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, USA

22-24 April 2012

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  1. Research

    RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia

    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 ...

    Junzhe Xu, Jingchun Sun, Jingchun Chen, Lily Wang, Anna Li, Matthew Helm, Steven L Dubovsky, Silviu-Alin Bacanu, Zhongming Zhao and Xiangning Chen

    BMC Genomics 2012 13(Suppl 8):S2

    Published on: 17 December 2012

  2. Research

    Analysis of high-throughput RNAi screening data in identifying genes mediating sensitivity to chemotherapeutic drugs: statistical approaches and perspectives

    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 ...

    Fei Ye, Joshua A Bauer, Jennifer A Pietenpol and Yu Shyr

    BMC Genomics 2012 13(Suppl 8):S3

    Published on: 17 December 2012

  3. Research

    Genomic sequence analysis and characterization of Sneathia amnii sp. nov

    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...

    Michael D Harwich, Myrna G Serrano, Jennifer M Fettweis, João MP Alves, Mark A Reimers, Gregory A Buck and Kimberly K Jefferson

    BMC Genomics 2012 13(Suppl 8):S4

    Published on: 17 December 2012

  4. Research

    Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes

    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...

    Michael P Trimarchi, Mark Murphy, David Frankhouser, Benjamin AT Rodriguez, John Curfman, Guido Marcucci, Pearlly Yan and Ralf Bundschuh

    BMC Genomics 2012 13(Suppl 8):S6

    Published on: 17 December 2012

  5. Research

    Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data

    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...

    Ao Zhou, Marcus R Breese, Yangyang Hao, Howard J Edenberg, Lang Li, Todd C Skaar and Yunlong Liu

    BMC Genomics 2012 13(Suppl 8):S10

    Published on: 17 December 2012

  6. Research

    DFI: gene feature discovery in RNA-seq experiments from multiple sources

    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 ...

    Hatice Gulcin Ozer, Jeffrey D Parvin and Kun Huang

    BMC Genomics 2012 13(Suppl 8):S11

    Published on: 17 December 2012

  7. Research

    Combining multiple ChIP-seq peak detection systems using combinatorial fusion

    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...

    Christina Schweikert, Stuart Brown, Zuojian Tang, Phillip R Smith and D Frank Hsu

    BMC Genomics 2012 13(Suppl 8):S12

    Published on: 17 December 2012

  8. Research

    A Bayesian decision fusion approach for microRNA target prediction

    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...

    Dong Yue, Maozu Guo, Yidong Chen and Yufei Huang

    BMC Genomics 2012 13(Suppl 8):S13

    Published on: 17 December 2012

  9. Research

    Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma

    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...

    Lingyao Zeng, Jian Yu, Tao Huang, Huliang Jia, Qiongzhu Dong, Fei He, Weilan Yuan, Lunxiu Qin, Yixue Li and Lu Xie

    BMC Genomics 2012 13(Suppl 8):S14

    Published on: 17 December 2012

  10. Research

    Automatically clustering large-scale miRNA sequences: methods and experiments

    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...

    Linxia Wan, Jiandong Ding, Ting Jin, Jihong Guan and Shuigeng Zhou

    BMC Genomics 2012 13(Suppl 8):S15

    Published on: 17 December 2012

  11. Research

    Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study

    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...

    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, Kenneth S Kendler…

    BMC Genomics 2012 13(Suppl 8):S16

    Published on: 17 December 2012

  12. Research

    Species-level classification of the vaginal microbiome

    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...

    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

    BMC Genomics 2012 13(Suppl 8):S17

    Published on: 17 December 2012

  13. Research

    CTF: a CRF-based transcription factor binding sites finding system

    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...

    Yupeng He, Yizhe Zhang, Guangyong Zheng and Chaochun Wei

    BMC Genomics 2012 13(Suppl 8):S18

    Published on: 17 December 2012

  14. Research

    Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics

    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...

    Suping Deng, Yixiang Shi, Liyun Yuan, Yixue Li and Guohui Ding

    BMC Genomics 2012 13(Suppl 8):S19

    Published on: 17 December 2012

  15. Research

    GLAD4U: deriving and prioritizing gene lists from PubMed literature

    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. ...

    Jérôme Jourquin, Dexter Duncan, Zhiao Shi and Bing Zhang

    BMC Genomics 2012 13(Suppl 8):S20

    Published on: 17 December 2012

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 The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Axios Review or Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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