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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. Content type: Research article

    Non-alcoholic fatty liver disease (NAFLD) is a major health burden in need for new medication. To identify potential drug targets a genomic study was performed in lipid-laden primary human hepatocyte (PHH) and...

    Authors: Stephanie Breher-Esch, Nishika Sahini, Anna Trincone, Christin Wallstab and Jürgen Borlak

    Citation: BMC Medical Genomics 2018 11:111

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  2. Content type: Research article

    Large-scale “omics” datasets have not been leveraged and integrated with functional analyses to discover potential drivers of cardiomyopathy. This study addresses the knowledge gap.

    Authors: Nzali V. Campbell, David A. Weitzenkamp, Ian L. Campbell, Ronald F. Schmidt, Chindo Hicks, Michael J. Morgan, David C. Irwin and John J. Tentler

    Citation: BMC Medical Genomics 2018 11:110

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  3. Content type: Research article

    BAP1 is a histone deubiquitinase that acts as a tumor and metastasis suppressor associated with disease progression in human cancer. We have used the “Calling Card System” of transposase-directed transposon in...

    Authors: Matthew Yen, Zongtai Qi, Xuhua Chen, John A. Cooper, Robi D. Mitra and Michael D. Onken

    Citation: BMC Medical Genomics 2018 11:97

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  4. Content type: Research article

    Cellular changes described in human gastroparesis have revealed a role for immune dysregulation, however, a mechanistic understanding of human gastroparesis and the signaling pathways involved are still unclear.

    Authors: Madhusudan Grover, Simon J. Gibbons, Asha A. Nair, Cheryl E. Bernard, Adeel S. Zubair, Seth T. Eisenman, Laura A. Wilson, Laura Miriel, Pankaj J. Pasricha, Henry P. Parkman, Irene Sarosiek, Richard W. McCallum, Kenneth L. Koch, Thomas L. Abell, William J. Snape, Braden Kuo…

    Citation: BMC Medical Genomics 2018 11:62

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  5. Content type: Research article

    Cerebral palsy (CP) is the leading cause of motor disability in children; however, its pathogenesis is unknown in most cases. Growing evidence suggests that Nitric oxide synthase 1 (NOS1) is involved in neural...

    Authors: Ting Yu, Lei Xia, Dan Bi, Yangong Wang, Qing Shang, Dengna Zhu, Juan Song, Yong Wang, Xiaoyang Wang, Changlian Zhu and Qinghe Xing

    Citation: BMC Medical Genomics 2018 11:56

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  6. Content type: Research article

    The most frequent chromosomal aneuploidy is trisomy 21 (T21) that is caused by an extra copy of chromosome 21. The imbalance of whole genome including genes and microRNAs contributes to the various phenotypes ...

    Authors: Ji Hyae Lim, You Jung Han, Hyun Jin Kim, Moon Young Kim, So Yeon Park, Youl-Hee Cho and Hyun Mee Ryu

    Citation: BMC Medical Genomics 2018 11:46

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  7. Content type: Case report

    Parental balanced reciprocal translocations can result in partial aneuploidies in the offspring due to unbalanced meiotic segregation during gametogenesis. Herein, we report the phenotypic and molecular cytoge...

    Authors: C. S. Paththinige, N. D. Sirisena, U. G. I. U. Kariyawasam, R. C. Ediriweera, P. Kruszka, M. Muenke and V. H. W. Dissanayake

    Citation: BMC Medical Genomics 2018 11:44

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  8. Content type: Research article

    Decapping of mRNA is an important step in the regulation of mRNA turnover and therefore of gene expression, which is a key process controlling development and homeostasis of all organisms. It has been shown th...

    Authors: Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, André Reis, Rami Jamra and Fulvia Ferrazzi

    Citation: BMC Medical Genomics 2018 11:41

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  9. Content type: Research article

    Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To fi...

    Authors: Alain Calender, Pierre Antoine Rollat Farnier, Adrien Buisson, Stéphane Pinson, Abderrazzaq Bentaher, Serge Lebecque, Harriet Corvol, Rola Abou Taam, Véronique Houdouin, Claire Bardel, Pascal Roy, Gilles Devouassoux, Vincent Cottin, Pascal Seve, Jean-François Bernaudin, Clarice X. Lim…

    Citation: BMC Medical Genomics 2018 11:23

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  10. Content type: Research article

    Asthma exacerbations are an important cause of morbidity in asthma. Respiratory infections are often involved in asthma exacerbations in both children and adults. Some individuals with asthma have increased su...

    Authors: Jose L. Gomez, Maria P. Diaz, Gustavo Nino and Clemente J. Britto

    Citation: BMC Medical Genomics 2018 11:21

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  11. Content type: Research article

    Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that vi...

    Authors: Na Zhang, Yun-Juan Bao, Amy Hin-Yan Tong, Scott Zuyderduyn, Gary D. Bader, J. S. Malik Peiris, Si Lok and Suki Man-Yan Lee

    Citation: BMC Medical Genomics 2018 11:20

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  12. Content type: Research article

    Human aging is a hot topic in biology, and it has been associated with DNA methylation changes at specific genomic sites. We aimed to study the changes of DNA methylation at a single-CpG-site resolution using ...

    Authors: Qian Zeng, Xiaoping Chen, Chaoxue Ning, Qiao Zhu, Yao Yao, Yali Zhao and Fuxin Luan

    Citation: BMC Medical Genomics 2018 11:7

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  13. Content type: Research article

    We intended to evaluate diagnostic utility of a targeted gene sequencing by using next generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytica...

    Authors: John Hoon Rim, Se Hee Kim, In Sik Hwang, Soon Sung Kwon, Jieun Kim, Hyun Woo Kim, Min Jung Cho, Ara Ko, Song Ee Youn, Jihun Kim, Young Mock Lee, Hee Jung Chung, Joon Soo Lee, Heung Dong Kim, Jong Rak Choi, Seung-Tae Lee…

    Citation: BMC Medical Genomics 2018 11:6

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  14. Content type: Research article

    Obsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO...

    Authors: Edna Grünblatt, Beatrice Oneda, Arif B. Ekici, Juliane Ball, Julia Geissler, Steffen Uebe, Marcel Romanos, Anita Rauch and Susanne Walitza

    Citation: BMC Medical Genomics 2017 10:68

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  15. Content type: Research article

    Inhibition of nonsense-mediated mRNA decay (NMD) in tumor cells can suppress tumor growth through expressing new antigens whose mRNAs otherwise are degraded by NMD. Thus NMD inhibition is a promising approach ...

    Authors: Meng Wang, Peiwei Zhang, Yufei Zhu, Xiangyin Kong, Zhenguo Zhang and Landian Hu

    Citation: BMC Medical Genomics 2017 10:55

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  16. Content type: Research article

    The implantation of mechanical circulatory support devices in heart failure patients is associated with a systemic inflammatory response, potentially leading to death from multiple organ dysfunction syndrome. ...

    Authors: Nicholas Wisniewski, Galyna Bondar, Christoph Rau, Jay Chittoor, Eleanor Chang, Azadeh Esmaeili, Martin Cadeiras and Mario Deng

    Citation: BMC Medical Genomics 2017 10:52

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  17. Content type: Research article

    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 ...

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

    Citation: BMC Medical Genomics 2017 10:38

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  18. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Medical Genomics 2017 10:25

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  19. Content type: Research article

    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...

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

    Citation: BMC Medical Genomics 2017 10:11

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  20. Content type: Research article

    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...

    Authors: 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…

    Citation: BMC Medical Genomics 2017 10:2

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  21. Content type: Research article

    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...

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

    Citation: BMC Medical Genomics 2016 9:60

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  22. Content type: Research article

    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...

    Authors: 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…

    Citation: BMC Medical Genomics 2016 9:59

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  23. Content type: Research article

    The high cost and the long time required to bring drugs into commerce is driving efforts to repurpose FDA approved drugs—to find new uses for which they weren’t intended, and to thereby reduce the overall cost...

    Authors: Hsiao-Rong Chen, David H. Sherr, Zhenjun Hu and Charles DeLisi

    Citation: BMC Medical Genomics 2016 9:51

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  24. Content type: Research article

    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...

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

    Citation: BMC Medical Genomics 2015 8:61

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  25. Content type: Research article

    Molecular stratification of bladder cancer has revealed gene signatures differentially expressed across tumor subtypes. While these signatures provide important insights into subtype biology, the transcription...

    Authors: Pontus Eriksson, Mattias Aine, Srinivas Veerla, Fredrik Liedberg, Gottfrid Sjödahl and Mattias Höglund

    Citation: BMC Medical Genomics 2015 8:25

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  26. Content type: Research article

    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...

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

    Citation: BMC Medical Genomics 2015 8:22

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  27. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Medical Genomics 2015 8:20

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  28. Content type: Research article

    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 ...

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

    Citation: BMC Medical Genomics 2015 8:17

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  29. Content type: Research article

    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...

    Authors: James C Ryan, Qingzhong Wu and Ritchie C Shoemaker

    Citation: BMC Medical Genomics 2015 8:15

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  30. Content type: Research article

    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...

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

    Citation: BMC Medical Genomics 2015 8:12

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  31. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Medical Genomics 2015 8:10

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  32. Content type: Research article

    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...

    Authors: 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…

    Citation: BMC Medical Genomics 2015 8:7

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  33. Content type: Research article

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

    Authors: 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

    Citation: BMC Medical Genomics 2014 7:73

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  34. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Medical Genomics 2014 7:61

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  35. Content type: Research article

    Obesity is a complex metabolic condition in strong association with various diseases, like type 2 diabetes, resulting in major public health and economic implications. Obesity is the result of environmental an...

    Authors: Lisette J A Kogelman, Susanna Cirera, Daria V Zhernakova, Merete Fredholm, Lude Franke and Haja N Kadarmideen

    Citation: BMC Medical Genomics 2014 7:57

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  36. Content type: Research article

    Human prion diseases are caused by abnormal accumulation of misfolded prion protein in the brain tissue. Inherited prion diseases, including familial Creutzfeldt-Jakob disease (fCJD), are associated with mutat...

    Authors: Sol Moe Lee, Myungguen Chung, Kyu Jam Hwang, Young Ran Ju, Jae Wook Hyeon, Jun-Sun Park, Chi-Kyeong Kim, Sangho Choi, Jeongmin Lee and Su Yeon Kim

    Citation: BMC Medical Genomics 2014 7:52

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  37. Content type: Research article

    The molecular characteristics of human diseases are often represented by a list of genes termed “signature genes”. A significant challenge facing this approach is that of reproducibility: signatures developed ...

    Authors: Feng Tian, Yajie Wang, Michael Seiler and Zhenjun Hu

    Citation: BMC Medical Genomics 2014 7:45

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  38. Content type: Research article

    The role of copy number variation (CNV) has been poorly explored in essential hypertension in part due to technical difficulties in accurately assessing absolute numbers of DNA copies. Droplet digital PCR (ddP...

    Authors: Francine Z Marques, Priscilla R Prestes, Leonardo B Pinheiro, Katrina Scurrah, Kerry R Emslie, Maciej Tomaszewski, Stephen B Harrap and Fadi J Charchar

    Citation: BMC Medical Genomics 2014 7:44

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  39. Content type: Research article

    Dent disease 1 represents a hereditary disorder of renal tubular epithelial function associated with mutations in the CLCN5 gene that encoded the ClC-5 Cl-/H+ antiporter. All of the reported disease-causing mutat...

    Authors: Enrica Tosetto, Alberto Casarin, Leonardo Salviati, Alessandra Familiari, John C Lieske and Franca Anglani

    Citation: BMC Medical Genomics 2014 7:41

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  40. Content type: Research article

    Chiari Type I Malformation (CMI) is characterized by herniation of the cerebellar tonsils through the foramen magnum at the base of the skull, resulting in significant neurologic morbidity. As CMI patients dis...

    Authors: Christina A Markunas, Eric Lock, Karen Soldano, Heidi Cope, Chien-Kuang C Ding, David S Enterline, Gerald Grant, Herbert Fuchs, Allison E Ashley-Koch and Simon G Gregory

    Citation: BMC Medical Genomics 2014 7:39

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  41. Content type: Research article

    Mechanisms underlying the development of virus-induced asthma exacerbations remain unclear. To investigate if epigenetic mechanisms could be involved in virus-induced asthma exacerbations, we undertook DNA met...

    Authors: Peter McErlean, Silvio Favoreto Jr, Fabricio F Costa, Junqing Shen, Jihan Quraishi, Assel Biyasheva, Jocelyn J Cooper, Denise M Scholtens, Elio F Vanin, Maria F de Bonaldo, Hehuang Xie, Marcelo B Soares and Pedro C Avila

    Citation: BMC Medical Genomics 2014 7:37

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  42. Content type: Research article

    Cardiac pathological hypertrophy is associated with a significantly increased risk of coronary heart disease and has been observed in diabetic patients treated with rosiglitazone whereas most published studies...

    Authors: Lars Verschuren, Peter Y Wielinga, Thomas Kelder, Marijana Radonjic, Kanita Salic, Robert Kleemann, Ben van Ommen and Teake Kooistra

    Citation: BMC Medical Genomics 2014 7:35

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  43. Content type: Research article

    Aberrant epigenetic profiles are concomitant with a spectrum of developmental defects and diseases. Role of methylation is an increasingly accepted factor in the pathophysiology of diabetes and its associated ...

    Authors: Sher Zaman Safi, Rajes Qvist, Gracie Ong Siok Yan and Ikram Shah Bin Ismail

    Citation: BMC Medical Genomics 2014 7:29

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  44. Content type: Research article

    Type 1 diabetes (T1D) is an autoimmune disease, while type 2 (T2D) and gestational diabetes (GDM) are considered metabolic disturbances. In a previous study evaluating the transcript profiling of peripheral mo...

    Authors: Adriane F Evangelista, Cristhianna VA Collares, Danilo J Xavier, Claudia Macedo, Fernanda S Manoel-Caetano, Diane M Rassi, Maria C Foss-Freitas, Milton C Foss, Elza T Sakamoto-Hojo, Catherine Nguyen, Denis Puthier, Geraldo A Passos and Eduardo A Donadi

    Citation: BMC Medical Genomics 2014 7:28

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  45. Content type: Research article

    Genome-scale studies of psoriasis have been used to identify genes of potential relevance to disease mechanisms. For many identified genes, however, the cell type mediating disease activity is uncertain, which...

    Authors: William R Swindell, Philip E Stuart, Mrinal K Sarkar, John J Voorhees, James T Elder, Andrew Johnston and Johann E Gudjonsson

    Citation: BMC Medical Genomics 2014 7:27

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  46. Content type: Research article

    Non-coding small RNA molecules play pivotal roles in cellular and developmental processes by regulating gene expression at the post-transcriptional level. In human diseases, the roles of the non-coding small R...

    Authors: Bruna De Felice, Paolo Mondola, Anna Sasso, Giuseppe Orefice, Vincenzo Bresciamorra, Giovanni Vacca, Elio Biffali, Marco Borra and Raimondo Pannone

    Citation: BMC Medical Genomics 2014 7:26

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