Volume 13 Supplement 8
The International Conference on Intelligent Biology and Medicine (ICIBM): Genomics
Research
Edited by Zhongming Zhao, Yufei Huang, Hua Xu, Bing Zhang and Yu Shyr
The conference was supported by a grant from National Science Foundation, USA (1141979) and financial support from the Center for Quantitative Sciences, Vanderbilt University. There was no sponsorship or other external funding for publication of the supplement.
The International Conference on Intelligent Biology and Medicine (ICIBM). Go to
conference site.
Nashville, TN, USA22-24 April 2012
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Content type: Introduction
We present a report of the 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) and the editorial report of the supplement to BMC Genomics that includes 22 research papers selected from ...
Authors: Zhongming Zhao, Yufei Huang, Bing Zhang, Yu Shyr and Hua Xu
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Content type: Research
While genome-wide association studies identified some promising candidates for schizophrenia, the majority of risk genes remained unknown. We were interested in testing whether integration gene expression and ...
Authors: Junzhe Xu, Jingchun Sun, Jingchun Chen, Lily Wang, Anna Li, Matthew Helm, Steven L Dubovsky, Silviu-Alin Bacanu, Zhongming Zhao and Xiangning Chen
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Content type: Research
High-throughput RNA interference (RNAi) screens have been used to find genes that, when silenced, result in sensitivity to certain chemotherapy drugs. Researchers therefore can further identify drug-sensitive ...
Authors: Fei Ye, Joshua A Bauer, Jennifer A Pietenpol and Yu Shyr
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Content type: Research
Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the...
Authors: Michael D Harwich Jr, Myrna G Serrano, Jennifer M Fettweis, João MP Alves, Mark A Reimers, Gregory A Buck and Kimberly K Jefferson
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Content type: Research
Histone modification plays an important role in cell differentiation and tissue development. A recent study has shown that the dimethylation of lysine 4 residue on histone 3 (H3K4me2) marks the gene body area ...
Authors: Jie Zhang, Jeffrey Parvin and Kun Huang
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Content type: Research
DNA methylation is an important epigenetic mark and dysregulation of DNA methylation is associated with many diseases including cancer. Advances in next-generation sequencing now allow unbiased methylome profi...
Authors: Michael P Trimarchi, Mark Murphy, David Frankhouser, Benjamin AT Rodriguez, John Curfman, Guido Marcucci, Pearlly Yan and Ralf Bundschuh
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Content type: Research
DNA methylation, which mainly occurs at CpG dinucleotides, is a dynamic epigenetic regulation mechanism in most eukaryotic genomes. It is already known that methylated CpG dinucleotides can lead to a high rate...
Authors: Junfeng Xia, Leng Han and Zhongming Zhao
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Content type: Research
Accurate calling of SNPs and genotypes from next-generation sequencing data is an essential prerequisite for most human genetics studies. A number of computational steps are required or recommended when transl...
Authors: Qi Liu, Yan Guo, Jiang Li, Jirong Long, Bing Zhang and Yu Shyr
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Content type: Research
RNA sequencing (RNA-seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignm...
Authors: Yuan Yuan, Clift Norris, Yanxun Xu, Kam-Wah Tsui, Yuan Ji and Han Liang
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Content type: Research
Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understan...
Authors: Ao Zhou, Marcus R Breese, Yangyang Hao, Howard J Edenberg, Lang Li, Todd C Skaar and Yunlong Liu
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Content type: Research
Differential expression detection for RNA-seq experiments is often biased by normalization algorithms due to their sensitivity to parametric assumptions on the gene count distributions, extreme values of gene ...
Authors: Hatice Gulcin Ozer, Jeffrey D Parvin and Kun Huang
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Content type: Research
Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount o...
Authors: Christina Schweikert, Stuart Brown, Zuojian Tang, Phillip R Smith and D Frank Hsu
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Content type: Research
MicroRNAs (miRNAs) are 19-25 nucleotides non-coding RNAs known to have important post-transcriptional regulatory functions. The computational target prediction algorithm is vital to effective experimental test...
Authors: Dong Yue, Maozu Guo, Yidong Chen and Yufei Huang
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Content type: Research
Hepatocellular carcinoma (HCC) is one of the most fatal cancers in the world, and metastasis is a significant cause to the high mortality in patients with HCC. However, the molecular mechanism behind HCC metas...
Authors: Lingyao Zeng, Jian Yu, Tao Huang, Huliang Jia, Qiongzhu Dong, Fei He, Weilan Yuan, Lunxiu Qin, Yixue Li and Lu Xie
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Content type: Research
Since the initial annotation of microRNAs (miRNAs) in 2001, many studies have sought to identify additional miRNAs experimentally or computationally in various species. MiRNAs act with the Argonaut family of p...
Authors: Linxia Wan, Jiandong Ding, Ting Jin, Jihong Guan and Shuigeng Zhou
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Content type: Research
A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to prod...
Authors: Zhongming Zhao, An-Yuan Guo, Edwin JCG van den Oord, Fazil Aliev, Peilin Jia, Howard J Edenberg, Brien P Riley, Danielle M Dick, Jill C Bettinger, Andrew G Davies, Michael S Grotewiel, Marc A Schuckit, Arpana Agrawal, John Kramer, John I Nurnberger Jr, Kenneth S Kendler…
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Content type: Research
The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacteria...
Authors: Jennifer M Fettweis, Myrna G Serrano, Nihar U Sheth, Carly M Mayer, Abigail L Glascock, J Paul Brooks, Kimberly K Jefferson and Gregory A Buck
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Content type: Research
Identifying the location of transcription factor bindings is crucial to understand transcriptional regulation. Currently, Chromatin Immunoprecipitation followed with high-throughput Sequencing (ChIP-seq) is ab...
Authors: Yupeng He, Yizhe Zhang, Guangyong Zheng and Chaochun Wei
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Content type: Research
Detecting the borders between coding and non-coding regions is an essential step in the genome annotation. And information entropy measures are useful for describing the signals in genome sequence. However, th...
Authors: Suping Deng, Yixiang Shi, Liyun Yuan, Yixue Li and Guohui Ding
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Content type: Research
Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. ...
Authors: Jérôme Jourquin, Dexter Duncan, Zhiao Shi and Bing Zhang
