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  1. Content type: Review

    The microRNA miR-155 is prominent in cancer biology. Among microRNAs that have been linked to cancer, it is the most commonly overexpressed in malignancies (PNAS 109:20047-20052, 2012). Since its discovery, mi...

    Authors: Gadareth Higgs and Frank Slack

    Citation: Journal of Clinical Bioinformatics 2013 3:17

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  2. Content type: Methodology

    Immunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation an...

    Authors: Miri Michaeli, Michal Barak, Lena Hazanov, Hila Noga and Ramit Mehr

    Citation: Journal of Clinical Bioinformatics 2013 3:15

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  3. Content type: Research

    Quantification and normalization of RT-qPCR data critically depends on the expression of so called reference genes. Our goal was to develop a strategy for the selection of reference genes that utilizes microar...

    Authors: Diana V Maltseva, Nadezda A Khaustova, Nikita N Fedotov, Elona O Matveeva, Alexey E Lebedev, Maxim U Shkurnikov, Vladimir V Galatenko, Udo Schumacher and Alexander G Tonevitsky

    Citation: Journal of Clinical Bioinformatics 2013 3:13

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  4. Content type: Short report

    Next-generation sequencing has enabled examination of variation at the DNA sequence level and can be further enhanced by evaluation of the variants at the protein level. One powerful method is to visualize the...

    Authors: Tychele Turner

    Citation: Journal of Clinical Bioinformatics 2013 3:14

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  5. Content type: Research

    DNA copy number variations (CNV) constitute an important source of genetic variability. The standard method used for CNV detection is array comparative genomic hybridization (aCGH).

    Authors: Maciej Sykulski, Tomasz Gambin, Magdalena Bartnik, Katarzyna Derwińska, Barbara Wiśniowiecka-Kowalnik, Paweł Stankiewicz and Anna Gambin

    Citation: Journal of Clinical Bioinformatics 2013 3:12

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  6. Content type: Methodology

    Biological networks are important for elucidating disease etiology due to their ability to model complex high dimensional data and biological systems. Proteomics provides a critical data source for such models...

    Authors: David L Gibbs, Arie Baratt, Ralph S Baric, Yoshihiro Kawaoka, Richard D Smith, Eric S Orwoll, Michael G Katze and Shannon K McWeeney

    Citation: Journal of Clinical Bioinformatics 2013 3:11

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  7. Content type: Research

    Whole genome microarray gene expression profiling is the ‘gold standard’ for the discovery of prognostic and predictive genetic markers for human cancers. However, suitable research material is lacking as most...

    Authors: Marlene Thomas, Manuela Poignée-Heger, Martin Weisser, Stephanie Wessner and Anton Belousov

    Citation: Journal of Clinical Bioinformatics 2013 3:10

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  8. Content type: Methodology

    Like all other neurodegenerative diseases, Alzheimer’s disease (AD) remains a very challenging and difficult problem for diagnosis and therapy. For many years, only historical, behavioral and psychiatric measu...

    Authors: Wen-Chin Hsu, Christopher Denq and Su-Shing Chen

    Citation: Journal of Clinical Bioinformatics 2013 3:9

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  9. Content type: Research

    Exploring stromal changes associated with tumor growth and development is a growing area of oncologic research. In order to study molecular changes in the stroma it is recommended to separate tumor tissue from...

    Authors: Camilo Valdes, Pearl Seo, Nicholas Tsinoremas and Jennifer Clarke

    Citation: Journal of Clinical Bioinformatics 2013 3:8

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  10. Content type: Database

    MicroRNAs were found to play an important role in cancers and several literatures exist to describe the relationship between microRNA and cancer, but the expression pattern was still faintly. There is a need f...

    Authors: Lei Dong, Min Luo, Fang Wang, Junwu Zhang, Tingting Li and Jia Yu

    Citation: Journal of Clinical Bioinformatics 2013 3:7

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  11. Content type: Reviewer acknowledgement

    The editors of Journal of Clinical Bioinformatics would like to thank all our reviewers who have contributed to the journal in Volume 2 (2012).

    Authors: Xiangdong Wang

    Citation: Journal of Clinical Bioinformatics 2013 3:5

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  12. Content type: Review

    MicroRNAs (miRNAs) are remarkable molecules that appear to have a fundamental role in the biology of the cell. They constitute a class of non-protein encoding RNA molecules which have now emerged as key player...

    Authors: Rishabh Kala, Gregory W Peek, Tabitha M Hardy and Trygve O Tollefsbol

    Citation: Journal of Clinical Bioinformatics 2013 3:6

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  13. Content type: Methodology

    Single nucleotide polymorphisms (SNPs) in genes derived from distinct pathways are associated with a breast cancer risk. Identifying possible SNP-SNP interactions in genome-wide case–control studies is an impo...

    Authors: Li-Yeh Chuang, Hsueh-Wei Chang, Ming-Cheng Lin and Cheng-Hong Yang

    Citation: Journal of Clinical Bioinformatics 2013 3:4

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  14. Content type: Research

    The recent introduction of high throughput sequencing technologies into clinical genetics has made it practical to simultaneously sequence many genes. In contrast, previous technologies limited sequencing base...

    Authors: Perry G Ridge, Christine Miller, Pinar Bayrak-Toydemir, D Hunter Best, Rong Mao, Jeffrey J Swensen, Elaine Lyon and Karl V Voelkerding

    Citation: Journal of Clinical Bioinformatics 2013 3:3

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  15. Content type: Research

    Mass spectrometry is an important analytical tool for clinical proteomics. Primarily employed for biomarker discovery, it is increasingly used for developing methods which may help to provide unambiguous diagn...

    Authors: Dario Di Silvestre, Italo Zoppis, Francesca Brambilla, Valeria Bellettato, Giancarlo Mauri and Pierluigi Mauri

    Citation: Journal of Clinical Bioinformatics 2013 3:1

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  16. Content type: Database

    Identification of prognostic biomarkers is hallmark of cancer genomics. Since miRNAs regulate expression of multiple genes, they act as potent biomarkers in several cancers. Identification of miRNAs that are p...

    Authors: Chirayu Pankaj Goswami and Harikrishna Nakshatri

    Citation: Journal of Clinical Bioinformatics 2012 2:23

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  17. Content type: Methodology

    Cancer outlier profile analysis (COPA) has proven to be an effective approach to analyzing cancer expression data, leading to the discovery of the TMPRSS2 and ETS family gene fusion events in prostate cancer. ...

    Authors: Chenwei Wang, Alperen Taciroglu, Stefan R Maetschke, Colleen C Nelson, Mark A Ragan and Melissa J Davis

    Citation: Journal of Clinical Bioinformatics 2012 2:22

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  18. Content type: Methodology

    Second generation RNA sequencing technology (RNA-seq) offers the potential to interrogate genome-wide differential RNA splicing in cancer. However, since short RNA reads spanning spliced junctions cannot be ma...

    Authors: Subhashini Srinivasan, Arun H Patil, Mohit Verma, Jonathan L Bingham and Raghunathan Srivatsan

    Citation: Journal of Clinical Bioinformatics 2012 2:21

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  19. Content type: Research

    Inflammatory bowel diseases, ulcerative colitis and Crohn’s disease are considered to be of autoimmune origin, but the etiology of irritable bowel syndrome remains elusive. Furthermore, classifying patients in...

    Authors: Philip S Crooke, John T Tossberg, Sara N Horst, John L Tauscher, Melodie A Henderson, Dawn B Beaulieu, David A Schwartz, Nancy J Olsen and Thomas M Aune

    Citation: Journal of Clinical Bioinformatics 2012 2:20

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  20. Content type: Database

    Next generation sequencing provides clinical research scientists with direct read out of innumerable variants, including personal, pathological and common benign variants. The aim of resequencing studies is to...

    Authors: Andrew Stubbs, Elizabeth A McClellan, Sebastiaan Horsman, Saskia D Hiltemann, Ivo Palli, Stephan Nouwens, Anton HJ Koning, Frits Hoogland, Joke Reumers, Daphne Heijsman, Sigrid Swagemakers, Andreas Kremer, Jules Meijerink, Diether Lambrechts and Peter J van der Spek

    Citation: Journal of Clinical Bioinformatics 2012 2:19

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  21. Content type: Short report

    Drug discovery typically starts with the identification of a potential target that is then tested and validated either through high-throughput screening against a library of drug compounds or by rational drug ...

    Authors: Eric di Luccio and Patrice Koehl

    Citation: Journal of Clinical Bioinformatics 2012 2:18

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  22. Content type: Review

    Autism is the fastest growing developmental disorder in the world today. The prevalence of autism in the US has risen from 1 in 2500 in 1970 to 1 in 88 children today. People with autism present with repetitiv...

    Authors: Mary Randolph-Gips and Pramila Srinivasan

    Citation: Journal of Clinical Bioinformatics 2012 2:17

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  23. Content type: Short report

    Ovarian cancer is the most deadly gynecological cancer because of late diagnosis, frequently with diffuse peritoneal metastases. Recent findings have shown that serous epithelial ovarian cancer has a narrow mu...

    Authors: Arash Rafii, Najeeb M Halabi and Joel A Malek

    Citation: Journal of Clinical Bioinformatics 2012 2:15

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