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  1. With the rapid development of biological technology, measurement of thousands of genes or SNPs can be carried out simultaneously. Improved procedures for multiple hypothesis testing when the number of tests is...

    Authors: Jiang Gui, Tor D Tosteson and Mark Borsuk

    Citation: BioData Mining 2012 5:4

    Content type: Review

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  2. Multifactor Dimensionality Reduction (MDR) is a popular and successful data mining method developed to characterize and detect nonlinear complex gene-gene interactions (epistasis) that are associated with dise...

    Authors: Hongying Dai, Madhusudan Bhandary, Mara Becker, J Steven Leeder, Roger Gaedigk and Alison A Motsinger-Reif

    Citation: BioData Mining 2012 5:3

    Content type: Methodology

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  3. Graph drawing is an integral part of many systems biology studies, enabling visual exploration and mining of large-scale biological networks. While a number of layout algorithms are available in popular networ...

    Authors: Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S Nevalainen and Tero Aittokallio

    Citation: BioData Mining 2012 5:2

    Content type: Research

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  4. Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that...

    Authors: Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Carolina Wanderley-Nogueira, Nina Mota Soares-Cavalcanti and Reinhard Schneider

    Citation: BioData Mining 2012 5:1

    Content type: Software article

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  5. Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their c...

    Authors: J Nikolaj Dybowski, Mona Riemenschneider, Sascha Hauke, Martin Pyka, Jens Verheyen, Daniel Hoffmann and Dominik Heider

    Citation: BioData Mining 2011 4:26

    Content type: Research

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  6. A goal of human genetics is to discover genetic factors that influence individuals' susceptibility to common diseases. Most common diseases are thought to result from the joint failure of two or more interacti...

    Authors: Daniel S Himmelstein, Casey S Greene and Jason H Moore

    Citation: BioData Mining 2011 4:21

    Content type: Methodology

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    The Erratum to this article has been published in BioData Mining 2016 9:9

  7. One important concept in traditional Chinese medicine (TCM) is "treating different diseases with the same therapy". In TCM practice, some patients with Rheumatoid Arthritis (RA) and some other patients with Co...

    Authors: Guang Zheng, Miao Jiang, Xiaojuan He, Jing Zhao, Hongtao Guo, Gao Chen, Qinglin Zha and Aiping Lu

    Citation: BioData Mining 2011 4:18

    Content type: Methodology

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  8. MicroRNAs (miRNAs) mediate posttranscriptional regulation of protein-coding genes by binding to the 3' untranslated region of target mRNAs, leading to translational inhibition, mRNA destabilization or degradat...

    Authors: Jun-ichi Satoh and Hiroko Tabunoki

    Citation: BioData Mining 2011 4:17

    Content type: Research

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  9. To make sense out of gene expression profiles, such analyses must be pushed beyond the mere listing of affected genes. For example, if a group of genes persistently display similar changes in expression levels...

    Authors: Pablo C Echeverría, Fedor Forafonov, Deo P Pandey, Guillaume Mühlebach and Didier Picard

    Citation: BioData Mining 2011 4:15

    Content type: Research

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  10. DNA methylation plays a very important role in the silencing of tumor suppressor genes in various tumor types. In order to gain a genome-wide understanding of how changes in methylation affect tumor growth, th...

    Authors: Shuying Sun, Yi-Wen Huang, Pearlly S Yan, Tim HM Huang and Shili Lin

    Citation: BioData Mining 2011 4:13

    Content type: Methodology

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  11. The ability to accurately classify cancer patients into risk classes, i.e. to predict the outcome of the pathology on an individual basis, is a key ingredient in making therapeutic decisions. In recent years g...

    Authors: Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Marco Antoniotti, Paolo Provero and Mario Giacobini

    Citation: BioData Mining 2011 4:12

    Content type: Research

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  12. Understanding complex systems often requires a bottom-up analysis towards a systems biology approach. The need to investigate a system, not only as individual components but as a whole, emerges. This can be do...

    Authors: Georgios A Pavlopoulos, Maria Secrier, Charalampos N Moschopoulos, Theodoros G Soldatos, Sophia Kossida, Jan Aerts, Reinhard Schneider and Pantelis G Bagos

    Citation: BioData Mining 2011 4:10

    Content type: Review

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  13. Copy number variants are >1 kb genomic amplifications or deletions that can be identified using array platforms. However, arrays produce substantial background noise that contributes to high false discovery ra...

    Authors: Britney L Grayson and Thomas M Aune

    Citation: BioData Mining 2011 4:8

    Content type: Methodology

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  14. Gene expression microarray data have been organized and made available as public databases, but the utilization of such highly heterogeneous reference datasets in the interpretation of data from individual tes...

    Authors: Sami K Kilpinen, Kalle A Ojala and Olli P Kallioniemi

    Citation: BioData Mining 2011 4:5

    Content type: Methodology

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  15. Several methods have been presented for the analysis of complex interactions between genetic polymorphisms and/or environmental factors. Despite the available methods, there is still a need for alternative met...

    Authors: Thorsten Lehr, Jing Yuan, Dirk Zeumer, Supriya Jayadev and Marylyn D Ritchie

    Citation: BioData Mining 2011 4:4

    Content type: Research

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  16. Measurements on gene level are widely used to gain new insights in complex diseases e.g. cancer. A promising approach to understand basic biological mechanisms is to combine gene expression profiles and classi...

    Authors: Christian W Martin, Anika Tauchen, Anke Becker and Tim W Nattkemper

    Citation: BioData Mining 2011 4:2

    Content type: Research

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  17. The present knowledge of protein structures at atomic level derives from some 60,000 molecules. Yet the exponential ever growing set of hypothetical protein sequences comprises some 10 million chains and this ...

    Authors: Marco Vassura, Pietro Di Lena, Luciano Margara, Maria Mirto, Giovanni Aloisio, Piero Fariselli and Rita Casadio

    Citation: BioData Mining 2011 4:1

    Content type: Research

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  18. Initial genome-wide association study (GWAS) discoveries are being further explored through the use of large cohorts across multiple and diverse populations involving meta-analyses within large consortia and n...

    Authors: Sarah A Pendergrass, Scott M Dudek, Dana C Crawford and Marylyn D Ritchie

    Citation: BioData Mining 2010 3:10

    Content type: Software article

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  19. A fundamental goal of human genetics is the discovery of polymorphisms that predict common, complex diseases. It is hypothesized that complex diseases are due to a myriad of factors including environmental exp...

    Authors: Alison A Motsinger-Reif, Sushamna Deodhar, Stacey J Winham and Nicholas E Hardison

    Citation: BioData Mining 2010 3:8

    Content type: Methodology

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  20. Growing interest and burgeoning technology for discovering genetic mechanisms that influence disease processes have ushered in a flood of genetic association studies over the last decade, yet little heritabili...

    Authors: Stephen D Turner, Scott M Dudek and Marylyn D Ritchie

    Citation: BioData Mining 2010 3:5

    Content type: Research

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  21. Massively parallel sequencing allows for genome-wide hypothesis-free investigation of for instance transcription factor binding sites or histone modifications. Although nucleotide resolution detailed informati...

    Authors: Stefan Enroth, Robin Andersson, Claes Wadelius and Jan Komorowski

    Citation: BioData Mining 2010 3:4

    Content type: Software article

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  22. Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological da...

    Authors: Rex T Nelson, Shulamit Avraham, Randy C Shoemaker, Gregory D May, Doreen Ware and Damian DG Gessler

    Citation: BioData Mining 2010 3:3

    Content type: Research

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  23. Affymetrix GeneChips utilize 25-mer oligonucleotides probes linked to a silica surface to detect targets in solution. Mismatches due to single nucleotide polymorphisms (SNPs) can affect the hybridization betwe...

    Authors: Fenghai Duan, Mark A Pauley, Eliot R Spindel, Li Zhang and Robert B Norgren Jr

    Citation: BioData Mining 2010 3:2

    Content type: Research

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  24. The quantities of data obtained by the new high-throughput technologies, such as microarrays or ChIP-Chip arrays, and the large-scale OMICS-approaches, such as genomics, proteomics and transcriptomics, are bec...

    Authors: Georgios A Pavlopoulos, Theodoros G Soldatos, Adriano Barbosa-Silva and Reinhard Schneider

    Citation: BioData Mining 2010 3:1

    Content type: Review

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  25. Protein families could be related to each other at broad levels that group them as superfamilies. These relationships are harder to detect at the sequence level due to high evolutionary divergence. Sequence se...

    Authors: Khader Shameer, Paramasivam Nagarajan, Kumar Gaurav and Ramanathan Sowdhamini

    Citation: BioData Mining 2009 2:8

    Content type: Research

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  26. Gene-centric analysis tools for genome-wide association study data are being developed both to annotate single locus statistics and to prioritize or group single nucleotide polymorphisms (SNPs) prior to analys...

    Authors: William S Bush, Guanhua Chen, Eric S Torstenson and Marylyn D Ritchie

    Citation: BioData Mining 2009 2:7

    Content type: Methodology

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  27. Genome-wide association studies are becoming the de facto standard in the genetic analysis of common human diseases. Given the complexity and robustness of biological networks such diseases are unlikely to be ...

    Authors: Casey S Greene, Nadia M Penrod, Jeff Kiralis and Jason H Moore

    Citation: BioData Mining 2009 2:5

    Content type: Methodology

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  28. Quality assessment methods, that are common place in engineering and industrial production, are not widely spread in large-scale proteomics experiments. But modern technologies such as Multi-Dimensional Liquid...

    Authors: Ole Schulz-Trieglaff, Egidijus Machtejevas, Knut Reinert, Hartmut Schlüter, Joachim Thiemann and Klaus Unger

    Citation: BioData Mining 2009 2:4

    Content type: Methodology

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  29. The fidelity of DNA replication serves as the nidus for both genetic evolution and genomic instability fostering disease. Single nucleotide polymorphisms (SNPs) constitute greater than 80% of the genetic varia...

    Authors: Eric Arehart, Scott Gleim, Bill White, John Hwa and Jason H Moore

    Citation: BioData Mining 2009 2:2

    Content type: Research

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