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Full-privacy secured search engine empowered by efficient genome-mapping algorithms [article]

Yuan-Yu Chang, Sheng-Tang Wong, Emmanuel O Salawu, Yu-Xuan Wang, Jui-Hung Hung, Lee-Wei Yang
2022 arXiv   pre-print
scheme and an efficient FM-index search routine that is generally used in the NGS of genomes.  ...  In short, search engine privacy has not been an option for web exploration in the past decades.  ...  Part of this work was financially supported by the National Tsing Hua University, Taiwan (10020B002).  ... 
arXiv:2201.00696v2 fatcat:lexisazibzharol25mo7sq3zqe

Deep data plane programming and AI for zero-trust self-driven networking in beyond 5G

Othmane Hireche, Chafika Benzaid, Tarik Taleb
2021 Computer Networks  
In this vein, this article proposes a novel framework to empower fully distributed trustworthy SelfDNs across multiple domains.  ...  The framework vision is achieved by exploiting (i) the capabilities of programmable data planes to enable real-time in-network telemetry collection; (ii) the potential of P4 -as an important example of  ...  Acknowledgment This work was supported in part by the European Union's Horizon 2020 research and innovation programme under the MonB5G project (Grant No. 871780); and the Academy of Finland Project 6Genesis  ... 
doi:10.1016/j.comnet.2021.108668 fatcat:5sf3vpjrlbag7bhpos2vc45oeq

Social networks, web-based tools and diseases: implications for biomedical research

Fabricio F. Costa
2013 Drug Discovery Today  
The security system indicates the encryption and/or algorithms used for data privacy and they are shown in yellow circles.  ...  Search engines and social media can be helpful in predicting epidemic outbreaks of a disease caused by any viruses or bacteria.  ... 
doi:10.1016/j.drudis.2012.10.006 pmid:23103282 fatcat:citthrjhkfhvlbsn252egtaswu

Biomedical Informatics on the Cloud

Peipei Ping, Henning Hermjakob, Jennifer S. Polson, Panagiotis V. Benos, Wei Wang
2018 Circulation Research  
A unified computational platform leverages metadata to not only provide direction but also empower researchers to mine a wealth of biomedical information and forge novel mechanistic insights.  ...  This review takes the opportunity to present an overview of the cloud-based computational environment, including the functional roles of metadata, the architecture schema of indexing and search, and the  ...  An efficient strategy by a search engine is to transform these metadata into a harmonized metadata schema so that digital objects can be efficiently indexed and examined on a unified platform.  ... 
doi:10.1161/circresaha.117.310967 pmid:29700073 pmcid:PMC6192708 fatcat:kekqc3gegvcc3hm56xzw3cosmu

Blockchain for Genomics: A Systematic Literature Review [article]

Mohammed Alghazwi, Fatih Turkmen, Joeri van der Velde, Dimka Karastoyanova
2021 arXiv   pre-print
Our study is driven by five research questions that we aim to answer in our review.  ...  In order to provide secure and accountable infrastructure, blockchain technologies offer a promising alternative to traditional distributed systems.  ...  Each data record is inserted into the smart contract and assigned a unique ID to be used as mapping key. An index-based, multi-mapping approach is used to efficiently query the genomic data.  ... 
arXiv:2111.10153v1 fatcat:xuitghgmg5adlfsgz6v5dqqkfy

A scoping review of distributed ledger technology in genomics: thematic analysis and directions for future research

Mikael Beyene, Philipp A Toussaint, Scott Thiebes, Matthias Schlesner, Benedikt Brors, Ali Sunyaev
2022 JAMIA Journal of the American Medical Informatics Association  
the application of DLT in genomics.  ...  healthcare information systems; (6) Investigate alternative consensus mechanisms based on Proof of Useful Work; and (7) Explore DLT-enabled approaches for the protection of genetic data ensuring user privacy  ...  Table 1 . 1 Overview of the search strategy Search string ("distributed ledger" OR "blockchain" OR "block chain") AND ("genome" OR "genomes" OR "genomic" OR "genomics" OR "gene" OR "genes" OR "genetic"  ... 
doi:10.1093/jamia/ocac077 pmid:35595301 pmcid:PMC9277639 fatcat:e77pmmdhfjd2himmbmd3nojoh4

Cloud Computing in Healthcare and Biomedicine

Barbara Calabrese, Mario Cannataro
2015 Scalable Computing : Practice and Experience  
However, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine.  ...  laboratories, such as magnetic resonance imaging, microarray, mass spectrometry and next-generation sequencing, are producing an increasing volume of clinical and omics data that poses new issues in terms of secure  ...  CloudBurst 14 is a new parallel read-mapping algorithm optimized for mapping next-generation sequence (NGS) data to the human genome and other reference genomes, for use in a variety of biological analyses  ... 
doi:10.12694/scpe.v16i1.1057 fatcat:k5s2o37zcrge5pvbwimhotbsca

Integration of Genomics Data and Electronic Health Records Toward Personalized Medicine: A Targeted Review

Ali Najafi, Neda Emami, Taha Samad-Soltani
2021 Frontiers in Health Informatics  
of all available literature in English was conducted on the topic through a search in the databases of Medline, Web of Science, Institute of Electrical and Electronics Engineers (IEEE), Scopus, and Cochrane  ...  Therefore, system developers could guarantee the success of systems by overcoming the given challenges.  ...  [23] highly recommended a web-based, user-friendly, and secure portal to empower patients.  ... 
doi:10.30699/fhi.v10i1.299 fatcat:5rzxdhkovrhbbnsave35i2i42a

Applications of blockchain in the medical field: A narrative review (Preprint)

Zhewei Ye, Yi Xie, Jiayao Zhang, Honglin Wang, Lin Lu, Tongtong Huo, Zhe Dong, Yu-Yu Duan, Pengran Liu, Songxiang Liu
2021 Journal of Medical Internet Research  
Moreover, potential challenges are mentioned, including the confidentiality of privacy, the efficiency of the system, security issues and regulatory policy.  ...  Not only can it be a mechanism to secure electronic health records (EHRs), but it provides a powerful tool that can empower users to control their own health data, enabling a fool-proof health data history  ...  , privacy, and security [89].  ... 
doi:10.2196/28613 pmid:34533470 pmcid:PMC8555946 fatcat:xwugcaipjnbv5fst3tjzvbr5ru

29th International Conference on Data Engineering [book of abstracts]

2013 2013 IEEE 29th International Conference on Data Engineering Workshops (ICDEW)  
r27 shortest & Direct Query (p. 98) On Shortest Unique Substring Queries Engineering Generalized Shortest Path Queries Efficient Direct Search on Compressed Genomic Data r28 skyline & snapshot  ...  Experiments also validate the high efficiency of the privacy protection algorithm.  ...  At the conference, volunteers may be identified by their black ICDE-13 shirts.  ... 
doi:10.1109/icdew.2013.6547409 fatcat:wadzpuh3b5htli4mgb4jreoika

Accelerating Genomic Data Generation and Facilitating Genomic Data Access Using Decentralization, Privacy-Preserving Technologies and Equitable Compensation

Dennis Grishin, Kamal Obbad, Preston Estep, Kevin Quinn, Sarah Wait Zaranek, Alexander Wait Zaranek, Ward Vandewege, Tom Clegg, Nico César, Mirza Cifric, George Church
2018 Blockchain in Healthcare Today  
data sets further compounds the search for links between genetics and disease. 29 The scarcity of genomic data is exacerbated by difficulty in data access due to fragmentation of genomic data across  ...  Many people are deterred by the costs of personal genome sequencing, as well as concerns over genomic data privacy.  ...  Conflict of Interest All authors are employees, advisors, or collaborators of Nebula Genomics. Funding Statement Development of the Nebula platform is funded by Nebula Foundation.  ... 
doi:10.30953/bhty.v1.34 fatcat:bgjyvrf54vglljkwskkl5dvwfu

Genomics big data hybrid depositories architecture to unlock precision medicine: a conceptual framework

Ummul H. Mohamad, Mohamad T. Ijab, Rabiah A. Kadir
2018 International Journal of Engineering & Technology  
As the genome sequencing cost becomes more affordable, genomics studies are extensively carried out to empower the ultimate healthcare goal which is the precision medicine.  ...  processing engine and decision support, to carry out their purpose of merging the genomics data with the healthcare data.  ...  High concern on the genomics big data privacy and protection Addressing the concern on the genomics data security, certain data depositories such as the Biobank applied a different approach to prevent  ... 
doi:10.14419/ijet.v7i4.16893 fatcat:4lgua7ixtbcxhhcwvenadbc2va

Citizen-Centered, Auditable, and Privacy-Preserving Population Genomics [article]

Dennis Grishin, Jean Louis Raisaro, Juan Ramón Troncoso-Pastoriza, Kamal Obbad, Kevin Quinn, Mickaël Misbach, Jared Gollhardt, Joao Sa, Jacques Fellay, George M. Church, Jean-Pierre Hubaux
2019 bioRxiv   pre-print
This approach provides strong security guarantees against realistic threat models by empowering individual citizens to decide who can query and access their genomic data and by ensuring end-to-end data  ...  To enable a secure exploration of genomic datasets with controlled and transparent data access, we propose a novel approach that combines cryptographic privacy-preserving technologies, such as homomorphic  ...  Acknowledgments: We are grateful to the Bitfury Exonum engineering team for running part of the performance measurements described in the paper.  ... 
doi:10.1101/799999 fatcat:hhwjh2t5ljh6zon5pd77eh6rhi

Big data privacy: a technological perspective and review

Priyank Jain, Manasi Gyanchandani, Nilay Khare
2016 Journal of Big Data  
However, there is an obvious contradiction between the security and privacy of big data and the widespread use of big data. which permits unrestricted use, distribution, and reproduction in any medium,  ...  day by day.  ...  security and privacy models by exploiting the map reduce framework.  ... 
doi:10.1186/s40537-016-0059-y fatcat:hol5lhemzvawzc6yyxe4paa7zu

Quantum Biotech and Internet of Virus Things: Towards A Theoretical Framework

Prafulla Kumar Padhi, Feranando Charrua-Santos
2021 Applied System Innovation  
This research disseminates the QBIoVT system paradigm, including architectural aspects, priority areas, challenges, applications, and QmRNA research engine design to accelerate QmRNA vaccines discovery  ...  Additionally, the massive amount of data managed within the IoVT perspective poses research challenges in the trust, security, and privacy domain.  ...  The web search engine (Google Scholar) indexes the full-text scholarly articles. 2.  ... 
doi:10.3390/asi4020027 fatcat:6f3qwzkozzakvkbcuiefo3ubvy
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