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Volume 12 Supplement 1

Selected articles from the Ninth Asia Pacific Bioinformatics Conference (APBC 2011)

Research

Edited by Yi-Ping Phoebe Chen and Kwang-Hyun Cho

The Ninth Asia Pacific Bioinformatics Conference (APBC 2011). Go to conference site.

Inchon, Korea11-14 January 2011

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  3. Peptide identification from tandem mass spectrometry (MS/MS) data is one of the most important problems in computational proteomics. This technique relies heavily on the accurate assessment of the quality of p...

    Authors: Zengyou He, Hongyu Zhao and Weichuan Yu
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S2
    Content type: Research Published on:

  5. We present a data structure enabling rapid heuristic solution to the ancestral genome reconstruction problem for given phylogenies under genomic rearrangement metrics. The efficiency of the greedy algorithm is...

    Authors: Chunfang Zheng and David Sankoff
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S4
    Content type: Research Published on:

  7. Ancestral Recombinations Graph (ARG) is a phylogenetic structure that encodes both duplication events, such as mutations, as well as genetic exchange events, such as recombinations: this captures the (genetic)...

    Authors: Laxmi Parida, Pier Francesco Palamara and Asif Javed
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S6
    Content type: Research Published on:

  10. Un-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequ...

    Authors: Sung-Chou Li, Wen-Ching Chan, Chun-Hung Lai, Kuo-Wang Tsai, Chun-Nan Hsu, Yuh-Shan Jou, Hua-Chien Chen, Chun-Hong Chen and Wen-chang Lin
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S9
    Content type: Research Published on:

  11. Complex diseases are commonly caused by multiple genes and their interactions with each other. Genome-wide association (GWA) studies provide us the opportunity to capture those disease associated genes and gen...

    Authors: Pengyi Yang, Joshua WK Ho, Yee Hwa Yang and Bing B Zhou
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S10
    Content type: Research Published on:

  12. The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated gr...

    Authors: Wangshu Zhang, Fengzhu Sun and Rui Jiang
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S11
    Content type: Research Published on:

  13. Determining the disulfide (S-S) bond pattern in a protein is often crucial for understanding its structure and function. In recent research, mass spectrometry (MS) based analysis has been applied to this probl...

    Authors: William Murad, Rahul Singh and Ten-Yang Yen
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S12
    Content type: Research Published on:

  14. Measuring similarities between tree structured data is important for analysis of RNA secondary structures, phylogenetic trees, glycan structures, and vascular trees. The edit distance is one of the most widely...

    Authors: Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S13
    Content type: Research Published on:

  15. The gene duplication (GD) problem seeks a species tree that implies the fewest gene duplication events across a given collection of gene trees. Solving this problem makes it possible to use large gene families...

    Authors: Wen-Chieh Chang, Gordon J Burleigh, David F Fernández-Baca and Oliver Eulenstein
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S14
    Content type: Research Published on:

  16. The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based ...

    Authors: Pawel Górecki, Gordon J Burleigh and Oliver Eulenstein
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S15
    Content type: Research Published on:

  18. Signal transduction is the major mechanism through which cells transmit external stimuli to evoke intracellular biochemical responses. Understanding relationship between external stimuli and corresponding cell...

    Authors: Chu Chun Kang, Yung Jen Chuang, Kai Che Tung, Chun Cheih Chao, Chuan Yi Tang, Shih Chi Peng and David Shan Hill Wong
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S17
    Content type: Research Published on:

  20. Human immunodeficiency virus type one (HIV-1) is the major pathogen that causes the acquired immune deficiency syndrome (AIDS). With the availability of large-scale protein-protein interaction (PPI) measuremen...

    Authors: Xiaoning Qian and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S19
    Content type: Research Published on:

  22. Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the num...

    Authors: Suparna Mitra, Paul Rupek, Daniel C Richter, Tim Urich, Jack A Gilbert, Folker Meyer, Andreas Wilke and Daniel H Huson
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S21
    Content type: Research Published on:

  23. Phosphorylation motifs represent common patterns around the phosphorylation site. The discovery of such kinds of motifs reveals the underlying regulation mechanism and facilitates the prediction of unknown pho...

    Authors: Zengyou He, Can Yang, Guangyu Guo, Ning Li and Weichuan Yu
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S22
    Content type: Research Published on:

  25. Humans are diploid, carrying two copies of each chromosome, one from each parent. Separating the paternal and maternal chromosomes is an important component of genetic analyses such as determining genetic asso...

    Authors: Christine Lo, Ali Bashir, Vikas Bansal and Vineet Bafna
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S24
    Content type: Research Published on:

  26. Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways o...

    Authors: Kyoohyoung Rho, Bumjin Kim, Youngjun Jang, Sanghyun Lee, Taejeong Bae, Jihae Seo, Chaehwa Seo, Jihyun Lee, Hyunjung Kang, Ungsik Yu, Sunghoon Kim, Sanghyuk Lee and Wan Kyu Kim
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S25
    Content type: Research Published on:

  27. In genome-wide association studies (GWAS), the number of single-nucleotide polymorphisms (SNPs) typically ranges between 500,000 and 1,000,000. Accordingly, detecting gene-gene interactions in GWAS is computat...

    Authors: Can Yang, Xiang Wan, Zengyou He, Qiang Yang, Hong Xue and Weichuan Yu
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S26
    Content type: Research Published on:

  29. Beta-site amyloid precursor protein cleaving enzyme (BACE-1) is a single-membrane protein belongs to the aspartyl protease class of catabolic enzymes. This enzyme involved in the processing of the amyloid prec...

    Authors: Shalini John, Sundarapandian Thangapandian, Sugunadevi Sakkiah and Keun Woo Lee
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S28
    Content type: Research Published on:

  30. The differentiation process from stem cells to fully differentiated cell types is controlled by the interplay of chromatin modifications and transcription factor activity. Histone modifications or transcriptio...

    Authors: Ivan G Costa, Helge G Roider, Thais G do Rego and Francisco de AT de Carvalho
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S29
    Content type: Research Published on:

  31. HSPs (Heat shock proteins) are highly conserved ubiquitous proteins among species which are involved in maintaining appropriate folding and conformation of other proteins and are thus referred to as molecular ...

    Authors: Abhinav Grover, Ashutosh Shandilya, Vibhuti Agrawal, Piyush Pratik, Divya Bhasme, Virendra S Bisaria and Durai Sundar
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S30
    Content type: Research Published on:

  33. A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with s...

    Authors: Yi-Zhong Weng, Darby Tien-Hao Chang, Yu-Feng Huang and Chih-Wei Lin
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S32
    Content type: Research Published on:

  34. Pharmacological interactions are useful for understanding ligand binding mechanisms of a therapeutic target. These interactions are often inferred from a set of active compounds that were acquired experimental...

    Authors: Kai-Cheng Hsu, Yen-Fu Chen, Shen-Rong Lin and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S33
    Content type: Research Published on:

  35. Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to ...

    Authors: Igor Chikalov, Peggy Yao, Mikhail Moshkov and Jean-Claude Latombe
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S34
    Content type: Research Published on:

  36. A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly ...

    Authors: Maxim Totrov
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S35
    Content type: Research Published on:

  37. Metabolite profiles can be used for identifying molecular signatures and mechanisms underlying diseases since they reflect the outcome of complex upstream genomic, transcriptomic, proteomic and environmental e...

    Authors: Gang Su, Charles F Burant, Christopher W Beecher, Brian D Athey and Fan Meng
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S36
    Content type: Research Published on:

  38. With the availability of large scale expression compendia it is now possible to view own findings in the light of what is already available and retrieve genes with an expression profile similar to a set of gen...

    Authors: Hui Zhao, Lore Cloots, Tim Van den Bulcke, Yan Wu, Riet De Smet, Valerie Storms, Pieter Meysman, Kristof Engelen and Kathleen Marchal
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S37
    Content type: Research Published on:

  40. Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the y...

    Authors: Hiroyuki Monji, Satoshi Koizumi, Tomonobu Ozaki and Takenao Ohkawa
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S39
    Content type: Research Published on:

  41. The Gene Ontology (GO) provides a controlled vocabulary for describing genes and gene products. In spite of the undoubted importance of GO, several drawbacks associated with GO and GO-based annotations have be...

    Authors: Yu Rang Park, Jihun Kim, Hye Won Lee, Young Jo Yoon and Ju Han Kim
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S40
    Content type: Research Published on:

  42. MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression at the post-transcriptional level. Recent studies have suggested that miRNAs and transcription factors are primary metazoan gene regulat...

    Authors: Cho-Yi Chen, Shui-Tein Chen, Chiou-Shann Fuh, Hsueh-Fen Juan and Hsuan-Cheng Huang
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S41
    Content type: Research Published on:

  43. In recent years, information about protein structure and function is described in a large amount of articles. However, a naive full-text search by specific keywords often fails to find desired articles, becaus...

    Authors: Riku Kyogoku, Ryo Fujimoto, Tomonobu Ozaki and Takenao Ohkawa
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S42
    Content type: Research Published on:

  44. HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure...

    Authors: Sanmin Liu, Lantao Liu, Ugur Uzuner, Xin Zhou, Manxi Gu, Weibing Shi, Yixiang Zhang, Susie Y Dai and Joshua S Yuan
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S43
    Content type: Research Published on:

  47. Protein quantification is an essential step in many proteomics experiments. A number of labeling approaches have been proposed and adopted in mass spectrometry (MS) based relative quantification. The mTRAQ, on...

    Authors: Joo Young Yoon, Jeonghun Yeom, Heebum Lee, Kyutae Kim, Seungjin Na, Kunsoo Park, Eunok Paek and Cheolju Lee
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S46
    Content type: Research Published on:

  48. Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical proper...

    Authors: Hui-Lin Huang, I-Che Lin, Yi-Fan Liou, Chia-Ta Tsai, Kai-Ti Hsu, Wen-Lin Huang, Shinn-Jang Ho and Shinn-Ying Ho
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S47
    Content type: Research Published on:

  49. Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several hierarchical clustering methods have been developed using similarity measures based on ...

    Authors: Yutaka Saito, Kengo Sato and Yasubumi Sakakibara
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S48
    Content type: Research Published on:
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