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Topic Evolution Analysis for Omics Data Integration in Cancers

Li Ning, He Huixin
2021 Frontiers in Cell and Developmental Biology  
The topic extraction results indicate that, with the rapid development of omics data integration research, multi-omics analysis (Topic 11) and genomics of colorectal cancer (Topic 10) have more studies  ...  From the topic prediction view, research findings in multi-omics data processing and novel biomarker discovery for cancer prediction (Topic 2, 3, 10, 11) will be heavily focused in the future.  ...  contents of integrating omics data in cancer research.  ... 
doi:10.3389/fcell.2021.631011 pmid:33898421 pmcid:PMC8058380 fatcat:inytqh6ywfarjh2neryg7jpu5m

Next-Generation Pathology [chapter]

Peter D. Caie, David J. Harrison
2016 Msphere  
The integration of standardised multi-omics Big-Data and the retention of valuable information on spatial heterogeneity is imperative to model complex disease mechanisms.  ...  Next generation pathology will incorporate Big-Data with systems medicine in order to personalise clinical practise for both prognostic and predictive patient care.  ...  labelled colorectal cancer tissue utilizing Definiens image analysis software.  ... 
doi:10.1007/978-1-4939-3283-2_4 pmid:26677179 fatcat:uithnzbsuraetn3y4spt52vqd4

Discovery of colorectal cancer PIK3CA mutation as potential predictive biomarker: power and promise of molecular pathological epidemiology

S Ogino, P Lochhead, E Giovannucci, J A Meyerhardt, C S Fuchs, A T Chan
2013 Oncogene  
Regular use of aspirin reduces incidence and mortality of various cancers, including colorectal cancer. Anticancer effect of aspirin represents one of the 'Provocative Questions' in cancer research.  ...  MPE represents an interdisciplinary integrative science, conceptually defined as 'epidemiology of molecular heterogeneity of disease'.  ...  DISCLAIMER The content is solely the responsibility of the authors and does not necessarily represent the official views of NIH.  ... 
doi:10.1038/onc.2013.244 pmid:23792451 pmcid:PMC3818472 fatcat:iavt7jdp4rh6nhy6vaujfzgdwy

Integrative analysis of exogenous, endogenous, tumour and immune factors for precision medicine

Shuji Ogino, Jonathan A Nowak, Tsuyoshi Hamada, Amanda I Phipps, Ulrike Peters, Danny A Milner Jr, Edward L Giovannucci, Reiko Nishihara, Marios Giannakis, Wendy S Garrett, Mingyang Song
2018 Gut  
Proof-of-principle studies on colorectal cancer provided insights into immunomodulating effects of aspirin, vitamin D, inflammatory diets and omega-3 polyunsaturated fatty acids.  ...  The integrated immunology-MPE model can contribute to better understanding of environment-tumour-immune interactions, and effective immunoprevention and immunotherapy strategies for precision medicine.  ...  We propose an integrated multilevel analysis of environment, tumour and immunity for improving cancer prevention and treatment.  ... 
doi:10.1136/gutjnl-2017-315537 pmid:29437869 fatcat:5p7jqj7mqvdrph57xmcb2re6gi

Molecular subtyping of colorectal cancer: Recent progress, new challenges and emerging opportunities

Wei Wang, Raju Kandimalla, Hao Huang, Lina Zhu, Ying Li, Feng Gao, Ajay Goel, Xin Wang
2018 Seminars in Cancer Biology  
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide.  ...  Recently, pembrolizumab, an anti-PD1 immunotherapy, has been approved by FDA for treatment of MSI-H or dMMR colorectal cancer.  ...  Acknowledgments The present work was supported by a start-up grant for new faculty (7200455) and a VPRT grant (9610337)  ... 
doi:10.1016/j.semcancer.2018.05.002 pmid:29775690 pmcid:PMC6240404 fatcat:jtfffdfoznenfmigdydgekqxby

Elucidating the Reprograming of Colorectal Cancer Metabolism Using Genome-Scale Metabolic Modeling

Cheng Zhang, Mohammed Aldrees, Muhammad Arif, Xiangyu Li, Adil Mardinoglu, Mohammad Azhar Aziz
2019 Frontiers in Oncology  
Colorectal cancer is the third most incidental cancer worldwide, and the response rate of current treatment for colorectal cancer is very low.  ...  We also investigated these genes in independent colorectal cancer patients and cell lines and found that many of these genes showed elevated level in colorectal cancer and exhibited adverse effect in patients  ...  integrated the personalized colorectal cancer GEMs and generated a generic GEM for colorectal cancer.  ... 
doi:10.3389/fonc.2019.00681 pmid:31417867 pmcid:PMC6682621 fatcat:wntjpuvbbbhelcgrn4cn6to47i

crcTRP: A Translational Research Platform for Colorectal Cancer

Ning Deng, Ling Zheng, Fang Liu, Li Wang, Huilong Duan
2013 Computational and Mathematical Methods in Medicine  
In this paper, a translational research platform for colorectal cancer, named crcTRP, is introduced. crcTRP serves the colorectal cancer translational research by providing various types of biomedical  ...  Transforming basic research results into clinical practice is one of the key tasks of translational research, which will greatly improve the diagnosis and treatments of colorectal cancer.  ...  a lot to colorectal cancer translational research.  ... 
doi:10.1155/2013/930362 pmid:23431356 pmcid:PMC3575041 fatcat:2uj7tg6plrarlm2qkbslsz54ju

Effect of perioperative intravenous lidocaine on postoperative outcomes in patients undergoing resection of colorectal cancer: a protocol for systematic review and meta-analysis

Wentao JI, Xiaoting Zhang, Guolin Sun, Xiandong Wang, Jia Liu, Jinjun Bian, Lulong Bo
2021 BMJ Open  
undergoing resection of colorectal cancer before August 2021.  ...  the data used for this systematic review will be exclusively extracted from published studies, ethical approval and informed consent of patients will not be required.  ...  SG and LB provided statistical and epidemiological support. JW wrote the article with the support of LB and ZX. All the authors revised and approved the final version of the manuscript.  ... 
doi:10.1136/bmjopen-2021-048803 pmid:34426465 pmcid:PMC8383864 fatcat:owahkjtvq5djpfht6cswypb6q4

Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues

David Chisanga, Shivakumar Keerthikumar, Mohashin Pathan, Dinuka Ariyaratne, Hina Kalra, Stephanie Boukouris, Nidhi Abraham Mathew, Haidar Al Saffar, Lahiru Gangoda, Ching-Seng Ang, Oliver M. Sieber, John M. Mariadason (+3 others)
2015 Nucleic Acids Research  
A database which integrates data from heterogeneous resources and enables analysis of the multidimensional data sets, specifically pertaining to CRC is currently lacking.  ...  In order to advance our understanding of colorectal cancer (CRC) development and progression, biomedical researchers have generated large amounts of OMICS data from CRC patient samples and representative  ...  COLORECTAL CANCER ATLAS PROVIDES AN INTE-GRATED VIEW OF MULTIPLE DATA TYPES Colorectal Cancer Atlas provides an integrated view of the sequence variations and the proteomic data.  ... 
doi:10.1093/nar/gkv1097 pmid:26496946 pmcid:PMC4702801 fatcat:zav42smdurfsrbm3py7nehrcuu

Bulk and Single-Cell Next-Generation Sequencing: Individualizing Treatment for Colorectal Cancer

Ioannis D. Kyrochristos, Demosthenes E. Ziogas, Anna Goussia, Georgios K. Glantzounis, Dimitrios H. Roukos
2019 Cancers  
Explosive integration of next-generation sequencing (NGS) systems into basic, translational and, more recently, basket trials is transforming biomedical and cancer research, aiming for substantial clinical  ...  This review describes latest advancements and future perspectives of integrated sequencing systems for genome and transcriptome exploration to overcome unmet research and clinical challenges towards Precision  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cancers11111809 pmid:31752125 pmcid:PMC6895993 fatcat:dcwutfgl4vhc7ctxd2p4ls5jcu

Immunohistochemical detection of cancer-associated fibroblasts in gastrointestinal cancer as a potential prognostic biomarker of survival: meta-analysis

Junjie Gu, Chenyu Wang, Xiuxiu Xu, Lin Zhao, Jianfeng Zhou, Chunmei Bai, Zhao Sun
2020 Translational Cancer Research  
The meta-analysis indicates that high proportion of CAFs is a valuable predictor of the prognosis in gastrointestinal cancer patients, and it may provide new ideas for targeted therapy in gastrointestinal  ...  The association between cancer-associated fibroblasts (CAFs) and prognosis of gastrointestinal cancer patients remains controversial.  ...  Acknowledgments We thank all the authors of the enrolled published papers for their valued contributions to the field. Funding: None.  ... 
doi:10.21037/tcr-20-2365 pmid:35117273 pmcid:PMC8798960 fatcat:n27ahv37kngvtdt6ngtaja64mm

Identification of biomarkers for the diagnosis and treatment of primary colorectal cancer based on microarray technology

Zhi Gang Zheng, Bao Qing Ma, Yu Xiao, Tian Xi Wang, Tian Yu, Yu Hu Huo, Qing Qing Wang, Meng Jie Shan, Ling Bing Meng, Jing Han
2020 Translational Cancer Research  
Primary colorectal cancer (PCRC) is one of the most common malignant tumors in clinic, and is characterized by high heterogeneity occurring between tumors and intracellularly.  ...  Differently expressed genes (DEGs) were identified with GEO2R, and the gene set enrichment analysis (GSEA) was implemented for enrichment analysis.  ...  distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and  ... 
doi:10.21037/tcr-19-2290 pmid:35117711 pmcid:PMC8798183 fatcat:ztvj56z5ibhfdeheoflsmzmfny

Precision Prevention of Cancer

T. R. Rebbeck
2014 Cancer Epidemiology, Biomarkers and Prevention  
analysis, and dissemination and implementation research.  ...  in precision prevention research and translation.  ... 
doi:10.1158/1055-9965.epi-14-1058 pmid:25362191 fatcat:m72phbvizfgz3mf2xuzm3oouqu

Lipidomics: a promising cancer biomarker

Furong Yan, Hong Zhao, Yiming Zeng
2018 Clinical and Translational Medicine  
Previous researches indicated that lipids may serve as a promising biomarker in the early diagnoses and individualized treatment of cancer.  ...  The prevention, diagnosis and targeted therapies of cancer are important in cancer controlling and treatment.  ...  The study about lipids as biomarkers for cancer is gradually translated from basic research to clinical application.  ... 
doi:10.1186/s40169-018-0199-0 pmid:30058036 pmcid:PMC6064713 fatcat:2f5x34h4kzgsnhhmlp5o27v3fm

Proceedings of the third international molecular pathological epidemiology (MPE) meeting

Peter T. Campbell, Timothy R. Rebbeck, Reiko Nishihara, Andrew H. Beck, Colin B. Begg, Alexei A. Bogdanov, Yin Cao, Helen G. Coleman, Gordon J. Freeman, Yujing J. Heng, Curtis Huttenhower, Rafael A. Irizarry (+19 others)
2017 Cancer Causes and Control  
Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases.  ...  Special topics included integration of MPE with immunology and health disparity research.  ...  He illustrated the use of the new method in the analysis of colorectal cancer data from the Nurses' Health Study. The auxiliary covariate was tumor location, which is commonly accrued for most cases.  ... 
doi:10.1007/s10552-016-0845-z pmid:28097472 pmcid:PMC5303153 fatcat:izydmxu5wrfhdh67qv3rre4zpu
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