Functional and structural genomics

Section edited by Kun Huang

This section considers studies of change in the expression and regulation of genes and genomes conducted at a genomic scale in relation to health and disease states.

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  1. 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

  2. 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

  3. Research article

    Epigenetic modifications and glucocorticoid sensitivity in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

    Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating idiopathic disease characterized by unexplained fatigue that fails to resolve with sufficient rest. Diagnosis is based on a list of...

    Wilfred C. de Vega, Santiago Herrera, Suzanne D. Vernon and Patrick O. McGowan

    BMC Medical Genomics 2017 10:11

    Published on: 23 February 2017

  4. Research article

    A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients

    Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are forms of hepatic autoimmunity, and risk for both diseases has a strong genetic component. This study aimed to define the genetic a...

    Agnieszka Paziewska, Andrzej Habior, Agnieszka Rogowska, Włodzimierz Zych, Krzysztof Goryca, Jakub Karczmarski, Michalina Dabrowska, Filip Ambrozkiewicz, Bozena Walewska-Zielecka, Marek Krawczyk, Halina Cichoz-Lach, Piotr Milkiewicz, Agnieszka Kowalik, Krzysztof Mucha, Joanna Raczynska, Joanna Musialik…

    BMC Medical Genomics 2017 10:2

    Published on: 6 January 2017

  5. Research article

    Genome-wide positioning of bivalent mononucleosomes

    Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only...

    Subhojit Sen, Kirsten F. Block, Alice Pasini, Stephen B. Baylin and Hariharan Easwaran

    BMC Medical Genomics 2016 9:60

    Published on: 15 September 2016

  6. Research article

    Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells

    The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene ex...

    Andréanne Morin, Tony Kwan, Bing Ge, Louis Letourneau, Maria Ban, Karolina Tandre, Maxime Caron, Johanna K. Sandling, Jonas Carlsson, Guillaume Bourque, Catherine Laprise, Alexandre Montpetit, Ann-Christine Syvanen, Lars Ronnblom, Stephen J. Sawcer, Mark G. Lathrop…

    BMC Medical Genomics 2016 9:59

    Published on: 13 September 2016

  7. Research article

    Associations of circulating plasma microRNAs with age, body mass index and sex in a population-based study

    Non-cellular blood circulating microRNAs (plasma miRNAs) represent a promising source for the development of prognostic and diagnostic tools owing to their minimally invasive sampling, high stability, and simp...

    Sabine Ameling, Tim Kacprowski, Ravi Kumar Chilukoti, Carolin Malsch, Volkmar Liebscher, Karsten Suhre, Maik Pietzner, Nele Friedrich, Georg Homuth, Elke Hammer and Uwe Völker

    BMC Medical Genomics 2015 8:61

    Published on: 14 October 2015

  8. Research article

    Radiation dose-rate effects on gene expression for human biodosimetry

    The effects of dose-rate and its implications on radiation biodosimetry methods are not well studied in the context of large-scale radiological scenarios. There are significant health risks to individuals expo...

    Shanaz A. Ghandhi, Lubomir B. Smilenov, Carl D. Elliston, Mashkura Chowdhury and Sally A. Amundson

    BMC Medical Genomics 2015 8:22

    Published on: 12 May 2015

  9. Research article

    Metabolic changes in type 2 diabetes are reflected in peripheral blood cells, revealing aberrant cytotoxicity, a viral signature, and hypoxia inducible factor activity

    Metabolic syndrome (MetS) is characterized by central obesity, insulin resistance, dysglycemia, and a pro-atherogenic plasma lipid profile. MetS creates a high risk for development of type 2 diabetes (T2DM) an...

    Tineke C. T. M. van der Pouw Kraan, Weena J. Chen, Mathijs C. M. Bunck, Daniel H. van Raalte, Nynke J. van der Zijl, Renate E. van Genugten, Liselotte van Bloemendaal, Josefien M. Baggen, Erik H. Serné, Michaela Diamant and Anton J. G. Horrevoets

    BMC Medical Genomics 2015 8:20

    Published on: 9 May 2015

  10. Research article

    DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks

    Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in ...

    Christina A Castellani, Benjamin I Laufer, Melkaye G Melka, Eric J Diehl, Richard L O’Reilly and Shiva M Singh

    BMC Medical Genomics 2015 8:17

    Published on: 6 May 2015

  11. Research article

    Transcriptomic signatures in whole blood of patients who acquire a chronic inflammatory response syndrome (CIRS) following an exposure to the marine toxin ciguatoxin

    Ciguatoxins (CTXs) are polyether marine neurotoxins found in multiple reef-fish species and are potent activators of voltage-gated sodium channels. It is estimated that up to 500,000 people annually experience...

    James C Ryan, Qingzhong Wu and Ritchie C Shoemaker

    BMC Medical Genomics 2015 8:15

    Published on: 2 April 2015

  12. Research article

    Effects of statin on circulating microRNAome and predicted function regulatory network in patients with unstable angina

    Statin therapy plays a pivotal role in stabilizing the plaque for unstable angina (UA) patients although its mechanism(s) remains largely unexplored. Here we aim to identify microRNAs (miRNAs) mediating the pr...

    Jingjin Li, Hong Chen, Jingyi Ren, Junxian Song, Feng Zhang, Jing Zhang, Chongyou Lee, Sufang Li, Qiang Geng, Chengfu Cao and Ning Xu

    BMC Medical Genomics 2015 8:12

    Published on: 13 March 2015

  13. Research article

    miR-10b-5p expression in Huntington’s disease brain relates to age of onset and the extent of striatal involvement

    MicroRNAs (miRNAs) are small non-coding RNAs that recognize sites of complementarity of target messenger RNAs, resulting in transcriptional regulation and translational repression of target genes. In Huntingto...

    Andrew G Hoss, Adam Labadorf, Jeanne C Latourelle, Vinay K Kartha, Tiffany C Hadzi, James F Gusella, Marcy E MacDonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel and Richard H Myers

    BMC Medical Genomics 2015 8:10

    Published on: 1 March 2015

  14. Research article

    The DNA methylation drift of the atherosclerotic aorta increases with lesion progression

    Atherosclerosis severity-independent alterations in DNA methylation, a reversible and highly regulated DNA modification, have been detected in aortic atheromas, thus supporting the hypothesis that epigenetic m...

    María del Pilar Valencia-Morales, Silvio Zaina, Holger Heyn, F Javier Carmona, Nuray Varol, Sergi Sayols, Enric Condom, José Ramírez-Ruz, Antonio Gomez, Sebastian Moran, Gertrud Lund, Dalia Rodríguez-Ríos, Gladys López-González, Magda Ramírez-Nava, Carmen de la Rocha, Alejandro Sanchez-Flores…

    BMC Medical Genomics 2015 8:7

    Published on: 27 February 2015

  15. Research article

    Systematic analysis of the clinical and biochemical characteristics of maternally inherited hypertension in Chinese Han families associated with mitochondrial

    Mitochondrial DNA mutations may be associated with cardiovascular disease, including the common cardiac vascular disease, hypertension.

    Yuqi Liu, Qinglei Zhu, Chao Zhu, Xueping Wang, Jie Yang, Tong Yin, Jinliao Gao, Zongbin Li, Qinghua Ma, Minxin Guan, Yang Li and Yundai Chen

    BMC Medical Genomics 2014 7:73

    Published on: 24 December 2014

  16. Research article

    Sleep quality, BDNF genotype and gene expression in individuals with chronic abdominal pain

    Sleep quality and genetics may contribute to the etiology of gastrointestinal (GI) symptoms. Individuals with impaired sleep often have a number of associated symptoms including chronic abdominal pain (CAP). T...

    Swarnalatha Y Reddy, Nat A Rasmussen, Nicolaas H Fourie, Rebecca S Berger, Angela C Martino, Jessica Gill, Ryan Longchamps, Xiao Min Wang, Margaret M Heitkemper and Wendy A Henderson

    BMC Medical Genomics 2014 7:61

    Published on: 31 October 2014

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