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2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

3-5 Feb. 2011

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Displaying Results 1 - 25 of 100
  • [Front cover]

    Publication Year: 2011, Page(s): c1
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  • [Copyright notice]

    Publication Year: 2011, Page(s): i
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  • Message from the General Chair

    Publication Year: 2011, Page(s):ii - vi
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  • Table of contents

    Publication Year: 2011, Page(s):vii - xii
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  • Keynote: A systems biology approach to integrative cancer genomics

    Publication Year: 2011, Page(s): 1
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (90 KB) | HTML iconHTML

    Summary form only given: Computational analysis of the recent onslaught of cancer molecular profile data is producing an unprecedented repertoire of genetic and epigenetic alterations contributing to tumorigenesis and progression. Yet, the direct impact of this knowledge on tumor treatment and prevention is still largely unproven. Loss of tumor suppressor function is difficult to target pharmacolo... View full abstract»

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  • Keynote: High-resolution sequence and chromatin signatures predict transcription factor binding in the human genome

    Publication Year: 2011, Page(s): 2
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (96 KB) | HTML iconHTML

    Accurately modeling the DNA sequence preferences of transcription factors and predicting their genomic binding sites are key problems in regulatory genomics. These efforts have long been frustrated by the limited availability and accuracy of TF binding site motifs. Today, protein binding microarray (PBM) experiments and chromatin immunoprecipitation followed by sequencing (ChlP-seq) experiments ar... View full abstract»

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  • Keynote: DNA-based molecular devices

    Publication Year: 2011, Page(s): 3
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (118 KB) | HTML iconHTML

    We overview recent work in the field of DNA-based autonomous biomolecular devices. We particularly emphasize molecular assemblies and molecular devices that are (i) self-assembled: that is they assemble into DNA nanostructures in one stage without explicit external control, (ii) programmable: the tasks the molecular devices execute can be modified without an entire redesign and (ii) autonomous: th... View full abstract»

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  • Invited: A novel perspective in algorithmic combinatorial methods for phasing populations in a coalescent model

    Publication Year: 2011, Page(s): 4
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (43 KB) | HTML iconHTML

    The goal of the present talk is to discuss some recent perspectives and challenges in facing the emerging computational problems related to phasing on datasets produced by new-generation technologies.It also discusess the need to develop new models, as well as some relevant concepts related to new datasets, such as Identity by Descent (IBD) which happens when two haplotypes are the same because th... View full abstract»

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  • Invited: Fast and theoretically strong algorithms for kinship discovery

    Publication Year: 2011, Page(s): 5
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (41 KB) | HTML iconHTML

    In kinship inference, genealogical relationships among organisms, typically in naturally-occurring populations, based on genetic marker information are identified. This task is crucial to conservation of endangered species and to understand the diversity of populations. Some of the simplest problems in this domain are sib group and half-sibgroup discover. Natural objectives in this domain are stat... View full abstract»

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  • Invited: Reconciled gene trees and their applications

    Publication Year: 2011, Page(s): 6
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (40 KB) | HTML iconHTML

    Phylogenetic trees describe the evolutionary history among various organisms. Studies on such trees have provided many valuable insights into a host of issues in biology, ecology, and medicine, and promise even more. As we enter the second decade of the post genomic era the enormous amount of genomic sequence information available provides us with an unprecedented opportunity for inferring novel p... View full abstract»

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  • Invited: Searching massive epigenome data for evolutionarily conserved sequence motifs

    Publication Year: 2011, Page(s): 7
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (138 KB) | HTML iconHTML

    The epigenome, such as nucleosome structure and DNA methylation, regulates expression of genes. Searching for evolutionarily conserved sequence motifs essential for controlling the epigenome is a fundamental problem in biology. Collecting massive epigenome data has been becoming increasingly feasible because of the wide-spread availability of next-generation sequencing technology. Thus, there have... View full abstract»

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  • Invited: Comparative microbial genomics

    Publication Year: 2011, Page(s): 8
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (47 KB) | HTML iconHTML

    As microbial sequencing data starts to pour in at an increasing rate, comparative genomics holds the keys to decipher and mine this wealth of information. We discuss the diverse ways in which the availability of comparative genomics data allows us to answer more questions with greater ease and greater confidence. View full abstract»

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  • Invited: Challenges in metagenomic assembly

    Publication Year: 2011, Page(s): 9
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (128 KB) | HTML iconHTML

    Genome assembly research has been `reborn' in recent years, in part due to rapid advances in sequencing technologies, but also due to the application of assembly to non-traditional tasks. Here we overview some of the challenges to genome assembly posed by data generated by metagenomic experiments. View full abstract»

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  • Invited: Multiclass RNA function classification using next-generation sequencing

    Publication Year: 2011, Page(s): 10
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (142 KB) | HTML iconHTML

    RNA-seq produces detailed information including length, strand and pairing states, which can be leveraged to characterize RNA functional categories using machine-learning approaches. Using fruit fly small-RNA-seq data, we demonstrate that by combining read length correlation with multi-class classifier models, we can classify four non-coding RNA function classes with high precision. View full abstract»

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  • Invited: “Going viral” with biological sequence analysis

    Publication Year: 2011, Page(s): 11
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (108 KB) | HTML iconHTML

    Summary form only given: Viruses have been implicated as the causative agents for a variety of cancers as well as diseases of the major physiological systems (e.g., nervous, respiratory, immune, reproductive, etc.), and viral infections have consistently ranked among the leading causes of death worldwide. Although viruses exhibit extreme biological diversity, plainly evidenced by the Baltimore cla... View full abstract»

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  • Invited: Metabolic network alignments

    Publication Year: 2011, Page(s): 12
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (59 KB) | HTML iconHTML

    A general network alignment problem: a pathway forms a pattern and a cellular network (usually from another species) forms the text, and how to find the best correspondence between the text and the pattern, is investigated. A representation of metabolic network/pathway by a graph in which vertices are labeled by enzymes which they represent and each of its directed edges connects enzymes catalyzin... View full abstract»

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  • Bcl::Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System

    Publication Year: 2011, Page(s):13 - 18
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (460 KB) | HTML iconHTML

    Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with mil... View full abstract»

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  • Identifying differentially regulated genes

    Publication Year: 2011, Page(s):19 - 25
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (222 KB) | HTML iconHTML

    Microarray experiments often measure expressions of genes taken from sample tissues in the presence of external perturbations such as medication, radiation, or disease. Typically in such experiments, gene expressions are measured before and after the application of external perturbation. In this paper, we focus on an important class of such microarray experiments that inherently have two groups of... View full abstract»

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  • High-performance biocomputing for simulating the spread of contagion over large contact networks

    Publication Year: 2011, Page(s):26 - 32
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (391 KB) | HTML iconHTML

    Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This paper shows how the EpiSimdemics interaction-based simulation system can be applied to the general contagion diffusion problem. Two specific problems, computational epidemiology and human immune system modeling, are given as examples. We then show how the graphics processing unit (GPU... View full abstract»

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  • PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text

    Publication Year: 2011, Page(s):33 - 39
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (140 KB) | HTML iconHTML

    A challenging issue in designing computational methods for predicting the gene structure into exons and introns from a cluster of transcript (EST, mRNA) sequences, is guaranteeing both accuracy and efficiency in time and space, when large clusters of over than 20,000 ESTs and genes longer than 1Mb are processed. Traditionally, the problem has been faced by combining different tools, not specifical... View full abstract»

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  • SIPPER: A flexible method to integrate heterogeneous data into a metabolic network

    Publication Year: 2011, Page(s):40 - 45
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (155 KB) | HTML iconHTML

    With the accumulation of available `omics' data, developing automatic methods for integrating and analyzing them into a common context has become a key goal in bioinformatics. In this paper, we propose a general framework (called SIPPER) to integrate heterogeneous information from one or several external data sources into a metabolic network, and to perform an automatic, data-independent analysis.... View full abstract»

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  • From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects

    Publication Year: 2011, Page(s):46 - 51
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (282 KB) | HTML iconHTML

    Recent findings of extensive alternative splicing events occurring in eukaryotic organisms have provided a possible explanation for the puzzling discrepancy between the number of genes and high genome complexity. Most alternative splicing events in eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as expressed sequence tags (EST) sequen... View full abstract»

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  • Studying disorder-to-order transitions from structural analysis

    Publication Year: 2011, Page(s):52 - 56
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (212 KB) | HTML iconHTML

    Many proteins and protein regions have been reported to be intrinsically disordered. Such disordered regions have been found to have conformational changes in various biological processes. Comprehensive studies on these disordered regions provide useful clues in understanding the mechanisms of a living cell. However, previous analyses only provided an overall number of disorder residues without de... View full abstract»

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  • Maximum likelihood parameter estimation in a stochastic resonate-and-fire neuronal model

    Publication Year: 2011, Page(s):57 - 62
    Cited by:  Papers (8)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (222 KB) | HTML iconHTML

    Recent work has shown that resonate-and-fire model is both computationally efficient and suitable for large network simulations. In this paper, we examine the estimation problem of a resonate-and-fire model with random threshold. The model parameters are divided into two sets. The first set is associated with subthreshold behavior and can be optimized by a nonlinear least squares algorithm. The ot... View full abstract»

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  • An algorithm for mining frequent patterns in biological sequence

    Publication Year: 2011, Page(s):63 - 68
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (299 KB) | HTML iconHTML

    Most of the existing algorithms for mining frequent patterns could produce lots of projected databases and short patterns which could increase the time and memory cost of mining. In order to overcome such shortcoming, a fast and efficient algorithm named FBPM for mining frequent patterns in biological sequence is proposed. We first present the concept of primary pattern, and then use prefix tree f... View full abstract»

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