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  1. Research article

    Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis

    Preeclampsia is a multifactorial disease with unknown pathogenesis. Even when recent studies explored this disease using several bioinformatics tools, the main objective was not directed to pathogenesis. Addit...

    Eduardo Tejera, Maykel Cruz-Monteagudo, Germán Burgos, María-Eugenia Sánchez, Aminael Sánchez-Rodríguez, Yunierkis Pérez-Castillo, Fernanda Borges, Maria Natália Dias Soeiro Cordeiro, César Paz-y-Miño and Irene Rebelo

    BMC Medical Genomics 2017 10:50

    Published on: 8 August 2017

  2. Research

    Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services

    Genomic data is increasingly collected by a wide array of organizations. As such, there is a growing demand to make summary information about such collections available more widely. However, over the past deca...

    Zhiyu Wan, Yevgeniy Vorobeychik, Murat Kantarcioglu and Bradley Malin

    BMC Medical Genomics 2017 10(Suppl 2):39

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  3. Research

    Efficient and secure outsourcing of genomic data storage

    Cloud computing is becoming the preferred solution for efficiently dealing with the increasing amount of genomic data. Yet, outsourcing storage and processing sensitive information, such as genomic data, comes...

    João Sá Sousa, Cédric Lefebvre, Zhicong Huang, Jean Louis Raisaro, Carlos Aguilar-Melchor, Marc-Olivier Killijian and Jean-Pierre Hubaux

    BMC Medical Genomics 2017 10(Suppl 2):46

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  4. Research

    BLOOM: BLoom filter based oblivious outsourced matchings

    Whole genome sequencing has become fast, accurate, and cheap, paving the way towards the large-scale collection and processing of human genome data. Unfortunately, this dawning genome era does not only promise...

    Jan Henrik Ziegeldorf, Jan Pennekamp, David Hellmanns, Felix Schwinger, Ike Kunze, Martin Henze, Jens Hiller, Roman Matzutt and Klaus Wehrle

    BMC Medical Genomics 2017 10(Suppl 2):44

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  5. Research

    Private queries on encrypted genomic data

    One of the tasks in the iDASH Secure Genome Analysis Competition in 2016 was to demonstrate the feasibility of privacy-preserving queries on homomorphically encrypted genomic data. More precisely, given a list...

    Gizem S. Çetin, Hao Chen, Kim Laine, Kristin Lauter, Peter Rindal and Yuhou Xia

    BMC Medical Genomics 2017 10(Suppl 2):45

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  6. Research

    Aftermath of bustamante attack on genomic beacon service

    With the enormous need for federated eco-system for holding global genomic and clinical data, Global Alliance for Genomic and Health (GA4GH) has created an international website called beacon service which all...

    Md Momin Al Aziz, Reza Ghasemi, Md Waliullah and Noman Mohammed

    BMC Medical Genomics 2017 10(Suppl 2):43

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  7. Research

    Secure approximation of edit distance on genomic data

    Edit distance is a well established metric to quantify how dissimilar two strings are by counting the minimum number of operations required to transform one string into the other. It is utilized in the domain ...

    Md Momin Al Aziz, Dima Alhadidi and Noman Mohammed

    BMC Medical Genomics 2017 10(Suppl 2):41

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  8. Research

    PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

    Advances in DNA sequencing technologies have prompted a wide range of genomic applications to improve healthcare and facilitate biomedical research. However, privacy and security concerns have emerged as a cha...

    Feng Chen, Chenghong Wang, Wenrui Dai, Xiaoqian Jiang, Noman Mohammed, Md Momin Al Aziz, Md Nazmus Sadat, Cenk Sahinalp, Kristin Lauter and Shuang Wang

    BMC Medical Genomics 2017 10(Suppl 2):48

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  9. Case report

    Identification of trunk mutations in gastric carcinoma: a case study

    Intratumor heterogeneity (ITH) poses an urgent challenge for cancer precision medicine because it can cause drug resistance against cancer target therapy and immunotherapy. The search for trunk mutations that ...

    Zhan Zhou, Shanshan Wu, Jun Lai, Yuan Shi, Chixiao Qiu, Zhe Chen, Yufeng Wang, Xun Gu, Jie Zhou and Shuqing Chen

    BMC Medical Genomics 2017 10:49

    Published on: 17 July 2017

  10. Research article

    In silico identification of potential key regulatory factors in smoking-induced lung cancer

    Lung cancer is a leading cause of cancer-related death worldwide and is the most commonly diagnosed cancer. Like other cancers, it is a complex and highly heterogeneous disease involving multiple signaling pat...

    Salem A. El-aarag, Amal Mahmoud, Medhat H. Hashem, Hatem Abd Elkader, Alaa E. Hemeida and Mahmoud ElHefnawi

    BMC Medical Genomics 2017 10:40

    Published on: 7 June 2017

  11. Research article

    Quantitative analysis of cryptic splicing associated with TDP-43 depletion

    Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral ...

    Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs and Vincent Plagnol

    BMC Medical Genomics 2017 10:38

    Published on: 26 May 2017

  12. Software

    CVE: an R package for interactive variant prioritisation in precision oncology

    An increasing number of precision oncology programmes are being launched world-wide. To support this development, we present the Cancer Variant Explorer (CVE), an R package with an interactive Shiny web browse...

    Andreas Mock, Suzanne Murphy, James Morris, Francesco Marass, Nitzan Rosenfeld and Charlie Massie

    BMC Medical Genomics 2017 10:37

    Published on: 25 May 2017

  13. Research

    Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population

    Aspirin Exacerbated Respiratory Disease (AERD) is a chronic medical condition that encompasses asthma, nasal polyposis, and hypersensitivity to aspirin and other non-steroidal anti-inflammatory drugs. Several ...

    Sehee Wang, Hyun-hwan Jeong, Dokyoon Kim, Kyubum Wee, Hae-Sim Park, Seung-Hyun Kim and Kyung-Ah Sohn

    BMC Medical Genomics 2017 10(Suppl 1):31

    Published on: 24 May 2017

    This article is part of a Supplement: Volume 10 Supplement 1

  14. Research

    Identifying subtype-specific associations between gene expression and DNA methylation profiles in breast cancer

    Breast cancer is a complex disease in which different genomic patterns exists depending on different subtypes. Recent researches present that multiple subtypes of breast cancer occur at different rates, and pl...

    Garam Lee, Lisa Bang, So Yeon Kim, Dokyoon Kim and Kyung-Ah Sohn

    BMC Medical Genomics 2017 10(Suppl 1):28

    Published on: 24 May 2017

    This article is part of a Supplement: Volume 10 Supplement 1

  15. Research

    N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes

    Transcriptome analytic tools are commonly used across patient cohorts to develop drugs and predict clinical outcomes. However, as precision medicine pursues more accurate and individualized treatment decisions...

    Qike Li, A. Grant Schissler, Vincent Gardeux, Ikbel Achour, Colleen Kenost, Joanne Berghout, Haiquan Li, Hao Helen Zhang and Yves A. Lussier

    BMC Medical Genomics 2017 10(Suppl 1):27

    Published on: 24 May 2017

    This article is part of a Supplement: Volume 10 Supplement 1

  16. Research

    Identification of epigenetic interactions between miRNA and DNA methylation associated with gene expression as potential prognostic markers in bladder cancer

    One of the fundamental challenges in cancer is to detect the regulators of gene expression changes during cancer progression. Through transcriptional silencing of critical cancer-related genes, epigenetic chan...

    Manu Shivakumar, Younghee Lee, Lisa Bang, Tullika Garg, Kyung-Ah Sohn and Dokyoon Kim

    BMC Medical Genomics 2017 10(Suppl 1):30

    Published on: 24 May 2017

    This article is part of a Supplement: Volume 10 Supplement 1

  17. Research

    Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers

    Many genetic diseases are caused by mutations in non-coding regions of the genome. These mutations are frequently found in enhancer sequences, causing disruption to the regulatory program of the cell. Enhancer...

    Julia Herman-Izycka, Michal Wlasnowolski and Bartek Wilczynski

    BMC Medical Genomics 2017 10(Suppl 1):34

    Published on: 24 May 2017

    This article is part of a Supplement: Volume 10 Supplement 1

  18. Research

    Association analysis of rare variants near the APOE region with CSF and neuroimaging biomarkers of Alzheimer’s disease

    The APOE ε4 allele is the most significant common genetic risk factor for late-onset Alzheimer’s disease (LOAD). The region surrounding APOE on chromosome 19 has also shown consistent association with LOAD. Howev...

    Kwangsik Nho, Sungeun Kim, Emrin Horgusluoglu, Shannon L. Risacher, Li Shen, Dokyoon Kim, Seunggeun Lee, Tatiana Foroud, Leslie M. Shaw, John Q. Trojanowski, Paul S. Aisen, Ronald C. Petersen, Clifford R. Jack Jr., Michael W. Weiner, Robert C. Green, Arthur W. Toga…

    BMC Medical Genomics 2017 10(Suppl 1):29

    Published on: 24 May 2017

    This article is part of a Supplement: Volume 10 Supplement 1

  19. Research article

    Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network

    To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthes...

    Nina R. Sperber, Janet S. Carpenter, Larisa H. Cavallari, Laura J. Damschroder, Rhonda M. Cooper-DeHoff, Joshua C. Denny, Geoffrey S. Ginsburg, Yue Guan, Carol R. Horowitz, Kenneth D. Levy, Mia A. Levy, Ebony B. Madden, Michael E. Matheny, Toni I. Pollin, Victoria M. Pratt, Marc Rosenman…

    BMC Medical Genomics 2017 10:35

    Published on: 22 May 2017

  20. Technical advance

    Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing

    The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mu...

    Donavan T. Cheng, Meera Prasad, Yvonne Chekaluk, Ryma Benayed, Justyna Sadowska, Ahmet Zehir, Aijazuddin Syed, Yan Elsa Wang, Joshua Somar, Yirong Li, Zarina Yelskaya, Donna Wong, Mark E. Robson, Kenneth Offit, Michael F. Berger, Khedoudja Nafa…

    BMC Medical Genomics 2017 10:33

    Published on: 19 May 2017

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