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BMC Medical Genomics | Bioinformatic and algorithmical studies

BMC Medical Genomics | Bioinformatic and algorithmical studies
Biomed Central
BMC Medical Genomics

Bioinformatic and algorithmical studies

Section edited by Youping Deng
This section considers studies on the development and application of novel computational and statistical methods to the analysis of genomic data for the study of health and disease.
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    A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without

    Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus ...
    Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner and Nicki Tiffin
    BMC Medical Genomics 2016 9:66
    Published on: 15 November 2016

    Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing

    The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adeq...
    Lei Wei, Antonios Papanicolau-Sengos, Song Liu, Jianmin Wang, Jeffrey M. Conroy, Sean T. Glenn, Elizabeth Brese, Qiang Hu, Kiersten Marie Miles, Blake Burgher, Maochun Qin, Karen Head, Angela R. Omilian, Wiam Bshara, John Krolewski, Donald L. Trump…
    BMC Medical Genomics 2016 9:64
    Published on: 19 October 2016

    Protecting genomic data analytics in the cloud: state of the art and opportunities

    The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, ...
    Haixu Tang, Xiaoqian Jiang, Xiaofeng Wang, Shuang Wang, Heidi Sofia, Dov Fox, Kristin Lauter, Bradley Malin, Amalio Telenti, Li Xiong and Lucila Ohno-Machado
    BMC Medical Genomics 2016 9:63
    Published on: 13 October 2016

    An adaptive detection method for fetal chromosomal aneuploidy using cell-free DNA from 447 Korean women

    Noninvasive prenatal testing (NIPT) using massively parallel sequencing of cell-free DNA (cfDNA) is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predicti...
    Sunshin Kim, HeeJung Jung, Sung Hee Han, SeungJae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Kyudong Han, Hwanjong Kwak, Sunghoon Park, Hee Jae Joo, Minae An, Jungsu Ha, Kyusang Lee, Byung Chul Kim, Hailing Zheng…
    BMC Medical Genomics 2016 9:61
    Published on: 3 October 2016

    Explorations to improve the completeness of exome sequencing

    Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a defin...
    Chen Du, Barbara N. Pusey, Christopher J. Adams, C. Christopher Lau, William P. Bone, William A. Gahl, Thomas C. Markello and David R. Adams
    BMC Medical Genomics 2016 9:56
    Published on: 27 August 2016

    Dealing with prognostic signature instability: a strategy illustrated for cardiovascular events in patients with end-stage renal disease

    Identification of prognostic gene expression markers from clinical cohorts might help to better understand disease etiology. A set of potentially important markers can be automatically selected when linking ge...
    Harald Binder, Thorsten Kurz, Sven Teschner, Clemens Kreutz, Marcel Geyer, Johannes Donauer, Annette Kraemer-Guth, Jens Timmer, Martin Schumacher and Gerd Walz
    BMC Medical Genomics 2016 9:43
    Published on: 20 July 2016

    Study design and data analysis considerations for the discovery of prognostic molecular biomarkers: a case study of progression free survival in advanced serous ovarian cancer

    Accurate discovery of molecular biomarkers that are prognostic of a clinical outcome is an important yet challenging task, partly due to the combination of the typically weak genomic signal for a clinical outc...
    Li-Xuan Qin and Douglas A. Levine
    BMC Medical Genomics 2016 9:27
    Published on: 10 June 2016

    A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer

    Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significa...
    Eliseos J. Mucaki, Natasha G. Caminsky, Ami M. Perri, Ruipeng Lu, Alain Laederach, Matthew Halvorsen, Joan H. M. Knoll and Peter K. Rogan
    BMC Medical Genomics 2016 9:19
    Published on: 11 April 2016

    Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia

    Schizophrenia is a neurodevelopmental disorder with genetic and environmental factors contributing to its pathogenesis, although the mechanism is unknown due to the difficulties in accessing diseased tissue du...
    Mariana Maschietto, Ana C Tahira, Renato Puga, Leandro Lima, Daniel Mariani, Bruna da Silveira Paulsen, Paulo Belmonte-de-Abreu, Henrique Vieira, Ana CV Krepischi, Dirce M Carraro, Joana A Palha, Stevens Rehen and Helena Brentani
    BMC Medical Genomics 2015 8:23
    Published on: 16 May 2015

    ASEQ: fast allele-specific studies from next-generation sequencing data

    Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. S...
    Alessandro Romanel, Sara Lago, Davide Prandi, Andrea Sboner and Francesca Demichelis
    BMC Medical Genomics 2015 8:9
    Published on: 1 March 2015

    Fuzzy logic selection as a new reliable tool to identify molecular grade signatures in breast cancer – the INNODIAG study

    Personalized medicine has become a priority in breast cancer patient management. In addition to the routinely used clinicopathological characteristics, clinicians will have to face an increasing amount of data...
    Tatiana Kempowsky-Hamon, Carine Valle, Magali Lacroix-Triki, Lyamine Hedjazi, Lidwine Trouilh, Sophie Lamarre, Delphine Labourdette, Laurence Roger, Loubna Mhamdi, Florence Dalenc, Thomas Filleron, Gilles Favre, Jean-Marie François, Marie-Véronique Le Lann and Véronique Anton-Leberre
    BMC Medical Genomics 2015 8:3
    Published on: 7 February 2015

    Meta-analysis of prostate cancer gene expression data identifies a novel discriminatory signature enriched for glycosylating enzymes

    Tumorigenesis is characterised by changes in transcriptional control. Extensive transcript expression data have been acquired over the last decade and used to classify prostate cancers. Prostate cancer is, how...
    Stefan J Barfeld, Phil East, Verena Zuber and Ian G Mills
    BMC Medical Genomics 2014 7:513
    Published on: 31 December 2014

    A 3-biomarker-panel predicts renal outcome in patients with proteinuric renal diseases

    Clinical and histological parameters are valid prognostic markers in renal disease, although they may show considerable interindividual variability and sometimes limited prognostic value. Novel molecular marke...
    Hannes Neuwirt, Paul Perco, Alexander Kainz, Irmgard Mühlberger, Johannes Leierer, Suzie-Jane Braniff, Bernd Mayer, Gert Mayer and Michael Rudnicki
    BMC Medical Genomics 2014 7:75
    Published on: 24 December 2014

    Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS)

    The incidence of Acute Megakaryoblastic Leukemia (AMKL) is 500-fold higher in children with Down Syndrome (DS) compared with non-DS children, but the relevance of trisomy 21 as a specific background of AMKL in...
    Maria Chiara Pelleri, Allison Piovesan, Maria Caracausi, Anna Concetta Berardi, Lorenza Vitale and Pierluigi Strippoli
    BMC Medical Genomics 2014 7:63
    Published on: 5 December 2014

    Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel

    Improvements in both performance and cost for next-generation sequencing (NGS) have spurred its rapid adoption for clinical applications. We designed and optimized a pan-cancer target-enrichment panel for 51 w...
    Ashish Choudhary, Elizabeth Mambo, Tiffany Sanford, Michael Boedigheimer, Brian Twomey, Joseph Califano, Andrew Hadd, Kelly S Oliner, Sylvie Beaudenon, Gary J Latham and Alex T Adai
    BMC Medical Genomics 2014 7:62
    Published on: 14 November 2014

    Global transcriptome-wide analysis of CIK cells identify distinct roles of IL-2 and IL-15 in acquisition of cytotoxic capacity against tumor

    Cytokine-induced killer (CIK) cells are an emerging approach of cancer treatment. Our previous study have shown that CIK cells stimulated with combination of IL-2 and IL-15 displayed improved proliferation cap...
    Wenju Wang, Mingyao Meng, Yayong Zhang, Chuanyu Wei, Yanhua Xie, Lihong Jiang, Chunhui Wang, Fang Yang, Weiwei Tang, Xingfang Jin, Dai Chen, Jie Zong, Zongliu Hou and Ruhong Li
    BMC Medical Genomics 2014 7:49
    Published on: 9 August 2014

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