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  1. With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human disea...

    Authors: Xiao-Long Wu, Yun Heo, Izzat El Hajj, Wen-Mei Hwu, Deming Chen and Jian Ma
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  2. Understanding the history of a gene family that evolves through duplication, speciation, and loss is a fundamental problem in comparative genomics. Features such as function, position, and structural similarit...

    Authors: Olivier Tremblay-Savard and Krister M Swenson
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  3. Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binar...

    Authors: Ján Maňuch, Murray Patterson, Roland Wittler, Cedric Chauve and Eric Tannier
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  4. Many cancer genome sequencing efforts are underway with the goal of identifying the somatic mutations that drive cancer progression. A major difficulty in these studies is that tumors are typically heterogeneo...

    Authors: Ahmad Mahmoody, Crystal L Kahn and Benjamin J Raphael
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  5. The comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. Methods for gene or...

    Authors: Daniel Doerr, Annelyse Thévenin and Jens Stoye
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  6. The computational prediction of Transcription Factor Binding Sites (TFBS) remains a challenge due to their short length and low information content. Comparative genomics approaches that simultaneously consider...

    Authors: Mathieu Blanchette
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  19. The report summarizes the scientific content of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB) held in conjunction with the Intelligent Syst...

    Authors: Alexander Goncearenco, Priscila Grynberg, Olga B Botvinnik, Geoff Macintyre and Thomas Abeel
    Citation: BMC Bioinformatics 2012 13(Suppl 18):A1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 13 Supplement 18

  20. Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to u...

    Authors: Lei Sun, Zhihua Zhang, Timothy L Bailey, Andrew C Perkins, Michael R Tallack, Zhao Xu and Hui Liu
    Citation: BMC Bioinformatics 2012 13:331
    Content type: Research article Published on:

  21. The Nymphaeales (waterlilly and relatives) lineage has diverged as the second branch of basal angiosperms and comprises of two families: Cabombaceae and Nymphaceae. The classification of Nymphaeales and phylog...

    Authors: Devendra Kumar Biswal, Manish Debnath, Shakti Kumar and Pramod Tandon
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S26
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  22. Freshwater algae can be used as indicators to monitor freshwater ecosystem condition. Algae react quickly and predictably to a broad range of pollutants. Thus they provide early signals of worsening environmen...

    Authors: Mogeeb AA Mosleh, Hayat Manssor, Sorayya Malek, Pozi Milow and Aishah Salleh
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S25
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  23. The transcriptome of an organism can be studied with the analysis of expressed sequence tag (EST) data sets that offers a rapid and cost effective approach with several new and updated bioinformatics approache...

    Authors: Ranjeeta Menon, Gagan Garg, Robin B Gasser and Shoba Ranganathan
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  24. Multidimensional scaling (MDS) is a widely used approach to dimensionality reduction. It has been applied to feature selection and visualization in various areas. Among diverse MDS methods, the classical MDS i...

    Authors: Sungin Park, Soo-Yong Shin and Kyu-Baek Hwang
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  25. Bioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cop...

    Authors: Mohamed El-Kalioby, Mohamed Abouelhoda, Jan Krüger, Robert Giegerich, Alexander Sczyrba, Dennis P Wall and Peter Tonellato
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  26. The definition of artificial immunity, realized through vaccinations, is nowadays a practice widely developed in order to eliminate cancer disease. The present paper deals with an improved version of a mathema...

    Authors: Carlo Bianca, Ferdinando Chiacchio, Francesco Pappalardo and Marzio Pennisi
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  27. Prediction of B-cell epitopes from antigens is useful to understand the immune basis of antibody-antigen recognition, and is helpful in vaccine design and drug development. Tremendous efforts have been devoted...

    Authors: Liang Zhao, Limsoon Wong, Lanyuan Lu, Steven CH Hoi and Jinyan Li
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  28. When studying genetic diseases in which genetic variations are passed on to offspring, the ability to distinguish between paternal and maternal alleles is essential. Determining haplotypes from genotype data i...

    Authors: En-Yu Lai, Wei-Bung Wang, Tao Jiang and Kun-Pin Wu
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  29. Current malaria diagnosis relies primarily on microscopic examination of Giemsa-stained thick and thin blood films. This method requires vigorously trained technicians to efficiently detect and classify the ma...

    Authors: Saowaluck Kaewkamnerd, Chairat Uthaipibull, Apichart Intarapanich, Montri Pannarut, Sastra Chaotheing and Sissades Tongsima
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  30. The metabolic network is an aggregation of enzyme catalyzed reactions that converts one compound to another. Paths in a metabolic network are a sequence of enzymes that describe how a chemical compound of inte...

    Authors: Kevin Lim and Limsoon Wong
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  31. Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. With the advent of high-throughput techniques, signif...

    Authors: Sriganesh Srihari and Hon Wai Leong
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  32. Statistical model checking techniques have been shown to be effective for approximate model checking on large stochastic systems, where explicit representation of the state space is impractical. Importantly, t...

    Authors: Chuan Hock Koh, Sucheendra K Palaniappan, PS Thiagarajan and Limsoon Wong
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  33. Metamorphosis in insects transforms the larval into an adult body plan and comprises the destruction and remodeling of larval and the generation of adult tissues. The remodeling of larval into adult muscles pr...

    Authors: Rambabu Chinta, Joo Huang Tan and Martin Wasser
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  34. Identification of subcellular localization in proteins is crucial to elucidate cellular processes and molecular functions in a cell. However, given a tremendous amount of sequence data generated in the post-ge...

    Authors: Emily Chia-Yu Su, Jia-Ming Chang, Cheng-Wei Cheng, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  35. Biclustering has been utilized to find functionally important patterns in biological problem. Here a bicluster is a submatrix that consists of a subset of rows and a subset of columns in a matrix, and contains...

    Authors: Je-Gun Joung, Soo-Jin Kim, Soo-Yong Shin and Byoung-Tak Zhang
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  36. Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug dis...

    Authors: Felix A Kruger, Raghd Rostom and John P Overington
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  37. Given a set of DNA sequences s1, ..., s t , the (l, d) motif problem is to find an l-length motif sequence M , not necessary existing in any of the input sequences, such that...

    Authors: Mostafa M Abbas, Mohamed Abouelhoda and Hazem M Bahig
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  38. Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since...

    Authors: Atima Tharatipyakul, Somrak Numnark, Duangdao Wichadakul and Supawadee Ingsriswang
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  39. Prediction of biochemical (metabolic) pathways has a wide range of applications, including the optimization of drug candidates, and the elucidation of toxicity mechanisms. Recently, several methods have been d...

    Authors: Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato and Yasubumi Sakakibara
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  40. Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target biomolecule and candidate hits and make it possible to desi...

    Authors: B Jayaram, Tanya Singh, Goutam Mukherjee, Abhinav Mathur, Shashank Shekhar and Vandana Shekhar
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  41. Reverse docking approaches have been explored in previous studies on drug discovery to overcome some problems in traditional virtual screening. However, current reverse docking approaches are problematic in th...

    Authors: Minho Lee and Dongsup Kim
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  42. The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its applica...

    Authors: Mahmoud ElHefnawi, Mohammad ElGamacy and Mohamed Fares
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  43. Rheumatoid arthritis (RA) is an autoimmune disease with unknown etiology. Anticitrullinated protein autoantibody has been documented as a highly specific autoantibody associated with RA. Protein arginine deimi...

    Authors: Chian Ying Teo, Steven Shave, Adam Leow Thean Chor, Abu Bakar Salleh, Mohd Basyaruddin Bin Abdul Rahman, Malcolm D Walkinshaw and Bimo A Tejo
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  44. Existing methods for predicting protein solubility on overexpression in Escherichia coli advance performance by using ensemble classifiers such as two-stage support vector machine (SVM) based classifiers and a nu...

    Authors: Hui-Ling Huang, Phasit Charoenkwan, Te-Fen Kao, Hua-Chin Lee, Fang-Lin Chang, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Wen-Liang Chen and Shinn-Ying Ho
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  45. Isocitrate Dehydrogenases (IDHs) are important enzymes present in all living cells. Three subfamilies of functionally dimeric IDHs (subfamilies I, II, III) are known. Subfamily I are well-studied bacterial IDH...

    Authors: Rithvik Vinekar, Chandra Verma and Indira Ghosh
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  46. Ten years ago when Asia-Pacific Bioinformatics Network held the first International Conference on Bioinformatics (InCoB) in Bangkok its theme was North-South Networking. At that time InCoB aimed to provide bio...

    Authors: Christian Schönbach, Sissades Tongsima, Jonathan Chan, Vladimir Brusic, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 13 Supplement 17

  47. In studies of case-parent trios, we define copy number variants (CNVs) in the offspring that differ from the parental copy numbers as de novo and of interest for their potential functional role in disease. Amo...

    Authors: Robert B Scharpf, Terri H Beaty, Holger Schwender, Samuel G Younkin, Alan F Scott and Ingo Ruczinski
    Citation: BMC Bioinformatics 2012 13:330
    Content type: Methodology article Published on:

  48. Illumina BeadArray technology includes non specific negative control features that allow a precise estimation of the background noise. As an alternative to the background subtraction proposed in BeadStudio whi...

    Authors: Sandra Plancade, Yves Rozenholc and Eiliv Lund
    Citation: BMC Bioinformatics 2012 13:329
    Content type: Research article Published on:

  50. Biomarker panels derived separately from genomic and proteomic data and with a variety of computational methods have demonstrated promising classification performance in various diseases. An open question is h...

    Authors: Oliver P Günther, Virginia Chen, Gabriela Cohen Freue, Robert F Balshaw, Scott J Tebbutt, Zsuzsanna Hollander, Mandeep Takhar, W Robert McMaster, Bruce M McManus, Paul A Keown and Raymond T Ng
    Citation: BMC Bioinformatics 2012 13:326
    Content type: Methodology article Published on:

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