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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  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 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

  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 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

  5. 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

  6. 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 IV, Sergio P. Cordero, Daniel L. Rubin and Joshua M. Stuart

    BMC Medical Genomics 2017 10:20

    Published on: 31 March 2017

  7. 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

  8. Research article

    Computational analysis of the mesenchymal signature landscape in gliomas

    Epithelial to mesenchymal transition, and mimicking processes, contribute to cancer invasion and metastasis, and are known to be responsible for resistance to various therapeutic agents in many cancers. While ...

    Orieta Celiku, Anita Tandle, Joon-Yong Chung, Stephen M. Hewitt, Kevin Camphausen and Uma Shankavaram

    BMC Medical Genomics 2017 10:13

    Published on: 9 March 2017

  9. Research article

    Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine

    Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, ther...

    Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T. Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang and Gholson J. Lyon

    BMC Medical Genomics 2017 10:10

    Published on: 23 February 2017

  10. Research article

    Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes

    Type 1 diabetes (T1D) is an autoimmune disease and extensive evidence has indicated a critical role of both the innate and the adaptive arms of immune system in disease development. To date most clinical trial...

    Shouguo Gao, Nathaniel Wolanyk, Ye Chen, Shuang Jia, Martin J. Hessner and Xujing Wang

    BMC Medical Genomics 2017 10:7

    Published on: 31 January 2017

  11. Research article

    Multidisciplinary insight into clonal expansion of HTLV-1–infected cells in adult T-cell leukemia via modeling by deterministic finite automata coupled with high-throughput sequencing

    Clonal expansion of leukemic cells leads to onset of adult T-cell leukemia (ATL), an aggressive lymphoid malignancy with a very poor prognosis. Infection with human T-cell leukemia virus type-1 (HTLV-1) is the...

    Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kenta Nakai, Kaoru Uchimaru and Toshiki Watanabe

    BMC Medical Genomics 2017 10:4

    Published on: 31 January 2017

  12. Research article

    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

  13. Research article

    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

  14. Technical advance

    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

  15. Research article

    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

  16. Debate

    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

  17. Research Article

    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

  18. Research article

    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

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