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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

    The mechanisms underlying neurodegeneration in the striatum of Huntingon’s Disease (HD) brain are currently unknown. While the striatum is massively degenerated in symptomatic individuals, which makes cellular...

    Authors: Filisia Agus, Diego Crespo, Richard H. Myers and Adam Labadorf

    Citation: BMC Medical Genomics 2019 12:137

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  2. Content type: Research article

    Diabetic retinopathy (DR) is the leading cause of blindness in the working age population. Transthyretin (TTR) showed a significantly decreased concentration in DR patients and exerted a visual protective effe...

    Authors: Jun Shao, Yunbin Zhang, Guangming Fan, Yu Xin and Yong Yao

    Citation: BMC Medical Genomics 2019 12:134

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  3. Content type: Research article

    Genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) that may be genetic factors underlying Alzheimer’s disease (AD). However, how these AD-associated SNPs (AD SNPs) c...

    Authors: Masataka Kikuchi, Norikazu Hara, Mai Hasegawa, Akinori Miyashita, Ryozo Kuwano, Takeshi Ikeuchi and Akihiro Nakaya

    Citation: BMC Medical Genomics 2019 12:128

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  4. Content type: Research article

    Burkholderia mallei (Bm) is a facultative intracellular bacterial pathogen causing highly-fatal glanders in solipeds and humans. The ability of Bm to thrive intracellularly is thought to be related to exploitatio...

    Authors: Sophie A. Aschenbroich, Eric R. Lafontaine, Maria Cecilia Lopez, Henry V. Baker and Robert J. Hogan

    Citation: BMC Medical Genomics 2019 12:127

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  5. Content type: Research article

    Identifying molecular biomarkers characteristic of ischemic stroke has the potential to aid in distinguishing stroke cases from stroke mimicking symptoms, as well as advancing the understanding of the physiolo...

    Authors: Konstantinos Theofilatos, Aigli Korfiati, Seferina Mavroudi, Matthew C. Cowperthwaite and Max Shpak

    Citation: BMC Medical Genomics 2019 12:118

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  6. Content type: Case report

    Balanced structural variants are mostly described in disease with gene disruption or subtle rearrangement at breakpoints.

    Authors: Kevin Yauy, Anouck Schneider, Bee Ling Ng, Jean-Baptiste Gaillard, Satish Sati, Christine Coubes, Constance Wells, Magali Tournaire, Thomas Guignard, Pauline Bouret, David Geneviève, Jacques Puechberty, Franck Pellestor and Vincent Gatinois

    Citation: BMC Medical Genomics 2019 12:116

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  7. Content type: Research article

    Population studies suggest that genetic factors play an important role in refractive error development; however, the precise role of genetic background and the composition of the signaling pathways underlying ...

    Authors: Tatiana V. Tkatchenko, Rupal L. Shah, Takayuki Nagasaki and Andrei V. Tkatchenko

    Citation: BMC Medical Genomics 2019 12:113

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  8. Content type: Research article

    Synthetic lethal interactions (SLIs) that occur between gene pairs are exploited for cancer therapeutics. Studies in the model eukaryote yeast have identified ~ 550,000 negative genetic interactions that have ...

    Authors: Morgan W. B. Kirzinger, Frederick S. Vizeacoumar, Bjorn Haave, Cristina Gonzalez-Lopez, Keith Bonham, Anthony Kusalik and Franco J. Vizeacoumar

    Citation: BMC Medical Genomics 2019 12:112

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  9. Content type: Research article

    A normally developed placenta is integral to a successful pregnancy. Preeclampsia (PE) and intrauterine growth restriction (IUGR) are two common pregnancy related complications that maybe a result of abnormal ...

    Authors: Zain Awamleh, Gregory B. Gloor and Victor K. M. Han

    Citation: BMC Medical Genomics 2019 12:91

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  10. Content type: Research article

    Gastric emptying is impaired in patients with gastroparesis whereas it is either unchanged or accelerated in obese individuals. The goal of the current study was to identify changes in gene expression in the s...

    Authors: B. Paul Herring, Meng Chen, Plamen Mihaylov, April M. Hoggatt, Anita Gupta, Attila Nakeeb, Jennifer N. Choi and John M. Wo

    Citation: BMC Medical Genomics 2019 12:89

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  11. Content type: Research article

    Large granular lymphocyte (LGL) leukemia is an uncommon cancer characterized by sustained clonal proliferation of LGL cells. Antibodies reactive to retroviruses have been documented in the serum of patients wi...

    Authors: Weiling Li, Lei Yang, Robert S. Harris, Lin Lin, Thomas L. Olson, Cait E. Hamele, David J. Feith, Thomas P. Loughran Jr and Mary Poss

    Citation: BMC Medical Genomics 2019 12:88

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  12. Content type: Case report

    The vast majority of cases with Beckwith-Wiedemann syndrome (BWS) are caused by a molecular defect in the imprinted chromosome region 11p15.5. The underlying mechanisms include epimutations, uniparental disomy...

    Authors: Caroline Lekszas, Indrajit Nanda, Barbara Vona, Julia Böck, Farah Ashrafzadeh, Nahid Donyadideh, Farnoosh Ebrahimzadeh, Najmeh Ahangari, Reza Maroofian, Ehsan Ghayoor Karimiani and Thomas Haaf

    Citation: BMC Medical Genomics 2019 12:83

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  13. Content type: Research article

    Clinical data identified an association between the use of HMG-CoA reductase inhibitors (statins) and incident diabetes in patients with underlying diabetes risk factors such as obesity, hypertension and dysli...

    Authors: Daniel Margerie, Philippe Lefebvre, Violeta Raverdy, Uwe Schwahn, Hartmut Ruetten, Philip Larsen, Alain Duhamel, Julien Labreuche, Dorothée Thuillier, Bruno Derudas, Céline Gheeraert, Hélène Dehondt, Quentin Dhalluin, Jérémy Alexandre, Robert Caiazzo, Pamela Nesslany…

    Citation: BMC Medical Genomics 2019 12:80

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  14. Content type: Research article

    Intra-tumor heterogeneity stems from genetic, epigenetic, functional, and environmental differences among tumor cells. A major source of genetic heterogeneity comes from DNA sequence differences and/or whole c...

    Authors: Yanding Zhao, Robert Carter, Sivaraman Natarajan, Frederick S. Varn, Duane A. Compton, Charles Gawad, Chao Cheng and Kristina M. Godek

    Citation: BMC Medical Genomics 2019 12:79

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  15. Content type: Research article

    The co-occurrence of multiple de novo copy number variations (CNVs) is a rare phenomenon in the human genome. Recently, an “organismal CNV mutator phenotype” has been reported to result in transient genomic in...

    Authors: Atsushi Hattori, Kohji Okamura, Yumiko Terada, Rika Tanaka, Yuko Katoh-Fukui, Yoichi Matsubara, Keiko Matsubara, Masayo Kagami, Reiko Horikawa and Maki Fukami

    Citation: BMC Medical Genomics 2019 12:77

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  16. Content type: Case report

    Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF).

    Authors: Angélica Martínez-Hernández, Julieta Larrosa, Francisco Barajas-Olmos, Humberto García-Ortíz, Elvia C. Mendoza-Caamal, Cecilia Contreras-Cubas, Elaheh Mirzaeicheshmeh, José Luis Lezana and Lorena Orozco

    Citation: BMC Medical Genomics 2019 12:68

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  17. Content type: Research article

    Chemoresistance is a primary clinical challenge for the management of small cell lung cancer. Additionally, transcriptional regulation by super enhancer (SE) has an important role in tumor evolution. The funct...

    Authors: Jiarong Bao, Man Li, Shumei Liang, Yunchu Yang, Jingfang Wu, Qingqing Zou, Shun Fang, Size Chen and Linlang Guo

    Citation: BMC Medical Genomics 2019 12:67

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  18. Content type: Research article

    In cystic fibrosis (CF), impaired immune cell responses, driven by the dysfunctional CF transmembrane conductance regulator (CFTR) gene, may determine the disease severity but clinical heterogeneity remains a maj...

    Authors: Justin E. Ideozu, Vittobai Rangaraj, Hiam Abdala-Valencia, Xi Zhang, Manoj Kandpal, Marc A. Sala, Ramana V. Davuluri and Hara Levy

    Citation: BMC Medical Genomics 2019 12:66

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  19. Content type: Research article

    Transcriptome wide changes have been assessed extensively during the progression of neurodegenerative diseases. Alternative polyadenylation (APA) occurs in over 70% of human protein coding genes and it has rec...

    Authors: Radhika Patel, Cillian Brophy, Mark Hickling, Jonathan Neve and André Furger

    Citation: BMC Medical Genomics 2019 12:60

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  20. Content type: Research article

    Endometrial cancer (EMCA) is the fifth most common cancer among women in the world. Identification of potentially pathogenic germline variants from individuals with EMCA will help characterize genetic features...

    Authors: Jason E. Miller, Raghu P. Metpally, Thomas N. Person, Sarathbabu Krishnamurthy, Venkata Ramesh Dasari, Manu Shivakumar, Daniel R. Lavage, Adam M. Cook, David J. Carey, Marylyn D. Ritchie, Dokyoon Kim and Radhika Gogoi

    Citation: BMC Medical Genomics 2019 12:59

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    The Correction to this article has been published in BMC Medical Genomics 2019 12:65

  21. Content type: Research article

    Human Endogenous Retroviruses type K HML-2 (HK2) are integrated into 117 or more areas of human chromosomal arms while two newly discovered HK2 proviruses, K111 and K222, spread extensively in pericentromeric ...

    Authors: Mark H. Kaplan, Mark Kaminski, Judith M. Estes, Scott D. Gitlin, Joseph Zahn, James T. Elder, Trilokraj Tejasvi, Elizabeth Gensterblum, Amr H. Sawalha, Joseph Patrick McGowan, Michael H. Dosik, Haner Direskeneli, Guher Saruhan Direskeneli, Sally N. Adebamowo, Clement A. Adebamowo, Mohammad Sajadi…

    Citation: BMC Medical Genomics 2019 12:58

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  22. Content type: Research article

    Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and ...

    Authors: Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Heather Geiger, Vanessa Felice, Esra Dikoglu, Sadia Rahman, Alice Fang, Vladimir Vacic, Ewa A. Bergmann…

    Citation: BMC Medical Genomics 2019 12:56

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    The Correction to this article has been published in BMC Medical Genomics 2019 12:114

  23. Content type: Research article

    Preterm birth (PTB), defined as infant delivery before 37 weeks of completed gestation, results from the interaction of both genetic and environmental components and constitutes a complex multifactorial syndro...

    Authors: Silvana Pereyra, Claudio Sosa, Bernardo Bertoni and Rossana Sapiro

    Citation: BMC Medical Genomics 2019 12:53

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  24. Content type: Technical advance

    Preimplantation genetic testing (PGT) has already been applied in chromosomally balanced translocation carriers to improve the clinical outcome of assisted reproduction. However, traditional methods could not ...

    Authors: Shuo Zhang, Dingding Zhao, Jun Zhang, Yan Mao, Lingyin Kong, Yueping Zhang, Bo Liang, Xiaoxi Sun and Congjian Xu

    Citation: BMC Medical Genomics 2019 12:52

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  25. Content type: Research article

    Currently, chromosomal microarrays (CMA) are recommended as first-tier test in the investigation of developmental disorders to examine copy number variations. The modern platforms also include probes for singl...

    Authors: Tiago Fernando Chaves, Luan Freitas Oliveira, Maristela Ocampos, Ingrid Tremel Barbato, Gisele Rozone de Luca, Jorge Humbeto Barbato Filho, Louise Lapagesse de Camargo Pinto, Pricila Bernardi and Angelica Francesca Maris

    Citation: BMC Medical Genomics 2019 12:50

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  26. Content type: Research article

    Oesophageal adenocarcinoma (EAC) incidence is increasing and has a poor survival rate. Barrett’s oesophagus (BE) is a precursor condition that is associated with EAC and often occurs in conjunction with chroni...

    Authors: Felicity Newell, Kalpana Patel, Michael Gartside, Lutz Krause, Sandra Brosda, Lauren G. Aoude, Kelly A. Loffler, Vanessa F. Bonazzi, Ann-Marie Patch, Stephen H. Kazakoff, Oliver Holmes, Qinying Xu, Scott Wood, Conrad Leonard, Guy Lampe, Reginald V. Lord…

    Citation: BMC Medical Genomics 2019 12:31

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  27. Content type: Research article

    Non-random chromosome positioning has been observed in the nuclei of several different tissue types, including human spermatozoa. The nuclear arrangement of chromosomes can be altered in men with decreased sem...

    Authors: Marta Olszewska, Ewa Wiland, Nataliya Huleyuk, Monika Fraczek, Alina T. Midro, Danuta Zastavna and Maciej Kurpisz

    Citation: BMC Medical Genomics 2019 12:30

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  28. Content type: Research article

    Glucocorticoids act on the glucocorticoid receptor (GR; NR3C1) to resolve inflammation and, as inhaled corticosteroids (ICS), are the cornerstone of treatment for asthma. However, reduced efficacy in severe di...

    Authors: Mahmoud M. Mostafa, Christopher F. Rider, Suharsh Shah, Suzanne L. Traves, Paul M. K. Gordon, Anna Miller-Larsson, Richard Leigh and Robert Newton

    Citation: BMC Medical Genomics 2019 12:29

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  29. Content type: Research article

    The past few decades have witnessed a tremendous development in the field of genetics. The implementation of next generation sequencing (NGS) technologies revolutionized the field of molecular biology and made...

    Authors: Nadine Jalkh, Sandra Corbani, Zahraa Haidar, Nadine Hamdan, Elias Farah, Joelle Abou Ghoch, Rouba Ghosn, Nabiha Salem, Ali Fawaz, Claudia Djambas Khayat, Mariam Rajab, Chebl Mourani, Adib Moukarzel, Simon Rassi, Bernard Gerbaka, Hicham Mansour…

    Citation: BMC Medical Genomics 2019 12:11

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  30. Content type: Research article

    It has been found that chronic rhinosinusitis (CRS) increases the risk of developing nasopharyngeal carcinoma (NPC). CRS can be caused by gastro-oesophageal reflux (GOR) that may reach nasopharynx. The major c...

    Authors: Sang-Nee Tan and Sai-Peng Sim

    Citation: BMC Medical Genomics 2019 12:9

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  31. Content type: Case report

    Two interstitial microdeletions Xp11.22 including the CLCN5 and SHROOM4 genes were recently reported in a male individual affected with Dent disease, short stature, psychomotor delay and minor facial anomalies. D...

    Authors: Magdalena Danyel, Eun Kyung Suk, Vera Raile, Jutta Gellermann, Alexej Knaus and Denise Horn

    Citation: BMC Medical Genomics 2019 12:6

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  32. Content type: Case report

    Mutations of SHOX represent the most frequent monogenic cause of short stature and related syndromes. The genetic alterations include point mutations and deletions/duplications spanning both SHOX and its regulato...

    Authors: Alice Monzani, Deepak Babu, Simona Mellone, Giulia Genoni, Antonella Fanelli, Flavia Prodam, Simonetta Bellone and Mara Giordano

    Citation: BMC Medical Genomics 2019 12:5

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  33. Content type: Research article

    In the absence of antiretroviral treatments (ARTs), a small group of individuals infected with HIV, including long-term non-progressors (LTNPs) who maintain high levels of CD4+ T cells for more than 7–10 years...

    Authors: Sun Young Lee, Yong Kwang Park, Cheol-Hee Yoon, Kisoon Kim and Kyung-Chang Kim

    Citation: BMC Medical Genomics 2019 12:3

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  34. Content type: Case report

    Silver-Russell Syndrome (SRS) is a rare growth-related genetic disorder mainly characterized by prenatal and postnatal growth failure. Although molecular causes are not clear in all cases, the most common mech...

    Authors: Yerai Vado, Javier Errea-Dorronsoro, Isabel Llano-Rivas, Nerea Gorria, Arrate Pereda, Blanca Gener, Laura Garcia-Naveda and Guiomar Perez de Nanclares

    Citation: BMC Medical Genomics 2018 11:124

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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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