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  1. 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

  2. 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

  3. 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

  4. 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, 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Research article

    Diet and exercise changes following direct-to-consumer personal genomic testing

    The impacts of direct-to-consumer personal genomic testing (PGT) on health behaviors such as diet and exercise are poorly understood. Our investigation aimed to evaluate diet and exercise changes following PGT...

    Daiva Elena Nielsen, Deanna Alexis Carere, Catharine Wang, J. Scott Roberts and Robert C. Green

    BMC Medical Genomics 2017 10:24

    Published on: 2 May 2017

  13. Research article

    Post-operative atrial fibrillation examined using whole-genome RNA sequencing in human left atrial tissue

    Both ambulatory atrial fibrillation (AF) and post-operative AF (poAF) are associated with substantial morbidity and mortality. Analyzing the tissue-specific gene expression in the left atrium (LA) can identify...

    Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K. Shernan, Jochen D. Muehlschlegel and Simon C. Body

    BMC Medical Genomics 2017 10:25

    Published on: 2 May 2017

  14. Research article

    Serum MicroRNA profile in patients with colon adenomas or cancer

    Colon cancer, one of the most common causes of cancer-related deaths, arises from adenomatous polyps. In these years, circulating microRNAs (miRNAs) have attracted increasing attention as novel biomarkers for ...

    Yajie Zhang, Min Li, Yijiang Ding, Zhimin Fan, Jinchun Zhang, Hongying Zhang, Bin Jiang and Yong Zhu

    BMC Medical Genomics 2017 10:23

    Published on: 20 April 2017

  15. Research article

    Patient complexity and genotype-phenotype correlations in biliary atresia: a cross-sectional analysis

    Biliary Atresia (BA) is rare and genetically complex, and the pathogenesis is elusive. The disease course is variable and can represent heterogeneity, which hinders effective disease management. Deciphering th...

    Guo Cheng, Patrick Ho-Yu Chung, Edwin Kin-Wai Chan, Man-Ting So, Pak-Chung Sham, Stacey S. Cherny, Paul Kwong-Hang Tam and Maria-Mercè Garcia-Barceló

    BMC Medical Genomics 2017 10:22

    Published on: 17 April 2017

  16. Research article

    GRMD cardiac and skeletal muscle metabolism gene profiles are distinct

    Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, which codes for the dystrophin protein. While progress has been made in defining the molecular basis and pathogenesis of DMD, major gaps r...

    Larry W. Markham, Candice L. Brinkmeyer-Langford, Jonathan H. Soslow, Manisha Gupte, Douglas B. Sawyer, Joe N. Kornegay and Cristi L. Galindo

    BMC Medical Genomics 2017 10:21

    Published on: 8 April 2017

  17. Research article

    Revealing cancer subtypes with higher-order correlations applied to imaging and omics data

    Patient stratification to identify subtypes with different disease manifestations, severity, and expected survival time is a critical task in cancer diagnosis and treatment. While stratification approaches usi...

    Kiley Graim, Tiffany Ting Liu, Achal S. Achrol, Evan O. Paull, Yulia Newton, Steven D. Chang, Griffith R. Harsh, Sergio P. Cordero, Daniel L. Rubin and Joshua M. Stuart

    BMC Medical Genomics 2017 10:20

    Published on: 31 March 2017

  18. Research article

    Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation sequencing

    The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platfor...

    Henry M. Wood, Joseph M. Foster, Morag Taylor, Emma Tinkler-Hundal, Fiona S. Togneri, Paula Wojtowicz, Assa Oumie, Karen G. Spink, Fiona Brew and Philip Quirke

    BMC Medical Genomics 2017 10:17

    Published on: 18 March 2017

  19. Research Article

    Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

    The distinct types of hematological malignancies have different biological mechanisms and prognoses. For instance, myelodysplastic syndrome (MDS) is generally indolent and low risk; however, it may transform i...

    Amir Foroushani, Rupesh Agrahari, Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan and Habil Zare

    BMC Medical Genomics 2017 10:16

    Published on: 16 March 2017

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