bioconductor: CancerSubtypes | Projects

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.3389/fonc.2020.555632

Comprehensive Characterization of Alternative mRNA Splicing Events in Glioblastoma: Implications for Prognosis, Molecular Subtypes, and Immune Microenvironment Remodeling
Cited by: 8
Author(s): Liang Zhao, Jiayue Zhang, Zhiyuan Liu, Yu Wang, Shurui Xuan, Peng Zhao
Software Mentions: 16
Published: almost 4 years ago

10.1016/j.cell.2019.10.007

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
Cited by: 375
Author(s): David Clark, Saravana M. Dhanasekaran, Francesca Petralia, Jianbo Pan, Xiaoyu Song, Yingwei Hu, Felipe da Veiga Leprevost, Boris Reva, Tung-Shing Mamie Lih, Hui-Yin Chang, Wanli Ma, Chen Huang, Christopher J. Ricketts, Lijun Chen, Azra Krek, Yize Li, Dmitry Rykunov, Qing Kay Li, Lin S. Chen, Umut Özbek, Suhas Vasaikar, Yige Wu, Seungyeul Yoo, Shrabanti Chowdhury, Matthew A. Wyczalkowski, Jiayi Ji, Michael Schnaubelt, Andy T. Kong, Sunantha Sethuraman, Dmitry M. Avtonomov, Minghui Ao, Antonio Colaprico, Song Cao, Kyung-Cho Cho, Selim Kalayci, Shiyong Ma, Wenke Liu, Kelly V. Ruggles, Anna Calinawan, Zeynep H. Gümüş, Daniel Geiszler, Emily Kawaler, Guo Ci Teo, Bo Wen, Yuping Zhang, Sarah Keegan, Kai Li, Feng Chen, Nathan Edwards, Phillip M. Pierorazio, Xi Steven Chen, Christian P. Pavlovich, A. Ari Hakimi, Gabriel Bromiński, James J. Hsieh, Andrzej Antczak, Tatiana Omelchenko, Jan Lubiński, Maciej Wiznerowicz, W. Marston Linehan, Christopher R. Kinsinger, Mathangi Thiagarajan, Emily S. Boja, Mehdi Mesri, Tara Hiltke, Ana I. Robles, Henry Rodriguez, Jiang Qian, David Fenyö, Bing Zhang, Ding Li, Eric E. Schadt, Arul M. Chinnaiyan, Zhen Zhang, Gilbert S. Omenn, Marcin Cieślik, Daniel W. Chan, Alexey I. Nesvizhskii, Pei Wang, Hui Zhang, A. Samad Hashimi, Alexander Pico, Alla Karpova, Alyssa Charamut, Amanda G. Paulovich, Amy M. Perou, Anna Malovannaya, Annette Marrero-Oliveras, Anupriya Agarwal, Barbara Hindenach, Barbara L. Pruetz, Beom-Jun Kim, Brian J. Druker, Chelsea J. Newton, Chet Birger, Corbin D. Jones, Cristina E. Tognon, D. R. Mani, Dana R. Valley, Daniel C. Rohrer, Daniel Cui Zhou, Darlene Tansil, David Chesla, David I. Heiman, David A. Wheeler, Donghui Tan, Doug W. Chan, Emek Demir, Ewa Malc, Francesmary Modugno, Gaddy Getz, Galen Hostetter, George Wilson, Gerald W. Hart, Heng Zhu, Hongwei Liu, Houston Culpepper, Hua Sun, Hua Zhou, Jacob Day, James Suh, Jasmine Huang, Jason McDermott, Jeffrey R. Whiteaker, Jeffrey W. Tyner, Jennifer Eschbacher, Jin Chen, John P. McGee, Jun Zhu, Karen A. Ketchum, Karin D. Rodland, Karl R. Clauser, Karna Robinson, Karsten Krug, Katherine A. Hoadley, Ki Sung Um, Kim Elburn, Kimberly Holloway, Liang-Bo Wang, Lili M. Blumenberg, Linda Hannick, Liqun Qi, Lori J. Sokoll, MacIntosh Cornwell, Marc Loriaux, Marcin J. Domagalski, Marina Gritsenko, Matthew L. Anderson, Matthew E. Monroe, Matthew J. Ellis, Maureen A. Dyer, Meenakshi Anurag, Meghan C. Burke, Melissa Borucki, Michael A. Gillette, Michael J. Birrer, Michael R. Lewis, Michael Ittmann, Michael J. Smith, Michael Vernon, Michelle Chaikin, Milan G. Chheda, Munziba Khan, Nancy Roche, Nathan Edwards, Negin Vatanian, Nicole Tignor, Noam D. Beckmann, Pamela Grady, Patricia Castro, Paul Piehowski, Peter B. McGarvey, Piotr A. Mieczkowski, Pushpa Hariharan, Qingsong Gao, Rajiv Dhir, Ramani B. Kothadia, Ratna R. Thangudu, Rebecca Montgomery, Reyka G. Jayasinghe, Richard Smith, Robert A. Edwards, Robert Zelt, Ross M. Bremner, Ruiyang Liu, Runyu Hong, Sailaja Mareedu, Samuel H. Payne, Sandra Cottingham, Sanford P. Markey, Scott D. Jewell, Shalin Patel, Shankha Satpathy, Shannon Richey, Sherri R. Davies, Shuang Cai, Simina M. Boca, Snehal Patil, Sohini Sengupta, Sonya Carter, Stacey Gabriel, Stefani N. Thomas, Stephanie Young, Stephen E. Stein, Steven A. Carr, Steven M. Foltz, S. G. Hilsenbeck, Tanya Krubit, Tao Liu, Tara Skelly, Thomas F. Westbrook, Uma Borate, Uma Velvulou, Vladislav Petyuk, William Bocik, Xi Chen, Yan Shi, Yifat Geffen, Yihao Lu, Ying Wang, Yosef E. Maruvka, Zhi Li, Zhiao Shi, Zhidong Tu
Software Mentions: 10
Published: about 5 years ago

10.1111/jcmm.14999

A stroma‐related lncRNA panel for predicting recurrence and adjuvant chemotherapy benefit in patients with early‐stage colon cancer
Cited by: 13
Author(s): Rui Zhou, Huiying Sun, Songbai Zheng, Jingwen Zhang, Dongqiang Zeng, Jianhua Wu, Zhenhua Huang, Xiaoxiang Rong, Jianping Bin, Yulin Liao, Min Shi, Wangjun Liao
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmolb.2020.598725

The Integrative Analysis Identifies Three Cancer Subtypes and Stemness Features in Cutaneous Melanoma
Cited by: 1
Author(s): Xiaoran Wang, Qi Wan, Lin Jin, Chengxiu Liu, Chang Liu, Yuanrong Cheng, Zhichong Wang
Software Mentions: 6
Published: almost 4 years ago

10.1002/cam4.3984

Signature based on metabolic‐related gene pairs can predict overall survival of osteosarcoma patients
Cited by: 8
Author(s): Long‐Qing Li, Liang‐Hao Zhang, Yongjie Yuan, Xin Lu, Yi Zhang, Yong‐Kui Liu, Wen Jiang, Manhas Abdul Khader, Tao Liu, Jiazhen Li, Yan Zhang
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2021.720841

Unsupervised Clustering Reveals Distinct Subtypes of Biliary Atresia Based on Immune Cell Types and Gene Expression
Cited by: 9
Author(s): Xiaoyan Pang, Jing Cao, Shuru Chen, Zhiliang Gao, Guangjian Liu, Yutian Chong, Zhuang‐Gui Chen, Jiao Gong, Xinhua Li
Software Mentions: 6
Published: about 3 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/s12859-021-04215-3

Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis
Cited by: 5
Author(s): Xiaomei Li, Buu Truong, Taosheng Xu, Lin Liu, Jiuyong Li, Thuc Duy Le
Software Mentions: 5
Published: over 3 years ago

10.1172/jci.insight.149257

Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort
Cited by: 27
Author(s): Flavia Flaviani, Natasha L. Hezelgrave, Tokuwa Kanno, Erica M. Prosdocimi, Evonne Chin-Smith, Alexandra Ridout, Djuna K von Maydell, Vikash Mistry, William Wade, Andrew Shennan, Konstantina Dimitrakopoulou, Paul Seed, A. James Mason, Rachel Tribe
Software Mentions: 5
Published: about 3 years ago

10.1186/s12859-019-2668-x

Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction
Cited by: 21
Author(s): Vu Viet Hoang Pham, Junpeng Zhang, Lin Liu, Buu Truong, Taosheng Xu, Trung Tin Nguyen, Jiuyong Li, Thuc Duy Le
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2021.692454

Unsupervised Hierarchical Clustering Identifies Immune Gene Subtypes in Gastric Cancer
Cited by: 9
Author(s): Jing Cao, Jiao Gong, Xinhua Li, Zhaoxia Hu, Yingjun Xu, Huading Shi, Danyang Li, Guangjian Liu, Yusheng Jie, Bo Hu, Yutian Chong
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2019.01285

Patterns of Immune Infiltration in HNC and Their Clinical Implications: A Gene Expression-Based Study
Cited by: 28
Author(s): Jukun Song, Zhili Deng, Jiaming Su, Dongbo Yuan, Jianguo Liu, Jianguo Zhu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fbioe.2020.00176

MicroRNAs Associated With Colon Cancer: New Potential Prognostic Markers and Targets for Therapy
Cited by: 25
Author(s): Junfeng Zhu, Ying Xü, Shanshan Liu, Qiao Li, Jianqiang Sun, Qi Zhao
Software Mentions: 3
Published: over 4 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

10.3390/curroncol28010091

A Histone Acetylation Modulator Gene Signature for Classification and Prognosis of Breast Cancer
Cited by: 5
Author(s): Mengping Long, Wei Hou, Yiqiang Liu, Taobo Hu
Software Mentions: 3
Published: almost 4 years ago

10.1042/BSR20193308

Genomic analysis and clinical implications of immune cell infiltration in gastric cancer
Cited by: 11
Author(s): Ming Wu, Yadong Wang, Huan Liu, Jukun Song, Jie Ding
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2020.574661

Multi-Omics Analysis Detects Novel Prognostic Subgroups of Breast Cancer
Cited by: 16
Author(s): Quang-Huy Nguyen, Hung Son Nguyen, Tin Nguyen, Duc-Hau Le
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2021.715460

DNA Damage Repair Profiles Alteration Characterize a Hepatocellular Carcinoma Subtype With Unique Molecular and Clinicopathologic Features
Cited by: 12
Author(s): Peng Lin, Ruizhi Gao, Rong Wen, Yun He, Hong Yang
Software Mentions: 2
Published: over 3 years ago

10.1042/BSR20201431

Identification of three molecular subtypes based on immune infiltration in ovarian cancer and its prognostic value
Cited by: 16
Author(s): Juan Liu, Zongjian Tan, Jun He, Tingting Jin, Yuanyuan Han, Li Hu, Jukun Song, Sheng‐Wen Huang
Software Mentions: 1
Published: about 4 years ago

10.3389/fgene.2019.00966

CEPICS: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping
Cited by: 7
Author(s): Ran Duan, Lin Gao, Xu Han, Kuo Song, Yuxuan Hu, Hongda Wang, Yun Dong, Chenxing Zhang, Songwei Jia
Software Mentions: 1
Published: about 5 years ago

Ecosyste.ms: Papers

Projects: bioconductor: CancerSubtypes

Papers Mentioning CancerSubtypes 22