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BioInformatics & Computational Biology (BICB 2011)

Academic Conferences - BioInformatics & Computational Biology (BICB 2011)
Academic Conferences

By : Global Science & Technology Forum

Date : 2011

Location : Singapore / Sigapore

PDF 50p
Description :

BICB conference presents the latest advances in the development of computing techniques and their application to life sciences.

Keywords :

Photobleaching, photoactivation, nuclear protein dynamics, live cell-imaging, intron sequence; intron length; number of GC; phylogenetics; hueristic algorithm, coding RNA; Long-range correlations in DNA; Wavelet Transforms; Detrended Fluctuation Analysis; Power Spectrum Analysis,

Keywords inside documents :

sequences ,sequence ,intron ,protein ,change ,expression ,pattern ,genes ,noncoding ,introns ,length ,number ,gamma ,statistic ,wavelet ,model ,function ,normal ,triplet ,fluorescence

Associated industries : Biotechnology - Biology - Software & Computing -

Proceedings from The Advances in Distributed and Parallel Computing (ADPC 2010) conference.

 

The aim of this BICB conference was to provide a platform for communication among top notch researchers, practitioners, and students from around the world in different fields of computer science, computer engineering, applied computing and computational biology to discuss the latest advances in the development of computing techniques and their application to life sciences.

 

The conference was featured original research in all areas of bio-informatics and computational biology, and covering the entire spectrum of underlying computational techniques in topics such as genome analysis sequence analysis, phylogenetics, analysis of high-throughput biological data, systems genetics, population analysis, as well as structural bioinformatics.

Abstracts of Proceedings included in The Advances in Distributed and Parallel Computing (ADPC 2010) conference proceedings. 

 

  1. Virtual Photo Activated Fluorescence (VPAF): obtaining PAF data from FRAP experiments

Gustavo Carrero, Centre for Science, Faculty of Science and Technology, Athabasca University, Edmonton, Alberta, Canada & Michael J. Hendzel, Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada

 

Kinetic dynamics of nuclear proteins in living cells are often studied using two inverse-related fluorescence microscopy techniques: Fluorescence Recovery After Photobleaching (FRAP) and Photo Activated Fluorescence (PAF). Motivated by the inverse relationship between FRAP and PAF, we now report a method, Virtual PAF (VPAF), for obtaining the equivalent of PAF results directly from FRAP experiments. The method, based on simple image arithmetic, is validated mathematically using partial differential equations. The analysis provides a closed algebraic relationship between PAF and FRAP curves that is used to generate a set of VPAF data from FRAP data.

 

  1. The Analysis of Pattern Change in Intron Sequences

Jinda Kongcharoen, Centre for Statistical and Survey Methodology, School of Mathematics and Applied Statistics, University of Wollongong, NSW, Australia & Rachel Caldwell, School of Biological Sciences, University of Wollongong, NSW, Australia & Yan-Xia Lin, Centre for Statistical and Survey Methodology, School of Mathematics and Applied Statistics, University of Wollongong, NSW, Australia & Yiren Yang, School of Biological Sciences, University of Wollongong, NSW, Australia & Ren Zhang, School of Biological Sciences, University of Wollongong, NSW, Australia

 

The Generalized Bernoulli Modeling approach is used to analyze the pattern change in intron sequences of a model plant species Arabidopsis thaliana. The influence of the intron length and the number of GC on the intron sequence pattern changes is examined. Two other gene properties, the gene expression level and the protein function encoded are also assessed. Among the random sampled intron sequences, 10.71% of them have been identified to have sequence pattern change. Our study shows that the number of GC and the intron length significantly influence the intron pattern change while the gene expression level and the protein function have little effect. Our results show that for Arabidopsis thaliana, the shorter intron with more number of GC might have a higher chance to have pattern changes detected on its sequence and this piece of information could be used for checking whether the intron is functional introns. This study may be benefit to the further study on functions of intron.

 

 

  1. Using multiple gene set enrichment analyses to support knowledge discovery in cancer transcriptome data

Frank Lin, Miew Keen Chong, Guy Tsafnat, Center for health informatics, The university of New South Wales, Sydney, Australia

 

Gene set enrichment analyses (GSEA) is a class of standard methods for the functional interpretation of transcriptome data. It is commonly used to examine the global perturbations in a genome-wide biological dataset [1,2]. We propose that by performing multiple GSEA on the same transcriptome dataset, the differences in the resulsts may be used to examine the potential "gaps" in our knowledge. Such discrepancies are potential candidates for futher validations by bench-side experiments. Here we illistrated by example how multiple GSEA ma be applied to re-analyse a cancer microarray dataset to potentially support knowledge discovery.

 

  1. Discovering Global propagation for Influenza A viruses based on robinson-foulds distance between phylogenetic trees

Kazeuya Sata, Kouichi Hirata, Kyushu Institute of technology, Japan & Kimihito Ito, Hokkaido University, Japan & Tetsuji Kuboyama, Gakushuin University, Japan

 

In this paper, we present a new method to discover the global propagation for influenza A viruses based on a Robinson-foulds distance between phylogenetic trees. First, we build a phylogenetic tree from amino acid sequences of influenza. A viruses for every region by an UPGMA and neighbor-joining mathod under the five dissimilarity measures newly introduced in this paper. Next, we extract the pair of the same leaves in the pair of the phylogeneticsubtrees based on a Robinson-fouldsdistance. Finally, we discover global prpopagation for influenza A viruses by analysing the occurrence time for every pair of the same leaves.

 

  1. Advantages of the D2 Statistic

C.J. Burden, J. Jing and S.R. Wilson, Mathematical Sciences Institute, Australian National University, Canberra, A.C.T. 0200, Australia

 

The D2 statistic, defined as the number of matches of words of some pre-specified length k, is a computationally fast alignment-free measure of biological sequence similarity. However there is some debate about its suitability for this purpose as it may be susceptible to single-sequence noise. We examine the extent of the problem and the effectiveness of overcoming it by using a mean-centred version of the statistic. We conclude that the D2 statistic is a useful measure of sequence similarity which can easily be extended to a mean-centred version which may perform better in some situations. Both the D2 statistic and its mean-centred version are well approximated by Gamma random variables under an i.i.d. null hypothesis, allowing for an accurate estimation of P-values.

 

  1. New Heuristic Algorithms for Constructing a Maximum Consensus Evolutionary Tree from a Set of Rooted Triplets

Soheil Jahangiri Tazehkand, Seyed Naser Hashemi, Department of Computer Science and Mathematics, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran & Hadi Poormohammadi, Department of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran

 

An evolutionary tree (phylogenetic tree) is a rooted tree, that models the evolutionary process history of currently living species, in which, leaves are labeled by species. The problem is to find the maximum consensus evolutionary tree from a set of given rooted triplets. A rooted triplet is a rooted binary tree on three leaves and shows the evolutionary relationship of the corresponding three species. The mentioned problem is known to be APX-hard. In this paper, we present two new heuristic algorithms. For a given set of m triplets on n species, the first algorithm runs in O(mn2) which is faster than any other previously known algorithm, although, the outcome is less satisfactory. The second algorithm runs in O(mn3) and in average performs better than any other previously known approximation algorithm.

 

 

  1. Predicting Mutations of Influenza Virus HA Genes - Using Dimensionality Reduction of Hamming Distance Space

Tetsuji KUBOYAMA, Gakushuin Univ. & Kimihito ITO, Hokkaido Univ., Kouichi HIRATA & Hiroshi SAKAMOTO, Kyushu Institute of Technology, JAPAN

 

Predicting mutation patterns of HA genes from the past gene sequences. A novel succinct method to predict the mutations: Biological knowledge is not required & Dimensionality Reduction of Hamming Distance Space.

 

  1. Spectral analysis of long noncoding RNAs

Vikram Singh, Center for Computational Biology and Bioinformatics, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110 067, India & Ramakrishna Ramaswamy, School of Physical Sciences and Center for Computational Biology and Bioinformatics, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.

 

We analyse symbolic sequences of a large number of known long noncoding genes in a variety of organisms via their Fourier and wavelet transforms. Although these do not have the striking correlation structure of protein coding genes, there are significant patterns within the sequences which can be detected through spectral methods. While these methods are not by themselves of sufficient accuracy to detect noncoding genes, they can provide useful filters to be used in conjunction with other tools for the identification of noncoding genes.

 

 

  1. C-ClustalW: An Integrated System for Multiple Sequence - Alignment in a Cloud Computing Environment

Hun-Gi Kim1, Yu-Jin Kang2, Seung-Hyun Jung3, Chi-Hwan Choi1, Wan-Sup Cho2

1Dept. of Bio-Information Technology, Chungbuk National University, Korea, & 2Dept. of Management Information Systems, u-BIZ BK21, Chungbuk National University, Korea, & 3Dept. of Information Industrial Engineering, Chungbuk National University, Korea.

 

ClustalW is a common tool of MSA(multiple sequence alignment) in the bioinformatics field. However, conventional MSA services are not well organized. Their performance is so weak and they require complicated manual labor frequently. In this paper, we propose an efficient MSA system, C-ClustlaW, based on highperformance cloud computing environment. To remove manual labor, various cumbersome activities related with post-processing for MSA such as experimental design, collecting sequence data, data refinement and, etc. Are automated on our system. Furthermore, each experiment is managed as a project and all the data and results in the experiment are accumulated in the server for providing personalized experimental environment via Internet. After finishing all alignment process, C-ClustalW could display sequence data in alignment as a tree structure. As a result, we can implement all processes of MSA on a single system.

 

  1. The binding properties of the human PKAI protein as inferred from molecular modeling and Molecular dynamics study

In Silico analysis of human PKAI protein, Karthikeyan Muthusamy* , Palani Kirubakaran and Selvaraman Nagamani, *Assistant Professor, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu – 630 003, India

 

PKAI or cAMP-dependent protein kinase type I-alpha (PRKAR1A) is a regulatory subunit, which is encoded by the gene PRKAR1A. PRKAR1A gene is over-expressed in different types of tumor and cancer cells. The PKAI protein is identified as a one of the potential candidate for anti cancer drug target. Human PKAI protein was modeled using comparative homology modeling using protein kinase A (Pdb id: 2QCS) as a reference template. The refinement of the model was carried out through molecular dynamics simulations by Desmond software. The reliability of the model was further assessed by PROCHECK and ProSa II analysis, which are in acceptable range. The PKAI binding groove was checked by small ligand molecules leading to inhibition. Virtual screening analysis was performed by various available small molecule databases (NCI and Asinex) and we have found that five of the compounds show promising docking score (glide sore and energy) which are in acceptable range of ADME properties. Further characterisation will be carried out by in vitro and in vivo assays.

 

 

  1. Identifying genes induced by different pathogen-associated molecular patterns

Jose C. Nacher, Department of Complex and Intelligent Systems, Future University Hakodate

Hokkaido, 041-8655, Japan & Vladimir B. Ryabov, Department of Complex and Intelligent Systems. Future University Hakodate, Hokkaido, 041-8655, Japan

 

Recent data analyses have highlighted the existence of simple laws that govern the transcriptional organization. In spite of its importance, theoretical frameworks have not always

kept pace with these findings and do not capture them simultaneously. Here we propose a simple probabilistic model that is able to reproduce two keystone statistical properties of the gene expression profiles: (1) Power-law decay of the expression level distribution function. (2) Approximately linear dependence between the temporal variation in the expression level and its initial value (also known as rich-travels-more). The developed statistical framework is based on the theory of random signals and noise (RSN) and it leads to new insights about the underlying dyna mics of the coupling between gene expression and external signals. The model not only makes predictions on the gene expression response to the action of different pathogen-associated molecular patterns but also leads to identification of genes that are most strongly induced by them.

 

 

  1. Meta-analysis of lung expansion maneuvers for the prevention of postoperative pulmonary complications for thoracic and abdominal patients

Pei-Hsin Chen, RN, 1. Graduate school of Nursing Department, Central University of Science and Technology, Taichung, Taiwan , 2. Nursing Department of Tzi Chi Hospital, Taiching Branch, Taiwan

     

This study aims to understand the effectiveness of different lung expansion maneuvers for prevention of pulmonary complications.

Pulmonary complication is a leading cause of death for patients post upper abdominal or thoracic surgery. Adequate lung expansion maneuvers can effectively prevent pulmonary complications. Although it had been studied extensively, there is no agreement on a specific regimen.

Virtual Photo Activated Fluorescence (VPAF): obtaining PAF data from FRAP experiments

Company Description : Kinetic dynamics of nuclear proteins in living cells are often studied using two inverse-related fluorescence microscopy techniques: Fluorescence Recovery After Photobleaching (FRAP) and Photo Activated Fluorescence (PAF). Motivated by the inverse relationship between FRAP and PAF, we now report a method, Virtual PAF (VPAF), for obtaining the equivalent of PAF results directly from FRAP experiments. The method, based on simple image arithmetic, is validated mathematically using partial differential equations. The analysis provides a closed algebraic relationship between PAF and FRAP curves that is used to generate a set of VPAF data from FRAP data.

Product Type : Academic Conferences

Author : Gustavo Carrero, Centre for Science, Faculty of Science and Tech

PDF 5p

Languages : English

The Analysis of Pattern Change in Intron Sequences

Company Description : The Generalized Bernoulli Modeling approach is used to analyze the pattern change in intron sequences of a model plant species Arabidopsis thaliana. The influence of the intron length and the number of GC on the intron sequence pattern changes is examined. Two other gene properties, the gene expression level and the protein function encoded are also assessed. Among the random sampled intron sequences, 10.71% of them have been identified to have sequence pattern change. Our study shows that the number of GC and the intron length significantly influence the intron pattern change while the gene expression level and the protein function have little effect. Our results show that for Arabidopsis thaliana, the shorter intron with more number of GC might have a higher chance to have pattern changes detected on its sequence and this piece of information could be used for checking whether the intron is functional introns. This study may be benefit to the further study on functions of intron.

Product Type : Academic Conferences

Author : Jinda Kongcharoen, Centre for Statistical and Survey Methodology

PDF 6p

Languages : English

Using multiple gene set enrichment analyses to support knowledge discovery in cancer transcri...

Company Description : Gene set enrichment analyses (GSEA) is a class of standard methods for the functional interpretation of transcriptome data. It is commonly used to examine the global perturbations in a genome-wide biological dataset [1,2]. We propose that by performing multiple GSEA on the same transcriptome dataset, the differences in the resulsts may be used to examine the potential "gaps" in our knowledge. Such discrepancies are potential candidates for futher validations by bench-side experiments. Here we illistrated by example how multiple GSEA ma be applied to re-analyse a cancer microarray dataset to potentially support knowledge discovery.

Product Type : Academic Conferences

Author : Frank Lin, Miew Keen Chong, Guy Tsafnat, Center for health infor

PDF 1p

Languages : English

Discovering Global propagation for Influenza A viruses based on robinson-foulds distance ...

Company Description : In this paper, we present a new method to discover the global propagation for influenza A viruses based on a Robinson-foulds distance between phylogenetic trees. First, we build a phylogenetic tree from amino acid sequences of influenza. A viruses for every region by an UPGMA and neighbor-joining mathod under the five dissimilarity measures newly introduced in this paper. Next, we extract the pair of the same leaves in the pair of the phylogeneticsubtrees based on a Robinson-fouldsdistance. Finally, we discover global prpopagation for influenza A viruses by analysing the occurrence time for every pair of the same leaves.

Product Type : Academic Conferences

Author : Kazeuya Sata, Kouichi Hirata, Kyushu Institute of technology, J

PDF 6p

Languages : English

Advantages of the D2 Statistic

Company Description : The D2 statistic, defined as the number of matches of words of some pre-specified length k, is a computationally fast alignment-free measure of biological sequence similarity. However there is some debate about its suitability for this purpose as it may be susceptible to single-sequence noise. We examine the extent of the problem and the effectiveness of overcoming it by using a mean-centred version of the statistic. We conclude that the D2 statistic is a useful measure of sequence similarity which can easily be extended to a mean-centred version which may perform better in some situations. Both the D2 statistic and its mean-centred version are well approximated by Gamma random variables under an i.i.d. null hypothesis, allowing for an accurate estimation of P-values.

Product Type : Academic Conferences

Author : C.J. Burden, J. Jing and S.R. Wilson, Mathematical Sciences Inst

PDF 7p

Languages : English

New Heuristic Algorithms for Constructing a Maximum Consensus Evolutionary Tree from a Set of...

Company Description : An evolutionary tree (phylogenetic tree) is a rooted tree, that models the evolutionary process history of currently living species, in which, leaves are labeled by species. The problem is to find the maximum consensus evolutionary tree from a set of given rooted triplets. A rooted triplet is a rooted binary tree on three leaves and shows the evolutionary relationship of the corresponding three species. The mentioned problem is known to be APX-hard. In this paper, we present two new heuristic algorithms. For a given set of m triplets on n species, the first algorithm runs in O(mn2) which is faster than any other previously known algorithm, although, the outcome is less satisfactory. The second algorithm runs in O(mn3) and in average performs better than any other previously known approximation algorithm.

Product Type : Academic Conferences

Author : Soheil Jahangiri Tazehkand, Seyed Naser Hashemi, Department of C

PDF 4p

Languages : English

Predicting Mutations of Influenza Virus HA Genes - Using Dimensionality Reduction of Hamming ...

Company Description : Predicting mutation patterns of HA genes from the past gene sequences. A novel succinct method to predict the mutations: Biological knowledge is not required & Dimensionality Reduction of Hamming Distance Space.

Product Type : Academic Conferences

Author : Tetsuji KUBOYAMA, Gakushuin Univ. & Kimihito ITO, Hokkaido Univ.

PDF 1p

Languages : English

Spectral analysis of long noncoding RNAs

Company Description : We analyse symbolic sequences of a large number of known long noncoding genes in a variety of organisms via their Fourier and wavelet transforms. Although these do not have the striking correlation structure of protein coding genes, there are significant patterns within the sequences which can be detected through spectral methods. While these methods are not by themselves of sufficient accuracy to detect noncoding genes, they can provide useful filters to be used in conjunction with other tools for the identification of noncoding genes.

Product Type : Academic Conferences

Author : Vikram Singh, Center for Computational Biology and Bioinformatic

PDF 8p

Languages : English

C-ClustalW: An Integrated System for Multiple Sequence - Alignment in a Cloud Computing Envir

Company Description : ClustalW is a common tool of MSA(multiple sequence alignment) in the bioinformatics field. However, conventional MSA services are not well organized. Their performance is so weak and they require complicated manual labor frequently. In this paper, we propose an efficient MSA system, C-ClustlaW, based on highperformance cloud computing environment. To remove manual labor, various cumbersome activities related with post-processing for MSA such as experimental design, collecting sequence data, data refinement and, etc. Are automated on our system. Furthermore, each experiment is managed as a project and all the data and results in the experiment are accumulated in the server for providing personalized experimental environment via Internet. After finishing all alignment process, C-ClustalW could display sequence data in alignment as a tree structure. As a result, we can implement all processes of MSA on a single system.

Product Type : Academic Conferences

Author : Hun-Gi Kim1, Yu-Jin Kang2, Seung-Hyun Jung3, Chi-Hwan Choi1, Wan

PDF 1p

Languages : English

The binding properties of the human PKAI protein as inferred from molecular modeling and Mol...

Company Description : PKAI or cAMP-dependent protein kinase type I-alpha (PRKAR1A) is a regulatory subunit, which is encoded by the gene PRKAR1A. PRKAR1A gene is over-expressed in different types of tumor and cancer cells. The PKAI protein is identified as a one of the potential candidate for anti cancer drug target. Human PKAI protein was modeled using comparative homology modeling using protein kinase A (Pdb id: 2QCS) as a reference template. The refinement of the model was carried out through molecular dynamics simulations by Desmond software. The reliability of the model was further assessed by PROCHECK and ProSa II analysis, which are in acceptable range. The PKAI binding groove was checked by small ligand molecules leading to inhibition. Virtual screening analysis was performed by various available small molecule databases (NCI and Asinex) and we have found that five of the compounds show promising docking score (glide sore and energy) which are in acceptable range of ADME properties. Further characterisation will be carried out by in vitro and in vivo assays.

Product Type : Academic Conferences

Author : In Silico analysis of human PKAI protein, Karthikeyan Muthusamy*

PDF 4p

Languages : English

Identifying genes induced by different pathogen-associated molecular patterns

Company Description : Recent data analyses have highlighted the existence of simple laws that govern the transcriptional organization. In spite of its importance, theoretical frameworks have not always kept pace with these findings and do not capture them simultaneously. Here we propose a simple probabilistic model that is able to reproduce two keystone statistical properties of the gene expression profiles: (1) Power-law decay of the expression level distribution function. (2) Approximately linear dependence between the temporal variation in the expression level and its initial value (also known as rich-travels-more). The developed statistical framework is based on the theory of random signals and noise (RSN) and it leads to new insights about the underlying dyna mics of the coupling between gene expression and external signals. The model not only makes predictions on the gene expression response to the action of different pathogen-associated molecular patterns but also leads to identification of genes that are most strongly induced by them.

Product Type : Academic Conferences

Author : Jose C. Nacher, Department of Complex and Intelligent Systems, F

PDF 6p

Languages : English

Meta-analysis of lung expansion maneuvers for the prevention of postoperative pulmonary comp...

Company Description : This study aims to understand the effectiveness of different lung expansion maneuvers for prevention of pulmonary complications. Pulmonary complication is a leading cause of death for patients post upper abdominal or thoracic surgery. Adequate lung expansion maneuvers can effectively prevent pulmonary complications. Although it had been studied extensively, there is no agreement on a specific regimen.

Product Type : Academic Conferences

Author : Pei-Hsin Chen, RN, 1. Graduate school of Nursing Department, Cen

PDF 1p

Languages : English

Organizer : Global Science & Technology Forum

GSTF provides a global intellectual platform for top notch academics and industry professionals to actively interact and share their groundbreaking research achievements. GSTF is dedicated to promoting research and development and offers an inter-disciplinary intellectual platform for leading scientists, researchers, academics and industry professionals across Asia Pacific to actively consult, network and collaborate with their counterparts across the globe.