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AN EXTENSIBLE BIOMARKER CURATION APPROACH AND SOFTWARE INFRASTRUCTURE FOR THE EARLY DETECTION OF CANCER
english

2009 Proceedings of the International Conference on Health Informatics   unpublished
The approach involves normalizing curated data through the use of a common information model for cancer biomarker research.  ...  The United States National Cancer Institute's (NCI) Early Detection Research Network (EDRN) is a distributed network of research institutions focused on the discovery of cancer biomarkers.  ...  The authors would like to thank Donald Johnsey, Christos Patriotis, and Sudhir Srivastava and the NCI leadership as a whole for their collaborative support in curation of data within the EDRN.  ... 
doi:10.5220/0001781103870392 fatcat:c6l6bmm6rvgajj7ea2fnod4a3e

The EDRN knowledge environment: an open source, scalable informatics platform for biological sciences research

Daniel Crichton, Ashish Mahabal, Kristen Anton, Luca Cinquini, Maureen Colbert, S. George Djorgovski, Heather Kincaid, Sean Kelly, David Liu, Thomas George, Achyut K. Dutta, M. Saif Islam
2017 Micro- and Nanotechnology Sensors, Systems, and Applications IX  
We describe here the Early Detection Research Network (EDRN) for Cancer's knowledge environment.  ...  It has accumulated data on hundreds of thousands of biospecemens and serves over 1300 registered users across the National Cancer Institute (NCI).  ...  AAM and SGD also acknowledge support from the Center for Data-Driven Discovery at Caltech, and from the Ajax Foundation.  ... 
doi:10.1117/12.2263842 fatcat:vosjphnqxbh67gdbomsuuvwwmq

The EARLY DETECTION RESEARCH NETWORK: A National Infrastructure to Support the Discovery, Development and Validation of Cancer Biomarkers

Sudhir Srivastava, Paul D. Wagner
2020 Cancer Epidemiology, Biomarkers and Prevention  
for the early cancer detection and risk assessment.  ...  In 2000, the US National Cancer Institute established the Early Detection Research Network (EDRN), an investigator-driven network to conduct translational research to identify, develop and validate biomarkers  ...  The authors also thank Dan Crichton of Jet Propulsion Laboratory for his contribution to the EDRN Informatics.  ... 
doi:10.1158/1055-9965.epi-20-0237 pmid:32357955 fatcat:s4ndl2dx4ndc7mbhdfatfzda24

Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

Jiajia Chen, Daqing Zhang, Wenying Yan, Dongrong Yang, Bairong Shen
2013 BioMed Research International  
We highlight some fundamental issues of translational bioinformatics and the potential use of cloud computing in NGS data processing for the improvement of prostate cancer treatment.  ...  The discovery of prostate cancer biomarkers has been boosted by the advent of next-generation sequencing (NGS) technologies.  ...  Conflict of Interests The authors declare that there is no conflict of interests. Authors' Contribution Jiajia Chen, Daqing Zhang, and Wenying Yan contributed equally to this work.  ... 
doi:10.1155/2013/901578 pmid:23957008 pmcid:PMC3727129 fatcat:wmsiqvou6vbqph5wox5sapgele

Radiomics Improves Cancer Screening and Early Detection

Robert J. Gillies, Matthew B. Schabath
2020 Cancer Epidemiology, Biomarkers and Prevention  
Imaging is a key technology in the early detection of cancers, including X-ray mammography, low dose CT for lung cancer, or optical imaging for skin, esophageal, or colorectal cancers.  ...  The first section of this review will briefly describe the various imaging modalities and their use as primary or secondary screens in an early detection pipeline.  ...  Acknowledgments This work was funded in part by the NIH grant U01 CA200464 (to R.J. Gillies and M.B. Schabath).  ... 
doi:10.1158/1055-9965.epi-20-0075 pmid:32917666 fatcat:36unqm2nrfcqbh7yhqedqz24ua

A Multidisciplinary, Model-Driven, Distributed Science Data System Architecture [chapter]

Daniel J. Crichton, Chris A. Mattmann, John S. Hughes, Sean C. Kelly, Andrew F. Hart
2011 Guide to e-Science  
OODT has enabled reuse of software for science data generation, capture and management, and delivery across highly distributed organizations for planetary science, earth science and cancer research.  ...  At the Jet Propulsion Laboratory in Pasadena, California, we have been developing science data systems for highly distributed communities in physical and life sciences that require extensive sharing of  ...  Acknowledgement The research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration.  ... 
doi:10.1007/978-0-85729-439-5_5 dblp:series/ccn/CrichtonMHKH11 fatcat:ntv2hwmvlngqbl3zd7issso4iy

Prevent Cancer Foundation quantitative CT imaging workshop XVI: lung cancer, COPD and cardiovascular disease - on the cusp of transformation, Arlington, VA

James L. Mulshine, Riccardo S. Avila, Daniel C. Sullivan, David F. Yankelevitz, Raúl San José Estépar, Laurie Fenton Ambrose, Bruce Pyenson, Carolyn R. Aldigé
2020 Translational Medicine Communications  
tools, including responsible AI development, to better detect and manage early lung cancer as well as other major tobacco-related thoracic diseases.  ...  Imaging researchers are positioned to develop much better workflow software tools to promote more efficient, outpatient management of the screening process for populations at-risk for lung cancer, especially  ...  All authors were involved with the writing and editing of this document. Author's Permission to Submit: All of the above authors have agreed to submit this manuscript for publication.  ... 
doi:10.1186/s41231-020-00069-8 fatcat:vjltwzsa3ndvbea2cgfehq4ig4

PRIMAGE project: predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers

Luis Martí-Bonmatí, Ángel Alberich-Bayarri, Ruth Ladenstein, Ignacio Blanquer, J. Damian Segrelles, Leonor Cerdá-Alberich, Polyxeni Gkontra, Barbara Hero, J. M. García-Aznar, Daniel Keim, Wolfgang Jentner, Karine Seymour (+22 others)
2020 European Radiology Experimental  
The project is constructed as an observational in silico study involving high-quality anonymised datasets (imaging, clinical, molecular, and genetics) for the training and validation of machine learning  ...  The open cloud-based platform will offer precise clinical assistance for phenotyping (diagnosis), treatment allocation (prediction), and patient endpoints (prognosis), based on the use of imaging biomarkers  ...  Acknowledgements PRIMAGE (PRedictive In-silico Multiscale Analytics to support cancer personalised diaGnosis and prognosis, empowered by imaging biomarkers) Business Place is a Horizon 2020 | RIA (Topic  ... 
doi:10.1186/s41747-020-00150-9 pmid:32246291 fatcat:qujua7cvcnbvvelwuolpaygduu

E-Science technologies in a workflow for personalized medicine using cancer screening as a case study

Ola Spjuth, Andreas Karlsson, Mark Clements, Keith Humphreys, Emma Ivansson, Jim Dowling, Martin Eklund, Alexandra Jauhiainen, Kamila Czene, Henrik Grönberg, Pär Sparén, Fredrik Wiklund (+7 others)
2017 JAMIA Journal of the American Medical Informatics Association  
We describe an e-Science initiative in Sweden, e-Science for Cancer Prevention and Control (eCPC), which supports biomarker discovery and offers decision support for personalized intervention strategies  ...  For breast cancer, new biomarkers based on breast density and molecular profiles are developed and the US multicenter Women Informed to Screen Depending on Measures (WISDOM) trial is referred to for evaluation  ...  Acknowledgments We thank the Swedish eScience Research Center community for numerous discussions, as well as Arnoldo Frigessi, University of Oslo, and Niklas Blomberg, Elixir UK, for excellent input as  ... 
doi:10.1093/jamia/ocx038 pmid:28444384 pmcid:PMC7651972 fatcat:m3nl5fujbzff7k26bldoff7nkm

A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers

Andrew J. Buckler, David Paik, Matt Ouellette, Jovanna Danagoulian, Gary Wernsing, Baris E. Suzek
2013 Journal of digital imaging  
We report on our current progress on developing an informatics infrastructure to store, query, and retrieve imaging biomarker data across a wide range of resources in a semantically meaningful way that  ...  With the availability of tools for automatic ontology-based annotation of datasets, coupled with image archives, and a means for batch selection and processing of image and clinical data, imaging will  ...  On the information side, various databases store information on ex vivo biomarkers (e.g., Early Detection Research Network Biomarker Database [8] , Infectious Disease Biomarker Database) [9] .  ... 
doi:10.1007/s10278-013-9598-3 pmid:23546775 pmcid:PMC3705009 fatcat:nkllru5k7fgbhb4bawn6zbllpq

Tissue Banking, Bioinformatics, and Electronic Medical Records: The Front-End Requirements for Personalized Medicine

K. Stephen Suh, Sreeja Sarojini, Maher Youssif, Kip Nalley, Natasha Milinovikj, Fathi Elloumi, Steven Russell, Andrew Pecora, Elyssa Schecter, Andre Goy
2013 Journal of Oncology  
The critical value of tissue bank samples, bioinformatics, and EMR in the early stages of the biomarker discovery process for personalized medicine is often overlooked.  ...  The approach relies on diagnostic and prognostic use of novel biomarkers discovered through combinations of tissue banking, bioinformatics, and electronic medical records (EMRs).  ...  If, for example, an institution wants to examine biomarkers associated with ovarian cancer, a query of the records of the tissue bank will return sample catalog numbers pertaining to ovarian cancer enabling  ... 
doi:10.1155/2013/368751 pmid:23818899 pmcid:PMC3683471 fatcat:xkctzzftgrdetnhrz6ojquhi3q

Ovarian cancer biomarkers for molecular biosensors and translational medicine

K Stephen Suh, Sang W Park, Angelica Castro, Hiren Patel, Patrick Blake, Michael Liang, Andre Goy
2010 Expert Review of Molecular Diagnostics  
The use of the NCI Cancer Gene Index is an excellent approach for generating a shortlist of candidate cancer biomarker genes and to extrapolate further in studying cancer gene-disease subtypes and cancer  ...  Some of the potential biomarkers for the purpose of early detection and community screening are listed in boxeS 1 & 2.  ...  References Papers of special note have been highlighted as:  ... 
doi:10.1586/erm.10.87 pmid:21080822 fatcat:y2phqtp5fzftvly64kto6uz4he

Proteomics in India: the clinical aspect

Somaditya Mukherjee, Arun Bandyopadhyay
2016 Clinical Proteomics  
It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives.  ...  It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human  ...  Competing interests The authors declare that they have no competing interests. Funding This work is supported by the grants from CSIR new Delhi (MLP113 and BSC 0118).  ... 
doi:10.1186/s12014-016-9122-0 pmid:27822170 pmcid:PMC5097398 fatcat:btgb2mendbh65abliajw5hc6cq

Report on the Evaluation-as-a-Service (EaaS) Expert Workshop

Frank Hopfgartner, Jimmy Lin, Krisztian Balog, Ivan Eggel, Allan Hanbury, Henning Müller, Noriko Kando, Simon Mercer, Jayashree Kalpathy-Cramer, Martin Potthast, Tim Gollub, Anastasia Krithara
2015 SIGIR Forum  
The objective of the meeting was to bring together initiatives that use cloud infrastructures, virtual machines, APIs (Application Programming Interface) and related projects that provide evaluation of  ...  In this report, we summarize the outcome of the "Evaluation-as-a-Service" workshop that was held on the 5th and 6th March 2015 in Sierre, Switzerland.  ...  Acknowledgements We acknowledge financial support by the European Science Foundation via its Research Network Program "Evaluating Information Access Systems" (ELIAS) and by the European Commission via  ... 
doi:10.1145/2795403.2795416 fatcat:fvruambvbjfqbpoigzfuxsq5ey

Bringing Greater Accuracy to Europe's Healthcare Systems: The Unexploited Potential of Biomarker Testing in Oncology

Denis Horgan, Gennaro Ciliberto, Pierfranco Conte, David Baldwin, Luis Seijo, Luis M. Montuenga, Luis Paz-Ares, Marina Garassino, Frederique Penault-Llorca, Fabrizia Galli, Isabelle Ray-Coquard, Denis Querleu (+37 others)
2020 Biomedicine Hub  
It offers case studies of biomarker testing in breast, ovarian, prostate, lung, thyroid and colon cancers, and derives specific lessons as to the potential and actual use of each of them.  ...  It urges a European evolution towards an initial minimum testing scenario, which would guarantee universal access to a suite of biomarker tests for the currently most common conditions, and, further into  ...  Acknowledgements We would like to thank the members of the European Alliance for Personalised Medicine, European representatives of the Commission and Member States for their kind input.  ... 
doi:10.1159/000511209 pmid:33564664 pmcid:PMC7841733 fatcat:vvwmksts5vdmnk42obiaqsvhge
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