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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: 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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  4. 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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  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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  24. Content type: Methodology

    In early-stage of cancer, primary treatment can be considered as effective at eliminating the tumor for a non-negligible proportion of patients whereas for the others it leads to a lower tumor burden and there...

    Authors: Philippe Broët and Thierry Moreau

    Citation: Journal of Clinical Bioinformatics 2012 2:14

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  25. Content type: Methodology

    A simple and fast computational model to describe the dynamics of tumour growth and metastasis formation is presented. The model is based on the calculation of successive generations of tumour cells and enable...

    Authors: Volker Haustein and Udo Schumacher

    Citation: Journal of Clinical Bioinformatics 2012 2:11

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  26. Content type: Methodology

    The identification of very small subsets of predictive variables is an important toπc that has not often been considered in the literature. In order to discover highly predictive yet compact gene set classifie...

    Authors: Xiaowei Guan, Mark R Chance and Jill S Barnholtz-Sloan

    Citation: Journal of Clinical Bioinformatics 2012 2:13

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  27. Content type: Research

    Hazelnut is reported as a causative agent of allergic reactions. However it is also an edible nut with health benefits. The allergenic characteristics of hazelnut-samples after autoclaving (AC) and high-pressu...

    Authors: Elena López, Carmen Cuadrado, Carmen Burbano, Maria Aranzazu Jiménez, Julia Rodríguez and Jesús F Crespo

    Citation: Journal of Clinical Bioinformatics 2012 2:12

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  28. Content type: Methodology

    Numerous biomedical software applications access databases maintained by the US National Center for Biotechnology Information (NCBI). To ease software automation, NCBI provides a powerful but complex Web-servi...

    Authors: Prakash M Nadkarni and Chirag R Parikh

    Citation: Journal of Clinical Bioinformatics 2012 2:9

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  29. Content type: Research

    3D domain swapping is a novel structural phenomenon observed in diverse set of protein structures in oligomeric conformations. A distinct structural feature, where structural segments in a protein dimer or hig...

    Authors: Khader Shameer and Ramanathan Sowdhamini

    Citation: Journal of Clinical Bioinformatics 2012 2:8

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  30. Content type: Review

    The 6th Benelux Bioinformatics Conference (BBC11) held in Luxembourg on 12 and 13 December 2011 attracted around 200 participants, including internationally-renowned guest speakers and more than 100 peer-reviewed...

    Authors: Francisco J Azuaje, Michaël Heymann, Anne-Marie Ternes, Anke Wienecke-Baldacchino, Daniel Struck, Danièle Moes and Reinhard Schneider

    Citation: Journal of Clinical Bioinformatics 2012 2:7

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  31. Content type: Research

    Peripheral arterial disease (PAD) is a relatively common manifestation of systemic atherosclerosis that leads to progressive narrowing of the lumen of leg arteries. Circulating monocytes are in contact with th...

    Authors: Rizwan Masud, Khader Shameer, Aparna Dhar, Keyue Ding and Iftikhar J Kullo

    Citation: Journal of Clinical Bioinformatics 2012 2:6

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  32. Content type: Research

    The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cu...

    Authors: Vladimir Lazarevic, Katrine Whiteson, Nadia Gaïa, Yann Gizard, David Hernandez, Laurent Farinelli, Magne Østerås, Patrice François and Jacques Schrenzel

    Citation: Journal of Clinical Bioinformatics 2012 2:4

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  33. Content type: Research

    High blood glucose and diabetes are amongst the conditions causing the greatest losses in years of healthy life worldwide. Therefore, numerous studies aim to identify reliable risk markers for development of i...

    Authors: Manuela Hische, Abdelhalim Larhlimi, Franziska Schwarz, Antje Fischer-Rosinský, Thomas Bobbert, Anke Assmann, Gareth S Catchpole, Andreas FH Pfeiffer, Lothar Willmitzer, Joachim Selbig and Joachim Spranger

    Citation: Journal of Clinical Bioinformatics 2012 2:3

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  34. Content type: Short report

    Translational and evidence based medicine can take advantage of biotechnology advances that offer a fast growing variety of high-throughput data for screening molecular activities of genomic, transcriptional, ...

    Authors: Raffaele Fronza, Michele Tramonti, William R Atchley and Christine Nardini

    Citation: Journal of Clinical Bioinformatics 2012 2:2

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  35. Content type: Research

    Systematic approach for drug discovery is an emerging discipline in systems biology research area. It aims at integrating interaction data and experimental data to elucidate diseases and also raises new issues...

    Authors: Shih-Heng Yeh, Hsiang-Yuan Yeh and Von-Wun Soo

    Citation: Journal of Clinical Bioinformatics 2012 2:1

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  36. Content type: Methodology

    Multivariate assays (MVAs) for assisting clinical decisions are becoming commonly available, but due to complexity, are often considered a high-risk approach. A key concern is that uncertainty on the assay's f...

    Authors: Mark TW Ebbert, Roy RL Bastien, Kenneth M Boucher, Miguel Martín, Eva Carrasco, Rosalía Caballero, Inge J Stijleman, Philip S Bernard and Julio C Facelli

    Citation: Journal of Clinical Bioinformatics 2011 1:37

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  37. Content type: Research

    It has been shown previously that glucocorticoids exert a dual mechanism of action, entailing cytotoxic, mitogenic as well as cell proliferative and anti-apoptotic responses, in a dose-dependent manner on CCRF...

    Authors: Emmanouil G Sifakis, George I Lambrou, Andriana Prentza, Spiros Vlahopoulos, Dimitris Koutsouris, Fotini Tzortzatou-Stathopoulou and Aristotelis A Chatziioannou

    Citation: Journal of Clinical Bioinformatics 2011 1:36

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  38. Content type: Short report

    In metabolomics, biomarker discovery is a highly data driven process and requires sophisticated computational methods for the search and prioritization of novel and unforeseen biomarkers in data, typically gat...

    Authors: Michael Netzer, Klaus M Weinberger, Michael Handler, Michael Seger, Xiaocong Fang, Karl G Kugler, Armin Graber and Christian Baumgartner

    Citation: Journal of Clinical Bioinformatics 2011 1:34

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  39. Content type: Research

    Health information exchange and health information integration has become one of the top priorities for healthcare systems across institutions and hospitals. Most organizations and establishments implement hea...

    Authors: Teeradache Viangteeravat, Matthew N Anyanwu, Venkateswara Ra Nagisetty, Emin Kuscu, Mark Eijiro Sakauye and Duojiao Wu

    Citation: Journal of Clinical Bioinformatics 2011 1:32

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  40. Content type: Research

    Pulmonary Langerhans-cell histiocytosis (PLCH) is a rare interstitial lung disease characterized by clusters of Langerhans cells, organized in granulomas, in the walls of distal bronchioles. It is a diffuse lu...

    Authors: Claudia Landi, Elena Bargagli, Barbara Magi, Antje Prasse, Joachim Muller-Quernheim, Luca Bini and Paola Rottoli

    Citation: Journal of Clinical Bioinformatics 2011 1:31

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  41. Content type: Review

    Atherosclerosis results from dyslipidemia and systemic inflammation, associated with the strong metabolism and interaction between diet and disease. Strategies based on the global profiling of metabolism would...

    Authors: Duo-jiao Wu, Bi-jun Zhu and Xiang-dong Wang

    Citation: Journal of Clinical Bioinformatics 2011 1:30

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  42. Content type: Methodology

    Dyslipidemia is an important risk factor for cardiovascular disease and type II diabetes. Lipoprotein diagnostics, such as LDL cholesterol and HDL cholesterol, help to diagnose these diseases. Lipoprotein prof...

    Authors: Daniël B van Schalkwijk, Ben van Ommen, Andreas P Freidig, Jan van der Greef and Albert A de Graaf

    Citation: Journal of Clinical Bioinformatics 2011 1:29

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  43. Content type: Methodology

    The immune response to viral infection is a temporal process, represented by a dynamic and complex network of gene and protein interactions. Here, we present a reverse engineering strategy aimed at capturing t...

    Authors: Konstantina Dimitrakopoulou, Charalampos Tsimpouris, George Papadopoulos, Claudia Pommerenke, Esther Wilk, Kyriakos N Sgarbas, Klaus Schughart and Anastasios Bezerianos

    Citation: Journal of Clinical Bioinformatics 2011 1:27

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