by: 55
Author(s): Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Zhe Sun, Matthew L. MacDonald, Robert A. Sweet, Jieru Wang, Wei Chen
Software Mentions: 4
Published: almost 9 years ago
10.1371/journal.pcbi.1004005
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
Cited by: 110
Author(s): James Mahoney, Jaclyn N. Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique Hinchcliff, Michael L. Whitfield
Software Mentions: 4
Published: almost 10 years ago
10.18632/aging.202173
A novel immune-related genes prognosis biomarker for hepatocellular carcinoma
Cited by: 7
Author(s): Kunpeng Wang, Xinyi Chen, Chong Jin, Jinggang Mo, Hao Jiang, Bin Yi, Xiang Chen
Software Mentions: 4
Published: almost 4 years ago
10.3389/fimmu.2021.716075
Transcriptome Analysis of Peripheral Blood Mononuclear Cells Reveals Distinct Immune Response in Asymptomatic and Re-Detectable Positive COVID-19 Patients
Cited by: 10
Author(s): Jiaqi Zhang, Dan Lin, Kui Li, Xiangming Ding, Lin Li, Yuntao Liu, Dongdong Liu, Jing Lin, Xiangyun Teng, Yizhe Li, Ming Liu, Jian Shen, Xiaodan Wang, He Dan, Yawei Shi, Dawei Wang, Jianhua Xu
Software Mentions: 4
Published: over 3 years ago
10.18632/oncotarget.23065
Transcriptome evolution from breast epithelial cells to basal-like tumors
Cited by: 11
Author(s): Gabriel Santpere, Ana Alcaráz-Sanabria, Verónica Corrales-Sánchez, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
Software Mentions: 4
Published: almost 7 years ago
10.1186/1471-2164-15-300
Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer
Cited by: 81
Author(s): Wei-Chun Chou, An‐Lin Cheng, Marco Brotto, Chun‐Yu Chuang
Software Mentions: 4
Published: over 10 years ago
10.18632/oncotarget.11788
Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics
Cited by: 64
Author(s): Zhibo Qu, Jingang Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qi Feng, Joy M. Raison, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: about 8 years ago
10.3389/fimmu.2019.00197
Inflation vs. Exhaustion of Antiviral CD8+ T-Cell Populations in Persistent Infections: Two Sides of the Same Coin?
Cited by: 16
Author(s): Emanuele Marchi, Lian Ni Lee, Paul Klenerman
Software Mentions: 4
Published: over 5 years ago
10.18632/oncotarget.14303
Pan-organ transcriptome variation across 21 cancer types
Cited by: 6
Author(s): Wangxiong Hu, Yanmei Yang, Xiaofen Li, Shu Zheng
Software Mentions: 4
Published: almost 8 years ago
10.3389/fgene.2021.563051
Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis
Cited by: 7
Author(s): Chunhong Hong, Shaohua Yang, Qiaojin Wang, Shiqiang Zhang, Wenhui Wu, Jinyao Chen, Danhui Zhong, Mingzhe Li, Liang Li, Jianfeng Li, Hong Yu, Hong Chen, Qianlin Zeng, Changhua Zhang
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2018.00328
Co-expression Network Analysis of Biomarkers for Adrenocortical Carcinoma
Cited by: 37
Author(s): Lushun Yuan, Guofeng Qian, Liang Chen, Chin‐Lee Wu, Dong Han, Yu Xiao, Xinghuan Wang
Software Mentions: 4
Published: over 6 years ago
10.1155/2020/3656841
Genetic Profiles Playing Opposite Roles of Pathogenesis in Schizophrenia and Glioma
Cited by: 3
Author(s): Yujie Wen, Zhiwei Xia, Dongjie Li, Quan Cheng, Qing Zhao, Hui Cao
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pbio.3000187
Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses
Cited by: 49
Author(s): Bo Lv, Qin An, Qiao Zeng, Xunyi Zhang, Ping Lü, Yanqiu Wang, Xianmin Zhu, Yao Ji, Guoping Fan, Zhigang Xue
Software Mentions: 4
Published: about 5 years ago
10.1155/2019/1785042
Low GAS5 Levels as a Predictor of Poor Survival in Patients with Lower-Grade Gliomas
Cited by: 18
Author(s): Yanfang Wang, Xin Shan, Kai Zhang, Run Shi, Xuanwen Bao
Software Mentions: 4
Published: almost 6 years ago
10.18632/oncotarget.15842
Identifying biomarkers of papillary renal cell carcinoma associated with pathological stage by weighted gene co-expression network analysis
Cited by: 29
Author(s): Zhong He, Min Sun, Ke Yuan, Rongjie Lin, Youde Xiao, Shaosheng Zhou, Hong Zhao, Yan Wang, Fuxiang Zhou, Youwen Zhou
Software Mentions: 4
Published: over 7 years ago
10.3389/fimmu.2019.02096
Plasmacytoid DCs From Patients With Sjögren's Syndrome Are Transcriptionally Primed for Enhanced Pro-inflammatory Cytokine Production
Cited by: 37
Author(s): Maarten R Hillen, Aridaman Pandit, Sofie L M Blokland, Sarita A. Y. Hartgring, Cornelis P. J. Bekker, Eefje Hanna Martine van der Heijden, Nila Hendrika Servaas, Marzia Rossato, Aike A. Kruize, Joël A G van Roon, Timothy R D J Radstake
Software Mentions: 4
Published: about 5 years ago
10.1186/s12864-020-6467-6
Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population
Cited by: 8
Author(s): Enoch Ng’oma, Patricka A. Williams-Simon, Aniqa Rahman, King Eg
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pbio.3000976
Cortical morphology at birth reflects spatiotemporal patterns of gene expression in the fetal human brain
Cited by: 33
Author(s): Gareth Ball, Jakob Seidlitz, Jonathan O’Muircheartaigh, Ralica Dimitrova, Daphna Fenchel, Antonios Makropoulos, Daan Christiaens, Andreas Schuh, Jonathan Passerat–Palmbach, Jana Hutter, Lucilio Cordero‐Grande, Emer Hughes, Anthony N. Price, Jo Hajnal, Daniel Rueckert, Emma C. Robinson, A. David Edwards
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pbio.3000711
Single-cell transcription analysis of Plasmodium vivax blood-stage parasites identifies stage- and species-specific profiles of expression
Cited by: 49
Author(s): Juliana M. Sá, Matthew Cannon, Ramoncito L. Caleon, Thomas E. Wellems, David Serre
Software Mentions: 4
Published: over 4 years ago
10.1186/s12974-020-02045-3
Transcriptional heterogeneity between primary adult grey and white matter astrocytes underlie differences in modulation of in vitro myelination
Cited by: 10
Author(s): Inge Werkman, Marissa Dubbelaar, Pieter van der Vlies, Jelkje J. de Boer-Bergsma, Bart J. L. Eggen, Wia Baron
Software Mentions: 4
Published: almost 4 years ago
10.3390/plants8120531
Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development
Cited by: 9
Author(s): Giulio Testone, Elena Baldoni, Maria Adelaide Iannelli, Chiara Nicolodi, Elisabetta Di Giacomo, Fabrizio Pietrini, Giovanni Mele, Donato Giannino, Giovanna Frugis
Software Mentions: 4
Published: about 5 years ago
10.3389/fgene.2020.603264
Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules
Cited by: 2
Author(s): James Lim, Chen Chen, Adam Grant, Megha Padi
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2021.628136
Breast Cancer Case Identification Based on Deep Learning and Bioinformatics Analysis
Cited by: 8
Author(s): Dongfang Jia, Cheng Chen, Fangfang Chen, Ningrui Zhang, Ziwei Yan
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2018.00183
Network-Based Predictors of Progression in Head and Neck Squamous Cell Carcinoma
Cited by: 20
Author(s): Nasim Sanati, Ovidiu D. Iancu, Guanming Wu, Jan Jacobs, Shannon K. McWeeney
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-016-2650-1
Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)
Cited by: 101
Author(s): Yuanda Lv, Zhikai Liang, Min Ge, Weicong Qi, Tifu Zhang, Feng Lin, Zhaohua Peng, Han Zhao
Software Mentions: 4
Published: over 8 years ago
10.1186/s12864-019-5428-4
New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: almost 6 years ago
10.3389/fgene.2019.01018
Transcriptome Analysis Identifies Piwi-Interacting RNAs as Prognostic Markers for Recurrence of Prostate Cancer
Cited by: 12
Author(s): Yuanli Zuo, Liang Yu, Jiting Zhang, You-Zeng Hao, Menglong Li, Zhining Wen, Yun Zhao
Software Mentions: 4
Published: about 5 years ago
10.3390/ijms22147266
Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts
Cited by: 12
Author(s): Weitao Li, Li Huang, Nian Liu, Manish K. Pandey, Yuning Chen, Cheng Ling, Jianbin Guo, Bin Yu, Huaiyong Luo, Xiaojing Zhou, Dongxin Huai, Weigang Chen, Liying Yan, Xin Wang, Yong Lei, Rajeev K. Varshney, Boshou Liao, Huifang Jiang
Software Mentions: 4
Published: over 3 years ago
10.3390/plants10040769
Transcriptome Analysis of Needle and Root of Pinus Massoniana in Response to Continuous Drought Stress
Cited by: 10
Author(s): Xiaozhou Feng, Zhao Yang, Xiurong Wang, Qiao Li, Jie Ran
Software Mentions: 4
Published: over 3 years ago
10.3390/ijms22158251
DIA-Based Quantitative Proteomics Reveals the Protein Regulatory Networks of Floral Thermogenesis in Nelumbo nucifera
Cited by: 5
Author(s): Yueyang Sun, Yu Zeng, Jing Jin, Hao Chen, Zhiying Liu, Qinru Zi, Zeyang Xiong, Ying Wang, Qian Li, Jing Peng, Yi Ding
Software Mentions: 4
Published: over 3 years ago
10.3390/ijms22094864
Characterization of Extracellular Vesicle Cargo in Sjögren’s Syndrome through a SWATH-MS Proteomics Approach
Cited by: 11
Author(s): Francesco Finamore, Antonella Cecchettini, Elisa Ceccherini, Giovanni Signore, Francesco Ferro, Silvia Rocchiccioli, Chiara Baldini
Software Mentions: 4
Published: over 3 years ago
10.3390/ijms22020574
The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes
Cited by: 7
Author(s): Michał Książkiewicz, Sandra Rychel-Bielska, Piotr Plewiński, Maria Nuc, Witold Irzykowski, M. Jędryczka, Paweł Krajewski
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2021.694777
Identification of Signature Genes Associated With Invasiveness and the Construction of a Prognostic Model That Predicts the Overall Survival of Bladder Cancer
Cited by: 10
Author(s): Yang He, Yu Wu, Zhe Liu, Boping Li, Ning Jiang, Peng Xu, Aiming Xu
Software Mentions: 4
Published: about 3 years ago
10.1186/s12915-020-00793-5
Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Cited by: 28
Author(s): Yang Zhou, Shuli Liu, Yan Hu, Lingzhao Fang, Yahui Gao, Han Xia, Steven G. Schroeder, Benjamin D. Rosen, Erin E. Connor, Congjun Li, R.L. Baldwin, John B. Cole, Curtis P. Van Tassell, Liguo Yang, Li Ma, George E. Liu
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-020-06793-7
Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress
Cited by: 8
Author(s): Caitlin M. A. Simopoulos, Mitchell MacLeod, Solmaz Irani, Wilson W L Sung, Marc J. Champigny, Peter S. Summers, G. Brian Golding, Elizabeth A. Weretilnyk
Software Mentions: 4
Published: over 4 years ago
10.1128/mSphere.01044-20
Gut Bacteria Shared by Children and Their Mothers Associate with Developmental Level and Social Deficits in Autism Spectrum Disorder
Cited by: 5
Author(s): Yu Chen, Hui Fang, Chunyan Li, Guojun Wu, Ting Xu, Xin Yang, Liping Zhao, Xiaoyan Ke, Chenhong Zhang
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12915-020-00862-9
Genome-enabled insights into the biology of thrips as crop pests
Cited by: 44
Author(s): Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G.C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis, Simon Snoeck, Clauvis Nji Tizi Taning, Dong Wei, Shirani M. K. Widana Gamage, Daniel Hughes, Shwetha C. Murali, Samuel T. Bailey, Nicolás Bejerman, Christopher J. Holmes, Emily C. Jennings, Andrew J. Rosendale, Andrew E. Rosselot, Kaylee Hervey, Brandi A. Schneweis, Sammy Cheng, Christopher P. Childers, Felipe A. Simão, Ralf G. Dietzgen, Hsu Chao, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Yi Han, Sandra L. Lee, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Joshua B. Benoit, Markus Friedrich, Jeffery W. Jones, Kristen A. Panfilio, Yoonseong Park, Hugh M. Robertson, Guy Smagghe, Diane E. Ullman, Maurijn van der Zee, Thomas Van Leeuwen, Jan A. Veenstra, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Anna E. Whitfield, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: about 4 years ago
10.3389/fgene.2020.00478
Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer
Cited by: 25
Author(s): Weigang Chen, Chang Gao, Yong Liu, Ying Wen, Xiaoling Hong, Zunnan Huang
Software Mentions: 4
Published: over 4 years ago
10.1038/s41398-021-01431-6
Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders
Cited by: 3
Author(s): Pei‐Fen Kuan, Xiaohua Yang, Ruwei Xu, Chang Che, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: over 3 years ago
10.1038/s41398-020-01096-7
Gestational diabetes induces behavioral and brain gene transcription dysregulation in adult offspring
Cited by: 11
Author(s): Keren Aviel-Shekler, Yara Hamshawi, Worood Sirhan, Dmitriy Getselter, Kannan Srikanth, Assaf Malka, Ron Piran, Evan Elliott
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41398-019-0472-z
DLPFC transcriptome defines two molecular subtypes of schizophrenia
Cited by: 26
Author(s): Elijah F. W. Bowen, Jack L. Burgess, Richard Granger, Joel E. Kleinman, C. Harker Rhodes
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-016-3390-y
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: almost 8 years ago
10.18632/aging.202634
Long non-coding RNAs ENST00000429730.1 and MSTRG.93125.4 are associated with metabolic activity in tuberculosis lesions of sputum-negative tuberculosis patients
Cited by: 5
Author(s): Lin Wang, Wen Zhu, Hui Ma, Liwei Wu, Hui Chen, Yijun Zhu, Liangfei Niu, Qihang Wu, Hongwei Li, Lei Shi, Leilei Li, Leiyi Wan, Jun Wang, Ka-Wing Wong, Yanzheng Song
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2105-13-S10-S7
A systematic comparison of genome-scale clustering algorithms
Cited by: 45
Author(s): Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, Michael A. Langston
Software Mentions: 4
Published: over 12 years ago
10.3389/fgene.2021.628192
KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs
Cited by: 7
Author(s): Tao Wang, Yuanyuan Guo, Shengwei Liu, Chaoxin Zhang, Tongyan Cui, Kun Ding, Peng Wang, Xibiao Wang, Zhipeng Wang
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2020.00934
Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma
Cited by: 8
Author(s): Sijie Zhou, Jiuyuan Fang, Yan Sun, Huixiang Li
Software Mentions: 4
Published: about 4 years ago
10.1128/mBio.00586-21
Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits
Cited by: 13
Author(s): Joshua M. Wang, Andrew L. Woodruff, Matthew J. Dunn, Robert J. Fillinger, Richard J. Bennett, Matthew Anderson
Software Mentions: 4
Published: over 3 years ago
10.1128/mSystems.00596-19
Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 5 years ago
10.3390/ijms221910390
Upregulation of the APOBEC3 Family Is Associated with a Poor Prognosis and Influences Treatment Response to Raf Inhibitors in Low Grade Glioma
Cited by: 4
Author(s): Cheng Luo, Songmao Wang, Weijie Liao, Shikuan Zhang, Ning Xu, Weidong Xie, Yaou Zhang
Software Mentions: 4
Published: about 3 years ago
10.3389/fgene.2021.633059
Prediction of a Competing Endogenous RNA Co-expression Network by Comprehensive Methods in Systemic Sclerosis-Related Interstitial Lung Disease
Cited by: 2
Author(s): Yue-Mei Yan, Ji-Na Zheng, Liwei Wu, Qianwen Rao, Qiaorong Yang, Di Gao, Qiang Wang
Software Mentions: 4
Published: over 3 years ago
10.1038/s41398-017-0058-6
Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons
Cited by: 43
Author(s): Ping Wang, Dejian Zhao, Herbert M. Lachman, Deyou Zheng
Software Mentions: 4
Published: almost 7 years ago
10.3389/fgene.2021.630215
Comparing Statistical Tests for Differential Network Analysis of Gene Modules
Cited by: 2
Author(s): Jaron Arbet, Yaxu Zhuang, Elizabeth Litkowski, Laura Saba, Katerina Kechris
Software Mentions: 4
Published: over 3 years ago