Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference |
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Authors: | Cava Claudia Zoppis Italo Gariboldi Manuela Castiglioni Isabella Mauri Giancarlo Antoniotti Marco |
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Affiliation: | 1. Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan 2. Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan 4. Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan 5. Mackay Medicine, Nursing and Management College, Taipei, Taiwan 6. Department of Medicine, Mackay Medical College, >New Taipei City, Taiwan 3. Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, 300, Taiwan
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Abstract: | Background 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 availability of many methods to identify bacteria, most of them are only applicable to specific and cultivable bacteria and are also tedious. Based on high throughput sequencing technology, this work derives 16S rRNA sequences of bacteria and analyzes probiotics and pathogens species. Results We constructed a database that recorded the species of probiotics and pathogens from literature, along with a modified Smith-Waterman algorithm for assigning the taxonomy of the sequenced 16S rRNA sequences. We also constructed a bacteria disease risk model for seven diseases based on 98 samples. Applicability of the proposed platform is demonstrated by collecting the microbiome in human gut of 13 samples. Conclusions The proposed platform provides a relatively easy means of identifying a certain amount of bacteria and their species (including uncultivable pathogens) for clinical microbiology applications. That is, detecting how probiotics and pathogens inhabit humans and how affect their health can significantly contribute to develop a diagnosis and treatment method. |
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