Hindawi Publishing Corporation EURASIP Journal on Bioinformatics and Systems Biology Volume 2009, Article ID 250306, 2 pages doi:10.1155/2009/250306
Editorial Applications of Signal Processing Techniques to Bioinformatics, Genomics, and Proteomics Erchin Serpedin (EURASIP Member),1 Javier Garcia-Frias,2 Yufei Huang,3 and Ulisses Braga-Neto1 1 Department
of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, USA of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716-7501, USA 3 Department of Electrical and Computer Engineering, University of Texas at San-Antonio, TX 78249-2057, USA 2 Department
Correspondence should be addressed to Erchin Serpedin,
[email protected] Received 17 February 2009; Accepted 17 February 2009 Copyright © 2009 Erchin Serpedin et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
The recent development of high-throughput molecular genetics technologies has brought a major impact to bioinformatics and systems biology. These technologies have made possible the measurement of the expression profiles of genes and proteins in a highly parallel and integrated fashion. The examination of the huge amounts of genomic and proteomic data holds the promise for understanding the complex interactions between genes and proteins, the functional processes of a cell, and the impact of various factors on a cell, and ultimately, for enabling the design of new technologies for intelligent management of diseases. This special issue focuses on modeling and processing of data arising in bioinformatics, genomics, and proteomics using signal processing methods. The importance of signal processing techniques is due to their important role in extracting, processing, and interpreting the information contained in genomic and proteomic data. It is our hope that signal processing methods will lead to new advances and insights in uncovering the structure, functioning and evolution of biological systems. The special issue consists of nine papers that span a wide range of problems and applications in bioinformatics, genomics, and proteomics such as design of compressive sensing microarrays, analysis of missing values in microarray data, and effect of imputation techniques on post genomic inference methods, RNA sequence alignment, detection of periodicity in genomic sequences and gene expression profiles, clustering and classification of gene and protein expression data, and intervention in probabilistic Boolean
networks. Next, we will briefly introduce the papers reported in this special issue. W. Dai et al. analyze how to design a microarray that it is fit for compressive sensing and that captures also the biochemistry of probe-target DNA hybridization. Algorithms and design results are reported for determining probe sequences that satisfy the binding requirements and for evaluating the target concentrations. M. S. B. Sehgal et al. address the general problem of improving post genomic knowledge discovery procedures such as the selection of the most significant genes and inference of gene regulatory networks using missing microarray data imputation techniques. It is shown that instead of neglecting missing data, recycling microarray data via robust imputation techniques can yield substantial performance improvements in the subsequent post genomic discovery procedures. B.-J. Yoon developed a novel efficient and robust approach for fast and accurate structural alignment of RNAs, including pseudoknots. The proposed method turns out to accelerate the dynamic programming algorithm for familyspecific models such as profile-csHMMs and CMs, and to be robust to small parameter changes that are present in the model used to predict the constraint. The paper by J. Epps explains in detail the origins of ambiguity in period estimation for symbolic sequences, and proposes a novel hybrid autocorrelation-IPDFT technique for periodicity characterization of sequences. W. Zhao et al. developed a novel algorithm for identification of genes involved in cyclic processes by combining
2
EURASIP Journal on Bioinformatics and Systems Biology
gene expression analysis and prior knowledge. The proposed cyclic-genes detection algorithm is validated on data sets corresponding to Saccharomyces cerevisiae and Drosophila melanogaster, and shown to represent a valuable technique for unveiling pathways related to cyclic processes. T. J. Hestilow and Y. Huang propose a novel method for gene clustering using the shape information of gene expression profiles. The shape information which is represented in terms of normalized and time-scaled forward first-order differences is then exploited by a variational Bayes clustering approach and a non-Bayesian (Silhouette) cluster statistic, and shown to yield promising results in clustering time-series microarray data. The paper by W. Zhao et al. proposes a new clustering approach to combine the traditional clustering methods with power spectral analysis of time series gene expression measurements. Simulation results confirm that the proposed clustering approach provides superior performance relative to hierarchical, K-means, and self-organizing maps, and yields additional information about temporal regulated genetic processes, for example, cell-cycle. T. T. Vu and U. M. Braga-Neto address the important problem of assessing the effectiveness of bagging in the classification of small-sample genomic and proteomic data sets. Representative experimental results are presented and discussed. Finally, the paper by B. Faryabi et al. studies the effects on intervention performance in the context of probabilistic Boolean networks due to a reduction in the values of the model parameters.
Acknowledgments The authors would like to thank the Editor-in-Chief Dr. Ioan Tabus for the opportunity to prepare this special issue, and the reviewers for their help and constructive criticism in preparing this special issue. Erchin Serpedin Javier Garcia-Frias Yufei Huang Ulisses Braga-Neto
Photographȱ©ȱTurismeȱdeȱBarcelonaȱ/ȱJ.ȱTrullàs
Preliminaryȱcallȱforȱpapers
OrganizingȱCommittee
The 2011 European Signal Processing Conference (EUSIPCOȬ2011) is the nineteenth in a series of conferences promoted by the European Association for Signal Processing (EURASIP, www.eurasip.org). This year edition will take place in Barcelona, capital city of Catalonia (Spain), and will be jointly organized by the Centre Tecnològic de Telecomunicacions de Catalunya (CTTC) and the Universitat Politècnica de Catalunya (UPC). EUSIPCOȬ2011 will focus on key aspects of signal processing theory and applications li ti as listed li t d below. b l A Acceptance t off submissions b i i will ill be b based b d on quality, lit relevance and originality. Accepted papers will be published in the EUSIPCO proceedings and presented during the conference. Paper submissions, proposals for tutorials and proposals for special sessions are invited in, but not limited to, the following areas of interest.
Areas of Interest • Audio and electroȬacoustics. • Design, implementation, and applications of signal processing systems. • Multimedia l d signall processing and d coding. d • Image and multidimensional signal processing. • Signal detection and estimation. • Sensor array and multiȬchannel signal processing. • Sensor fusion in networked systems. • Signal processing for communications. • Medical imaging and image analysis. • NonȬstationary, nonȬlinear and nonȬGaussian signal processing.
Submissions Procedures to submit a paper and proposals for special sessions and tutorials will be detailed at www.eusipco2011.org. Submitted papers must be cameraȬready, no more than 5 pages long, and conforming to the standard specified on the EUSIPCO 2011 web site. First authors who are registered students can participate in the best student paper competition.
ImportantȱDeadlines: P Proposalsȱforȱspecialȱsessionsȱ l f i l i
15 D 2010 15ȱDecȱ2010
Proposalsȱforȱtutorials
18ȱFeb 2011
Electronicȱsubmissionȱofȱfullȱpapers
21ȱFeb 2011
Notificationȱofȱacceptance SubmissionȱofȱcameraȬreadyȱpapers Webpage:ȱwww.eusipco2011.org
23ȱMay 2011 6ȱJun 2011
HonoraryȱChair MiguelȱA.ȱLagunasȱ(CTTC) GeneralȱChair AnaȱI.ȱPérezȬNeiraȱ(UPC) GeneralȱViceȬChair CarlesȱAntónȬHaroȱ(CTTC) TechnicalȱProgramȱChair XavierȱMestreȱ(CTTC) TechnicalȱProgramȱCo Technical Program CoȬChairs Chairs JavierȱHernandoȱ(UPC) MontserratȱPardàsȱ(UPC) PlenaryȱTalks FerranȱMarquésȱ(UPC) YoninaȱEldarȱ(Technion) SpecialȱSessions IgnacioȱSantamaríaȱ(Unversidadȱ deȱCantabria) MatsȱBengtssonȱ(KTH) Finances MontserratȱNájarȱ(UPC) Montserrat Nájar (UPC) Tutorials DanielȱP.ȱPalomarȱ (HongȱKongȱUST) BeatriceȱPesquetȬPopescuȱ(ENST) Publicityȱ StephanȱPfletschingerȱ(CTTC) MònicaȱNavarroȱ(CTTC) Publications AntonioȱPascualȱ(UPC) CarlesȱFernándezȱ(CTTC) IIndustrialȱLiaisonȱ&ȱExhibits d i l Li i & E hibi AngelikiȱAlexiouȱȱ (UniversityȱofȱPiraeus) AlbertȱSitjàȱ(CTTC) InternationalȱLiaison JuȱLiuȱ(ShandongȱUniversityȬChina) JinhongȱYuanȱ(UNSWȬAustralia) TamasȱSziranyiȱ(SZTAKIȱȬHungary) RichȱSternȱ(CMUȬUSA) RicardoȱL.ȱdeȱQueirozȱȱ(UNBȬBrazil)
