Volume 10, supplement issue 1, January 2009
Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)
- Issue editors
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- Michael Q Zhang
- Michael S Waterman
- Xuegong Zhang
75 articles in this issue
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Genome aliquoting with double cut and join
Authors
- Robert Warren
- David Sankoff
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S2
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Pathogenic Bacillus anthracis in the progressive gene losses and gains in adaptive evolution
Authors
- GX Yu
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S3
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SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
Authors (first, second and last of 4)
- Chin-Hsien Tai
- James J Vincent
- Byungkook Lee
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S4
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ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets
Authors (first, second and last of 5)
- Guan Ning Lin
- Zhipeng Cai
- Dong Xu
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S5
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Maximum independent sets of commuting and noninterfering inversions
Authors (first, second and last of 4)
- Krister M Swenson
- Yokuki To
- Bernard ME Moret
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S6
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Inversion-based genomic signatures
Authors
- Krister M Swenson
- Bernard ME Moret
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S7
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Triplet supertree heuristics for the tree of life
Authors
- Harris T Lin
- J Gordon Burleigh
- Oliver Eulenstein
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S8
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Sorting by reversals, block interchanges, tandem duplications, and deletions
Authors
- Martin Bader
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S9
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Improved algorithms for approximate string matching (extended abstract)
Authors
- Dimitris Papamichail
- Georgios Papamichail
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S10
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Simultaneous phylogeny reconstruction and multiple sequence alignment
Authors
- Feng Yue
- Jian Shi
- Jijun Tang
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S11
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Methods for comparative metagenomics
Authors (first, second and last of 5)
- Daniel H Huson
- Daniel C Richter
- Stephan C Schuster
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S12
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DNA motif alignment by evolving a population of Markov chains
Authors
- Chengpeng Bi
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S13
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Parallel short sequence assembly of transcriptomes
Authors
- Benjamin G Jackson
- Patrick S Schnable
- Srinivas Aluru
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S14
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Finding optimal threshold for correction error reads in DNA assembling
Authors (first, second and last of 4)
- Francis YL Chin
- Henry CM Leung
- Siu-Ming Yiu
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S15
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Crystallizing short-read assemblies around seeds
Authors
- Mohammad Sajjad Hossain
- Navid Azimi
- Steven Skiena
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S16
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Short read DNA fragment anchoring algorithm
Authors
- Wendi Wang
- Peiheng Zhang
- Xinchun Liu
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S17
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REMAS: a new regression model to identify alternative splicing events from exon array data
Authors (first, second and last of 7)
- Hao Zheng
- Xingyi Hang
- Minghua Deng
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S18
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A voting approach to identify a small number of highly predictive genes using multiple classifiers
Authors (first, second and last of 6)
- Md Rafiul Hassan
- M Maruf Hossain
- Kotagiri Ramamohanarao
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S19
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Knowledge driven decomposition of tumor expression profiles
Authors
- Martin H van Vliet
- Lodewyk FA Wessels
- Marcel JT Reinders
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S20
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Network-based support vector machine for classification of microarray samples
Authors
- Yanni Zhu
- Xiaotong Shen
- Wei Pan
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S21
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Using random forest for reliable classification and cost-sensitive learning for medical diagnosis
Authors (first, second and last of 5)
- Fan Yang
- Hua-zhen Wang
- Wei-wen Cai
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S22
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A statistical framework for integrating two microarray data sets in differential expression analysis
Authors
- Yinglei Lai
- Sarah E Eckenrode
- Jin-Xiong She
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S23
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Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations
Authors (first, second and last of 6)
- Reija Autio
- Sami Kilpinen
- Jaakko Astola
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S24
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Integrative disease classification based on cross-platform microarray data
Authors (first, second and last of 5)
- Chun-Chi Liu
- Jianjun Hu
- Xianghong Jasmine Zhou
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S25
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Principal component tests: applied to temporal gene expression data
Authors
- Wensheng Zhang
- Hong-Bin Fang
- Jiuzhou Song
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S26
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Biclustering of gene expression data using reactive greedy randomized adaptive search procedure
Authors
- Smitha Dharan
- Achuthsankar S Nair
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S27
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Identification of histone modifications in biomedical text for supporting epigenomic research
Authors
- Corinna Kolářik
- Roman Klinger
- Martin Hofmann-Apitius
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S28
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Searching for bidirectional promoters in Arabidopsis thaliana
Authors (first, second and last of 6)
- Quan Wang
- Lin Wan
- Minghua Deng
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S29
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ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules
Authors (first, second and last of 9)
- Hong Sun
- Tijl De Bie
- Kathleen Marchal
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S30
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Transcriptional interaction-assisted identification of dynamic nucleosome positioning
Authors (first, second and last of 7)
- Zhiming Dai
- Xianhua Dai
- Caisheng He
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S31
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Predicting microRNA targets in time-series microarray experiments via functional data analysis
Authors
- Brian J Parker
- Jiayu Wen
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S32
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A structural interpretation of the effect of GC-content on efficiency of RNA interference
Authors (first, second and last of 7)
- Chi Yu Chan
- C Steven Carmack
- Ye Ding
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S33
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Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information
Authors
- Je-Gun Joung
- Zhangjun Fei
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S34
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HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models
Authors
- Sabah Kadri
- Veronica Hinman
- Panayiotis V Benos
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S35
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Computational prediction of novel non-coding RNAs in Arabidopsis thaliana
Authors (first, second and last of 8)
- Dandan Song
- Yang Yang
- Tao Jiang
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S36
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Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA
Authors (first, second and last of 6)
- Fei Xia
- Yong Dou
- Yang Zhang
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S37
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Prediction of RNA secondary structure with pseudoknots using integer programming
Authors
- Unyanee Poolsap
- Yuki Kato
- Tatsuya Akutsu
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S38
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Sequence-structure relations of pseudoknot RNA
Authors
- Fenix WD Huang
- Linda YM Li
- Christian M Reidys
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S39
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Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures
Authors
- Weitao Sun
- Jing He
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S40
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Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses
Authors
- Jhang-Wei Huang
- Chwan-Chuen King
- Jinn-Moon Yang
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S41
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Predicting disordered regions in proteins using the profiles of amino acid indices
Authors
- Pengfei Han
- Xiuzhen Zhang
- Zhi-Ping Feng
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S42
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A method to improve protein subcellular localization prediction by integrating various biological data sources
Authors
- Thai Quang Tung
- Doheon Lee
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S43
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Studying the unfolding process of protein G and protein L under physical property space
Authors (first, second and last of 4)
- Liling Zhao
- Jihua Wang
- Zanxia Cao
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S44
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Prediction of amyloid fibril-forming segments based on a support vector machine
Authors (first, second and last of 4)
- Jian Tian
- Ningfeng Wu
- Yunliu Fan
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S45
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Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity
Authors (first, second and last of 5)
- Yi Jia
- Jun Huan
- Leonidas N Carayannopoulos
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S46
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Semi-supervised protein subcellular localization
Authors (first, second and last of 5)
- Qian Xu
- Derek Hao Hu
- Qiang Yang
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S47
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A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism
Authors (first, second and last of 6)
- Krongsakda Phakthanakanok
- Khanok Ratanakhanokchai
- Surapong Pinitglang
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S48
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Quality assessment of tandem mass spectra using support vector machine (SVM)
Authors (first, second and last of 4)
- An-Min Zou
- Fang-Xiang Wu
- Guy G Poirier
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S49
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Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences
Authors (first, second and last of 15)
- Yan Fu
- Wei Jia
- Si-Min He
- Content type: Research
- Open Access
- Published: 30 January 2009
- Article: S50