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Volume 13 Supplement 1

Selected articles from the Tenth Asia Pacific Bioinformatics Conference (APBC 2012)


Edited by Yi-Ping Phoebe Chen and Peer Bork

The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). Go to conference site.

Melbourne, Australia17-19 January 2012

  1. Content type: Proceedings

    Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly being applied to study genome-wide binding sites of transcription factors. There is an increasing interest in...

    Authors: Hatice Ulku Osmanbeyoglu, Ryan J Hartmaier, Steffi Oesterreich and Xinghua Lu

    Citation: BMC Genomics 2012 13(Suppl 1):S1

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  2. Content type: Proceedings

    Sequence features in promoter regions are involved in regulating gene transcription initiation. Although numerous computational methods have been developed for predicting transcriptional start sites (TSSs) or ...

    Authors: Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Tzu-Hao Chang and Dray-Ming Shien

    Citation: BMC Genomics 2012 13(Suppl 1):S3

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  3. Content type: Proceedings

    Neglected tropical diseases, especially those caused by helminths, constitute some of the most common infections of the world's poorest people. Development of techniques for automated, high-throughput drug scr...

    Authors: Hyokyeong Lee, Asher Moody-Davis, Utsab Saha, Brian M Suzuki, Daniel Asarnow, Steven Chen, Michelle Arkin, Conor R Caffrey and Rahul Singh

    Citation: BMC Genomics 2012 13(Suppl 1):S4

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  4. Content type: Proceedings

    We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-...

    Authors: Narges Sharif Razavian, Hetunandan Kamisetty and Christopher J Langmead

    Citation: BMC Genomics 2012 13(Suppl 1):S5

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  5. Content type: Proceedings

    In the analysis of effects by cell treatment such as drug dosing, identifying changes on gene network structures between normal and treated cells is a key task. A possible way for identifying the changes is to...

    Authors: Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh and Satoru Miyano

    Citation: BMC Genomics 2012 13(Suppl 1):S6

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  6. Content type: Proceedings

    Inferring gene orders of ancestral genomes has the potential to provide detailed information about the recent evolution of species descended from them. Current popular tools to infer ancestral genome data (suc...

    Authors: Yiwei Zhang, Fei Hu and Jijun Tang

    Citation: BMC Genomics 2012 13(Suppl 1):S7

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  7. Content type: Proceedings

    Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversi...

    Authors: David Sankoff, Chunfang Zheng and Baoyong Wang

    Citation: BMC Genomics 2012 13(Suppl 1):S8

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  8. Content type: Proceedings

    Plant n on-s pecific l ipid t ransfer p roteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, partici...

    Authors: Nai-Jyuan Wang, Chi-Ching Lee, Chao-Sheng Cheng, Wei-Cheng Lo, Ya-Fen Yang, Ming-Nan Chen and Ping-Chiang Lyu

    Citation: BMC Genomics 2012 13(Suppl 1):S9

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  9. Content type: Proceedings

    Bayesian networks (BNs) have been widely used to estimate gene regulatory networks. Many BN methods have been developed to estimate networks from microarray data. However, two serious problems reduce the effec...

    Authors: Yukito Watanabe, Shigeto Seno, Yoichi Takenaka and Hideo Matsuda

    Citation: BMC Genomics 2012 13(Suppl 1):S12

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  10. Content type: Proceedings

    MicroRNAs (miRNAs) are small non-protein-coding RNAs. miRNA genes need several biogenesis steps to form function miRNAs. However, the precise mechanism and biology involved in the mature miRNA molecules are no...

    Authors: Sung-Chou Li, Yu-Lun Liao, Meng-Ru Ho, Kuo-Wang Tsai, Chun-Hung Lai and Wen-chang Lin

    Citation: BMC Genomics 2012 13(Suppl 1):S13

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  11. Content type: Proceedings

    Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization f...

    Authors: Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma and Dan Zou

    Citation: BMC Genomics 2012 13(Suppl 1):S14

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  12. Content type: Proceedings

    Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics,...

    Authors: Trupti Joshi, Kapil Patil, Michael R Fitzpatrick, Levi D Franklin, Qiuming Yao, Jeffrey R Cook, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry T Nguyen and Dong Xu

    Citation: BMC Genomics 2012 13(Suppl 1):S15

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