cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1038/s41396-020-00874-x

Specificity of assemblage, not fungal partner species, explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants
Cited by: 8
Author(s): Zhongtao Zhao, Xiaojuan Li, Ming Fai Liu, Vincent Merckx, Richard M. Saunders, Dianxiang Zhang
Software Mentions: 3
Published: almost 6 years ago

10.7150/jca.49138

LINC00184 involved in the regulatory network of ANGPT2 via ceRNA mediated miR-145 inhibition in gastric cancer
Cited by: 13
Author(s): Haiyan Piao, Shuai Guo, Haoyi Jin, Yue Wang, Jun Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1093/jxb/erx391

Sugar metabolism reprogramming in a non-climacteric bud mutant of a climacteric plum fruit during development on the tree
Cited by: 36
Author(s): Macarena Farcuh, Bosheng Li, Rosa M. Rivero, Lyudmila Shlizerman, Avi Sadka, Eduardo Blumwald
Software Mentions: 3
Published: almost 9 years ago

10.7150/jca.52170

Five-gene signature associating with Gleason score serve as novel biomarkers for identifying early recurring events and contributing to early diagnosis for Prostate Adenocarcinoma
Cited by: 10
Author(s): Lingyu Zhang, Li Yu, Xuchu Wang, Ying Ping, Danhua Wang, Ying Cao, Yibei Dai, Weiwei Liu, Zhihua Tao
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2016.00169

Genetic Networks in Mouse Retinal Ganglion Cells
Cited by: 15
Author(s): Felix L Struebing, Richard K. Lee, Robert W. Williams, Eldon E. Geisert
Software Mentions: 3
Published: about 10 years ago

10.1042/BSR20191247

HPO-Shuffle: an associated gene prioritization strategy and its application in drug repurposing for the treatment of canine epilepsy
Cited by: 5
Author(s): Shuguang Wang, Xiangyu Meng, Yuxing Wang, Ye-Mao Liu, Jingbo Xia
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1009270

Physiological and genetic convergence supports hypoxia resistance in high-altitude songbirds
Cited by: 10
Author(s): Ying Xiong, Liqing Fan, Yan Hao, Yalin Cheng, Ying Chang, Jing Wang, Haiyan Lin, Gang Song, Yanhua Qu, Fumin Lei
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1005963

De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects
Cited by: 87
Author(s): James R. Priest, Kazutoyo Osoegawa, Nebil Mohammed, Vivek Nanda, Ramendra K. Kundu, Kathleen Schultz, Edward J. Lammer, Santhosh Girirajan, Todd E. Scheetz, Daryl Waggott, François Haddad, Sushma Reddy, Daniel Bernstein, Trudy L. Burns, Jeffrey D. Steimle, Xinan Yang, Ivan P. Moskowitz, Matthew E. Hurles, Richard P. Lifton, Debbie Nickerson, Michael J. Bamshad, Evan E. Eichler, Seema Mital, Val C. Sheffield, Thomas Quertermous, Bruce D. Gelb, Michael A. Portman, Euan A. Ashley
Software Mentions: 3
Published: over 10 years ago

10.1042/BSR20193938

Weighted gene correlation network analysis reveals novel regulatory modules associated with recurrent early pregnancy loss
Cited by: 5
Author(s): Xiaoxiao Li, Yuanqi He, Cuifang Hao, Xiaona Li, Xue Li
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008768

Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum
Cited by: 30
Author(s): Eva L. Koch, Frédéric Guillaume
Software Mentions: 3
Published: over 6 years ago

10.1038/s41438-019-0120-z

Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus × domestica)
Cited by: 17
Author(s): Katchen Julliany Pereira Silva, Jugpreet Singh, Ryland Bednarek, Zhangjun Fei, Awais Khan
Software Mentions: 3
Published: over 7 years ago

10.1042/BSR20181925

Co-expression of key gene modules and pathways of human breast cancer cell lines
Cited by: 13
Author(s): Yadong Wu, Lin Feng, Siyang Luo, Xinhai Yin, He Dan, Jianguo Liu, Zhao-hui Yue, Jukun Song
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1008513

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1
Cited by: 34
Author(s): Zhejun Ji, Marianthi Kiparaki, Virginia Folgado, Amit Kumar, Jorge Polo Blanco, Gerard Rimesso, Jacky Chuen, Yang Liu, Deyou Zheng, Nicholas E. Baker
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1006745

GRHL3 binding and enhancers rearrange as epidermal keratinocytes transition between functional states
Cited by: 39
Author(s): Rachel Herndon Klein, Ziguang Lin, Amelia Soto Hopkin, William Gordon, Lam C. Tsoi, Yun Liang, Jóhann E. Guðjónsson, Bogi Andersen
Software Mentions: 3
Published: over 9 years ago

10.1042/BSR20200514

Identification of co-expressed genes associated with <i>MLL</i> rearrangement in pediatric acute lymphoblastic leukemia
Cited by: 2
Author(s): Hao Zhang, Bei Liu, Juan Cheng, Haizhen Ma, Zijian Li, Yuandi Xi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07690-3

Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection
Cited by: 0
Author(s): Bahiyah Azli, Sharanya Ravi, M. Hair-Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-76762-3

Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203
Cited by: 7
Author(s): Juansheng Ren, Fan Zhang, Fangyuan Gao, Lihua Zeng, Xianjun Lu, Xiuqin Zhao, Jian Lv, Xiangwen Su, Liping Liu, Mingli Dai, Jianlong Xu, Guangjun Ren
Software Mentions: 3
Published: almost 6 years ago

10.1155/2019/8265958

Competing Endogenous RNA and Coexpression Network Analysis for Identification of Potential Biomarkers and Therapeutics in association with Metastasis Risk and Progression of Prostate Cancer
Cited by: 9
Author(s): Xu Pang, Ying Zhao, Jinhua Wang, Wan Li, Qian Xiang, Zhuo Zhang, Shi-Liang Wu, Ailin Liu, Guanhua Du, Yimin Chen
Software Mentions: 3
Published: about 7 years ago

10.7150/ijbs.33735

Co-expression network analysis of lncRNAs and mRNAs in rat liver tissue reveals the complex interactions in response to pathogenic cytotoxicity
Cited by: 3
Author(s): Dongliang Leng, Chen Huang, Kuan Cheok Lei, Shixue Sun, Baoqing Sun, Xiaohua Douglas Zhang
Software Mentions: 3
Published: almost 8 years ago

10.1042/BSR20202921

Immune-associated biomarkers for early diagnosis of Parkinson’s disease based on hematological lncRNA–mRNA co-expression
Cited by: 8
Author(s): Kecheng Lei, Liwen Zhang, Yijing He, Hui Sun, Weifang Tong, Yawei Xu, Lingjing Jin
Software Mentions: 3
Published: almost 6 years ago

10.1093/jxb/erx010

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Cited by: 48
Author(s): Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jérôme Verdier, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-020-76139-6

Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability
Cited by: 16
Author(s): Geoffrey Finch, Sonya Nandyal, Carlie Perretta, Benjamin Davies, Andrew J. Rosendale, Christopher J. Holmes, J. D. Gantz, Drew E. Spacht, Samuel T. Bailey, Marc E. Rothenberg, Kennan Oyen, Elise M. Didion, Souvik Chakraborty, Richard Lee, David L. Denlinger, Stephen F. Matter, Geoffrey M. Attardo, Matthew T. Weirauch, Joshua B. Benoit
Software Mentions: 3
Published: almost 6 years ago

10.3390/nu13093210

Association Study among Comethylation Modules, Genetic Polymorphisms and Clinical Features in Mexican Teenagers with Eating Disorders: Preliminary Results
Cited by: 1
Author(s): Germán Alberto Nolasco-Rosales, José Jaime Martínez‐Magaña, Isela Esther Juárez‐Rojop, Thelma Beatríz González-Castro, Carlos Alfonso Tóvilla-Zárate, Ana Rosa Sepúlveda García, Emmanuel Sarmiento, David Ruiz‐Ramos, Alma Delia Genis‐Mendoza, Humberto Nicolini
Software Mentions: 2
Published: about 5 years ago

10.1186/s13568-021-01288-4

Growth performances, gastrointestinal epithelium and bacteria responses of Yellow-feathered chickens to kudzu-leaf flavonoids supplement
Cited by: 3
Author(s): Fuguang Xue, Gen Wan, Yunsen Xiao, Chuanbin Chen, Mei Qu, Long Xu
Software Mentions: 2
Published: about 5 years ago

10.1186/s13568-019-0763-z

Altered diversity and composition of the gut microbiome in patients with cervical cancer
Cited by: 45
Author(s): Zhongqiu Wang, Qingxin Wang, Jing Zhao, Lei Gong, Yan Zhang, Xia Wang, Zhiyong Yuan
Software Mentions: 2
Published: over 7 years ago

10.1007/s00401-018-1830-2

Tumour compartment transcriptomics demonstrates the activation of inflammatory and odontogenic programmes in human adamantinomatous craniopharyngioma and identifies the MAPK/ERK pathway as a novel therapeutic target
Cited by: 96
Author(s): John Apps, Gabriela Carreno, José Mario González-Meljem, Scott Haston, Romain Guiho, Jayne Cooper, Saba Manshaei, Nital Jani, Annett Hölsken, Benedetta Pettorini, Robert J. Beynon, Deborah M. Simpson, Helen C. Fraser, Ying Hong, Shirleen Hallang, T. J. Stone, Alex Virasami, Andrew M. Donson, David R. Jones, Kristian Aquilina, Helen Spoudeas, Abhijit Joshi, Richard G. Grundy, Lisa Storer, Márta Korbonits, David A. Hilton, Kyoko Tossell, Selvam Thavaraj, Mark A. Ungless, Jesús Gil, Rolf Buslei, Todd C. Hankinson, Darren Hargrave, Colin R. Goding, Cynthia L. Andoniadou, Paul A. Brogan, Thomas S. Jacques, Williams Hj, Juan Pedro Martinez-Barbera
Software Mentions: 2
Published: over 8 years ago

10.1007/s00401-018-1900-5

Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy
Cited by: 43
Author(s): Mariet Allen, Xue Wang, Daniel J. Serie, Samantha L. Strickland, Jeremy D. Burgess, Shunsuke Koga, Curtis S. Younkin, Thuy Nguyen, Kimberly G. Malphrus, Sarah Lincoln, Melissa Alamprese, Kuixi Zhu, Rui Chang, Minerva M. Carrasquillo, Naomi Kouri, Melissa E. Murray, Joseph S. Reddy, Cory C. Funk, Nathan D. Price, Todd E. Golde, Steven G. Younkin, Yan W. Asmann, Julia E. Crook, Dennis W. Dickson, Nilüfer Ertekin-Taner
Software Mentions: 2
Published: about 8 years ago

10.1186/s40478-018-0606-1

Modulation of astrocyte reactivity improves functional deficits in mouse models of Alzheimer’s disease
Cited by: 122
Author(s): Kelly Ceyzériat, Lucile Ben Haim, Audrey Denizot, Dylan Pommier, Marco Matos, Océane Guillemaud, Marie-Ange Palomares, Laurene Abjean, Fanny Petit, Pauline Gipchtein, Marie-Claude Gaillard, Martine Guillermier, Suéva Bernier, Mylène Gaudin, Gwenaëlle Aurégan, Charlène Joséphine, Nathalie Déchamps, Julien Veran, Valentin Langlais, Karine Cambon, Alexis Bémelmans, Jan Baijer, Gilles Bonvento, Marc Dhénain, Jean‐François Deleuze, Stéphane H. R. Oliet, Emmanuel Brouillet, Philippe Hantraye, María-Angeles Carrillo-de Sauvage, Robert Olaso, Aude Panatier, Carole Escartin
Software Mentions: 2
Published: about 8 years ago

10.1186/s40478-019-0705-7

Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis
Cited by: 14
Author(s): Jeroen Melief, Marie Orre, Koen Bossers, C.G. van Eden, Karianne Schuurman, Matthew R. J. Mason, Joost Verhaagen, Jörg Hamann, Inge Huitinga
Software Mentions: 2
Published: over 7 years ago

10.1186/s40478-017-0424-x

A data-driven approach links microglia to pathology and prognosis in amyotrophic lateral sclerosis
Cited by: 54
Author(s): Johnathan Cooper‐Knock, Claire Green, Gabriel Altschuler, Wenbin Wei, Joanna J. Bury, Paul R. Heath, Matthew Wyles, Catherine Gelsthorpe, J. Robin Highley, Alejandro Lorente-Pons, Tim Beck, Kathryn Doyle, Karel Otero, Bryan J. Traynor, Janine Kirby, Pamela J. Shaw, Winston Hide
Software Mentions: 2
Published: over 9 years ago

10.18632/aging.203457

N6-methyladenosine (m6A) modification and its clinical relevance in cognitive dysfunctions
Cited by: 15
Author(s): Bingying Du, Yanbo Zhang, Meng Liang, Zengkan Du, Haibo Li, Cong Fan, Hailing Zhang, Yan Jiang, Xiaoying Bi
Software Mentions: 2
Published: about 5 years ago

10.18632/aging.103362

Serum metabolites associate with physical performance among middle-aged adults: Evidence from the Bogalusa Heart Study
Cited by: 10
Author(s): Jovia L. Nierenberg, Jiang He, Changwei Li, Xiaoqing Gu, Mengyao Shi, Alexander C. Razavi, Xuenan Mi, Shengxu Li, Lydia A. Bazzano, Amanda H. Anderson, Hua He, Wei Chen, Jack M. Guralnik, Jason M. Kinchen, Tanika N. Kelly
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.103775

Coupled immune stratification and identification of therapeutic candidates in patients with lung adenocarcinoma
Cited by: 9
Author(s): Wenquan Hu, Guosheng Wang, Yundi Chen, Lonny Yarmus, Biao Liu, Yuan Wan
Software Mentions: 2
Published: about 6 years ago

10.18632/aging.202303

Knockdown of CENPF inhibits the progression of lung adenocarcinoma mediated by ERβ2/5 pathway
Cited by: 8
Author(s): Huiping Tang, Yuquan Bai, Lei Xiong, Yanhong Wei, Li Shen, Weidong Hu, Meifeng Xu, Xuefeng Zhou, Guoqing Pan, Zhang Li, Minghua Zhu, Zheng Tang, Zhaohui Yang, Zhijie Xiao, Yi Cai, Michael Lanuti, Jinping Zhao
Software Mentions: 2
Published: almost 6 years ago

10.18632/aging.102230

Epigenome-wide association study of leukocyte telomere length
Cited by: 16
Author(s): Yunsung Lee, Dianjianyi Sun, Anil P.S. Ori, Ake T. Lu, Anne Seeboth, Sarah E. Harris, Ian J. Deary, Riccardo E. Marioni, Mette Soerensen, Jonas Mengel‐From, Jacob Hjelmborg, Kaare Christensen, James G. Wilson, Daniel Levy, Alex P. Reiner, Wei Chen, Shengxu Li, Jennifer R. Harris, Per Magnus, Abraham Aviv, Astanand Jugessur, Steve Horvath
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.102000

Rh type C-glycoprotein functions as a novel tumor suppressor gene by inhibiting tumorigenicity and metastasis in head and neck squamous cell carcinoma
Cited by: 7
Author(s): Wenguang Xu, Zou Huixian, Wei Zheng, Chuanhui Song, Chuanchao Tang, Xiteng Yin, Yufeng Wang, Shengwei Han, Yu Cai, Wei Han
Software Mentions: 2
Published: over 7 years ago

10.18632/aging.203360

A combined hypoxia and immune gene signature for predicting survival and risk stratification in triple-negative breast cancer
Cited by: 28
Author(s): Yang Xia, Xin Weng, Yong Yang, Meng Zhang, Yingjie Xiu, Wenfeng Peng, Xuhui Liao, Meiquan Xu, Yan Sun, Xia Liu
Software Mentions: 2
Published: about 5 years ago

10.18632/aging.101127

Induction of fibroblast senescence generates a non-fibrogenic myofibroblast phenotype that differentially impacts on cancer prognosis
Cited by: 79
Author(s): Massimiliano Mellone, Christopher J. Hanley, Steve Thirdborough, Toby Mellows, Edwin Garcia, Jeongmin Woo, Jo Tod, Steven J. Frampton, Veronika Jenei, Karwan A. Moutasim, Tasnuva D. Kabir, Peter A. Brennan, Giulia Venturi, Kirsty Ford, Nicolás Herranz, Ka Keat Lim, James Clarke, D Lambert, Stephen S. Prime, Tim Underwood, Pandurangan Vijayanand, Kevin W. Eliceiri, Christopher H. Woelk, Emma V. King, Jesús Gil, Christian Ottensmeier, Gareth J. Thomas
Software Mentions: 2
Published: almost 10 years ago

10.18632/aging.102366

TIMP1 mRNA in tumor-educated platelets is diagnostic biomarker for colorectal cancer
Cited by: 40
Author(s): Yang Liu, Qian Jiang, Dongzheng Li, Xin Zhou, Dongsheng Yu, Jian Zhong
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.202879

Characterizing a long-term chronic heart failure model by transcriptomic alterations and monitoring of cardiac remodeling
Cited by: 2
Author(s): Yingqi Zhu, Qiancheng Wang, Hairuo Lin, Kaitong Chen, Cankun Zheng, Lin Chen, Siyuan Ma, Wangjun Liao, Jianping Bin, Yulin Liao
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.102419

Characterization of long non-coding RNA and messenger RNA profiles in laryngeal cancer by weighted gene co-expression network analysis
Cited by: 26
Author(s): Huanhuan Liu, Yi Sun, Huan Tian, Xiaolian Xiao, Jiaqi Zhang, Yongzhen Wang, Fang Yu
Software Mentions: 2
Published: almost 7 years ago

10.18632/aging.102483

Competing endogenous network analysis identifies lncRNA Meg3 activates inflammatory damage in UVB induced murine skin lesion by sponging miR-93-5p/epiregulin axis
Cited by: 10
Author(s): Nan Zhang, Zhong Zhang, Yujia Wang, Li Yang, Fengbo Wu, Cheng Peng, Wei Huang, Gu He
Software Mentions: 2
Published: almost 7 years ago

10.18632/aging.101005

Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels
Cited by: 174
Author(s): Steve Horvath, Peter Langfelder, Seung Kwak, Jeff Aaronson, Jim Rosinski, Thomas Vogt, M Eszes, Richard L.M. Faull, Maurice A. Curtis, Henry J. Waldvogel, Oi-Wa Choi, Steve Tung, Harry V. Vinters, Giovanni Coppola, X. William Yang
Software Mentions: 2
Published: over 10 years ago

10.18632/aging.102397

Identifying hub genes of clear cell renal cell carcinoma associated with the proportion of regulatory T cells by weighted gene co-expression network analysis
Cited by: 11
Author(s): Ye‐Hui Chen, Shao‐Hao Chen, Jian Hou, Zhi‐Bin Ke, Yupeng Wu, Tingting Lin, Yong Wei, Xue-Yi Xue, Qing‐Shui Zheng, Jiaofeng Huang, Ning Xu
Software Mentions: 2
Published: almost 7 years ago

10.18632/aging.202494

Identification of novel candidate biomarkers for pancreatic adenocarcinoma based on TCGA cohort
Cited by: 5
Author(s): Jie Yang, Peng Wang, Yuanyuan Li
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.101592

Sirtuin 3 attenuates amyloid-β induced neuronal hypometabolism
Cited by: 18
Author(s): Jun Yin, Shiping Li, Megan Nielsen, Tanner Carcione, Winnie S. Liang, Jiong Shi
Software Mentions: 2
Published: about 8 years ago

10.18632/aging.203378

Identification of inflammation-related DNA methylation biomarkers in periodontitis patients based on weighted co-expression analysis
Cited by: 6
Author(s): Pengcheng Wang, Bingbing Wang, Zheng Zhang, Zuomin Wang
Software Mentions: 2
Published: about 5 years ago

10.18632/aging.103712

Chloride intracellular channel protein 2: prognostic marker and correlation with PD-1/PD-L1 in breast cancer
Cited by: 14
Author(s): Tao Xu, Zhi Wang, Menglu Dong, Di Wu, Shujie Liao, Xingrui Li
Software Mentions: 2
Published: about 6 years ago

10.18632/aging.102780

Immune-related key gene CLDN10 correlates with lymph node metastasis but predicts favorable prognosis in papillary thyroid carcinoma
Cited by: 16
Author(s): Zhaoyin Xiang, Cheng Zhong, Aoshuang Chang, Junjun Ling, Hou-Yu Zhao, Wei Zhou, Xianlu Zhuo
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.202969

Ketogenic diet-mediated steroid metabolism reprogramming improves the immune microenvironment and myelin growth in spinal cord injury rats according to gene and co-expression network analyses
Cited by: 4
Author(s): Hong Zeng, Yao Lu, Meng-jie Huang, Yanyan Yang, Huayi Xing, Xiao-xie Liu, Mouwang Zhou
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.102168

Copy number variations primed lncRNAs deregulation contribute to poor prognosis in colorectal cancer
Cited by: 22
Author(s): Huimin Liu, Xiaoyu Gu, Guihua Wang, Ying Huang, Shaoqing Ju, Jianfei Huang, Xudong Wang
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.202440

High expression of vinculin predicts poor prognosis and distant metastasis and associates with influencing tumor-associated NK cell infiltration and epithelial-mesenchymal transition in gastric cancer
Cited by: 14
Author(s): Huafu Li, Chunming Wang, Linxiang Lan, Axel Behrens, Mona Tomaschko, Josue Ruiz, Shan Qiao, Guangying Zhao, Yuan Cheng, Xing Xiao, Bo Li, Le-Ping Yan, Wei Wu, Wuguo Li, Junzong Chen, Yulong He, Changhua Zhang
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.102978

Klotho antagonizes pulmonary fibrosis through suppressing pulmonary fibroblasts activation, migration, and extracellular matrix production: a therapeutic implication for idiopathic pulmonary fibrosis
Cited by: 13
Author(s): Qiqing Huang, Yan Chen, Shaoran Shen, Yuanyuan Wang, Liya Liu, Shuangshuang Wu, Wei Xu, Weihong Zhao, Mingyan Lin, Jianzhong Wu
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.202304

Genomic and transcriptomic analysis of pituitary adenomas reveals the impacts of copy number variations on gene expression and clinical prognosis among prolactin-secreting subtype
Cited by: 4
Author(s): Yiyuan Chen, Hua Gao, Weiyan Xie, Jing Guo, Qiuyue Fang, Peng Zhao, Chunhui Liu, Haibo Zhu, Zhuang Wang, Jichao Wang, Songbai Gui, Yazhou Zhang, Chuzhong Li
Software Mentions: 2
Published: almost 6 years ago

10.18632/aging.101062

LncRNA mediated regulation of aging pathways in Drosophila melanogaster during dietary restriction
Cited by: 33
Author(s): Deying Yang, Ting Lian, Jianbo Tu, Uma Gaur, Xueping Mao, Xiaolan Fan, Diyan Li, Ying Li, Mingyao Yang
Software Mentions: 2
Published: about 10 years ago

10.18632/aging.102231

TPM2 as a potential predictive biomarker for atherosclerosis
Cited by: 39
Author(s): Ling‐Bing Meng, Mengjie Shan, Yong Qiu, Ruomei Qi, Zemou Yu, Peng Guo, Chen-Yi Di, Tao Gong
Software Mentions: 2
Published: about 7 years ago

10.1111/acel.13229

Underlying features of epigenetic aging clocks in vivo and in vitro
Cited by: 84
Author(s): Zuyun Liu, Diana Leung, Kyra Thrush, Wei Zhao, Scott Ratliff, Toshiko Tanaka, Lauren Schmitz, Jennifer A. Smith, Luigi Ferrucci, Morgan E. Levine
Software Mentions: 2
Published: about 6 years ago

10.1111/acel.12386

Integration of ‘omics’ data in aging research: from biomarkers to systems biology
Cited by: 94
Author(s): Jonas Zierer, Cristina Menni, Gabi Kastenmüller, Tim D. Spector
Software Mentions: 2
Published: about 11 years ago

10.1186/s13223-017-0192-y

Canadian Society of Allergy and Clinical Immunology annual scientific meeting 2016
Cited by: 5
Author(s): Mohammad A. Alsayegh, Hanan Alshamali, Mousa Khadada, A Ciccolini, Anne K. Ellis, Diana Quint, William Powley, Laurie Lee, Yahya Fiteih, Shairaz Baksh, Harissios Vliagoftis, Sebastien K. Gerega, Brad Millson, Katia Charland, Stéphane Barakat, Xichun Sun, Ricardo Jiménez, Susan Waserman, Mark FitzGerald, Jacques Hébert, Josiane Cognet-Sicé, Kevin E. Renahan, S. Huq, Rishma Chooniedass, Scott Sawyer, Hans Pasterkamp, Allan B. Becker, Steven G. Smith, Shiyuan Zhang, Kavisha Jayasundara, Claire E. Tacon, Alex Simidchiev, Gilbert Nadeau, Necdet Gunsoy, Hana Müllerová, Frank Albers, Young Woong Kim, Casey P. Shannon, Amrit Singh, Helen Neighbour, Mark Larché, Scott J. Tebbutt, Annika Klopp, Lorena Vehling, Allan B. Becker, Padmaja Subbarao, Piushkumar J. Mandhane, Stuart E. Turvey, Malcolm R. Sears, Meghan B. Azad, Keely Loewen, Barret A. Monchka, Salaheddin M. Mahmud, Geert ’t Jong, Cristina Longo, Gillian Bartlett, Francine M Ducharme, Tibor Schuster, Brenda MacGibbon, Tracie A. Barnett, Michelle L. North, Jeff Brook, Elizabeth Lee, Vanessa Omana, Jenny Thiele, Lisa M. Steacy, Greg J. Evans, Miriam L. Diamond, Gordon Sussman, Yann Amistani, Kathy Abiteboul, Mark W. Tenn, Chenxi Yang, Christopher Carlsten, Edward M. Conway, Douglas G. Mack, Rofina Yasmin Othman, Colin Barber, Chrystyna Kalicinsky, Andrea E. Burke, Mary Messieh, Parameswaran Nair, Thomas H. Chun, Lindsay Douglas, Joel Liem, Lucy Duan, Charlotte E. Miller, Pascale Dupuis, Lori Connors, Michael Fein, Joseph Shuster, Hani Hadi, Brooke I. Polk, Nikita Raje, Roxane Labrosse, Philippe Bégin, Louis Paradis, Anne Des Roches, Jonathan Lacombe-Barrios, Sanju Mishra, Gina Lacuesta, Meredith Chiasson, Babar Haroon, Kara Robertson, Thomas B. Issekutz, Desmond Leddin, Stephen Couban, Lori Connors, Adrienne M. Roos, Amin Kanani, Edmond S. Chan, R. Robert Schellenberg, Lana Rosenfield, Anna Cvetkovic, K. N. Woodward, Jaclyn Quirt, Wade Watson, Edson Castilho, Jennifer Sullivan, Beverley Temple, Donna Martin, Victoria E. Cook, Christopher Mills, Elodie Portales‐Casamar, Lisa Fu, Alexander Ho, Jeffrey S. Zaltzman, Lucy Chen, Peter Vadas, Sofianne Gabrielli, Ann E. Clarke, Harley Eisman, Judy Morris, Lawrence Joseph, Sebastien LaVieille, Moshe Ben‐Shoshan, François Graham, Charles S. Barnes, Jay M. Portnoy, Vincent Stagg, Elinor Simons, Diana L. Lefebvre, David Dai, Piushkumar J. Mandhane, Malcolm R. Sears, Herman Tam, F. Estelle R. Simons, Dhaifallah S Alotaibi, Bassel Dawod, Matthew Tunis, Jean S. Marshall, Marylin Desjardins, Marianne Béland, Duncan Lejtenyi, Jean-Phillipe Drolet, Martine Lemire, Christos Tsoukas, Francisco Noya, Reza Alizadehfar, Christine McCusker, Bruce Mazer, Danay Maestre‐Batlle, Evelyn Gunawan, Christopher F. Rider, Anette Kocbach Bølling, Olga M. Pena, Daniel Suez, Isaac Melamed, Iftikhar Hussaın, Mark R. Stein, Sudhir Gupta, Kenneth Paris, Sandor Fritsch, Christelle Bourgeois, Heinz Leibl, Barbara McCoy, Martin Noël, Leman Yel, Ori Scott, Brenda Reid, Adelle Atkinson, Vy Hong-Diep Kim, Chaim M. Roifman, Eyal Grunebaum, Eiman Al-Selahi, Fernando Alemán, Amber Oberle, Mike Trus, Gordon Sussman, Amin Kanani, Olivier Chambenoi, Sima Chiva-Razavi, Savannah Grodecki, Nikhil Joshi, Peter Menikefs, David W. Holt, Teresa Pun, Damian Tworek, Raphael Hanna, Delia Heroux, Elli Rosenberg, Leah T. Stiemsma, Stuart E. Turvey, Judah A. Denburg, Christopher Mill, Timothy Teoh, Preeti Zimmer, Vishal Avinashi, Mihaela Paina, Ahmed A. Darwish Hassan, John Paul Oliveria, Chris Olesovsky, Gail M. Gauvreau, Linda Pedder, Paul K. Keith, Greg Plunkett, Michelle L. Bolner, Persia Pourshahnazari, Donald Stark, Kateryna Vostretsova, Andrew Moses, A. Maurice Wakeman, Alexander Singer, Thomas Gerstner, Elissa M. Abrams, Sara F. Johnson, Roberta L. Woodgate
Software Mentions: 2
Published: over 9 years ago

10.1186/s42523-020-00041-9

Microbiome–host co-oscillation patterns in remodeling of colonic homeostasis during adaptation to a high-grain diet in a sheep model
Cited by: 8
Author(s): Limei Lin, Yue Wang, Liping Xu, Junhua Liu, Weiyun Zhu, Shengyong Mao
Software Mentions: 2
Published: over 6 years ago

10.3390/ani11082311

Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development
Cited by: 8
Author(s): Hao Ding, Yueyue Lin, Tao Zhang, Lan Chen, Genxi Zhang, Jinyu Wang, Kaizhou Xie, Guojun Dai
Software Mentions: 2
Published: about 5 years ago

10.3390/antibiotics10020097

Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages
Cited by: 7
Author(s): Lu Lu, Ranlei Wei, Sanjib Bhakta, Simon J. Waddell, Ester Boix
Software Mentions: 2
Published: almost 6 years ago

10.3390/antibiotics10070792

Correction: Lu et al. Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages. Antibiotics 2021, 10, 97
Cited by: 1
Author(s): Lu Lu, Ranlei Wei, Sanjib Bhakta, Simon J. Waddell, Ester Boix
Software Mentions: 2
Published: over 5 years ago

10.1007/s00204-016-1824-6

Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity
Cited by: 20
Author(s): Salil N. Pendse, Alexandra Maertens, Michael Rosenberg, Dipanwita Roy, Rick A. Fasani, Marguerite M. Vantangoli, Samantha J. Madnick, Kim Boekelheide, Albert J. Fornace, Shelly Odwin, James D. Yager, Thomas Hartung, Melvin E. Andersen, Patrick D. McMullen
Software Mentions: 2
Published: about 10 years ago

10.1007/s00204-018-2354-1

Characterisation of the NRF2 transcriptional network and its response to chemical insult in primary human hepatocytes: implications for prediction of drug-induced liver injury
Cited by: 21
Author(s): Ian M. Copple, Wouter den Hollander, Giulia Callegaro, Fiona Mutter, James L. Maggs, Amy Schofield, Lucille Rainbow, Yongxiang Fang, Jeffrey J. Sutherland, Ewa Ellis, Magnus Ingelman‐Sundberg, Stephen Fenwick, Christopher E. Goldring, Bob van de Water, James Stevens, B. Kevin Park
Software Mentions: 2
Published: almost 8 years ago

10.1186/ar4081

Systems analysis of primary Sjögren's syndrome pathogenesis in salivary glands identifies shared pathways in human and a mouse model
Cited by: 47
Author(s): Steve Horvath, Abu N M Nazmul-Hossain, Rodney P. E. Pollard, Franciscus Kroese, Arjan Vissink, Cornelis Kallenberg, Frederik Spijkervet, Hendrika Bootsma, Sara A. Michie, Sven Ulrik Gorr, Ammon B. Peck, Chaochao Cai, Hui Zhou, David T. Wong
Software Mentions: 2
Published: almost 15 years ago

10.31557/APJCP.2020.21.9.2771

Network-Based Analysis Reveals Association of FOXE1 Gene Polymorphisms in Thyroid Cancer Patients; A Case-Control Study in Southeast of Iran
Cited by: 1
Author(s): Ahmad Mehrazin, Hossein Safarpour, Seyedeh Tahmineh Davoudi, Negin Parsamanesh, Farhad Saeedi, Ebrahim Miri‐Moghaddam
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2105-12-296

Differential C3NET reveals disease networks of direct physical interactions
Cited by: 35
Author(s): Gökmen Altay, Mohammad Asim, Florian Markowetz, David E. Neal
Software Mentions: 2
Published: over 15 years ago

10.1186/s12859-017-1890-7

Identification and characterization of conserved lncRNAs in human and rat brain
Cited by: 20
Author(s): Dan Li, Mary Qu Yang
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-12-322

Strategies for aggregating gene expression data: The collapseRows R function
Cited by: 257
Author(s): Jeremy A. Miller, Chaochao Cai, Peter Langfelder, Daniel H. Geschwind, Sunil M. Kurian, Daniel R. Salomon, Steve Horvath
Software Mentions: 2
Published: about 15 years ago

10.1186/s12859-021-03987-y

ComHub: Community predictions of hubs in gene regulatory networks
Cited by: 9
Author(s): Julia Åkesson, Zelmina Lubovac-Pilav, Rasmus Magnusson, Mika Gustafsson
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-15-S10-I1

Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014
Cited by: 0
Author(s): Eric C. Rouchka, Julia H. Chariker
Software Mentions: 2
Published: about 12 years ago

10.1186/s12859-018-2553-z

Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency
Cited by: 38
Author(s): Suraya Mohamad Salleh, Gianluca Mazzoni, Peter Løvendahl, Haja N. Kadarmideen
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-019-2733-5

Generalized gene co-expression analysis via subspace clustering using low-rank representation
Cited by: 5
Author(s): Tongxin Wang, Jie Zhang, Kun Huang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-018-2536-0

MicroRNA dysregulational synergistic network: discovering microRNA dysregulatory modules across subtypes in non-small cell lung cancers
Cited by: 9
Author(s): Nhat Tran, Vinay V. Abhyankar, Kytai T. Nguyen, Jon A. Weidanz, Jean Gao
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-14-42

A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data
Cited by: 21
Author(s): Marie Verbanck, Sébastien Lê, Jacques Pagès
Software Mentions: 2
Published: over 13 years ago

10.1186/s12859-017-1889-0

Repositioning drugs by targeting network modules: a Parkinson’s disease case study
Cited by: 24
Author(s): Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent A. Laufer, S. Louis Bridges, Jake Y. Chen
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-016-1387-9

Prior knowledge guided eQTL mapping for identifying candidate genes
Cited by: 0
Author(s): Yunli Wang, René Richard, Youlian Pan
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-13-328

Comparison of co-expression measures: mutual information, correlation, and model based indices
Cited by: 362
Author(s): Song Lin, Peter Langfelder, Steve Horvath
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12859-018-2291-2

WISH-R– a fast and efficient tool for construction of epistatic networks for complex traits and diseases
Cited by: 11
Author(s): Victor Adriano Okstoft Carmelo, Lisette J. A. Kogelman, Majbritt Busk Madsen, Haja N. Kadarmideen
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-016-0913-0

Netter: re-ranking gene network inference predictions using structural network properties
Cited by: 8
Author(s): Joeri Ruyssinck, Piet Demeester, Tom Dhaene, Yvan Saeys
Software Mentions: 2
Published: over 10 years ago

10.1186/s12915-021-01118-w

An increase of phosphatidylcholines in follicular fluid implies attenuation of embryo quality on day 3 post-fertilization
Cited by: 6
Author(s): Ju Wang, Wei Zheng, Shuoping Zhang, Kunlun Yan, Miao Jin, Huiling Hu, Zhen Ma, Fei Gong, Guangxiu Lu, Yan Ren, Liang Lin, Ge Lin, Liang Hu, Siqi Liu
Software Mentions: 2
Published: about 5 years ago

10.1186/s12885-021-08434-y

Comprehensive analysis of suppressor of cytokine signaling proteins in human breast Cancer
Cited by: 9
Author(s): Mingyu Sun, Cheng Tang, Jun Li, Wenli Jiang, Haifeng Yu, Dong Fang, Chun Huang, Youlutuziayi Rixiati
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-019-5885-9

Epithelial-mesenchymal transition markers screened in a cell-based model and validated in lung adenocarcinoma
Cited by: 27
Author(s): Jing Song, Wenqing Wang, Yingyan Wang, Yongxin Qin, Yingzi Wang, Jian Zhou, Xuelian Wang, Yi Zhang, Qi Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12885-021-08604-y

Seven key hub genes identified by gene co-expression network in cutaneous squamous cell carcinoma
Cited by: 13
Author(s): Huizhen Chen, Jiankang Yang, Wenjuan Wu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-021-07972-9

Identification and validation of a five-lncRNA prognostic signature related to Glioma using bioinformatics analysis
Cited by: 8
Author(s): Chunyu Zhang, Haitao Liu, Pengfei Xu, Yinqiu Tan, Yang Xu, Long Wang, Baohui Liu, Daofeng Tian
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-021-08034-w

Identification of the potential novel biomarkers as susceptibility gene for Wilms tumor
Cited by: 2
Author(s): Li Liu, Zhe Song, Xudong Gao, Xian Chen, Xiaobin Wu, Mi Wang, Yu-De Hong
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-020-6676-z

Identification of potential novel biomarkers to differentiate malignant thyroid nodules with cytological indeterminate
Cited by: 9
Author(s): Dandan Wu, Shudong Hu, Yongzhong Hou, Yingying He, Shubai Liu
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2407-11-230

Protein expression based multimarker analysis of breast cancer samples
Cited by: 35
Author(s): Angela P. Presson, Nam Yoon, Lora Bagryanova, Vei Mah, Mohammad Alavi, Erin L. Maresh, Ayyappan K. Rajasekaran, Lee Goodglick, David Chia, Steve Horvath
Software Mentions: 2
Published: over 15 years ago

10.1186/s12872-021-01960-4

A 2 miRNAs-based signature for the diagnosis of atherosclerosis
Cited by: 7
Author(s): Xiujiang Han, Huimin Wang, Yongjian Li, Lina Liu, Sheng Gao
Software Mentions: 2
Published: over 5 years ago

10.1186/s12872-021-02108-0

Exploration and validation of hub genes and pathways in the progression of hypoplastic left heart syndrome via weighted gene co-expression network analysis
Cited by: 2
Author(s): Xuelan Liu, Honglei Shang, Bin Li, Lei Zhao, Ying Huang, Kaiyuan Wu, Manman Hu, Taibing Fan
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-213X-13-29

Stage-specific transcription during development of Aedes aegypti
Cited by: 19
Author(s): Brent W. Harker, Susanta K. Behura, Becky deBruyn, Diane D. Lovin, Akio Mori, Jeanne Romero‐Severson, David W. Severson
Software Mentions: 2
Published: over 13 years ago

10.1186/s12862-021-01794-w

Region-specific expression of young small-scale duplications in the human central nervous system
Cited by: 4
Author(s): Solène Brohard, Vincent Frouin, Vincent Meyer, Smahane Chalabi, Jean‐François Deleuze, Édith Le Floch, Christophe Battail
Software Mentions: 2
Published: over 5 years ago

10.1186/s12862-021-01787-9

Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity
Cited by: 14
Author(s): Pooja Singh, Ehsan Pashay Ahi, Christian Sturmbauer
Software Mentions: 2
Published: over 5 years ago

10.1186/s12862-020-01633-4

Evolution and transition of expression trajectory during human brain development
Cited by: 9
Author(s): Mingli Li, Hui Tang, Yong Shao, Mingshan Wang, Haibo Xu, Sheng Wang, David M. Irwin, Adeniyi C. Adeola, Tao Zeng, Luonan Chen, Yan Li, Dong‐Dong Wu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-6167-2

The anti-phytoalexin gene Bx-cathepsin W supports the survival of Bursaphelenchus xylophilus under Pinus massoniana phytoalexin stress
Cited by: 9
Author(s): Feng Wang, Qiaoli Chen, Ruizhi Zhang, Danlei Li, Yaming Ling, Ruiqing Song
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2164-13-636

Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects
Cited by: 184
Author(s): Kristel R. van Eijk, Simone de Jong, Marco P. Boks, Terry Langeveld, Fabrice Colas, Jan H. Veldink, Carolien G.F. de Kovel, Esther Janson, Eric Strengman, Peter Langfelder, René S. Kahn, Leonard H van den Berg, Steve Horvath, Roel A. Ophoff
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-021-07923-5

Transcriptome sequencing and differential expression analysis of seed starch accumulation in Chinese chestnut Metaxenia
Cited by: 7
Author(s): Shengxing Li, Shi Z, Qiqi Zhu, Liang Tao, Wenhui Liang, Zhiheng Zhao
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-14-840

Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes
Cited by: 25
Author(s): Ram Kumar Basnet, Natalia M. Moreno-Pachon, Keqin Lin, Johan Bucher, Richard G. F. Visser, Chris Maliepaard, Guusje Bonnema
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-017-3761-z

Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis
Cited by: 48
Author(s): Rong Liu, Wei Zhang, Zhao‐Qian Liu, Hong‐Hao Zhou
Software Mentions: 2
Published: over 9 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479