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Volume 10 Supplement 1

Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)

Research

Edited by Michael Q Zhang, Michael S Waterman and Xuegong Zhang

The Seventh Asia Pacific Bioinformatics Conference (APBC 2009). Go to conference site.

Beijing, China13-16 January 2009

Page 1 of 2

  2. The genome aliquoting probem is, given an observed genome A with n copies of each gene, presumed to descend from an n-way polyploidization event from an ordinary diploid genome B, followed by a history of chromos...

    Authors: Robert Warren and David Sankoff
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S2
    Content type: Research Published on:

  4. Generating sequence alignments from superimposed structures is an important part of many structure comparison programs. The accuracy of the alignment affects structure recognition, classification and possibly ...

    Authors: Chin-Hsien Tai, James J Vincent, Changhoon Kim and Byungkook Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S4
    Content type: Research Published on:

  5. With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite...

    Authors: Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty and Dong Xu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S5
    Content type: Research Published on:

  6. Given three signed permutations, an inversion median is a fourth permutation that minimizes the sum of the pairwise inversion distances between it and the three others. This problem is NP-hard as well as hard ...

    Authors: Krister M Swenson, Yokuki To, Jijun Tang and Bernard ME Moret
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S6
    Content type: Research Published on:

  7. Reconstructing complete ancestral genomes (at least in terms of their gene inventory and arrangement) is attracting much interest due to the rapidly increasing availability of whole genome sequences. While mod...

    Authors: Krister M Swenson and Bernard ME Moret
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S7
    Content type: Research Published on:

  8. There is much interest in developing fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlapping sets of taxa to make a comprehensive phylogene...

    Authors: Harris T Lin, J Gordon Burleigh and Oliver Eulenstein
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S8
    Content type: Research Published on:

  12. Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as ...

    Authors: Daniel H Huson, Daniel C Richter, Suparna Mitra, Alexander F Auch and Stephan C Schuster
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S12
    Content type: Research Published on:

  14. The de novo assembly of genomes and transcriptomes from short sequences is a challenging problem. Because of the high coverage needed to assemble short sequences as well as the overhead of modeling the assembly p...

    Authors: Benjamin G Jackson, Patrick S Schnable and Srinivas Aluru
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S14
    Content type: Research Published on:

  15. DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DN...

    Authors: Francis YL Chin, Henry CM Leung, Wei-Lin Li and Siu-Ming Yiu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S15
    Content type: Research Published on:

  16. New short-read sequencing technologies produce enormous volumes of 25–30 base paired-end reads. The resulting reads have vastly different characteristics than produced by Sanger sequencing, and require differe...

    Authors: Mohammad Sajjad Hossain, Navid Azimi and Steven Skiena
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S16
    Content type: Research Published on:

  17. The emerging next-generation sequencing method based on PCR technology boosts genome sequencing speed considerably, the expense is also get decreased. It has been utilized to address a broad range of bioinform...

    Authors: Wendi Wang, Peiheng Zhang and Xinchun Liu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S17
    Content type: Research Published on:

  18. Alternative splicing (AS) is an important regulatory mechanism for gene expression and protein diversity in eukaryotes. Previous studies have demonstrated that it can be causative for, or specific to splicing-...

    Authors: Hao Zheng, Xingyi Hang, Ji Zhu, Minping Qian, Wubin Qu, Chenggang Zhang and Minghua Deng
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S18
    Content type: Research Published on:

  19. Microarray gene expression profiling has provided extensive datasets that can describe characteristics of cancer patients. An important challenge for this type of data is the discovery of gene sets which can b...

    Authors: Md Rafiul Hassan, M Maruf Hossain, James Bailey, Geoff Macintyre, Joshua WK Ho and Kotagiri Ramamohanarao
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S19
    Content type: Research Published on:

  20. Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods h...

    Authors: Martin H van Vliet, Lodewyk FA Wessels and Marcel JT Reinders
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S20
    Content type: Research Published on:

  22. Most machine-learning classifiers output label predictions for new instances without indicating how reliable the predictions are. The applicability of these classifiers is limited in critical domains where inc...

    Authors: Fan Yang, Hua-zhen Wang, Hong Mi, Cheng-de Lin and Wei-wen Cai
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S22
    Content type: Research Published on:

  24. Gene expression microarray technologies are widely used across most areas of biological and medical research. Comparing and integrating microarray data from different experiments would be very useful, but is c...

    Authors: Reija Autio, Sami Kilpinen, Matti Saarela, Olli Kallioniemi, Sampsa Hautaniemi and Jaakko Astola
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S24
    Content type: Research Published on:

  25. Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generat...

    Authors: Chun-Chi Liu, Jianjun Hu, Mrinal Kalakrishnan, Haiyan Huang and Xianghong Jasmine Zhou
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S25
    Content type: Research Published on:

  26. Clustering analysis is a common statistical tool for knowledge discovery. It is mainly conducted when a project still is in the exploratory phase without any priori hypotheses. However, the statistical signifi...

    Authors: Wensheng Zhang, Hong-Bin Fang and Jiuzhou Song
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S26
    Content type: Research Published on:

  28. Posttranslational modifications of histones influence the structure of chromatine and in such a way take part in the regulation of gene expression. Certain histone modification patterns, distributed over the g...

    Authors: Corinna Kolářik, Roman Klinger and Martin Hofmann-Apitius
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S28
    Content type: Research Published on:

  29. A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region bet...

    Authors: Quan Wang, Lin Wan, Dayong Li, Lihuang Zhu, Minping Qian and Minghua Deng
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S29
    Content type: Research Published on:

  30. The detection of cis-regulatory modules (CRMs) that mediate transcriptional responses in eukaryotes remains a key challenge in the postgenomic era. A CRM is characterized by a set of co-occurring transcription fa...

    Authors: Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor and Kathleen Marchal
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S30
    Content type: Research Published on:

  31. Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucle...

    Authors: Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Yangyang Deng, Jiang Wang and Caisheng He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S31
    Content type: Research Published on:

  33. RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful technique for eukaryotic gene knockdown. siRNA GC-content negatively correlates with RNA...

    Authors: Chi Yu Chan, C Steven Carmack, Dang D Long, Anil Maliyekkel, Yu Shao, Igor B Roninson and Ye Ding
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S33
    Content type: Research Published on:

  34. MicroRNAs (miRNAs) are small and noncoding RNAs that play important roles in various biological processes. They regulate target mRNAs post-transcriptionally through complementary base pairing. Since the change...

    Authors: Je-Gun Joung and Zhangjun Fei
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S34
    Content type: Research Published on:

  35. MicroRNA s (miRNAs) are small non-coding single-stranded RNAs (20–23 nts) that are known to act as post-transcriptional and translational regulators of gene expression. Although, they were initially overlooked, t...

    Authors: Sabah Kadri, Veronica Hinman and Panayiotis V Benos
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S35
    Content type: Research Published on:

  36. Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using til...

    Authors: Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen and Tao Jiang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S36
    Content type: Research Published on:

  37. In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers o...

    Authors: Fei Xia, Yong Dou, Xingming Zhou, Xuejun Yang, Jiaqing Xu and Yang Zhang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S37
    Content type: Research Published on:

  39. The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-...

    Authors: Fenix WD Huang, Linda YM Li and Christian M Reidys
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S39
    Content type: Research Published on:

  40. Electron cryomicroscopy is a fast developing technique aiming at the determination of the 3-dimensional structures of large protein complexes. Using this technique, protein density maps can be generated with 6...

    Authors: Weitao Sun and Jing He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S40
    Content type: Research Published on:

  46. Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midn...

    Authors: Yi Jia, Jun Huan, Vincent Buhr, Jintao Zhang and Leonidas N Carayannopoulos
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S46
    Content type: Research Published on:

  47. Protein subcellular localization is concerned with predicting the location of a protein within a cell using computational method. The location information can indicate key functionalities of proteins. Accurate...

    Authors: Qian Xu, Derek Hao Hu, Hong Xue, Weichuan Yu and Qiang Yang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S47
    Content type: Research Published on:

  48. SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Underst...

    Authors: Krongsakda Phakthanakanok, Khanok Ratanakhanokchai, Khin Lay Kyu, Pornthep Sompornpisut, Aaron Watts and Surapong Pinitglang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S48
    Content type: Research Published on:

  50. Peptide identification via tandem mass spectrometry is the basic task of current proteomics research. Due to the complexity of mass spectra, the majority of mass spectra cannot be interpreted at present. The e...

    Authors: Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, Zuofei Yuan, Hao Chi, You Li, Liyun Xiu, Wenping Wang, Chao Liu, Leheng Wang, Ruixiang Sun, Wen Gao, Xiaohong Qian and Si-Min He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S50
    Content type: Research Published on:
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