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Volume 17 Supplement 7

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2015: genomics

Research

Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.

Indianapolis, IN, USA13-15 November 2015

Edited by Kun Huang, Yunlong Liu, Yufei Huang, Lang Li, Lee Cooper, Jianhua Ruan and Zhongming Zhao.

Related articles have been published in a supplement to BMC Systems Biology.

  1. Content type: Introduction

    We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected...

    Authors: Kun Huang, Yunlong Liu, Yufei Huang, Lang Li, Lee Cooper, Jianhua Ruan and Zhongming Zhao

    Citation: BMC Genomics 2016 17(Suppl 7):524

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  2. Content type: Research

    Ion Torrent and Ion Proton are semiconductor-based sequencing technologies that feature rapid sequencing speed and low upfront and operating costs, thanks to the avoidance of modified nucleotides and optical m...

    Authors: Weixing Feng, Sen Zhao, Dingkai Xue, Fengfei Song, Ziwei Li, Duojiao Chen, Bo He, Yangyang Hao, Yadong Wang and Yunlong Liu

    Citation: BMC Genomics 2016 17(Suppl 7):521

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  4. Content type: Research

    Most existing tools for detecting next-generation sequencing-based splicing events focus on generic splicing events. Consequently, special types of non-canonical splicing events of short mRNA regions (IRE1α ta...

    Authors: Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin R. Hassler and Randal J. Kaufman

    Citation: BMC Genomics 2016 17(Suppl 7):503

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  6. Content type: Research

    Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular responses. LPS pre-conditioning was previously shown to improve the therapeutic efficacy of bone marrow stromal ...

    Authors: Ao Zhou, Meng Li, Bo He, Weixing Feng, Fei Huang, Bing Xu, A. Keith Dunker, Curt Balch, Baiyan Li, Yunlong Liu and Yue Wang

    Citation: BMC Genomics 2016 17(Suppl 7):509

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  8. Content type: Research

    We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated...

    Authors: Chandirasegaran Massilamany, Akram Mohammed, John Dustin Loy, Tanya Purvis, Bharathi Krishnan, Rakesh H. Basavalingappa, Christy M. Kelley, Chittibabu Guda, Raúl G. Barletta, Etsuko N. Moriyama, Timothy P. L. Smith and Jay Reddy

    Citation: BMC Genomics 2016 17(Suppl 7):511

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  9. Content type: Research

    The objective of this research was to investigate the variation of gene expression in the blood transcriptome profile of Chinese Holstein cows associated to the milk yield traits.

    Authors: Xue Bai, Zhuqing Zheng, Bin Liu, Xiaoyang Ji, Yongsheng Bai and Wenguang Zhang

    Citation: BMC Genomics 2016 17(Suppl 7):512

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  10. Content type: Research

    Somatic mutations can be used as potential biomarkers for subtyping and predicting outcomes for cancer patients. However, cancer patients often carry many somatic mutations, which do not always concentrate on ...

    Authors: Jie Zhang, Zachary Abrams, Jeffrey D. Parvin and Kun Huang

    Citation: BMC Genomics 2016 17(Suppl 7):513

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  11. Content type: Research

    We considered the prediction of cancer classes (e.g. subtypes) using patient gene expression profiles that contain both systematic and condition-specific biases when compared with the training reference datase...

    Authors: Chifeng Ma, Konduru S. Sastry, Mario Flore, Salah Gehani, Issam Al-Bozom, Yusheng Feng, Erchin Serpedin, Lotfi Chouchane, Yidong Chen and Yufei Huang

    Citation: BMC Genomics 2016 17(Suppl 7):549

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  13. Content type: Research

    Sensitive detection of low-frequency single nucleotide variants carries great significance in many applications. In cancer genetics research, tumor biopsies are a mixture of normal and tumor cells from various...

    Authors: Yangyang Hao, Pengyue Zhang, Xiaoling Xuei, Harikrishna Nakshatri, Howard J. Edenberg, Lang Li and Yunlong Liu

    Citation: BMC Genomics 2016 17(Suppl 7):514

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  14. Content type: Research

    Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer. Recent large-scale next-generation sequencing analyses reveal that PBRM1 is the second most frequently mutated gene harboring many...

    Authors: Yuanyuan Wang, Xingyi Guo, Michael J. Bray, Zhiyong Ding and Zhongming Zhao

    Citation: BMC Genomics 2016 17(Suppl 7):515

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    The Erratum to this article has been published in BMC Genomics 2016 17:821

  16. Content type: Research

    Glioblastoma (GBM) is the most common and aggressive brain tumors. It has poor prognosis even with optimal radio- and chemo-therapies. Since GBM is highly heterogeneous, drugs that target on specific molecular...

    Authors: Yang Chen, Zhen Gao, Bingcheng Wang and Rong Xu

    Citation: BMC Genomics 2016 17(Suppl 7):516

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  17. Content type: Research

    In combination with gene expression profiles, the protein interaction network (PIN) constructs a dynamic network that includes multiple functional modules. Previous studies have demonstrated that rifampin can ...

    Authors: Jin Li, Ying Wang, Lei Wang, Xuefeng Dai, Wang Cong, Weixing Feng, Chengzhen Xu, Yulin Deng, Yue Wang, Todd C. Skaar, Hong Liang and Yunlong Liu

    Citation: BMC Genomics 2016 17(Suppl 7):517

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  19. Content type: Research

    Proper cell models for breast cancer primary tumors have long been the focal point in the cancer’s research. The genomic comparison between cell lines and tumors can investigate the similarity and dissimilarit...

    Authors: Guanglong Jiang, Shijun Zhang, Aida Yazdanparast, Meng Li, Aniruddha Vikram Pawar, Yunlong Liu, Sai Mounika Inavolu and Lijun Cheng

    Citation: BMC Genomics 2016 17(Suppl 7):525

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  20. Content type: Research

     Gene co-expression network analysis (GCNA) is widely adopted in bioinformatics and biomedical research with applications such as gene function prediction, protein-protein interaction inference, disease marker...

    Authors: Zhi Han, Jie Zhang, Guoyuan Sun, Gang Liu and Kun Huang

    Citation: BMC Genomics 2016 17(Suppl 7):519

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  21. Content type: Research

    The recent advent of the state-of-art high throughput sequencing technology, known as Methylated RNA Immunoprecipitation combined with RNA sequencing (MeRIP-seq) revolutionizes the area of mRNA epigenetics and...

    Authors: Xiaodong Cui, Jia Meng, Shaowu Zhang, Manjeet K. Rao, Yidong Chen and Yufei Huang

    Citation: BMC Genomics 2016 17(Suppl 7):520

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