[Bioclusters] Call for Papers: Special Issue on ComputingArchitectures and Acceleration for Bioinformatics Algorithms

Bertil Schmidt (Dr) ASBSchmidt at ntu.edu.sg
Thu Nov 16 21:52:53 EST 2006

Dear Colleagues,


This is a gentle reminder of submission deadline on 1 December 2006. We look forwards to receiving your submissions soon.


Best regards,


Guest Editors: Feng Lin, Heiko Schröder, Bertil Schmidt

Nanyang Technological University
School of Computer Engineering
N4-2A-04, Nanyang Avenue
Singapore 639798





Call for Papers:

Special Issue on Computing Architectures and Acceleration for Bioinformatics Algorithms

The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology (Elsevier)



Important Dates

Deadline for submission of full paper: 1 December 2006

Completion of review/notification of acceptance: 1 January 2007

Revised paper due: 1 February 2007

Notification of final decision: 15 February 2007

Publication of electronic version: February 2007

Publication of printed version: June 2007



The goal of this special issue is to present the current research and critical review on computing architectures, hardware-accelerated algorithms, and software systems for bioinformatics data processing tasks. During the last decades, research in the fields of molecular biology and biomedicine has provided the scientific community with huge amount of data through sequencing, genome-wide annotation, gene expression profiling and proteomics projects. The genetic databases have been growing exponentially and sophisticated computer algorithms have been developed to cater for needs of data mining, analysis and simulation. It is clear that development of high performance computing technologies has become crucial for deployment of the software systems to tackle various bioinformatics problems.


Papers published in this issue will address the compute-intensive bioinformatics algorithms and system development, and the applications ranging from fundamental computational biology to biomedical applications. Along with the data processing in genomics and proteomics, we are especially interested in the following computational solutions:

* DNA sequence alignment and assembly

* Heuristic sequence database searching

* Identification of structural and genetic features on a genome

* Genetic function mapping

* RNA secondary structure modeling

* SAGE and microarray data mining

* Clustering algorithms and gene profiling

* Protein folding and structural modeling

* Protein-ligand docking and inter-protein interaction

* Comparative genomics and molecular phylogeny

* Machine learning algorithms such as neural network, HMM and SVM for bioinformatics


Authors should emphasize exploratory work on the use of modern computing architectures, and different metric change rates such as compute versus communicate, and latency versus bandwidth. Computing architectures of interest include reconfigurable architectures such as Field-Programmable Gate Arrays, systolic architectures, multi-core architectures and chip level multiprocessing, SIMD and MIMD architectures, cluster and compute farm, grid computing, multi-thread and stream computing architectures, and multimedia architectures. Original research, significant improvement of previous methods and in-depth survey on the above topics are invited to the special issue. And as a general guideline to submission to The Journal of VLSI Signal Processing Systems, papers can be categorized into

* Architectural design and analysis

* Computation methodology

* System performance analysis (including measurement, modeling, and simulation)

* Review and prospect analysis


Online Manuscript Submission

Manuscripts for this special issue should be submitted online at the following URL: http://www.editorialmanager.com/vlsi. The instructions for the authors can be found there. Especially, when you are prompted to Select Article Type, choose "Special Issue - CompuArch & Bioinfo". All the papers will be reviewed by the Guest Editors and invited reviewers, and recommended to the Editorial Board for publication.


Guest Editors

Dr Feng Lin: asflin at ntu.edu.sg 

Dr Heiko Schröder: heiko at cs.rmit.edu.au 

Dr Bertil Schmidt: asbschmidt at ntu.edu.sg



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