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  1. Review

    Variations in genome-wide RNAi screens: lessons from influenza research

    Genome-wide RNA interference (RNAi) screening is an emerging and powerful technique for genetic screens, which can be divided into arrayed RNAi screen and pooled RNAi screen/selection based on different screen...

    Yu-Chi Chou, Michael MC Lai, Yi-Chen Wu, Nai-Chi Hsu, King-Song Jeng and Wen-Chi Su

    Journal of Clinical Bioinformatics 2015 5:2

    Published on: 3 March 2015

  2. Research

    K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores

    Network biology currently focuses primarily on metabolic pathways, gene regulatory, and protein-protein interaction networks. While these approaches have yielded critical information, alternative methods to ne...

    Arnold I Emerson, Simeon Andrews, Ikhlak Ahmed, Thasni KA Azis and Joel A Malek

    Journal of Clinical Bioinformatics 2015 5:1

    Published on: 3 March 2015

  3. Methodology

    Copy number variation analysis based on AluScan sequences

    AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirem...

    Jian-Feng Yang, Xiao-Fan Ding, Lei Chen, Wai-Kin Mat, Michelle Zhi Xu, Jin-Fei Chen, Jian-Min Wang, Lin Xu, Wai-Sang Poon, Ava Kwong, Gilberto Ka-Kit Leung, Tze-Ching Tan, Chi-Hung Yu, Yue-Bin Ke, Xin-Yun Xu, Xiao-Yan Ke…

    Journal of Clinical Bioinformatics 2014 4:15

    Published on: 5 December 2014

  4. Short report

    Analysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform

    Direct assessment of allelic phase for DNA and RNA features of diploid genomes has been challenging for Sanger sequencing, due to its allele-conflating base-calling signal. Massively parallel sequencing techno...

    Mercedeh Movassagh, Prakriti Mudvari, Maria Kokkinaki, Nathan J Edwards, Nady Golestaneh and Anelia Horvath

    Journal of Clinical Bioinformatics 2014 4:14

    Published on: 21 November 2014

  5. Research

    Extraction of echocardiographic data from the electronic medical record is a rapid and efficient method for study of cardiac structure and function

    Measures of cardiac structure and function are important human phenotypes that are associated with a range of clinical outcomes. Studying these traits in large populations can be time consuming and costly. Uti...

    Quinn S Wells, Eric Farber-Eger and Dana C Crawford

    Journal of Clinical Bioinformatics 2014 4:12

    Published on: 20 September 2014

  6. Research

    Interpretation for scales of measurement linking with abstract algebra

    The Stevens classification of levels of measurement involves four types of scale: “Nominal”, “Ordinal”, “Interval” and “Ratio”. This classification has been used widely in medical fields and has accomplished a...

    Jitsuki Sawamura, Shigeru Morishita and Jun Ishigooka

    Journal of Clinical Bioinformatics 2014 4:9

    Published on: 10 June 2014

  7. Methodology

    comoR: a software for disease comorbidity risk assessment

    The diagnosis of comorbidities, which refers to the coexistence of different acute and chronic diseases, is difficult due to the modern extreme specialisation of physicians. We envisage that a software dedicat...

    Mohammad Ali Moni and Pietro Liò

    Journal of Clinical Bioinformatics 2014 4:8

    Published on: 23 May 2014

  8. Research

    A novel molecular typing method of Mycobacteria based on DNA barcoding visualization

    Different subtypes of Mycobacterium tuberculosis (MTB) may induce diverse severe human infections, and some of their symptoms are similar to other pathogenes, e.g. Nontuberculosis mycobacteria (NTM). So determina...

    Bin Liu, Xiaotian Zhang, Honglan Huang, Ying Zhang, Fengfeng Zhou and Guoqing Wang

    Journal of Clinical Bioinformatics 2014 4:4

    Published on: 20 February 2014

  9. Research

    Development of detection method for novel fusion gene using GeneChip exon array

    Fusion genes have been recognized to play key roles in oncogenesis. Though, many techniques have been developed for genome-wide analysis of fusion genes, a more efficient method is desired.

    Yusaku Wada, Masaaki Matsuura, Minoru Sugawara, Masaru Ushijima, Satoshi Miyata, Koichi Nagasaki, Tetsuo Noda and Yoshio Miki

    Journal of Clinical Bioinformatics 2014 4:3

    Published on: 18 February 2014

  10. Research

    Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference

    Copy number alterations (CNAs) represent an important component of genetic variations. Such alterations are related with certain type of cancer including those of the pancreas, colon, and breast, among others....

    Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri and Marco Antoniotti

    Journal of Clinical Bioinformatics 2014 4:2

    Published on: 24 January 2014

  11. Methodology

    Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing

    The human body plays host to a vast array of bacteria, found in oral cavities, skin, gastrointestinal tract and the vagina. Some bacteria are harmful while others are beneficial to the host. Despite the availa...

    Chih-Min Chiu, Feng-Mao Lin, Tzu-Hao Chang, Wei-Chih Huang, Chao Liang, Ting Yang, Wei-Yun Wu, Tzu-Ling Yang, Shun-Long Weng and Hsien-Da Huang

    Journal of Clinical Bioinformatics 2014 4:1

    Published on: 13 January 2014

  12. Review

    Mathematical models for translational and clinical oncology

    In the context of translational and clinical oncology, mathematical models can provide novel insights into tumor-related processes and can support clinical oncologists in the design of the treatment regime, do...

    Ralf Gallasch, Mirjana Efremova, Pornpimol Charoentong, Hubert Hackl and Zlatko Trajanoski

    Journal of Clinical Bioinformatics 2013 3:23

    Published on: 7 November 2013

  13. Research

    In silicoanalysis of the molecular machinery underlying aqueous humor production: potential implications for glaucoma

    The ciliary body epithelia (CBE) of the eye produce the aqueous humor (AH). The equilibrium between the AH production by the CBE and the outflow through the trabecular meshwork ultimately determines the intrao...

    Sarah F Janssen, Theo GMF Gorgels, Peter J van der Spek, Nomdo M Jansonius and Arthur AB Bergen

    Journal of Clinical Bioinformatics 2013 3:21

    Published on: 28 October 2013

  14. Research

    A systematic analysis of a mi-RNA inter-pathway regulatory motif

    The continuing discovery of new types and functions of small non-coding RNAs is suggesting the presence of regulatory mechanisms far more complex than the ones currently used to study and design Gene Regulator...

    Stefano Di Carlo, Gianfranco Politano, Alessandro Savino and Alfredo Benso

    Journal of Clinical Bioinformatics 2013 3:20

    Published on: 24 October 2013

  15. Research

    Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks

    Large scale understanding of complex and dynamic alterations in cellular and subcellular levels during cancer in contrast to normal condition has facilitated the emergence of sophisticated systemic approaches ...

    Md Fahmid Islam, Md Moinul Hoque, Rajat Suvra Banik, Sanjoy Roy, Sharmin Sultana Sumi, F M Nazmul Hassan, Md Tauhid Siddiki Tomal, Ahmad Ullah and K M Taufiqur Rahman

    Journal of Clinical Bioinformatics 2013 3:19

    Published on: 6 October 2013

  16. Short report

    Using biomarkers to predict progression from clinically isolated syndrome to multiple sclerosis

    Detection of brain lesions disseminated in space and time by magnetic resonance imaging remains a cornerstone for the diagnosis of clinically definite multiple sclerosis. We have sought to determine if gene ex...

    John T Tossberg, Philip S Crooke, Melodie A Henderson, Subramaniam Sriram, Davit Mrelashvili, Saskia Vosslamber, Cor L Verweij, Nancy J Olsen and Thomas M Aune

    Journal of Clinical Bioinformatics 2013 3:18

    Published on: 3 October 2013

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