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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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