bioconductor: maftools | Projects

10.3389/fimmu.2021.645839

Multi-Omics Profiling Identifies Risk Hypoxia-Related Signatures for Ovarian Cancer Prognosis
Cited by: 11
Author(s): Xingyu Chen, Hua Lan, Dong He, Runshi Xu, Yao Zhang, Ying Cheng, Haotian Chen, Songshu Xiao, Ke Cao
Software Mentions: 6
Published: over 3 years ago

10.3390/cancers13143394

Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma
Cited by: 7
Author(s): Fereshteh Izadi, Benjamin Sharpe, Stella P. Breininger, Maria Secrier, Jane Gibson, Robert Walker, S Rahman, Ginny Devonshire, Matthew G. Lloyd, Zoë S. Walters, Rebecca Fitzgerald, Matthew Rose-Zerilli, Tim Underwood
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2021.685065

Comprehensive Landscape of Ovarian Cancer Immune Microenvironment Based on Integrated Multi-Omics Analysis
Cited by: 4
Author(s): Jiacheng Shen, Tingwei Liu, Qiaoli Bei, Shaohua Xu
Software Mentions: 6
Published: over 3 years ago

10.1186/s13046-019-1372-z

Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer
Cited by: 61
Author(s): Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz de Lucas, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos, Georgios D. Ayiomamitis
Software Mentions: 6
Published: over 5 years ago

10.7150/ijbs.51207

Development of a novel immune-related lncRNA signature as a prognostic classifier for endometrial carcinoma
Cited by: 25
Author(s): Jinhui Liu, Jie Mei, Yichun Wang, Xucheng Chen, Jiadong Pan, Laigen Tong, Yan Zhang
Software Mentions: 5
Published: almost 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

10.7717/peerj.11433

Analysis of multi-omics differences in left-side and right-side colon cancer
Cited by: 7
Author(s): Yanyi Huang, Jinzhong Duanmu, Yushu Liu, Mengyun Yan, Taiyuan Li, Qunguang Jiang
Software Mentions: 5
Published: over 3 years ago

10.3390/cancers12103054

A Methylation-Based Reclassification of Bladder Cancer Based on Immune Cell Genes
Cited by: 26
Author(s): Qizhan Luo, Thomas-Alexander Vögeli
Software Mentions: 5
Published: about 4 years ago

10.1038/s41420-021-00557-2

Identification of the pyroptosis‑related prognostic gene signature and the associated regulation axis in lung adenocarcinoma
Cited by: 119
Author(s): Wanli Lin, Ying Chen, Bomeng Wu, Zuwei Li
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.721873

Screening of DNA Damage Repair Genes Involved in the Prognosis of Triple-Negative Breast Cancer Patients Based on Bioinformatics
Cited by: 4
Author(s): Nan Wang, Yuanting Gu, Jiangrui Chi, Xinwei Li, Youyi Xiong, Chaochao Zhong, Fang Wang, Xinxing Wang, Lin Li
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-020-03691-3

Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma
Cited by: 31
Author(s): Talip Zengin, Tuğba Önal-Süzek
Software Mentions: 5
Published: about 4 years ago

10.1186/s12885-021-08115-w

Identification of PIK3CA multigene mutation patterns associated with superior prognosis in stomach cancer
Cited by: 5
Author(s): Yu Yu, Zhouqing Xie, Mingxin Zhao, Xiaohua Lian
Software Mentions: 5
Published: over 3 years ago

10.1186/s12885-019-6462-y

Systematical identifications of prognostic meaningful lung adenocarcinoma subtypes and the underlying mutational and expressional characters
Cited by: 6
Author(s): Zhenyang Lv, Ting Lei
Software Mentions: 5
Published: almost 5 years ago

10.3389/fcell.2021.707677

The Identification of the Metabolism Subtypes of Skin Cutaneous Melanoma Associated With the Tumor Microenvironment and the Immunotherapy
Cited by: 8
Author(s): Ronghua Yang, Zhengguang Wang, Jiehua Li, Xiaobing Pi, Gao Run-xing, Jun Ma, Yi Qu, Sitong Zhou
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.721505

Integrated Analysis of Copy Number Variation, Microsatellite Instability, and Tumor Mutation Burden Identifies an 11-Gene Signature Predicting Survival in Breast Cancer
Cited by: 5
Author(s): Xin Jin, Yan Junfeng, Chuanzhi Chen, Yi Chen, Wen‐Shih Huang
Software Mentions: 5
Published: about 3 years ago

10.3389/fcell.2021.665265

TP53 Mutational Status-Based Genomic Signature for Prognosis and Predicting Therapeutic Response in Pancreatic Cancer
Cited by: 4
Author(s): Feng Zhang, Wenhui Zhong, Honghao Li, Kaijun Huang, Min Yu, Yu-bin Liu
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.645482

Glycolysis Define Two Prognostic Subgroups of Lung Adenocarcinoma With Different Mutation Characteristics and Immune Infiltration Signatures
Cited by: 3
Author(s): Huo Chen, Mengyu Zhang, Rui Li, Tingting Liu, Jianping Li, Yi-Qing Qu
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.711348

Characterization of Molecular Subtypes in Head and Neck Squamous Cell Carcinoma With Distinct Prognosis and Treatment Responsiveness
Cited by: 10
Author(s): Pei Zhang, Shue Li, Tingting Zhang, Fengzhen Cui, Jihua Shi, Fengbo Zhao, Xia Sheng
Software Mentions: 5
Published: about 3 years ago

10.3389/fonc.2021.683951

The Epithelial to Mesenchymal Transition Related Gene Calumenin Is an Adverse Prognostic Factor of Bladder Cancer Correlated With Tumor Microenvironment Remodeling, Gene Mutation, and Ferroptosis
Cited by: 14
Author(s): Yueyao Du, WenHao Miao, Xiang Jiang, Jin Cao, Bo Wang, Yi Wang, Jian Yu, XiZhi Wang, Haitao Liu
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.570336

A Novel Immune-Related Prognostic Signature in Head and Neck Squamous Cell Carcinoma
Cited by: 10
Author(s): Yi Zhang, Ping Chen, Qiang Zhou, Hongyan Wang, Qingquan Hua, Jie Wang, Hongliang Zhong
Software Mentions: 5
Published: over 3 years ago

10.7150/ijms.39056

Identification of gene expression profiles and immune cell infiltration signatures between low and high tumor mutation burden groups in bladder cancer
Cited by: 33
Author(s): Zonglong Wu, Mu-Ru Wang, Qinggang Liu, Yaxiao Liu, Ke-Cheng Zhu, Lipeng Chen, Hongda Guo, Yan Li, Benkang Shi
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12935-020-01670-5

Development and validation of a VHL-associated immune prognostic signature for clear cell renal cell carcinoma
Cited by: 10
Author(s): Jin Zhang, Aiting Yan, Weimin Cao, Honglei Shi, Kai Cao, Xiaowu Liu
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12935-021-02046-z

Upregulation of ARNTL2 is associated with poor survival and immune infiltration in clear cell renal cell carcinoma
Cited by: 11
Author(s): Song Wang, Xueyou Ma, Yufan Ying, Jiazhu Sun, Zitong Yang, Jiangfeng Li, Ke Jin, Xiao Wang, Bo Xie, Xiangyi Zheng, Ben Liu, Liping Xie
Software Mentions: 5
Published: over 3 years ago

10.18632/aging.104204

ADRB1 was identified as a potential biomarker for breast cancer by the co-analysis of tumor mutational burden and immune infiltration
Cited by: 15
Author(s): Wang Jia, Xiaolu Zhang, Jie Li, Xiaoran Ma, Fubin Feng, Lijuan Liu, Jibiao Wu, Changgang Sun
Software Mentions: 5
Published: about 4 years ago

10.1002/cam4.1791

Analysis of solid tumor mutation profiles in liquid biopsy
Cited by: 19
Author(s): Sai A. Balaji, Ashwini Shanmugam, Anuradha Chougule, Srikant Sridharan, Kumar Prabhash, Anuradha Arya, Aditya Chaubey, Arun K Hariharan, Pandurang Kolekar, Manimala Sen, Aarthi Ravichandran, Shanmukh Katragadda, Satish Sankaran, Satish Bhargava, Prashanth Kulkarni, Suchitra Rao, Chinnababu Sunkavalli, Shripad Banavali, Amit Joshi, Vanita Noronha, Amit Dutt, Urvashi Bahadur, Ramesh Hariharan, Vamsi Veeramachaneni, Vaijayanti Gupta
Software Mentions: 5
Published: about 6 years ago

10.1186/s12935-020-01283-y

Identification and validation of m6A RNA methylation regulators with clinical prognostic value in Papillary thyroid cancer
Cited by: 34
Author(s): Xinyi Wang, Xiaorui Fu, Junjia Zhang, Xiong Cai, Shuyong Zhang, Yali Lv
Software Mentions: 5
Published: over 4 years ago

10.1111/1759-7714.14002

Significance of tumor mutation burden and immune infiltration in thymic epithelial tumors
Cited by: 8
Author(s): Zi-Ming Wang, Qiang Xu, David Kaul, Mahmoud Ismail, Harun Badakhshi
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.713569

Identification of Immune Cell Infiltration Landscape and Their Prognostic Significance in Uveal Melanoma
Cited by: 11
Author(s): Zaizhu Han, Yun Chen, Pan Shen, Lan Gong
Software Mentions: 4
Published: about 3 years ago

10.1111/jcmm.16221

Expression and prognostic characteristics of m 5 C regulators in low‐grade glioma
Cited by: 11
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 4
Published: almost 4 years ago

10.3389/fcell.2021.695533

Identification of a Costimulatory Molecule Gene Signature to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma
Cited by: 12
Author(s): Ling Aye, Xiaole Song, Jingyi Yang, Li Hu, Xicai Sun, Jiaju Zhou, Quan Liu, Hongmeng Yu, Dehui Wang
Software Mentions: 4
Published: over 3 years ago

10.1002/1878-0261.12651

Genetic alterations of malignant pleural mesothelioma: association with tumor heterogeneity and overall survival
Cited by: 66
Author(s): Lisa Quetel, Clément Meiller, Jean-Baptiste Assié, Yuna Blum, Sandrine Imbeaud, François Montagne, Robin Tranchant, Julien De Wolf, Stefano Caruso, Marie‐Christine Copin, Véronique Hofman, Laure Gibault, Cécile Badoual, Ecaterina Pintilie, Paul Hofman, I. Monnet, Arnaud Scherpereel, Françoise Le Pimpec‐Barthes, Jessica Zucman‐Rossi, Marie‐Claude Jaurand, Didier Jean
Software Mentions: 4
Published: over 4 years ago

10.1042/BSR20201491

Exploration of immune-related genes in high and low tumor mutation burden groups of chromophobe renal cell carcinoma
Cited by: 9
Author(s): Lei Li, Xi Chen, Lu Hao, Qiuyan Chen, Haosheng Liu, Qing Zhou
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.667875

TNF-Alpha Pathway Alternation Predicts Survival of Immune Checkpoint Inhibitors in Non-Small Cell Lung Cancer
Cited by: 9
Author(s): Anqi Lin, Hongman Zhang, Hua Meng, Ze Deng, Tianqi Gu, Peng Luo, Jian Zhang
Software Mentions: 4
Published: about 3 years ago

10.3389/fonc.2021.720125

Identification of the Prognosis Value and Potential Mechanism of Immune Checkpoints in Renal Clear Cell Carcinoma Microenvironment
Cited by: 18
Author(s): Guodong Liao, Ping Wang, Yuyong Wang
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3756

An immune‐related seven‐lncRNA signature for head and neck squamous cell carcinoma
Cited by: 11
Author(s): Yue Chen, Tianzhi Luo, Shihe Xu, Chunyan Chen, Ying Sun, Lin Li, Yan‐Ping Mao
Software Mentions: 4
Published: over 3 years ago

10.1111/jcmm.16553

Construction of a SUMOylation regulator‐based prognostic model in low‐grade glioma
Cited by: 3
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 4
Published: over 3 years ago

10.7150/ijms.50491

Multi‐omics analysis of tumor mutational burden combined with prognostic assessment in epithelial ovarian cancer based on TCGA database
Cited by: 18
Author(s): Jinhui Liu, Wei Xu, Siyue Li, Rui Sun, Wenjun Cheng
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2020.517637

The Landscape of Immune Cells Infiltrating in Prostate Cancer
Cited by: 54
Author(s): Zhicong Wu, Hua Chen, Wenyang Luo, Hanyun Zhang, Guihuan Li, Fanning Zeng, Fan Deng
Software Mentions: 4
Published: about 4 years ago

10.3389/fcell.2021.666376

MCM4 Is a Novel Biomarker Associated With Genomic Instability, BRCAness Phenotype, and Therapeutic Potentials in Soft-Tissue Sarcoma
Cited by: 2
Author(s): Qi Liu, Qiyuan Bao, Yanguang Xu, Yucheng Fu, Zhijian Jin, Jun Wang, Weibin Zhang, Yuhui Shen
Software Mentions: 4
Published: over 3 years ago

10.1186/s13046-019-1403-9

IFN-gamma-induced PD-L1 expression in melanoma depends on p53 expression
Cited by: 93
Author(s): Alexander Thiem, Sonja Hesbacher, Hermann Kneitz, Teresa di Primio, Markus V. Heppt, Heike M. Hermanns, Matthias Goebeler, Svenja Meierjohann, Roland Houben, David Schrama
Software Mentions: 4
Published: about 5 years ago

10.3389/fendo.2021.674616

Tumor Mutation Burden Predicts Relapse in Papillary Thyroid Carcinoma With Changes in Genes and Immune Microenvironment
Cited by: 7
Author(s): Mingming Guo, Zhe Chen, Yayi Li, Sijin Li, Fei Shen, Xiao‐Xiong Gan, Jianhua Feng, Wei Cai, Qingzhi Liu, Bo Xu
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2020.01374

Immunogenomic Profiling and Classification of Prostate Cancer Based on HIF-1 Signaling Pathway
Cited by: 8
Author(s): Jukun Song, Wei-Ming Chen, Guohua Zhu, Wei Wang, Fa Sun, Jianguo Zhu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12935-021-01792-4

Identification of a prognostic and therapeutic immune signature associated with hepatocellular carcinoma
Cited by: 42
Author(s): Yanan Peng, Chang Liu, Mengting Li, Wenjie Li, Mengna Zhang, Xiang Jiang, Ying Chang, Lan Liu, Wei Fan, Qiu Zhao
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2020.00796

Genome-Wide Profiling of Alternative Splicing Signature Reveals Prognostic Predictor for Esophageal Carcinoma
Cited by: 5
Author(s): Jian-Rong Sun, Chen-Fan Kong, Yanni Lou, Ran Yu, Xiang-Ke Qu, Liqun Jia
Software Mentions: 4
Published: over 4 years ago

10.7150/jca.50462

Classification of Clear Cell Renal Cell Carcinoma based on Tumor Suppressor Genomic Profiling
Cited by: 2
Author(s): Weimin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 4
Published: almost 4 years ago

10.1093/gigascience/gix015

Enhancing knowledge discovery from cancer genomics data with Galaxy
Cited by: 7
Author(s): Marco A. Albuquerque, Bruno M. Grande, Elie Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K. Grewal, Sohrab P. Shah, Paul C. Boutros, Ryan D. Morin
Software Mentions: 4
Published: over 7 years ago

10.1111/jcmm.16800

Prognostic signature and immune efficacy of m1A‐, m5C‐ and m6A‐related regulators in cutaneous melanoma
Cited by: 20
Author(s): Xian rui Wu, Zheng Chen, Yang Liu, Zi zi Chen, Fengjie Tang, Zhi zhao Chen, Jing Jing Li, Jun Liu, Ke Cao, Xiang Chen, Jianda Zhou
Software Mentions: 4
Published: over 3 years ago

10.1186/s12967-021-03054-3

Interferon regulatory factor family influences tumor immunity and prognosis of patients with colorectal cancer
Cited by: 15
Author(s): Yanjie Chen, Sushan Luo, Ling Dong, Taotao Liu, Xizhong Shen, Ning‐Ping Zhang, Li Liang
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-018-36319-x

Low mutation and neoantigen burden and fewer effector tumor infiltrating lymphocytes correlate with breast cancer metastasization to lymph nodes
Cited by: 17
Author(s): Zhigang Wang, Wei Liu, Chong Chen, Xiaolin Yang, Yunping Luo, Bailin Zhang
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.202811

Prognostic analysis of tumor mutation burden and immune infiltration in hepatocellular carcinoma based on TCGA data
Cited by: 6
Author(s): Shaoqing Liu, Qian-Jie Tang, Jianwen Huang, Meixiao Zhan, Wei Zhao, Xiangyu Yang, Li Yong, Lijuan Qiu, Fujun Zhang, Ligong Lu, Xueling He
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2021.685515

Regulatory Network Analysis of Mutated Genes Based on Multi-Omics Data Reveals the Exclusive Features in Tumor Immune Microenvironment Between Left-Sided and Right-Sided Colon Cancer
Cited by: 10
Author(s): Tianfei Yi, Yuwei Zhang, Derry Minyao Ng, Yang Xi, Meng Ye, Lvjun Cen, Jianjiong Li, Xiaoxiang Fan, Yanguo Li, Shiyun Hu, Hao Rong, Yangyang Xie, Guofang Zhao, Leyi Chen, Chen Chen, Shujing Ni, Jiaying Mi, Xiaoyu Dai, Qi Liao
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2020.557188

Bioinformatics Identification of the Expression and Clinical Significance of E2F Family in Endometrial Cancer
Cited by: 8
Author(s): YunZheng Zhang, Zihao Wang, Jian Ma, Jianing Huo, Yibing Li, YuShan Wang, Hao Chen, LuHe Shan, Xiaoxin Ma
Software Mentions: 4
Published: about 4 years ago

10.3389/fmolb.2021.688298

Identification of a Prognostic Signature Associated With the Homeobox Gene Family for Bladder Cancer
Cited by: 9
Author(s): Bingqi Dong, Jiaming Liang, Li Ding, Wenping Song, Jinbo Song, Mingkai Zhu, Shufang Zhao, Yongkang Ma, Tiejun Yang
Software Mentions: 4
Published: over 3 years ago

10.18632/aging.203184

The circadian clock is associated with prognosis and immune infiltration in stomach adenocarcinoma
Cited by: 13
Author(s): Zhihao Huang, Aoxiao He, Jiakun Wang, Hongmei Lü, Rongguiyi Zhang, Linquan Wu, Qian Feng
Software Mentions: 4
Published: over 3 years ago

10.1155/2019/1093815

Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis
Cited by: 9
Author(s): Yao Ma, Xiaofei Feng, Wan-Xia Yang, Chongge You
Software Mentions: 4
Published: about 5 years ago

10.1155/2021/3766659

Multiomics Differences in Lung Squamous Cell Carcinoma Patients with High Radiosensitivity Index Compared with Those with Low Radiosensitivity Index
Cited by: 2
Author(s): You Wei Du, Shengtao Yuan, Xibing Zhuang, Qi Zhang, Tiankui Qiao
Software Mentions: 4
Published: about 3 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 3 years ago

10.18632/aging.203380

Immune cell infiltration-associated signature in colon cancer and its prognostic implications
Cited by: 12
Author(s): Dan Deng, Xin Luo, Sifang Zhang, Zhijie Xu
Software Mentions: 4
Published: over 3 years ago

10.1038/s41408-021-00493-5

Genomic insights into the pathogenesis of Epstein–Barr virus-associated diffuse large B-cell lymphoma by whole-genome and targeted amplicon sequencing
Cited by: 17
Author(s): Niklas Gebauer, Axel Künstner, Julius Ketzer, Hanno M Witte, Tobias Rausch, Vladimír Beneš, Jürgen Zimmermann, Judith Gebauer, Hartmut Merz, Veronica Bernard, Lana Harder, Katharina Ratjen, Stefan Gesk, Wolfgang Peter, Yannik Busch, Peter Trojok, Nikolas von Bubnoff, Harald Biersack, Hauke Busch, Alfred C. Feller
Software Mentions: 4
Published: over 3 years ago

10.1002/2211-5463.12934

Novel immune subtypes of lung adenocarcinoma identified through bioinformatic analysis
Cited by: 4
Author(s): Fanglu Qin, Zhanyu Xu, Liqiang Yuan, Wenjie Chen, Jiangbo Wei, Yu Sun, Shikang Li
Software Mentions: 4
Published: about 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

10.1111/jcmm.16393

TTN/OBSCN ‘Double‐Hit’ predicts favourable prognosis, ‘immune‐hot’ subtype and potentially better immunotherapeutic efficacy in colorectal cancer
Cited by: 33
Author(s): Xinwei Han, Libo Wang, Chunguang Guo, Long Liu, Dechao Jiao, Zhenqiang Sun, Kunpeng Wu, Yanan Zhao
Software Mentions: 4
Published: over 3 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

10.3390/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

10.3390/biomedicines9020215

Reclassification of Kidney Clear Cell Carcinoma Based on Immune Cell Gene-Related DNA CpG Pairs
Cited by: 1
Author(s): Qizhan Luo, Thomas-Alexander Vögeli
Software Mentions: 4
Published: almost 4 years ago

10.3389/fonc.2021.680918

Hippo Pathway Core Genes Based Prognostic Signature and Immune Infiltration Patterns in Lung Squamous Cell Carcinoma
Cited by: 26
Author(s): Chang Gu, Jiafei Chen, Xuening Dang, Chunji Chen, Zhenyu Huang, Weidong Shen, Xin Shi, Chenyang Dai, Chang Chen
Software Mentions: 4
Published: over 3 years ago

10.1042/BSR20194337

Mining TCGA database for tumor mutation burden and their clinical significance in bladder cancer
Cited by: 71
Author(s): Jia Lv, Yongze Zhu, Alin Ji, Qi Zhang, Guodong Liao
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2021.741608

Identification of Key Regulators of Hepatitis C Virus-Induced Hepatocellular Carcinoma by Integrating Whole-Genome and Transcriptome Sequencing Data
Cited by: 7
Author(s): L. Chen, Wei Zhang, Yiran Ben
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2021.671179

Significance of N6-Methyladenosine RNA Methylation Regulators in Immune Infiltrates of Ovarian Cancer
Cited by: 9
Author(s): Jing Gu, Fangfang Bi
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2019.02451

Pan-Cancer Analysis Reveals Disrupted Circadian Clock Associates With T Cell Exhaustion
Cited by: 51
Author(s): Yingcheng Wu, Baorui Tao, Tianyang Zhang, Yihui Fan, Renfang Mao
Software Mentions: 4
Published: about 5 years ago

10.1002/cam4.2726

Analysis of the clinicopathological characteristics, genetic phenotypes, and prognostic of pure mucinous adenocarcinoma
Cited by: 6
Author(s): Zhencong Chen, Ming Li, Ke Ma, Guanning Shang, Jiaqi Liang, Jiacheng Yin, Jizhuang Luo, Cheng Zhan, Yu Shi, Qun Wang
Software Mentions: 3
Published: almost 5 years ago

10.18632/aging.202853

Comprehensive analysis of genomic and immunological profiles in Chinese and Western hepatocellular carcinoma populations
Cited by: 4
Author(s): Wei Li, Hong Wu, Xuewen Xu, Zhang Yange
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.203456

m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in hepatocellular carcinoma
Cited by: 13
Author(s): Xiongpei Huang, Zecheng Qiu, Liusheng Li, Bin Chen, Peiyuan Huang
Software Mentions: 3
Published: about 3 years ago

10.18632/aging.202267

The mutational pattern of homologous recombination-related (HRR) genes in Chinese colon cancer and its relevance to immunotherapy responses
Cited by: 13
Author(s): Pei Zhou, Xueying Wu, Huan Chen, Ying Hu, Henghui Zhang, Lijia Wu, Ying Yang, Beibei Mao, Huaqing Wang
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-021-04185-6

2-kupl: mapping-free variant detection from DNA-seq data of matched samples
Cited by: 1
Author(s): Yunfeng Wang, Haoliang Xue, Christine Pourcel, Yang Du, Daniel Gautheret
Software Mentions: 3
Published: over 3 years ago

10.1186/s12885-020-07159-8

The prognostic values of m6A RNA methylation regulators in uveal melanoma
Cited by: 22
Author(s): Jing Tang, Qi Wan, Jianqun Lu
Software Mentions: 3
Published: over 4 years ago

10.1186/s12885-020-07157-w

Network-based identification of biomarkers for colon adenocarcinoma
Cited by: 5
Author(s): Fuyan Hu, Qing Wang, Zhiyuan Yang, Zhen Zeng, Xiaoping Li
Software Mentions: 3
Published: over 4 years ago

10.1186/s12885-021-08229-1

Identification of NTRK3 as a potential prognostic biomarker associated with tumor mutation burden and immune infiltration in bladder cancer
Cited by: 13
Author(s): Zhao Zhang, Yizhi Yu, Pengfei Zhang, Guofeng Ma, Mingxin Zhang, Ye Liang, Wei Jiao, Haitao Niu
Software Mentions: 3
Published: over 3 years ago

10.1186/s12885-021-08765-w

A TP53 mutation model for the prediction of prognosis and therapeutic responses in head and neck squamous cell carcinoma
Cited by: 9
Author(s): Congyu Shi, Shan Liu, Xudong Tian, Xiaoyi Wang, Pan Gao
Software Mentions: 3
Published: about 3 years ago

10.1186/s12885-018-4567-3

Deep sequencing of human papillomavirus positive loco-regionally advanced oropharyngeal squamous cell carcinomas reveals novel mutational signature
Cited by: 13
Author(s): Christian Grónhøj Larsen, David Hebbelstrup Jensen, Tina Klitmøller Agander, Katalin Kiss, Estrid Høgdall, Lena Specht, Frederik Otzen Bagger, Finn Cilius Nielsen
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-021-01010-0

Identification of macrophage related gene in colorectal cancer patients and their functional roles
Cited by: 2
Author(s): Yingxiang Chen, Cui Zhang, Xiang Zou, Man Yu, Bo Yang, Chenfeng Ji, Shuangquan Gao, Jun Li, Bin Liu
Software Mentions: 3
Published: over 3 years ago

10.1155/2021/6653802

Multiomics Analysis of Transcriptome, Epigenome, and Genome Uncovers Putative Mechanisms for Dilated Cardiomyopathy
Cited by: 5
Author(s): Li Liu, Jianjun Huang, Yan Liu, Xingshou Pan, Zhile Li, Liufang Zhou, Tengfang Lai, Chengcai Chen, Baomin Wei, Jianjiao Mo, Qinjiang Wei, Yan Wang, Xian-Nan Huang, Zhen Zhang, Zhuohua Zhang, Meidan Huang, Fengzhen He, Zhaohe Huang
Software Mentions: 3
Published: over 3 years ago

10.1155/2021/8357585

Comprehensive Analysis of CD163 as a Prognostic Biomarker and Associated with Immune Infiltration in Glioblastoma Multiforme
Cited by: 3
Author(s): Hao Li, Di Wang, Bolong Yi, Heng Cai, Zhuo Xi, Xin Lou, Zhen Li
Software Mentions: 3
Published: over 3 years ago

10.1042/BSR20201533

Identification of immune-based prostate cancer subtypes using mRNA expression
Cited by: 5
Author(s): Jukun Song, Wei Wang, Yiwen Yuan, Yong Ban, Jiaming Su, Dongbo Yuan, Weihong Chen, Jianguo Zhu
Software Mentions: 3
Published: almost 4 years ago

10.20892/j.issn.2095-3941.2020.0089

The mutational pattern of homologous recombination (HR)-associated genes and its relevance to the immunotherapeutic response in gastric cancer
Cited by: 15
Author(s): Yue Fan, Ying Hui, Xueying Wu, Huan Chen, Ying Hu, Henghui Zhang, Lijia Wu, Ying Yang, Beibei Mao, Lan Zheng
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12935-020-01472-9

Significance of tumor mutation burden combined with immune infiltrates in the progression and prognosis of ovarian cancer
Cited by: 45
Author(s): Fangfang Bi, Ying Chen, Qing Yang
Software Mentions: 3
Published: over 4 years ago

10.1002/cam4.1905

Construction of immune-related risk signature for renal papillary cell carcinoma
Cited by: 42
Author(s): Zhongyu Wang, Qian Song, Zaixing Yang, Jianing Chen, Jun Shang, Wen Ju
Software Mentions: 3
Published: almost 6 years ago

10.3389/pore.2021.589662

Identification of Prognostic Related Genes of Tumor Microenvironment Derived From Esophageal Cancer Patients
Cited by: 3
Author(s): Wei Yuan, Jiaqin Yan, Hongtao Liu, Ling Li, Bowen Wu, Can Guo, Mingzhi Zhang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0224379

Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing
Cited by: 12
Author(s): Youngsub Chun, Jae Woo Choi, Min Hee Hong, Dongmin Jung, Hyeonju Son, Eun Kyung Cho, Young Joo Min, Sang‐We Kim, Keunchil Park, Sung Sook Lee, Sang Woo Kim, Hye Ryun Kim, Byoung Chul Cho
Software Mentions: 3
Published: almost 5 years ago

10.3390/cancers13010105

Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma Are Molecularly Distinct
Cited by: 6
Author(s): Alana Sorgini, Hugh Andrew Jinwook Kim, Peter YF. Zeng, M.A.Q. Shaikh, Neil Mundi, Farhad Ghasemi, Eric Di Gravio, Halema Khan, Danielle MacNeil, Michael A. Khan, Adrian Mendez, John Yoo, Kevin Fung, Pencilla Lang, Joe S. Mymryk, John W. Barrett, Krupal Patel, Paul C. Boutros, Anthony C. Nichols
Software Mentions: 3
Published: almost 4 years ago

10.1155/2020/8836493

Identification of Prognostic Biomarkers of Cutaneous Melanoma Based on Analysis of Tumor Mutation Burden
Cited by: 4
Author(s): Jiaqiong Lin, Ye Lin, Zhemin Huang, Xiaoyong Li
Software Mentions: 3
Published: about 4 years ago

10.1093/database/baz060

ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer
Cited by: 10
Author(s): Judith Pérez-Granado, Janet Piñero, Laura I. Furlong
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13550-020-00632-2

A pan-cancer analysis of the clinical and genetic portraits of somatostatin receptor expressing tumor as a potential target of peptide receptor imaging and therapy
Cited by: 11
Author(s): Hyun-Jong Lee, Minseok Suh, Hongyoon Choi, Seunggyun Ha, Jin Chul Paeng, Gi Jeong Cheon, Keon Wook Kang, Dong Hoon Lee
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.739509

Integrated Analysis of Stemness-Related LncRNAs Helps Predict the Immunotherapy Responsiveness of Gastric Cancer Patients
Cited by: 1
Author(s): Quan Jiang, Lingli Chen, Hao Chen, Zhaoqing Tang, Fenglin Liu, Yihong Sun
Software Mentions: 3
Published: about 3 years ago

10.3389/fgene.2021.630794

Integrative Analysis of TP53INP2 in Head and Neck Squamous Cell Carcinoma
Cited by: 3
Author(s): Ruoyan Cao, Suyang Liu, Jiayu Zhang, Xianyue Ren, Xijuan Chen, Bin Cheng, Juan Xia
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2021.711433

Landscape of Immune Microenvironment Under Immune Cell Infiltration Pattern in Breast Cancer
Cited by: 54
Author(s): Qianhui Xu, Shaohuai Chen, Yuanbo Hu, Wen Huang
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2021.722807

Integrated Profiling Identifies PLOD3 as a Potential Prognostic and Immunotherapy Relevant Biomarker in Colorectal Cancer
Cited by: 12
Author(s): Shi Jun-hong, Meiyu Bao, Weifeng Wang, Xuan Wu, Yueying Li, Chaofen Zhao, Weiwei Liu
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2021.653711

The N6-Methyladenosine-Modified Pseudogene HSPA7 Correlates With the Tumor Microenvironment and Predicts the Response to Immune Checkpoint Therapy in Glioblastoma
Cited by: 26
Author(s): Rongrong Zhao, Boyan Li, Shouji Zhang, Zheng He, Ziwen Pan, Qindong Guo, Wei Qiu, Yanhua Qi, Shulin Zhao, Shaobo Wang, Zihang Chen, Ping Zhang, Xing Guo, Hao Xue, Gang Li
Software Mentions: 3
Published: over 3 years ago

10.3389/fmed.2021.667543

m6A RNA Methylation Regulator YTHDF1 Correlated With Immune Microenvironment Predicts Clinical Outcomes and Therapeutic Efficacy in Breast Cancer
Cited by: 10
Author(s): Ying Hu, Qinwen Pan, Minghao Wang, Xiang Ai, Yuzhao Yan, Yuan Tian, Yuting Jing, Peng Tang, Jun Jiang
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.716854

Comprehensive Analysis of the Immune Infiltrates of Pyroptosis in Kidney Renal Clear Cell Carcinoma
Cited by: 17
Author(s): Zhuolun Sun, Changying Jing, Xudong Guo, Mingxiao Zhang, Feng Kong, Zhenqing Wang, Shaobo Jiang, Hanbo Wang
Software Mentions: 3
Published: about 3 years ago

Projects: bioconductor: maftools

Papers Mentioning maftools 288