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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. The identification of genes that predict in vitro cellular chemosensitivity of cancer cells is of great importance. Chemosensitivity related genes (CRGs) have been widely utilized to guide clinical and cancer ...

    Authors: Xin Chen, Wei Jiang, Qianghu Wang, Teng Huang, Peng Wang, Yan Li, Xiaowen Chen, Yingli Lv and Xia Li

    Citation: BMC Medical Genomics 2012 5:43

    Content type: Research article

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  2. MicroRNA is a naturally occurring class of non-coding RNA molecules that mediate posttranscriptional gene regulation and are strongly implicated in cellular processes such as cell proliferation, carcinogenesis...

    Authors: Iver Nordentoft, Karin Birkenkamp-Demtroder, Mads Agerbæk, Dan Theodorescu, Marie Stampe Ostenfeld, Arndt Hartmann, Michael Borre, Torben F Ørntoft and Lars Dyrskjøt

    Citation: BMC Medical Genomics 2012 5:40

    Content type: Research article

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  3. By regulating digestion and absorption of nutrients and providing a barrier against the external environment the intestine provides a crucial contribution to the maintenance of health. To what extent aging-rel...

    Authors: Wilma T Steegenga, Nicole JW de Wit, Mark V Boekschoten, Noortje IJssennagger, Carolien Lute, Shohreh Keshtkar, Mechteld M Grootte Bromhaar, Ellen Kampman, Lisette C de Groot and Michael Muller

    Citation: BMC Medical Genomics 2012 5:38

    Content type: Research article

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  4. Imatinib mesylate is currently the drug of choice to treat chronic myeloid leukemia. However, patient resistance and cytotoxicity make secondary lines of treatment, such as omacetaxine mepesuccinate, a necessi...

    Authors: Hemant Kulkarni, Harald H H Göring, Vincent Diego, Shelley Cole, Ken R Walder, Greg R Collier, John Blangero and Melanie A Carless

    Citation: BMC Medical Genomics 2012 5:37

    Content type: Research article

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  5. Transcriptomic studies in clinical research are essential tools for deciphering the functional elements of the genome and unraveling underlying disease mechanisms. Various technologies have been developed to d...

    Authors: Nalini Raghavachari, Jennifer Barb, Yanqin Yang, Poching Liu, Kimberly Woodhouse, Daniel Levy, Christopher J O‘Donnell, Peter J Munson and Gregory J Kato

    Citation: BMC Medical Genomics 2012 5:28

    Content type: Research article

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  6. MicroRNAs (miRNAs) are small non-coding RNAs that participate in the spatiotemporal regulation of messenger RNA (mRNA) and protein synthesis. Recent studies have shown that some miRNAs are involved in the prog...

    Authors: Zhaohui Luo, Liyang Zhang, Zheng Li, Xiayu Li, Gang Li, Haibo Yu, Chen Jiang, Yafei Dai, Xiaofang Guo, Juanjuan Xiang and Guiyuan Li

    Citation: BMC Medical Genomics 2012 5:3

    Content type: Research article

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  7. The progression towards type 2 diabetes depends on the allostatic response of pancreatic beta cells to synthesise and secrete enough insulin to compensate for insulin resistance. The endocrine pancreas is a pl...

    Authors: Yurena Vivas, Cristina Martínez-García, Adriana Izquierdo, Francisco Garcia-Garcia, Sergio Callejas, Ismael Velasco, Mark Campbell, Manuel Ros, Ana Dopazo, Joaquin Dopazo, Antonio Vidal-Puig and Gema Medina-Gomez

    Citation: BMC Medical Genomics 2011 4:86

    Content type: Research article

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  8. In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour sampl...

    Authors: Fatemeh Kaveh, Hege Edvardsen, Anne-Lise Børresen-Dale, Vessela N Kristensen and Hiroko K Solvang

    Citation: BMC Medical Genomics 2011 4:85

    Content type: Research article

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  9. Epigenetic alteration of gene expression is a common event in human cancer. DNA methylation is a well-known epigenetic process, but verifying the exact nature of epigenetic changes associated with cancer remai...

    Authors: Jung-Hoon Park, Jinah Park, Jung Kyoon Choi, Jaemyun Lyu, Min-Gyun Bae, Young-Gun Lee, Jae-Bum Bae, Dong Yoon Park, Han-Kwang Yang, Tae-You Kim and Young-Joon Kim

    Citation: BMC Medical Genomics 2011 4:82

    Content type: Research article

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  10. Bone morphogenetic proteins (BMPs) are members of the TGF-beta superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evid...

    Authors: Alejandra Rodriguez-Martinez, Emma-Leena Alarmo, Lilli Saarinen, Johanna Ketolainen, Kari Nousiainen, Sampsa Hautaniemi and Anne Kallioniemi

    Citation: BMC Medical Genomics 2011 4:80

    Content type: Research article

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  11. MicroRNAs are ~22-nt long regulatory RNAs that serve as critical modulators of post-transcriptional gene regulation. The diversity of miRNAs in endothelial cells (ECs) and the relationship of this diversity to...

    Authors: Matthew N McCall, Oliver A Kent, Jianshi Yu, Karen Fox-Talbot, Ari L Zaiman and Marc K Halushka

    Citation: BMC Medical Genomics 2011 4:78

    Content type: Research article

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  12. Gene fusions arising from chromosomal translocations have been implicated in cancer. However, the role of gene fusions in BRCA1-related breast cancers is not well understood. Mutations in BRCA1 are associated wit...

    Authors: Kevin CH Ha, Emilie Lalonde, Lili Li, Luca Cavallone, Rachael Natrajan, Maryou B Lambros, Costas Mitsopoulos, Jarle Hakas, Iwanka Kozarewa, Kerry Fenwick, Chris J Lord, Alan Ashworth, Anne Vincent-Salomon, Mark Basik, Jorge S Reis-Filho, Jacek Majewski…

    Citation: BMC Medical Genomics 2011 4:75

    Content type: Research article

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  13. Sporadic amyotrophic lateral sclerosis (sALS) is a motor neuron disease with poorly understood etiology. Results of gene expression profiling studies of whole blood from ALS patients have not been validated an...

    Authors: Jean-Luc C Mougeot, Zhen Li, Andrea E Price, Fred A Wright and Benjamin R Brooks

    Citation: BMC Medical Genomics 2011 4:74

    Content type: Research article

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  14. Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35. Within each repeat unit is a gene, DUX4, that can encode a protein co...

    Authors: Koji Tsumagari, Shao-Chi Chang, Michelle Lacey, Carl Baribault, Sridar V Chittur, Janet Sowden, Rabi Tawil, Gregory E Crawford and Melanie Ehrlich

    Citation: BMC Medical Genomics 2011 4:67

    Content type: Research article

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  15. Mesenchymal stem cell (MSC) found in bone marrow (BM-MSCs) and the Wharton's jelly matrix of human umbilical cord (WJ-MSCs) are able to transdifferentiate into neuronal lineage cells both in vitro and in vivo and...

    Authors: Shing-Jyh Chang, Shun-Long Weng, Jui-Yu Hsieh, Tao-Yeuan Wang, Margaret Dah-Tsyr Chang and Hsei-Wei Wang

    Citation: BMC Medical Genomics 2011 4:65

    Content type: Research article

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  16. Inflammation plays an important role in cardiac repair after myocardial infarction (MI). Nevertheless, the systems-level characterization of inflammation proteins in MI remains incomplete. There is a need to d...

    Authors: Francisco J Azuaje, Sophie Rodius, Lu Zhang, Yvan Devaux and Daniel R Wagner

    Citation: BMC Medical Genomics 2011 4:59

    Content type: Research article

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  17. Prostate tumor heterogeneity is a major factor in disease management. Heterogeneity could be due to multiple cancer cell types with distinct gene expression. Of clinical importance is the so-called cancer stem...

    Authors: Laura E Pascal, Ricardo ZN Vêncio, Robert L Vessella, Carol B Ware, Eneida F Vêncio, Gareth Denyer and Alvin Y Liu

    Citation: BMC Medical Genomics 2011 4:46

    Content type: Research article

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  18. Bladder cancer is the sixth most common cancer in the world and the incidence is particularly high in southwestern Taiwan. Previous studies have identified several tumor-related genes that are hypermethylated ...

    Authors: Pi-Che Chen, Ming-Hsuan Tsai, Sidney KH Yip, Yeong-Chin Jou, Chi-Fai Ng, Yanning Chen, Xiaoling Wang, Wei Huang, Chun-Liang Tung, Gary CW Chen, Martin MS Huang, Joanna HM Tong, Eing-Ju Song, De-Ching Chang, Cheng-Da Hsu, Ka-Fai To…

    Citation: BMC Medical Genomics 2011 4:45

    Content type: Research article

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  19. Traditional Chinese Medicine (TCM) has been used for thousands of years to treat or prevent diseases, including cancer. Good manufacturing practices (GMP) and sophisticated product analysis (PhytomicsQC) to en...

    Authors: Ena Wang, Scott Bussom, Jinguo Chen, Courtney Quinn, Davide Bedognetti, Wing Lam, Fulan Guan, Zaoli Jiang, Yichao Mark, Yingdong Zhao, David F Stroncek, Jeffrey White, Francesco M Marincola and Yung-Chi Cheng

    Citation: BMC Medical Genomics 2011 4:38

    Content type: Research article

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  20. Myostatin is a potent muscle growth inhibitor that belongs to the Transforming Growth Factor-β (TGF-β) family. Mutations leading to non functional myostatin have been associated with hypermuscularity in severa...

    Authors: Dwi U Kemaladewi, Willem MH Hoogaars, Sandra H van Heiningen, Samuel Terlouw, David JJ de Gorter, Johan T den Dunnen, Gert Jan B van Ommen, Annemieke Aartsma-Rus, Peter ten Dijke and Peter AC 't Hoen

    Citation: BMC Medical Genomics 2011 4:36

    Content type: Research article

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  21. Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their compara...

    Authors: Tracy Tucker, Alexandre Montpetit, David Chai, Susanna Chan, Sébastien Chénier, Bradley P Coe, Allen Delaney, Patrice Eydoux, Wan L Lam, Sylvie Langlois, Emmanuelle Lemyre, Marco Marra, Hong Qian, Guy A Rouleau, David Vincent, Jacques L Michaud…

    Citation: BMC Medical Genomics 2011 4:25

    Content type: Research article

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  22. An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years) in natural transiti...

    Authors: Wim Crielaard, Egija Zaura, Annemarie A Schuller, Susan M Huse, Roy C Montijn and Bart JF Keijser

    Citation: BMC Medical Genomics 2011 4:22

    Content type: Research article

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  23. The vascular disease in-stent restenosis (ISR) is characterized by formation of neointima and adverse inward remodeling of the artery after injury by coronary stent implantation. We hypothesized that the analy...

    Authors: Santhi K Ganesh, Jungnam Joo, Kimberly Skelding, Laxmi Mehta, Gang Zheng, Kathleen O'Neill, Eric M Billings, Anna Helgadottir, Karl Andersen, Gudmundur Thorgeirsson, Thorarinn Gudnason, Nancy L Geller, Robert D Simari, David R Holmes, William W O'Neill and Elizabeth G Nabel

    Citation: BMC Medical Genomics 2011 4:20

    Content type: Research article

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  24. Molecular alterations critical to development of cancer include mutations, copy number alterations (amplifications and deletions) as well as genomic rearrangements resulting in gene fusions. Massively parallel...

    Authors: Ewa Przybytkowski, Cristiano Ferrario and Mark Basik

    Citation: BMC Medical Genomics 2011 4:16

    Content type: Research article

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  25. Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcript...

    Authors: Serban Nacu, Wenlin Yuan, Zhengyan Kan, Deepali Bhatt, Celina Sanchez Rivers, Jeremy Stinson, Brock A Peters, Zora Modrusan, Kenneth Jung, Somasekar Seshagiri and Thomas D Wu

    Citation: BMC Medical Genomics 2011 4:11

    Content type: Research article

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  26. The molecular pathways involved in the interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches, with global expression data sets, were used to identify perturbed gene networks, to g...

    Authors: Ji-Hoon Cho, Richard Gelinas, Kai Wang, Alton Etheridge, Melissa G Piper, Kara Batte, Duaa Dakhlallah, Jennifer Price, Dan Bornman, Shile Zhang, Clay Marsh and David Galas

    Citation: BMC Medical Genomics 2011 4:8

    Content type: Research article

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  27. HCV infection frequently induces chronic liver diseases. The current standard treatment for chronic hepatitis (CH) C combines pegylated interferon (IFN) and ribavirin, and is less than ideal due to undesirable...

    Authors: Yoshiki Murakami, Masami Tanaka, Hidenori Toyoda, Katsuyuki Hayashi, Masahiko Kuroda, Atsushi Tajima and Kunitada Shimotohno

    Citation: BMC Medical Genomics 2010 3:48

    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.