bioconductor: MethylMix | Projects

10.1042/BSR20201604

Novel prognostic prediction model constructed through machine learning on the basis of methylation-driven genes in kidney renal clear cell carcinoma
Cited by: 11
Author(s): Weihao Tang, Ying Cao, Xiaoke Ma
Software Mentions: 9
Published: over 4 years ago

10.1002/cam4.2665

Genome‐wide screening of abberant methylated drivers combined with relative risk loci in bladder cancer
Cited by: 2
Author(s): Chuanjie Zhang, Kangjie Shen, Yuxiao Zheng, Feng Qi, Jun Luo
Software Mentions: 8
Published: about 5 years ago

10.1093/bfgp/elx018

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis
Cited by: 91
Author(s): Luciane T. Kagohara, Genevieve Stein-O’Brien, Dylan Z. Kelley, Emily Flam, Heather C. Wick, Ludmila Danilova, Hariharan Easwaran, Alexander V. Favorov, Jiang Qian, Daria A. Gaykalova, Elana J. Fertig
Software Mentions: 7
Published: over 7 years ago

10.3389/fcell.2020.576996

Development and Validation of a Novel DNA Methylation-Driven Gene Based Molecular Classification and Predictive Model for Overall Survival and Immunotherapy Response in Patients With Glioblastoma: A Multiomic Analysis
Cited by: 9
Author(s): Zihao Wang, Lu Gao, Xiaopeng Guo, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 7
Published: over 4 years ago

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: over 7 years ago

10.3389/fgene.2020.00099

A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma
Cited by: 4
Author(s): J Chen, X Wang, Wei Li, Chao Shang, T Chen, Y Chen
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pgen.1008749

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
Cited by: 29
Author(s): Heini M. Natri, Katalina Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S. Jacobs, Georgi Hudjashov, J. Stephen Lansing, Herawati Sudoyo, Nicholas E. Banovich, Murray P. Cox, Irene Gallego Romero
Software Mentions: 6
Published: over 4 years ago

10.1002/2211-5463.13211

Prognostic biomarker identification and tumor classification in breast cancer patients by methylation and transcriptome analysis
Cited by: 4
Author(s): Xiongdong Zhong, Guoying Zhong
Software Mentions: 6
Published: over 3 years ago

10.1289/EHP595

Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group
Cited by: 212
Author(s): Carrie V. Breton, Carmen J. Marsit, Elaine M. Faustman, Kari Nadeau, Jaclyn M. Goodrich, Dana C. Dolinoy, Julie B. Herbstman, Nina Holland, Janine M. LaSalle, Rebecca Jean Schmidt, Paul Yousefi, Frederica P. Perera, Bonnie R. Joubert, Joseph L. Wiemels, Miles G. Taylor, Ivana V. Yang, Rui Chen, Kinjal Hew, Deborah M. Hussey Freeland, Rachel L. Miller, Susan K. Murphy
Software Mentions: 6
Published: over 7 years ago

10.1089/cmb.2020.0081

GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis
Cited by: 5
Author(s): Xiao Wang, Dan Hao, Haja N. Kadarmideen
Software Mentions: 6
Published: almost 4 years ago

10.3389/fonc.2021.632430

Genomic Alteration Characterization in Colorectal Cancer Identifies a Prognostic and Metastasis Biomarker: FAM83A|IDO1
Cited by: 29
Author(s): Zaoqu Liu, Yuyuan Zhang, Qin Dang, Kunpeng Wu, Dechao Jiao, Zhen Li, Zhenqiang Sun, Xinwei Han
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2016.00002

Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges
Cited by: 16
Author(s): Louise B. Thingholm, Lars van Brakel Andersen, Enes Makalic, Melissa C. Southey, Mads Thomassen, Lise Lotte Hansen
Software Mentions: 6
Published: almost 9 years ago

10.18632/aging.102923

Integrative analysis of DNA methylation and gene expression reveals distinct hepatocellular carcinoma subtypes with therapeutic implications
Cited by: 10
Author(s): Xiaowen Huang, Chen Yang, Jilin Wang, Tiantian Sun, Hua Xiong
Software Mentions: 5
Published: over 4 years ago

10.1186/s12935-020-01294-9

A robust twelve-gene signature for prognosis prediction of hepatocellular carcinoma
Cited by: 46
Author(s): Guoqing Ouyang, Bin Yi, Guangdong Pan, Xiang Chen
Software Mentions: 5
Published: over 4 years ago

10.1186/s12935-021-02038-z

Identification of methylation-driven genes prognosis signature and immune microenvironment in uterus corpus endometrial cancer
Cited by: 10
Author(s): Jinhui Liu, Chengjian Ji, Yichun Wang, Cheng Zhang, Hongjun Zhu
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-014-0579-8

Pancancer analysis of DNA methylation-driven genes using MethylMix
Cited by: 102
Author(s): Olivier Gevaert, Robert Tibshirani, Sylvia K. Plevritis
Software Mentions: 5
Published: almost 10 years ago

10.3389/fgene.2020.00294

Methylation-Driven Genes Identified as Novel Prognostic Indicators for Thyroid Carcinoma
Cited by: 12
Author(s): Liting Lv, Liyu Cao, Guoqing Hu, Qinyan Shen, Jiaming Wu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12920-020-00780-3

Pan-cancer analysis of differential DNA methylation patterns
Cited by: 7
Author(s): Mai Shi, Stephen Kwok‐Wing Tsui, Hao Wu, Yingying Wei
Software Mentions: 4
Published: about 4 years ago

10.1002/2211-5463.13242

A methylation‐driven gene panel predicts survival in patients with colon cancer
Cited by: 6
Author(s): Yawen Peng, Jing Zhao, Fang‐Fang Yin, Gaowa Sharen, Qiyan Wu, Qi Chen, Xiaoxuan Sun, Juan Yang, Huan Wang, Dong Zhang
Software Mentions: 4
Published: over 3 years ago

10.1155/2021/6628391

Identification of Prognostic Risk Model Based on DNA Methylation-Driven Genes in Esophageal Adenocarcinoma
Cited by: 2
Author(s): Yuhua Chen, Jinjie Wang, Hao Zhou, Zhanghao Huang, Qian Li, Wei Shi
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2021.705547

Construction of Novel Methylation-Driven Gene Model and Investigation of PARVB Function in Glioblastoma
Cited by: 3
Author(s): Wanli Yu, Pengfei Wu, Fang Wang, Miao Li, Bo Han, Zhiqun Jiang
Software Mentions: 4
Published: about 3 years ago

10.1186/s12935-019-0950-7

A six-gene prognostic model predicts overall survival in bladder cancer patients
Cited by: 37
Author(s): Liwei Wang, Jiazhong Shi, Yaqin Huang, Sha Li, Jingqi Zhang, Hua Ding, Jin Yang, Zhiwen Chen
Software Mentions: 4
Published: about 5 years ago

10.1093/bib/bbz121

A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping
Cited by: 43
Author(s): Anita Sathyanarayanan, Rohit Gupta, Erik W. Thompson, Dale R. Nyholt, Denis C. Bauer, Shivashankar H. Nagaraj
Software Mentions: 4
Published: about 5 years ago

10.1186/s12935-020-01567-3

Identification and validation of methylation-driven genes prognostic signature for recurrence of laryngeal squamous cell carcinoma by integrated bioinformatics analysis
Cited by: 11
Author(s): Jie Cui, Liping Wang, Waisheng Zhong, Zhe Chen, Jie Chen, Hong Yang, Genglong Liu
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-017-17298-x

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma
Cited by: 59
Author(s): Kevin Brennan, June Ho Shin, Joshua K. Tay, Marcos Prunello, Andrew J. Gentles, John B. Sunwoo, Olivier Gevaert
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2020.00301

Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer
Cited by: 12
Author(s): Yanshen Kuang, Ying Wang, Wanli Zhai, Xuning Wang, Bingdong Zhang, Maolin Xu, Shaohua Guo, Mu Ke, Baoqing Jia, Hongyi Liu
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1007245

The impact of DNA methylation on the cancer proteome
Cited by: 8
Author(s): Majed Mohamed Magzoub, Marcos Prunello, Kevin Brennan, Olivier Gevaert
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0171694

An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology
Cited by: 2
Author(s): Buğra Özer, Uğur Sezerman
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13148-018-0451-x

Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma
Cited by: 20
Author(s): Thomas Sanford, Maxwell V. Meng, Reema Railkar, Piyush K. Agarwal, Sima P. Porten
Software Mentions: 3
Published: almost 7 years ago

10.1002/2211-5463.13093

Hypermethylation of the <i>PZP</i> gene is associated with hepatocellular carcinoma cell proliferation, invasion and migration
Cited by: 8
Author(s): Ming‐Chi Wu, Hui Y. Lan, Zhongwei Ye, Yonghui Wang
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-017-1490-6

Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data
Cited by: 51
Author(s): Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiaotai Huang, Wanxin Tang
Software Mentions: 3
Published: almost 8 years ago

10.3389/fonc.2021.629860

Integrative Analysis of Identifying Methylation-Driven Genes Signature Predicts Prognosis in Colorectal Carcinoma
Cited by: 8
Author(s): Hao Huang, Jinming Fu, Lei Zhang, Jing Xu, Dapeng Li, Justina Ucheojor Onwuka, Ding Zhang, Linjing Zhao, Simin Sun, Lin Zhu, Ting Zheng, Chenyang Jia, Binbin Cui, Yong Zhao
Software Mentions: 3
Published: over 3 years ago

10.1002/jcp.29046

Identification of methylation‐driven genes related to prognosis in clear‐cell renal cell carcinoma
Cited by: 11
Author(s): Jia Wang, Qiujing Zhang, Qingqing Zhu, Chengxiang Li, Xueli Nan, Fuxia Wang, Lihua Fang, Jie Liu, Chao Xie, Shuai Fu, Bao-Liang Song
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/5542485

PAR2 Promoter Hypomethylation Regulates PAR2 Gene Expression and Promotes Lung Adenocarcinoma Cell Progression
Cited by: 5
Author(s): Kwou-Yeung Wu, Lei Xu, Ling Cheng
Software Mentions: 2
Published: over 3 years ago

10.1186/s12935-020-01331-7

Identification of methylation-driven genes related to the prognosis of papillary renal cell carcinoma: a study based on The Cancer Genome Atlas
Cited by: 13
Author(s): Zeyu Liu, Yuxiang Wan, Ming Yang, Xuewei Qi, Zhenzhen Dong, Jinchang Huang, Jingnan Xu
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-018-2397-6

EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation
Cited by: 5
Author(s): Saverio Candido, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Valentina Di Salvatore, Massimo Libra, Francesco Pappalardo
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12967-019-2065-2

Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data
Cited by: 46
Author(s): Ning Xu, Yupeng Wu, Zhi‐Bin Ke, Yingchun Liang, Hai Cai, Wenting Su, Xuan Tao, Shao‐Hao Chen, Qing‐Shui Zheng, Yong Wei, Xue-Yi Xue
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2020.584733

A Prognostic Nomogram Model Based on mRNA Expression of DNA Methylation-Driven Genes for Gastric Cancer
Cited by: 5
Author(s): Zuhua Chen, Bo Liu, Minxiao Yi, Hong Qian, Xianglin Yuan
Software Mentions: 2
Published: about 4 years ago

10.1200/CCI.19.00125

Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes
Cited by: 6
Author(s): Olivier Gevaert, Mohsen Nabian, Shaimaa Bakr, Celine Everaert, Jayendra Shinde, Artur Manukyan, Ted Liefeld, Thorin Tabor, Jishu Xu, Joachim Lupberger, Brian J. Haas, Thomas F. Baumert, Mikel Hernáez, Michael Reich, Francisco J. Quintana, Erik J. Uhlmann, Anna M. Krichevsky, Jill P. Mesirov, Vincent J. Carey, Nathalie Pochet
Software Mentions: 2
Published: about 4 years ago

10.7150/jca.35641

LAT, HOXD3 and NFE2L3 identified as novel DNA methylation-driven genes and prognostic markers in human clear cell renal cell carcinoma by integrative bioinformatics approaches
Cited by: 25
Author(s): Jie Wang, Zhao Hu, Huiyue Dong, Ling Zhu, Shuiliang Wang, Ping Wang, Qun Ren, Honglin Zhu, Junqiu Chen, Zhijie Lin, Yuanhang Cheng, Benjiang Qian, Yi Zhang, Ruxue Jia, Weizheng Wu, Jun Lü, Ming Jen Tan
Software Mentions: 2
Published: almost 6 years ago

10.7150/thno.31155

DNA methylation-driven genes for constructing diagnostic, prognostic, and recurrence models for hepatocellular carcinoma
Cited by: 81
Author(s): Junyu Long, Peipei Chen, Jianzhen Lin, Yi Bai, Yang Xu, Jin Bian, Yu Hung Lin, Dongxu Wang, Xiaobo Yang, Yongchang Zheng, Xinting Sang, Hong Zhao
Software Mentions: 2
Published: almost 6 years ago

10.1155/2019/9379864

Combined Analysis of the Aberrant Epigenetic Alteration of Pancreatic Ductal Adenocarcinoma
Cited by: 11
Author(s): Rui Xu, Qian Xu, Guangwen Huang, Xinhai Yin, Jianguo Zhu, Yunsong Peng, Jukun Song
Software Mentions: 2
Published: almost 5 years ago

10.1155/2020/8817652

Prognostic Value of DNA Methylation-Driven Genes in Clear Cell Renal Cell Carcinoma: A Study Based on Methylation and Transcriptome Analyses
Cited by: 7
Author(s): Mao‐Lin Hu, Jian‐Wei Xie, Huiming Hou, Ming Liu, Qianqian Wang
Software Mentions: 2
Published: over 4 years ago

10.18632/aging.203249

DNA methylation biomarkers for diagnosis of primary liver cancer and distinguishing hepatocellular carcinoma from intrahepatic cholangiocarcinoma
Cited by: 6
Author(s): Yi Bai, Wen Tong, Fucun Xie, Liuyang Zhu, Hao Wu, Rui Shi, Lianjiang Wang, Long Yang, Zhisong Liu, Fei Miao, Qiang Zhao, Yamin Zhang
Software Mentions: 2
Published: over 3 years ago

10.1186/s12935-021-02053-0

Aberrantly methylated-differentially genes and pathways among Iranian patients with colorectal cancer
Cited by: 1
Author(s): Mahla Ghorbani, Marjan Azghandi, Mohammad Amin Kerachian
Software Mentions: 1
Published: over 3 years ago

10.1002/ctm2.45

Four methylation‐driven genes may be prognostic biomarkers in clear cell renal carcinoma
Cited by: 4
Author(s): Hang Yin, Haiyang Zhang, Xiaoyuan Wang, Qingyong Xu
Software Mentions: 1
Published: over 4 years ago

10.1186/s13040-019-0202-3

ClickGene: an open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration
Cited by: 12
Author(s): Jia Bi, Yi Tong, Zhe Qiu, Xing Yang, John D. Minna, Adi F. Gazdar, Kai Song
Software Mentions: 1
Published: over 5 years ago

10.1186/s12935-018-0691-z

Exploration of methylation-driven genes for monitoring and prognosis of patients with lung adenocarcinoma
Cited by: 33
Author(s): Chundi Gao, Jing Zhuang, Huayao Li, Cun Liu, Chao Zhou, Lijuan Liu, Changgang Sun
Software Mentions: 1
Published: about 6 years ago

10.18632/aging.104047

Integrative analysis reveals novel driver genes and molecular subclasses of hepatocellular carcinoma
Cited by: 14
Author(s): Liguang Yang, Zhengtao Zhang, Yidi Sun, Shichao Pang, Qianlan Yao, Ping Lin, Ju Chien Cheng, Jia Li, Guohui Ding, Lijian Hui, Yixue Li, Hong Li
Software Mentions: 1
Published: about 4 years ago

10.1186/s12935-019-0770-9

Identification of DNA methylation-driven genes in esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas
Cited by: 34
Author(s): Tong Lu, Di Chen, Yuanyong Wang, Xiao Sun, Shicheng Li, Shuncheng Miao, Yang Wo, Yanting Dong, Xiaoliang Leng, Weihua Du, Wenjie Jiao
Software Mentions: 1
Published: over 5 years ago

10.7150/ijms.43272

Integrative analysis of DNA methylation-driven genes for the prognosis of lung squamous cell carcinoma using MethylMix
Cited by: 11
Author(s): Rui Li, Yunhong Yin, Jia Jin, Xiao Liu, Mengyu Zhang, Yie Yang, Yi-Qing Qu
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12967-019-2068-z

Methylation and transcriptome analysis reveal lung adenocarcinoma-specific diagnostic biomarkers
Cited by: 49
Author(s): Rui Li, Yie Yang, Yunhong Yin, Meng-Yu Zhang, Hao Li, Yi-Qing Qu
Software Mentions: 1
Published: about 5 years ago

10.7150/ijbs.41587

Development and Validation of a Prognostic Nomogram for Gastric Cancer Based on DNA Methylation-Driven Differentially Expressed Genes
Cited by: 38
Author(s): Yi Bai, Chunlian Wei, Yi Zhong, Yamin Zhang, Junyu Long, Shan Huang, Fucun Xie, Yantao Tian, Xi Wang, Hong Zhao
Software Mentions: 1
Published: almost 5 years ago

Projects: bioconductor: MethylMix

Papers Mentioning MethylMix 53