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Volume 11 Supplement 1

Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

Research

Edited by Laxmi Parida and Gene Myers

The Eighth Asia Pacific Bioinformatics Conference (APBC 2010). Go to conference site.

Bangalore, India18-21 January 2010

Page 1 of 2

  3. MicroRNAs (miRNAs) play an essential task in gene regulatory networks by inhibiting the expression of target mRNAs. As their mRNA targets are genes involved in important cell functions, there is a growing inte...

    Authors: Vinod Chandra, Reshmi Girijadevi, Achuthsankar S Nair, Sreenadhan S Pillai and Radhakrishna M Pillai
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S2
    Content type: Research Published on:

  6. Feature selection techniques are critical to the analysis of high dimensional datasets. This is especially true in gene selection from microarray data which are commonly with extremely high feature-to-sample r...

    Authors: Pengyi Yang, Bing B Zhou, Zili Zhang and Albert Y Zomaya
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S5
    Content type: Research Published on:

  7. In supervised learning, traditional approaches to building a classifier use two sets of examples with pre-defined classes along with a learning algorithm. The main limitation of this approach is that examples fro...

    Authors: Nitin Bhardwaj, Mark Gerstein and Hui Lu
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S6
    Content type: Research Published on:

  8. Defensins comprise a group of antimicrobial peptides, widely recognized as important elements of the innate immune system in both animals and plants. Cationicity, rather than the secondary structure, is believ...

    Authors: Soja Saghar Soman, Krishnankutty Chandrika Sivakumar and Easwaran Sreekumar
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S7
    Content type: Research Published on:

  9. The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcr...

    Authors: Junhee Seok, Amit Kaushal, Ronald W Davis and Wenzhong Xiao
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S8
    Content type: Research Published on:

  10. Prediction of protein structural classes (α, β, α + β and α/β) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. Many methods have been ...

    Authors: Jian-Yi Yang, Zhen-Ling Peng and Xin Chen
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S9
    Content type: Research Published on:

  11. Post-translational modifications (PTMs) have a key role in regulating cell functions. Consequently, identification of PTM sites has a significant impact on understanding protein function and revealing cellular...

    Authors: Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida and Dongsup Kim
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S10
    Content type: Research Published on:

  14. This article has been withdrawn from the public domain because of significant plagiarism. In the light of this situation, BioMed Central regrets that this article is no longer available. The authors apologise ...

    Authors: Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra and Abhijit Datta
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S13
    Content type: Research Published on:

    The Retraction Note to this article has been published in BMC Bioinformatics 2010 11:258

  15. Small non-coding RNAs (21 to 24 nucleotides) regulate a number of developmental processes in plants and animals by silencing genes using multiple mechanisms. Among these, the most conserved classes are microRN...

    Authors: Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu and Gary Stacey
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S14
    Content type: Research Published on:

  19. Single nucleotide polymorphism (SNP) based association studies aim at identifying SNPs associated with phenotypes, for example, complex diseases. The associated SNPs may influence the disease risk individually...

    Authors: Can Yang, Xiang Wan, Qiang Yang, Hong Xue and Weichuan Yu
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S18
    Content type: Research Published on:

  20. Antibacterial peptides are one of the effecter molecules of innate immune system. Over the last few decades several antibacterial peptides have successfully approved as drug by FDA, which has prompted an inter...

    Authors: Sneh Lata, Nitish K Mishra and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S19
    Content type: Research Published on:

  22. Recombinant protein production is a useful biotechnology to produce a large quantity of highly soluble proteins. Currently, the most widely used production system is to fuse a target protein into different vec...

    Authors: Wen-Ching Chan, Po-Huang Liang, Yan-Ping Shih, Ueng-Cheng Yang, Wen-chang Lin and Chun-Nan Hsu
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S21
    Content type: Research Published on:

  23. MicroRNA (miRNA) expression profiling data has recently been found to be particularly important in cancer research and can be used as a diagnostic and prognostic tool. Current approaches of tumor classificatio...

    Authors: Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik and Michael Q Zhang
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S22
    Content type: Research Published on:

  25. Folding of a protein into its three dimensional structure is influenced by both local and global interactions within a protein. Higher order residue interactions, like pairwise, triplet and quadruplet ones, pl...

    Authors: Pandurangan Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar and Ramanathan Sowdhamini
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S24
    Content type: Research Published on:

  26. Many research results show that the biological systems are composed of functional modules. Members in the same module usually have common functions. This is useful information to understand how biological syst...

    Authors: Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko and Chung-Yen Lin
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S25
    Content type: Research Published on:

  27. Human Immunodeficiency Virus type 1 (HIV-1), the causative agent of Acquired Immune Deficiency Syndrome (AIDS), exhibits very high genetic diversity with different variants or subtypes prevalent in different p...

    Authors: Aridaman Pandit and Somdatta Sinha
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S26
    Content type: Research Published on:

  28. Finding sequences of evolutionary operations that transform one genome into another is a classical problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactl...

    Authors: Martin Bader
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S27
    Content type: Research Published on:

  30. It has been apparent in the last few years that small non coding RNAs (ncRNA) play a very significant role in biological regulation. Among these microRNAs (miRNAs), 22-23 nucleotide small regulatory RNAs, have...

    Authors: Sumeet Agarwal, Candida Vaz, Alok Bhattacharya and Ashwin Srinivasan
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S29
    Content type: Research Published on:

  31. The study of genome rearrangements has become a mainstay of phylogenetics and comparative genomics. Fundamental in such a study is the median problem: given three genomes find a fourth that minimizes the sum o...

    Authors: Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M Swenson and Bernard ME Moret
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S30
    Content type: Research Published on:

  32. Understanding of secondary metabolic pathway in plant is essential for finding druggable candidate enzymes. However, there are many enzymes whose functions are not yet discovered in organism-specific metabolic...

    Authors: Hiroto Saigo, Masahiro Hattori, Hisashi Kashima and Koji Tsuda
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S31
    Content type: Research Published on:

  34. Glycobiology pertains to the study of carbohydrate sugar chains, or glycans, in a particular cell or organism. Many computational approaches have been proposed for analyzing these complex glycan structures, wh...

    Authors: Limin Li, Wai-Ki Ching, Takako Yamaguchi and Kiyoko F Aoki-Kinoshita
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S33
    Content type: Research Published on:

  35. Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are...

    Authors: Zaixin Lu, Zhiyu Zhao and Bin Fu
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S34
    Content type: Research Published on:

  37. RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly uses highly coupled Dynamic Programming (D...

    Authors: SPT Krishnan, Sim Sze Liang and Bharadwaj Veeravalli
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S36
    Content type: Research Published on:

  38. Introduction of spaced speeds opened a way of sensitivity improvement in homology search without loss of search speed. Since then, the efforts of finding optimal seed which maximizes the sensitivity have been ...

    Authors: Won-Hyoung Chung and Seong-Bae Park
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S37
    Content type: Research Published on:

  39. Pathways provide topical descriptions of cellular circuitry. Comparing analogous pathways reveals intricate insights into individual functional differences among species. While previous works in the field perf...

    Authors: Adi Mano, Tamir Tuller, Oded Béjà and Ron Y Pinter
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S38
    Content type: Research Published on:

  43. Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for proc...

    Authors: Mukul S Bansal, J Gordon Burleigh and Oliver Eulenstein
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S42
    Content type: Research Published on:

  44. In the yeast Saccharomyces cerevisiae, interactions between galactose, Gal3p, Gal80p, and Gal4p determine the transcriptional status of the genes required for the galactose utilization. Increase in the cellular g...

    Authors: Vishwesh V Kulkarni, Venkatesh Kareenhalli, Pushkar Malakar, Lucy Y Pao, Michael G Safonov and Ganesh A Viswanathan
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S43
    Content type: Research Published on:

  47. Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures i...

    Authors: Lei Zhang, James Bailey, Arun S Konagurthu and Kotagiri Ramamohanarao
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S46
    Content type: Research Published on:
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