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A New Framework for Precise Identification of Prostatic Adenocarcinoma

Sarah M. Ayyad, Mohamed A. Badawy, Mohamed Shehata, Ahmed Alksas, Ali Mahmoud, Mohamed Abou Abou El-Ghar, Mohammed Ghazal, Moumen El-Melegy, Nahla B. Abdel-Hamid, Labib M. Labib, H. Arafat Ali, Ayman El-Baz
2022 Sensors  
In this paper, we introduce a new comprehensive framework to precisely differentiate between malignant and benign prostate cancer.  ...  different feature sets that lead to better identification of prostatic adenocarcinoma.  ...  To overcome the drawbacks of the aforementioned studies, we developed a new comprehensive framework (shown in Figure 1 ) for early identification of prostatic adenocarcinoma.  ... 
doi:10.3390/s22051848 pmid:35270995 pmcid:PMC8915102 fatcat:r2sypzk3z5ei5m3jg7cdusqcqa

LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer

K. Babalyan, R. Sultanov, E. Generozov, E. Sharova, E. Kostryukova, A. Larin, A. Kanygina, V. Govorun, G. Arapidi, Arne Elofsson
2018 PLoS ONE  
The algorithm produced an AUC of 0.97 (95% CI: 0.94-0.99, 9 sites) for prostate adenocarcinoma and an AUC of 1.0 (from 2 to 6 sites) for urothelial bladder carcinoma, two types of kidney carcinoma and  ...  For prostate adenocarcinoma we showed that identified differential variability methylation patterns distinguish cluster of samples with higher recurrence rate (hazard ratio for recurrence = 0.48, 95% CI  ...  Prostate adenocarcinoma.  ... 
doi:10.1371/journal.pone.0204371 fatcat:5mpstsftgvggdmv7rjddedu2ly

Tissue-associated microbial detection in cancer using human sequencing data

Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez, Youping Deng
2020 BMC Bioinformatics  
AbstractCancer is one of the leading causes of morbidity and mortality in the globe. Microbiological infections account for up to 20% of the total global cancer burden.  ...  With the advent of next generation sequencing (NGS) technologies, data generated from NGS is being used for pathogen detection in cancer.  ...  On the downside, the target reference genome must be present for precise identification of microbes.  ... 
doi:10.1186/s12859-020-03831-9 pmid:33272199 fatcat:hf33nubknzc5dj7cy4hqzqal34

TOOme: A Novel Computational Framework to Infer Cancer Tissue-of-Origin by Integrating Both Gene Mutation and Expression

Binsheng He, Jidong Lang, Bo Wang, Xiaojun Liu, Qingqing Lu, Jianjun He, Wei Gao, Pingping Bing, Geng Tian, Jialiang Yang
2020 Frontiers in Bioengineering and Biotechnology  
Thus, we developed a computational framework to infer tumor tissue-of-origin by integrating both gene mutation and expression (TOOme).  ...  However, the tissue-of-origin for around 5% tumors could not be identified by routine medical diagnosis according to a statistics in the United States.  ...  All authors approved the final version of this manuscript. 19A060 and 19C0185).  ... 
doi:10.3389/fbioe.2020.00394 pmid:32509741 pmcid:PMC7248358 fatcat:rjykpgsyu5drtlf7v2n4huptj4

Optimizing mouse models for precision cancer prevention

Clémentine Le Magnen, Aditya Dutta, Cory Abate-Shen
2016 Nature Reviews. Cancer  
This conceptual framework requires a precise understanding of the genetic, and epigenetic factors that promote cancer, and how these are influenced by environmental factors such as diet, hormones, pharmaceutical  ...  Herein we discuss opportunities and challenges for "precision mouse modeling", including their essential criteria of mouse models for prevention research, representative success stories, and opportunities  ...  framework that focuses on precision prevention.  ... 
doi:10.1038/nrc.2016.1 pmid:26893066 pmcid:PMC5517771 fatcat:5m6qpcezhvgtjnfexejksw2qvi

Prostate cancer screening research can benefit from network medicine: an emerging awareness

Valeria Panebianco, Martina Pecoraro, Giulia Fiscon, Paola Paci, Lorenzo Farina, Carlo Catalano
2020 npj Systems Biology and Applications  
Up to date, screening for prostate cancer (PCa) remains one of the most appealing but also a very controversial topics in the urological community.  ...  exploring new research pathways in a rational, highly reliable, and reproducible way.  ...  Similarly, Yang et al. 55 integrated somatic mutation profiles in a PPI network for stratifying prostate adenocarcinoma samples.  ... 
doi:10.1038/s41540-020-0133-0 pmid:32382028 pmcid:PMC7206063 fatcat:lvwcddrflzgsffcildn27wc3di

caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research

Rebecca S Crowley, Melissa Castine, Kevin Mitchell, Girish Chavan, Tara McSherry, Michael Feldman
2010 JAMIA Journal of the American Medical Informatics Association  
Implementation of the system at several Cancer Centers across the country is creating a potential network of caTIES repositories that could provide millions of de-identified clinical reports to users.  ...  The design of caTIES addresses three critical issues for informatics support of translational research: (1) federation of research data sources derived from clinical systems; (2) expressive graphical interfaces  ...  Acknowledgements We thank Lucy Cafeo at the University of Pittsburgh Department of Biomedical Informatics for expert preparation and review of the manuscript.  ... 
doi:10.1136/jamia.2009.002295 pmid:20442142 pmcid:PMC2995710 fatcat:cotiub7yfbahfarpfn3urykbaq

Cultivating Clinical Clarity through Computer Vision: A Current Perspective on Whole Slide Imaging and Artificial Intelligence

Ankush U. Patel, Nada Shaker, Sambit Mohanty, Shivani Sharma, Shivam Gangal, Catarina Eloy, Anil V. Parwani
2022 Diagnostics  
As computer vision shapes new constructs for the modern world and intertwines with clinical medicine, cultivating clarity of our new terrain through examining the trajectory and current scope of computational  ...  Through review of numerous studies, we find developmental efforts for ML migrating from research to standardized clinical frameworks while overcoming obstacles that have formerly curtailed adoption of  ...  Conflicts of Interest: The authors declare no conflict of interest. Diagnostics 2022, 12, 1778  ... 
doi:10.3390/diagnostics12081778 pmid:35892487 pmcid:PMC9332710 fatcat:4cgjt665zbgidnpoeklwsmr6iy

Deep Learning-Based Pan-Cancer Classification Model Reveals Tissue-of-Origin Specific Gene Expression Signatures

Mayur Divate, Aayush Tyagi, Derek J. Richard, Prathosh A. Prasad, Harsha Gowda, Shivashankar H. Nagaraj
2022 Cancers  
In conclusion, we present a robust neural network model for accurate classification of cancers based on gene expression data and also provide a list of gene signatures that are valuable for developing  ...  These gene signatures serve as valuable biomarkers for determining tissue-of-origin for cancers of unknown primary.  ...  For example, the expression of prostate-specific antigen (PSA) is elevated in prostate cancer patients [1] .  ... 
doi:10.3390/cancers14051185 pmid:35267493 pmcid:PMC8909043 fatcat:sdxauigxj5byrpbjmgzwdxaxjq

Liquid Biopsy is Instrumental for 3PM Dimensional Solutions in Cancer Management

Alena Liskova, Marek Samec, Lenka Koklesova, Frank A. Giordano, Peter Kubatka, Olga Golubnitschaja
2020 Journal of Clinical Medicine  
At any stage, application of early and predictive diagnostics, targeted prevention, and personalization of medical services are basic pillars making 3PM particularly attractive for the patients as well  ...  In view of the consequent severe socio-economic burden on society, the paradigm change from a reactive to a predictive, preventive, and personalized medical approach in the overall cancer management is  ...  Furthermore, circulating exosomal DNA could be used for fast and low-cost identification of cancer-driving mutations, as has been illustrated by a study evaluating a possible identification of KRAS and  ... 
doi:10.3390/jcm9092749 pmid:32854390 pmcid:PMC7563444 fatcat:3oaa27vppzdg3hhtythqubuqga

Deep learning-based pan-cancer classification model reveals cancer-specific gene expression signatures [article]

Mayur Divate, Aayush Tyagi, Derek J. Richard, Prathosh A Prasad, Harsha Gowda, Shivashankar H Nagaraj
2021 bioRxiv   pre-print
The identification of cancer-specific biomarkers and therapeutic targets is one of the primary goals of cancer genomics.  ...  We employed deep neural networks to train a model on the transcriptome profile datasets for all cancer types.  ...  Deep learning is a cutting-edge artificial intelligence technique that provides a very powerful framework for supervised learning [13] .  ... 
doi:10.1101/2021.03.15.435283 fatcat:stasu6xmm5hv3m55mttrtjpwcy

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

Himisha Beltran, Davide Prandi, Juan Miguel Mosquera, Matteo Benelli, Loredana Puca, Joanna Cyrta, Clarisse Marotz, Eugenia Giannopoulou, Balabhadrapatruni V S K Chakravarthi, Sooryanarayana Varambally, Scott A Tomlins, David M Nanus (+7 others)
2016 Nature Medicine  
An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, wherein tumor cells demonstrate low to absent AR  ...  Acknowledgements We would like to thank our patients and their families for participation in this study. We would also like to acknowledge R. Montgomery, A. Armstrong, R.  ...  Szmulewitz for contributing samples and S.S. Chae for his technical assistance. H. Beltran  ... 
doi:10.1038/nm.4045 pmid:26855148 pmcid:PMC4777652 fatcat:xtkrk3urzne4zfxgwueelyyvpi

Bacteria in Cancer Therapeutics: A Framework for Effective Therapeutic Bacterial Screening and Identification

Eta E. Ashu, Jianping Xu, Ze-Chun Yuan
2019 Journal of Cancer  
Here, we provided a four-step framework that can be used in screening and identifying bacteria with cancer therapeutic potential, including those that are uncultivable.  ...  Systematic methodologies such as the ones suggested here could prove valuable to new BMCT researchers, including experienced non-BMCT researchers in possession of extensive knowledge and resources of bacterial  ...  A four-step framework for screening and identifying bacteria with cancer therapeutic potential.  ... 
doi:10.7150/jca.31699 pmid:31205534 pmcid:PMC6547982 fatcat:dtaje4hrizgjpgrrqf4ejvkfvu

Multilineage plasticity in prostate cancer through expansion of stem–like luminal epithelial cells with elevated inflammatory signaling [article]

Samir Zaidi, Jimmy L. Zhao, Joseph M. Chan, Martine P. Roudier, Kristine M. Wadosky, Anuradha Gopalan, Wouter R. Karthaus, Jungmin Choi, Kayla Lawrence, Ojasvi Chaudhary, Tianhao Xu, Ignas Masilionis (+18 others)
2021 bioRxiv   pre-print
AbstractLineage plasticity is a well–established mechanism of resistance to targeted therapies in lung and prostate cancer, where tumors transition from adenocarcinoma to small–cell or neuroendocrine carcinoma  ...  Through single–cell analysis of a cohort of heavily–treated castration–resistant human prostate cancers (CRPC), we report a greater degree of plasticity than previously appreciated, with multiple distinct  ...  We further appreciate the efforts of the Memorial Sloan Kettering Cancer Center (MSK) Genitourinary faculty for recruitment of prostate cancer tumor specimens.  ... 
doi:10.1101/2021.11.01.466599 fatcat:hu6xk2mmrjb4dn2k4223qhmwne

CUP-AI-Dx: A tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence

Yue Zhao, Ziwei Pan, Sandeep Namburi, Andrew Pattison, Atara Posner, Shiva Balachander, Carolyn A. Paisie, Honey V Reddi, Jens Rueter, Anthony J Gill, Stephen Fox, Kanwal P.S. Raghav (+5 others)
2020 EBioMedicine  
Developing robust and accessible diagnostic methods for resolving cancer tissue of origin, therefore, has significant value for CUP patients.  ...  Cancer of unknown primary (CUP), representing approximately 3-5% of all malignancies, is defined as metastatic cancer where a primary site of origin cannot be found despite a standard diagnostic workup  ...  The authors would like to thank the University of Melbourne Centre for Cancer Research Genomics Core Facility and Genomics Platform Group for their support in generating and processing RNA-seq data.  ... 
doi:10.1016/j.ebiom.2020.103030 pmid:33039710 pmcid:PMC7553237 fatcat:3fvtatqorfdrvlb6pfiejv2w6e
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