cran: WGCNA | Projects | Ecosyste.ms: Papers

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 6 years ago

10.3389/fonc.2020.541479

Identification and Validation of Novel Biomarkers for Diagnosis and Prognosis of Hepatocellular Carcinoma
Cited by: 26
Author(s): Xiaoyi Hu, Mingyang Bao, Jiacheng Huang, Lin Zhou, Shusen Zheng
Software Mentions: 4
Published: about 6 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 6 years ago

10.3389/fonc.2020.00681

Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 50
Author(s): Chia‐Ying Li, Jia-Hua Cai, Jeffrey J. P. Tsai, Charles C.N. Wang
Software Mentions: 4
Published: over 6 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 6 years ago

10.1002/cam4.3372

Identification of prognostic biomarkers associated with stromal cell infiltration in muscle‐invasive bladder cancer by bioinformatics analyses
Cited by: 10
Author(s): Pan Li, Jinlong Cao, Jianpeng Li, Zhiqiang Yao, Dali Han, Lijun Ying, Zhiping Wang, Junqiang Tian
Software Mentions: 4
Published: about 6 years ago

10.1002/cam4.2969

Identification of hub methylated‐CpG sites and associated genes in oral squamous cell carcinoma
Cited by: 14
Author(s): Yuxin Dai, Qiao‐Li Lv, Tingting Qi, Jian Qu, Hongli Ni, Yongkang Liao, Peng Liu, Qiang Qu
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2020.541401

Prognosis Analysis and Validation of m6A Signature and Tumor Immune Microenvironment in Glioma
Cited by: 46
Author(s): Sheng Lin, Houshi Xu, Anke Zhang, Yunjia Ni, Yuanzhi Xu, Tong Meng, Mingjie Wang, Meiqing Lou
Software Mentions: 4
Published: about 6 years ago

10.3389/fnins.2020.562292

Human iPSC-Derived Neuronal Cells From CTBP1-Mutated Patients Reveal Altered Expression of Neurodevelopmental Gene Networks
Cited by: 5
Author(s): S. Vijayalingam, Uthayashanker R. Ezekiel, Fenglian Xu, T. Subramanian, Elizabeth Geerling, Brittany Hoelscher, KayKay San, Aravinda Ganapathy, Kyle Pemberton, Eric Tycksen, Amelia K. Pinto, James D. Brien, David B. Beck, Wendy K. Chung, Christina A. Gurnett, G. Chinnadurai
Software Mentions: 4
Published: about 6 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 6 years ago

10.3389/fonc.2020.560229

A Molecular Subtype Model for Liver HBV-Related Hepatocellular Carcinoma Patients Based on Immune-Related Genes
Cited by: 5
Author(s): Qiyao Zhang, Xiao Yu, Qingyuan Zheng, Yuting He, Wenzhi Guo
Software Mentions: 4
Published: about 6 years ago

10.3389/fnins.2021.639527

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders
Cited by: 5
Author(s): Junlin Shen, Bing‐Bing Yang, Zhonghua Xie, Heng Wu, Zhanye Zheng, Jianhua Wang, Ping Wang, Peng Zhang, Wei Li, Zhaoxiang Ye, Chunshui Yu
Software Mentions: 4
Published: over 5 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 6 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 10 years ago

10.1186/s12935-020-01352-2

Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma
Cited by: 19
Author(s): Naiqiang Zhu, Jingyi Hou, Guiyun Ma, Shuai Guo, Chengliang Zhao, Bin Chen
Software Mentions: 4
Published: over 6 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 5 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 14 years ago

10.1038/s42003-019-0391-9

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation
Cited by: 25
Author(s): Alborz Mazloomian, Shinsuke Araki, Momoko Ohori, Amal M. El-Naggar, Damian Yap, Ali Bashashati, Shigetomi Nakao, Poul H. Sorensen, Atsushi Nakanishi, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 4
Published: over 7 years ago

10.3389/fnins.2020.00774

Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala
Cited by: 19
Author(s): Marissa R Keever, Pan Zhang, Courtni R. Bolt, Adrienne M. Antonson, Haley E Rymut, Megan P. Caputo, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 4
Published: about 6 years ago

10.3389/fnins.2017.00112

Antidyskinetic Effects of MEK Inhibitor Are Associated with Multiple Neurochemical Alterations in the Striatum of Hemiparkinsonian Rats
Cited by: 21
Author(s): Guiqin Chen, Shuke Nie, Chao Han, Kai Ma, Xu Yan, Zhentao Zhang, Stella M. Papa, Xin Cao
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0185682

Meta-analysis of peripheral blood gene expression modules for COPD phenotypes
Cited by: 15
Author(s): Dominik Reinhold, Jarrett Morrow, Sean Jacobson, Junxiao Hu, Benjamin Ringel, Max A. Seibold, Craig P. Hersh, Katerina Kechris, Russell P. Bowler
Software Mentions: 4
Published: about 9 years ago

10.3389/fnins.2021.657465

Novel Insight Into the Role of Immune Dysregulation in Amyotrophic Lateral Sclerosis Based on Bioinformatic Analysis
Cited by: 7
Author(s): Yuanyang Xie, Ximei Luo, Hongping He, Min Tang
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/4348371

DHX36, BAX, and ARPC1B May Be Critical for the Diagnosis and Treatment of Tuberculosis
Cited by: 3
Author(s): Yunli Zhang, Yanming Liu, Hongling Li, Qingxia Liu, Wei Wang, Zijuan Jian, Wenen Liu
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0210672

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures
Cited by: 28
Author(s): Tingting Song, Keting Li, Ting Wu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Yuncong Yao, Zhenhai Han
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-019-6021-6

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)
Cited by: 17
Author(s): Liqing Zhou, Zhihong Liu, Yan Dong, Xiujun Sun, Biao Wu, Tao Yu, Yao Zheng, Aiguo Yang, Qing Zhao, Dan Zhao
Software Mentions: 4
Published: about 7 years ago

10.3389/fnmol.2021.639145

Post-stroke Delivery of Valproic Acid Promotes Functional Recovery and Differentially Modifies Responses of Peri-Infarct Microglia
Cited by: 6
Author(s): Tung‐Tai Kuo, Vicki Wang, Jui-Sheng Wu, Yuan-Hao Chen, Kuan-Yin Tseng
Software Mentions: 4
Published: over 5 years ago

10.3390/nu12123602

Epigenetic Patterns in Five-Year-Old Children Exposed to a Low Glycemic Index Dietary Intervention during Pregnancy: Results from the ROLO Kids Study
Cited by: 10
Author(s): Aisling A. Geraghty, A. Sexton-Oates, Eileen C. O’Brien, Richard Saffery, Fionnuala M. McAuliffe
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13058-018-0933-y

HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors
Cited by: 44
Author(s): Anneleen Daemen, Gerard Manning
Software Mentions: 4
Published: almost 9 years ago

10.1590/1414-431X2021e11363

Dysregulation of KIF14 regulates the cell cycle and predicts poor prognosis in cervical cancer: a study based on integrated approaches
Cited by: 4
Author(s): Xiao Li, Sisi Zhang, Qingyu Zheng, Shuirong Zhang
Software Mentions: 4
Published: almost 6 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 6 years ago

10.1186/1471-2164-14-728

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: about 13 years ago

10.1186/s12864-015-1522-4

Transcriptomic profiles of aging in purified human immune cells
Cited by: 57
Author(s): Lindsay M. Reynolds, Jingzhong Ding, Jeanette Taylor, Kurt Lohman, Nicola Soranzo, Alberto de la Fuente, Tie Fu Liu, Craig W. Johnson, R. Graham Barr, Thomas C. Register, Kathleen Donohue, Monica V. Talor, Daniela Čiháková, C. Charles Gu, Jasmin Divers, David S. Siscovick, Gregory L. Burke, Wendy S. Post, Steven Shea, David R. Jacobs, Ina Hoeschele, Charles E. McCall, Stephen B. Kritchevsky, David M. Herrington, Russell P. Tracy, Yongmei Liu
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0056228

canEvolve: A Web Portal for Integrative Oncogenomics
Cited by: 39
Author(s): Mehmet K. Samur, Zhenyu Yan, Xujun Wang, Qingyi Cao, Nikhil C. Munshi, Li Cheng, Parantu K. Shah
Software Mentions: 4
Published: over 13 years ago

10.18632/aging.202228

Identification of SCARA3 with potential roles in metabolic disorders
Cited by: 7
Author(s): Hui Peng, Qi Guo, Tian Su, Ye Xiao, Changjun Li, Yan Huang, Xiang‐Hang Luo
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0229308

Weighted gene co-expression network analysis identified six hub genes associated with rupture of intracranial aneurysms
Cited by: 6
Author(s): Qunhui Wang, Qiong Luo, Zhuo Yang, Yuhao Zhao, Jiaqi Li, Jian Wang, Jianmin Piao, Xuan Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fmolb.2021.708127

Glucotoxicity Activation of IL6 and IL11 and Subsequent Induction of Fibrosis May Be Involved in the Pathogenesis of Islet Dysfunction
Cited by: 6
Author(s): Laiwei Lu, Lili Zhuang, Xiaodong Shen, Liyong Yang
Software Mentions: 4
Published: about 5 years ago

10.3389/fmolb.2021.622643

Immune-Inhibitory Gene Expression is Positively Correlated with Overall Immune Activity and Predicts Increased Survival Probability of Cervical and Head and Neck Cancer Patients
Cited by: 10
Author(s): Megha Budhwani, Gavin Turrell, Meihua Yu, Ian H. Frazer, Ahmed M. Mehdi, Janin Chandra
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-020-02463-0

Identifying the pattern of immune related cells and genes in the peripheral blood of ischemic stroke
Cited by: 24
Author(s): Zijian Li, Yueran Cui, Juan Feng, Yanxia Guo
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0206665

Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer
Cited by: 11
Author(s): Kanthida Kusonmano, Mari K. Halle, Elisabeth Wik, Erling A. Høivik, Camilla Krakstad, Karen Klepsland Mauland, Ingvild L. Tangen, Ansgar Berg, Henrica M.J. Werner, Jone Trovik, Anne Margrete Øyan, Karl‐Henning Kalland, Inge Jonassen, Helga B. Salvesen, Kjell Petersen
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0253037

A meta-analysis of transcriptomic profiles of Huntington’s disease patients
Cited by: 14
Author(s): Manuel Seefelder, Stefan Kochanek
Software Mentions: 4
Published: over 5 years ago

10.3389/fmolb.2021.632950

Comprehensive Metabolomics Identified the Prominent Role of Glycerophospholipid Metabolism in Coronary Artery Disease Progression
Cited by: 10
Author(s): Hui Chen, Zixian Wang, Min Qin, Bin Zhang, Li Jen Lin, Qin Ma, Chen Liu, Xiaoping Chen, Hanping Li, Wen‐Ter Lai, Shilong Zhong
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-021-02870-x

High copy number variations, particular transcription factors, and low immunity contribute to the stemness of prostate cancer cells
Cited by: 9
Author(s): Zao Dai, Ping Liu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-020-02372-2

Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis
Cited by: 38
Author(s): Lixin Cheng, Chuanchuan Nan, Lin Kang, Ning Zhang, Sheng Liu, Huaisheng Chen, Chengying Hong, Youlian Chen, Zhen Liang, Xueyan Liu
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21249560

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses
Cited by: 2
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmolb.2021.719982

Identification of Mast Cell-Based Molecular Subtypes and a Predictive Signature in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Hanxiang Liu, Yi Yang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-021-07731-x

Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice
Cited by: 16
Author(s): Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiaowei Chi, Tongzuo Zhang
Software Mentions: 4
Published: over 5 years ago

10.1042/BSR20203020

Network-based approach to identify prognosis-related genes in tamoxifen-treated patients with estrogen receptor-positive breast cancer
Cited by: 4
Author(s): Yanyan Wang, Xiaonan Gong, Yujie Zhang
Software Mentions: 4
Published: about 5 years ago

10.1042/BSR20200516

Association between SNAP25 and human glioblastoma multiform: a comprehensive bioinformatic analysis
Cited by: 5
Author(s): Changhong Yu, Jianxing Yin, Xiefeng Wang, Lijiu Chen, Yutian Wei, Chenfei Lu, Yongping You
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5850-7

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks
Cited by: 6
Author(s): Kevin B. Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, D Lambert, Stephen Brown, James R. Bradford
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0177750

Inflammatory and apoptotic remodeling in autonomic nervous system following myocardial infarction
Cited by: 23
Author(s): Chen Gao, Kimberly Howard‐Quijano, Christoph Rau, Tatsuo Takamiya, Yang Song, Kalyanam Shivkumar, Yibin Wang, Aman Mahajan
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms20092177

Polysome Profiling of a Human Glioblastoma Reveals Intratumoral Heterogeneity
Cited by: 9
Author(s): Fernanda C. S. Lupinacci, Hellen Kuasne, Martín Roffé, Julia Avian Vassalakis, Fernanda Ferreira da Silva, Tiago G. Santos, Victor Piana de Andrade, Paulo Sanematsu, Vilma R. Martins, Sílvia Regina Rogatto, Glaucia Noeli Maroso Hajj
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0192613

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples
Cited by: 17
Author(s): Hua Yu, Bingke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang, Wei Liu
Software Mentions: 4
Published: over 8 years ago

10.1042/BSR20203235

Mining the key genes for ventilator-induced lung injury using co-expression network analysis
Cited by: 2
Author(s): Li Zhao, Yajun Xiao, Li Xu, Qingxiu Wang
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-020-01152-4

Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs
Cited by: 23
Author(s): Maxwell J. Scott, Joshua B. Benoit, Rebecca J. Davis, Samuel T. Bailey, Virág Varga, Ellen O. Martinson, Paul V. Hickner, Zainulabeuddin Syed, Gisele Antoniazzi Cardoso, Tatiana Teixeira Torres, Matthew T. Weirauch, Elizabeth H. Scholl, Adam M. Phillippy, Agustin Sagel, Mario Vasquez, Gladys Quintero, S. Skoda
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms20123101

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation
Cited by: 29
Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller‐Roeber, Tsanko Gechev
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.579290

Spatiotemporal Patterns in Diversity and Assembly Process of Marine Protist Communities of the Changjiang (Yangtze River) Plume and Its Adjacent Waters
Cited by: 8
Author(s): Xin Guo, Lianghuan Wu, Lingfeng Huang
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.68130

Cellular, circuit and transcriptional framework for modulation of itch in the central amygdala
Cited by: 19
Author(s): Vijay K. Samineni, Gary E. Grajales‐Reyes, Eric Tycksen, Bryan A. Copits, Christian Pedersen, Edem S Ankudey, Julian N Sackey, Sienna B Sewell, Michael R. Bruchas, Robert W. Gereau
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2016.01688

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways
Cited by: 19
Author(s): Sadegh Azimzadeh Jamalkandi, Sayed‐Hamidreza Mozhgani, Hamid Gholami Pourbadie, Mehdi Mirzaie, Farshid Noorbakhsh, Behrouz Vaziri, Alireza Gholami, Naser Ansari-Pour, Mohieddin Jafari
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.46149

Identification of potential biomarkers of vaccine inflammation in mice
Cited by: 23
Author(s): Paul F. McKay, Deniz Cizmeci, Yoann Aldon, Jeroen Maertzdorf, January Weiner, Stefan H. E. Kaufmann, David Lewis, Robert A. van den Berg, Giuseppe Del Giudice, Robin J. Shattock
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.46981

Transcriptional landscape of myogenesis from human pluripotent stem cells reveals a key role of TWIST1 in maintenance of skeletal muscle progenitors
Cited by: 27
Author(s): In Young Choi, Hotae Lim, Hyeon Jin Cho, Yohan Oh, Bin Kuan Chou, Hao Bai, Linzhao Cheng, Yong Jun Kim, Sang‐Hwan Hyun, Hyesoo Kim, Joo Heon Shin, Gabsang Lee
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.34613

Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues
Cited by: 93
Author(s): Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Marianne Wallace, Lance A. Riley, Collin M Douglas, Miguel A. Gutiérrez-Monreal, Nicholas F. Lahens, Ming Gong, Francisco H. Andrade, Karyn A. Esser, Michael Hughes
Software Mentions: 4
Published: over 8 years ago

10.1042/BSR20211280

Identification of hub genes in colorectal cancer based on weighted gene co-expression network analysis and clinical data from The Cancer Genome Atlas
Cited by: 23
Author(s): Yu Zhang, Jia Luo, Zhe Liu, Xudong Li, Ying Ma, Bohang Zhang, Yuxuan Chen, Xiaofeng Li, Zhi-Guo Feng, Ningning Yang, Dayun Feng, Lei Wang, Xiu–Peng Song
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.102275

Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice
Cited by: 52
Author(s): Huimin Li, Xinhui Wang, Xinyue Lu, Hongxin Zhu, Sheng Li, Shiwei Duan, Xinzhi Zhao, Fuquan Zhang, Gil Alterovitz, Fudi Wang, Qiang Li, Xiao-Li Tian, Mingqing Xu
Software Mentions: 4
Published: about 7 years ago

10.3390/biom10091230

The Transcriptomic Evidence on the Role of Abdominal Visceral vs. Subcutaneous Adipose Tissue in the Pathophysiology of Diabetes in Asian Indians Indicates the Involvement of Both
Cited by: 6
Author(s): Anshul Kumar, Prabhat Tiwari, Aditya Saxena, Naincy Purwar, Nitin Wahi, Balram Sharma, Sandeep Kumar Mathur
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.573829

Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici
Cited by: 2
Author(s): Arthur J. Jallet, Arnaud Le Rouzic, Anne Génissel
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-018-5115-x

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
Cited by: 19
Author(s): Bi Jun Li, Dan Jiang, Zhijun Meng, Yong Zhang, Zong Xian Zhu, Haoran Lin, Jun Xia
Software Mentions: 4
Published: about 8 years ago

10.3390/biom10091207

Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder
Cited by: 24
Author(s): Dongmei Ai, Yuduo Wang, Xiaoxin Li, Hongfei Pan
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2021.599261

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
Cited by: 53
Author(s): Komudi Singh, Yunching Chen, Shakiba Hassanzadeh, Han Kim, Jennifer Judy, Fayaz Seifuddin, Ilker Tunc, Michael N. Sack, Mehdi Pirooznia
Software Mentions: 4
Published: over 5 years ago

10.3390/biomedicines9010034

Shared Blood Transcriptomic Signatures between Alzheimer’s Disease and Diabetes Mellitus
Cited by: 14
Author(s): Taesic Lee, Hyunju Lee
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.65582

Neural correlates of ingroup bias for prosociality in rats
Cited by: 25
Author(s): Inbal Ben-Ami Bartal, Jocelyn Breton, Huanjie Sheng, Kimberly L.P. Long, Stella Chen, Aline Halliday, Justin W. Kenney, Anne L. Wheeler, Paul W. Frankland, Carrie Shilyansky, Karl Deisseroth, Dacher Keltner, Daniela Kaufer
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/4908427

Comprehensive Analysis of mRNA Expression Profiles in Head and Neck Cancer by Using Robust Rank Aggregation and Weighted Gene Coexpression Network Analysis
Cited by: 4
Author(s): Zijian Cao, Yin-Jie Ao, Yu Guo, Shui‐Hong Zhou
Software Mentions: 4
Published: almost 6 years ago

10.1155/2021/9921195

A Computational Framework to Identify Transcriptional and Network Differences between Hepatocellular Carcinoma and Normal Liver Tissue and Their Applications in Repositioning Drugs
Cited by: 0
Author(s): Aimin Hu, Wei Zheng, Zuxiang Zheng, Bichao Luo, Jieming Yi, Xinhong Zhou, Changjiang Zeng
Software Mentions: 4
Published: about 5 years ago

10.1155/2021/9933136

Identification of Biomarkers for Predicting Allograft Rejection following Kidney Transplantation Based on the Weighted Gene Coexpression Network Analysis
Cited by: 2
Author(s): Lijun Wang, Xiao-Bo Ma, Hongying Xia, Xun Sun, Yu Lu, Qian Yang, Zongqiang Hu, Yi‐Fang Zhao, Wei Hu, Jianghua Ran
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-6161-8

Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat
Cited by: 17
Author(s): Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David Konkin, Ron Knox, Yuefeng Ruan, Pierre R. Fobert
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2017.01561

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
Cited by: 211
Author(s): Luisa W. Hugerth, Anders F. Andersson
Software Mentions: 4
Published: about 9 years ago

10.1084/jem.20202446

GSAP regulates lipid homeostasis and mitochondrial function associated with Alzheimer’s disease
Cited by: 14
Author(s): Peng Xu, Jerry C. Chang, Xiaopu Zhou, Wei Wang, Michael Bamkole, Eitan Wong, Karima Bettayeb, LuLin Jiang, Timothy Huang, Wenjie Luo, Huaxi Xu, Angus C. Nairn, Marc Flajolet, Nancy Y. Ip, Yueming Li, Paul Greengard
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-019-2596-9

Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
Cited by: 8
Author(s): André Voigt, Eivind Almaas
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2020.549213

Stemness Related Genes Revealed by Network Analysis Associated With Tumor Immune Microenvironment and the Clinical Outcome in Lung Adenocarcinoma
Cited by: 41
Author(s): Hao Zeng, Jianrui Ji, Xindi Song, Yeqian Huang, Hui Li, Juan Huang, Xuelei Ma
Software Mentions: 4
Published: about 6 years ago

10.1084/jem.20170412

A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis
Cited by: 43
Author(s): Alma-Martina Cepika, Romain Banchereau, Élodie Segura, Marina Ohouo, Brandi L. Cantarel, Kristina Goller, V. Ashley Cantrell, Emily Ruchaud, Elizabeth Gatewood, Phuong Nguyen, Jin Gu, Esperanza Anguiano, Sandra Zurawski, Jeanine Baisch, Marilynn Punaro, Nicole Baldwin, Gerlinde Obermoser, Karolina Palucka, Jacques Banchereau, Sebastián Amigorena, Virginia Pascual
Software Mentions: 4
Published: about 9 years ago

10.1155/2020/4612158

CCNB2, TOP2A, and ASPM Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis
Cited by: 9
Author(s): Yuping Zeng, He He, Yu Zhang, Xia Wang, Yang Lin-de, Zhenmei An
Software Mentions: 4
Published: over 6 years ago

10.1186/s13046-020-01752-2

MiRNA-340-5p mediates the functional and infiltrative promotion of tumor-infiltrating CD8+ T lymphocytes in human diffuse large B cell lymphoma
Cited by: 9
Author(s): Yangyang Xu, Zhenchuan Liu, Lixin Lv, Ping Li, Bing Xu, Wenbin Qian, Aibin Liang
Software Mentions: 4
Published: almost 6 years ago

10.1084/jem.20190430

An anti-CRF antibody suppresses the HPA axis and reverses stress-induced phenotypes
Cited by: 7
Author(s): Hunter S. Futch, Karen N. McFarland, Brenda D. Moore, M. Zino Kuhn, Benoit I. Giasson, Thomas B. Ladd, Karen A. Scott, Melanie R. Shapiro, Rachel L. Nosacka, Marshall S. Goodwin, Yong Ran, Pedro Cruz, Doojin Ryu, Cara L. Croft, Yona Levites, Christopher Janus, Paramita Chakrabarty, Andrew R. Judge, Todd M. Brusko, Annette D. de Kloet, Eric G. Krause, Todd E. Golde
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: about 6 years ago

10.1155/2020/2123787

Identification of lncRNA and mRNA Biomarkers in Osteoarthritic Degenerative Meniscus by Weighted Gene Coexpression Network and Competing Endogenous RNA Network Analysis
Cited by: 4
Author(s): Jun Zhao, Yu Su, Jianfei Jiao, Zhengchun Wang, Xiangchun Fang, Xuefeng He, Xiaofeng Zhang, Zhao Liu, Xilin Xu
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.659788

RNA-Associated Co-expression Network Identifies Novel Biomarkers for Digestive System Cancer
Cited by: 7
Author(s): Zheng Chen, Zijie Shen, Zilong Zhang, Zhao Da, Lei Xu, Lijun Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.00225

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication
Cited by: 9
Author(s): Qi Zhou, Ping Fu, Shu-Shang Li, Changjiang Zhang, Qiuhan Yu, Chuan-Zhen Qiu, Hongbo Zhang, Ze Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.613744

Integrated Weighted Gene Co-expression Network Analysis Identified That TLR2 and CD40 Are Related to Coronary Artery Disease
Cited by: 6
Author(s): Bin Qi, Jianhong Chen, Tao Lin, Chuan-Meng Zhu, Yong Wang, Guo-Xiong Deng, Miao Liu
Software Mentions: 4
Published: almost 6 years ago

10.1155/2021/6644827

Multiomics Analysis of Genetics and Epigenetics Reveals Pathogenesis and Therapeutic Targets for Atrial Fibrillation
Cited by: 2
Author(s): Li Liu, Jianjun Huang, Baomin Wei, Jianjiao Mo, Qinjiang Wei, Chengcai Chen, Yan Wang, Xian-Nan Huang, Fengzhen He, Lingling Qin, Hehua Huang, Xue Li, Xingshou Pan
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.650874

Investigating Transcriptional Dynamics Changes and Time-Dependent Marker Gene Expression in the Early Period After Skeletal Muscle Injury in Rats
Cited by: 6
Author(s): Kangning Ren, Liangliang Wang, Liang Wang, Qiu-xiang Du, Jie Cao, Qianqian Jin, Guo-shuai An, Na Li, Li-hong Dang, Yingjie Tian, Ying-Yuan Wang, Jun-hong Sun
Software Mentions: 4
Published: over 5 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 6 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 7 years ago

10.1155/2020/7594098

Development and Validation of an Immune-Related Prognostic Signature for Ovarian Cancer Based on Weighted Gene Coexpression Network Analysis
Cited by: 6
Author(s): Yuanyuan An, Qing Yang
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/2137319

Identification of Four Pathological Stage-Relevant Genes in Association with Progression and Prognosis in Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Dengyong Xu, Yuzi Xu, Yiming Lv, Fei Wu, Yunlong Liu, Ming Zhu, Dake Chen, Bingjun Bai
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2018.00228

Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients
Cited by: 6
Author(s): Kuan Fu Ding, Darren Finlay, Hongwei Yin, William P.D. Hendricks, Chris Sereduk, Jeffrey Kiefer, Aleksandar Sekulić, Patricia LoRusso, Kristiina Vuori, Jeffrey M. Trent, Nicholas J. Schork
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0240975

RNA sequencing of whole blood in dogs with primary immune-mediated hemolytic anemia (IMHA) reveals novel insights into disease pathogenesis
Cited by: 5
Author(s): Corie Borchert, Adam Herman, Megan Roth, Aimee C. Brooks, Steven G. Friedenberg
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0178532

Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism
Cited by: 21
Author(s): Brian Gudenas, Anand Srivastava, Liangjiang Wang
Software Mentions: 4
Published: over 9 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 5 years ago

10.3390/ijms19092500

Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites
Cited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: about 8 years ago

10.1155/2020/8886914

An Integrative Analysis Reveals the Potential Mechanism between Herbal Medicine Yinchen and Immunoregulation in Hepatocellular Carcinoma
Cited by: 3
Author(s): Zhuomao Mo, Zhirui Cao, Ling Yu, Yongdan Wang, Pan Li, You-Wu Lin, Shijun Zhang
Software Mentions: 4
Published: almost 6 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479