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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. 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

    Content type: Research article

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  2. 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

    Content type: Research article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Research article

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  5. 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

    Content type: Research article

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  6. 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

    Content type: Research article

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  7. 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

    Content type: Research article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Research article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research article

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  20. DNA methylation is a crucial epigenetic modification of the genome which is involved in embryonic development, transcription, chromatin structure, X chromosome inactivation, genomic imprinting and chromosome s...

    Authors: Hong-Dan Wang, Qiao-Fang Hou, Qian-Nan Guo, Tao Li, Dong Wu, Xian-Ping Zhang, Yan Chu, Miao He, Hai Xiao, Liang-Jie Guo, Ke Yang, Shi-Xiu Liao and Bo-Feng Zhu

    Citation: BMC Medical Genomics 2014 7:18

    Content type: Research article

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  21. In more than 70% of families with a strong history of breast and ovarian cancers, pathogenic mutation in BRCA1 or BRCA2 cannot be identified, even though hereditary factors are expected to be involved. It has bee...

    Authors: Martin J Larsen, Mads Thomassen, Qihua Tan, Anne-Vibeke Lænkholm, Martin Bak, Kristina P Sørensen, Mette Klarskov Andersen, Torben A Kruse and Anne-Marie Gerdes

    Citation: BMC Medical Genomics 2014 7:9

    Content type: Research article

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  22. High-grade osteosarcoma is a primary malignant bone tumor mostly occurring in adolescents and young adults, with a second peak at middle age. Overall survival is approximately 60%, and has not significantly in...

    Authors: Marieke L Kuijjer, Brendy EWM van den Akker, Riet Hilhorst, Monique Mommersteeg, Emilie P Buddingh, Massimo Serra, Horst Bürger, Pancras CW Hogendoorn and Anne-Marie Cleton-Jansen

    Citation: BMC Medical Genomics 2014 7:4

    Content type: Research article

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  23. To gain biological insights into lung metastases from hepatocellular carcinoma (HCC), we compared the whole-genome sequencing profiles of primary HCC and paired lung metastases.

    Authors: Limei Ouyang, Jeeyun Lee, Cheol-Keun Park, Mao Mao, Yujian Shi, Zhuolin Gong, Hancheng Zheng, Yingrui Li, Yonggang Zhao, Guangbiao Wang, Huiling Fu, Jhingook Kim and Ho Yeong Lim

    Citation: BMC Medical Genomics 2014 7:2

    Content type: Research article

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  24. The presence of an extra whole or part of chromosome 21 in people with Down syndrome (DS) is associated with multiple neurological changes, including pathological aging that often meets the criteria for Alzhei...

    Authors: Meaghan J Jones, Pau Farré, Lisa M McEwen, Julia L MacIsaac, Kim Watt, Sarah M Neumann, Eldon Emberly, Max S Cynader, Naznin Virji-Babul and Michael S Kobor

    Citation: BMC Medical Genomics 2013 6:58

    Content type: Research article

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  25. To investigate associations between WW domain-containing oxidoreductase (WWOX), runt-related transcription factor 2 (RUNX2) and vascular endothelial growth factor alpha (VEGFA) in human osteosarcoma (OS).

    Authors: Jilong Yang, Linru Zhao, Wei Tian, Zhichao Liao, Hong Zheng, Guowen Wang and Kexin Chen

    Citation: BMC Medical Genomics 2013 6:56

    Content type: Research article

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  26. Structure and function of the human brain are subjected to dramatic changes during its development and aging. Studies have demonstrated that microRNAs (miRNAs) play an important role in the regulation of brain...

    Authors: Weiguo Li, Lina Chen, Wan Li, Xiaoli Qu, Weiming He, Yuehan He, Chenchen Feng, Xu Jia, Yanyan Zhou, Junjie Lv, Binhua Liang, Binbin Chen and Jing Jiang

    Citation: BMC Medical Genomics 2013 6:55

    Content type: Research article

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  27. Steatohepatitis occurs in alcoholic liver disease and may progress to liver cirrhosis and hepatocellular carcinoma. Its molecular pathogenesis is to a large degree unknown. Histone modifications play a key rol...

    Authors: Madhusudhan Bysani, Ola Wallerman, Susanne Bornelöv, Kurt Zatloukal, Jan Komorowski and Claes Wadelius

    Citation: BMC Medical Genomics 2013 6:50

    Content type: Research article

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  28. A wealth of nuclear receptor binding data has been generated by the application of chromatin immunoprecipitation (ChIP) techniques. However, there have been relatively few attempts to apply these datasets to h...

    Authors: Adam E Handel, Geir K Sandve, Giulio Disanto, Lahiru Handunnetthi, Gavin Giovannoni and Sreeram V Ramagopalan

    Citation: BMC Medical Genomics 2013 6:45

    Content type: Research article

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  29. Intratumoral heterogeneity is a major obstacle for the treatment of cancer, as the presence of even minor populations that are insensitive to therapy can lead to disease relapse. Increased clonal diversity has...

    Authors: Matthew Anaka, Christopher Hudson, Pu-Han Lo, Hongdo Do, Otavia L Caballero, Ian D Davis, Alexander Dobrovic, Jonathan Cebon and Andreas Behren

    Citation: BMC Medical Genomics 2013 6:40

    Content type: Research article

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  30. Hunter syndrome (HS) is a lysosomal storage disease caused by iduronate-2-sulfatase (IDS) deficiency and loss of ability to break down and recycle the glycosaminoglycans, heparan and dermatan sulfate, leading ...

    Authors: Gianluigi Mazzoccoli, Rosella Tomanin, Tommaso Mazza, Francesca D’Avanzo, Marika Salvalaio, Laura Rigon, Alessandra Zanetti, Valerio Pazienza, Massimo Francavilla, Francesco Giuliani, Manlio Vinciguerra and Maurizio Scarpa

    Citation: BMC Medical Genomics 2013 6:37

    Content type: Research article

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  31. Alterations in epigenetic marks, including methylation or acetylation, are common in human cancers. For many epigenetic pathways, however, direct measures of activity are unknown, making their role in various ...

    Authors: Adam L Cohen, Stephen R Piccolo, Luis Cheng, Rafaella Soldi, Bing Han, W Evan Johnson and Andrea H Bild

    Citation: BMC Medical Genomics 2013 6:35

    Content type: Research article

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  32. As part of the civil aviation safety program to define the adverse effects of ethanol on flying performance, we performed a DNA microarray analysis of human whole blood samples from a five-time point study of ...

    Authors: Doris M Kupfer, Vicky L White, David L Strayer, Dennis J Crouch and Dennis Burian

    Citation: BMC Medical Genomics 2013 6:26

    Content type: Research article

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  33. Down syndrome (DS) is a complex disorder caused by the trisomy of either the entire, or a critical region of chromosome 21 (21q22.1-22.3). Despite representing the most common cause of mental retardation, the ...

    Authors: Barbara Granese, Iris Scala, Carmen Spatuzza, Anna Valentino, Marcella Coletta, Rosa Anna Vacca, Pasquale De Luca and Generoso Andria

    Citation: BMC Medical Genomics 2013 6:24

    Content type: Research article

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  34. End-stage renal failure is associated with profound changes in physiology and health, but the molecular causation of these pleomorphic effects termed “uremia” is poorly understood. The genomic changes of uremi...

    Authors: Andreas Scherer, Oliver P Günther, Robert F Balshaw, Zsuzsanna Hollander, Janet Wilson-McManus, Raymond Ng, W Robert McMaster, Bruce M McManus and Paul A Keown

    Citation: BMC Medical Genomics 2013 6:23

    Content type: Research article

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  35. SCA28 is an autosomal dominant ataxia associated with AFG3L2 gene mutations. We performed a whole genome expression profiling using lymphoblastoid cell lines (LCLs) from four SCA28 patients and six unrelated heal...

    Authors: Cecilia Mancini, Paola Roncaglia, Alessandro Brussino, Giovanni Stevanin, Nicola Lo Buono, Helena Krmac, Francesca Maltecca, Elena Gazzano, Anna Bartoletti Stella, Maria Antonietta Calvaruso, Luisa Iommarini, Claudia Cagnoli, Sylvie Forlani, Isabelle Le Ber, Alexandra Durr, Alexis Brice…

    Citation: BMC Medical Genomics 2013 6:22

    Content type: Research article

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  36. Alternative splicing is critical for generating complex proteomes in response to extracellular signals. Nuclear receptors including estrogen receptor alpha (ERα) and their ligands promote alternative splicing....

    Authors: Poornima Bhat-Nakshatri, Eun-Kyung Song, Nikail R Collins, Vladimir N Uversky, A Keith Dunker, Bert W O’Malley, Tim R Geistlinger, Jason S Carroll, Myles Brown and Harikrishna Nakshatri

    Citation: BMC Medical Genomics 2013 6:21

    Content type: Research article

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  37. Cidofovir (CDV) proved efficacious in treatment of human papillomaviruses (HPVs) hyperplasias. Antiproliferative effects of CDV have been associated with apoptosis induction, S-phase accumulation, and increase...

    Authors: Tim De Schutter, Graciela Andrei, Dimitri Topalis, Lieve Naesens and Robert Snoeck

    Citation: BMC Medical Genomics 2013 6:18

    Content type: Research article

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  38. Chronic kidney disease (CKD) patients present a complex interaction between the innate and adaptive immune systems, in which immune activation (hypercytokinemia and acute-phase response) and immune suppression...

    Authors: Gianluigi Zaza, Simona Granata, Federica Rascio, Paola Pontrelli, Maria Pia Dell’Oglio, Sharon Natasha Cox, Giovanni Pertosa, Giuseppe Grandaliano and Antonio Lupo

    Citation: BMC Medical Genomics 2013 6:17

    Content type: Research article

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  39. Upon co-stimulation with CD3/CD28 antibodies, activated CD4 + T cells were found to lose their susceptibility to HIV-1 infection, exhibiting an induced resistant phenotype. This rather unexpected phenomenon ha...

    Authors: Wen-Wen Xu, Miao-Jun Han, Dai Chen, Ling Chen, Yan Guo, Andrew Willden, Di-Qiu Liu and Hua-Tang Zhang

    Citation: BMC Medical Genomics 2013 6:15

    Content type: Research article

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  40. Hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome (LS) is a cancer syndrome characterised by early-onset epithelial cancers, especially colorectal cancer (CRC) and endometrial cancer. The aim o...

    Authors: Bente A Talseth-Palmer, Elizabeth G Holliday, Tiffany-Jane Evans, Mark McEvoy, John Attia, Desma M Grice, Amy L Masson, Cliff Meldrum, Allan Spigelman and Rodney J Scott

    Citation: BMC Medical Genomics 2013 6:10

    Content type: Research article

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  41. Cryptorchidism is the most frequent congenital disorder in male children; however the genetic causes of cryptorchidism remain poorly investigated. Comparative integratomics combined with systems biology approa...

    Authors: Carlo V Cannistraci, Jernej Ogorevc, Minja Zorc, Timothy Ravasi, Peter Dovc and Tanja Kunej

    Citation: BMC Medical Genomics 2013 6:5

    Content type: Research article

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  42. Human Immunodeficiency Virus-1 (HIV) infection frequently results in neurocognitive impairment. While the cause remains unclear, recent gene expression studies have identified genes whose transcription is dysr...

    Authors: Andrew J Levine, Jeremy A Miller, Paul Shapshak, Benjamin Gelman, Elyse J Singer, Charles H Hinkin, Deborah Commins, Susan Morgello, Igor Grant and Steve Horvath

    Citation: BMC Medical Genomics 2013 6:4

    Content type: Research article

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  43. A number of neurodevelopmental syndromes are caused by mutations in genes encoding proteins that normally function in epigenetic regulation. Identification of epigenetic alterations occurring in these disorder...

    Authors: Daria Grafodatskaya, Barian HY Chung, Darci T Butcher, Andrei L Turinsky, Sarah J Goodman, Sana Choufani, Yi-An Chen, Youliang Lou, Chunhua Zhao, Rageen Rajendram, Fatima E Abidi, Cindy Skinner, James Stavropoulos, Carolyn A Bondy, Jill Hamilton, Shoshana Wodak…

    Citation: BMC Medical Genomics 2013 6:1

    Content type: Research article

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  44. Mitochondrial proteomic alterations of nasopharyngeal carcinoma metastasis remain unknown. Our purpose is to screen mitochondrial proteins for the elucidation of the molecular mechanisms of nasopharyngeal carc...

    Authors: Jianping Liu, Xianquan Zhan, Maoyu Li, Guoqing Li, Pengfei Zhang, Zhefeng Xiao, Meiying Shao, Fang Peng, Rong Hu and Zhuchu Chen

    Citation: BMC Medical Genomics 2012 5:62

    Content type: Research article

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  45. Anatomic and physiological similarities to the human make swine an excellent large animal model for human health and disease.

    Authors: Eric M Walters, Eckhard Wolf, Jeffery J Whyte, Jiude Mao, Simone Renner, Hiroshi Nagashima, Eiji Kobayashi, Jianguo Zhao, Kevin D Wells, John K Critser, Lela K Riley and Randall S Prather

    Citation: BMC Medical Genomics 2012 5:55

    Content type: Review

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  46. Epithelial ovarian cancer is characterized by multiple genomic alterations; most are passenger alterations which do not confer tumor growth. Like many cancers, it is a heterogeneous disease and can be broadly ...

    Authors: Ruby YunJu Huang, Geng Bo Chen, Noriomi Matsumura, Hung-Cheng Lai, Seiichi Mori, Jingjing Li, Meng Kang Wong, Ikuo Konishi, Jean-Paul Thiery and Liang Goh

    Citation: BMC Medical Genomics 2012 5:47

    Content type: Research article

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As a result of the significant disruption that is being caused by the COVID-19 pandemic we are very aware that many researchers will have difficulty in meeting the timelines associated with our peer review process during normal times.  Please do let us know if you need additional time. Our systems will continue to remind you of the original timelines but we intend to be highly flexible at this time.