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TABLE OF CONTENTS
Issue No. 03 - May-June (vol. 9)
ISSN: 1545-5963
Special Section on the Second International Workshop on High Performance Computational Systems Biology
Regular Papers

Clustering 100,000 Protein Structure Decoys in Minutes (Abstract)

Dongbo Bu , Inst. of Comput. Technol., Beijing, China
Shuai Cheng Li , Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
Ming Li , Sch. of Comput. Sci., Univ. of WaterlooWaterloo, Waterloo, ON, Canada
pp. 765-773

On the Application of Active Learning and Gaussian Processes in Postcryopreservation Cell Membrane Integrity Experiments (Abstract)

F. Barry , Nat. Centre for Biomed. Eng. Sci., Nat. Univ. of Ireland Galway, Galway, Ireland
M. J. Murphy , Nat. Centre for Biomed. Eng. Sci., Nat. Univ. of Ireland Galway, Galway, Ireland
D. Fay , Comput. Lab., Univ. of Cambridge, Cambridge, UK
M. Norkus , Electr. & Electron. Eng., Nat. Univ. of Ireland Galway, Galway, Ireland
G. Olaighin , Electr. & Electron. Eng., Nat. Univ. of Ireland Galway, Galway, Ireland
L. Kilmartin , Electr. & Electron. Eng., Nat. Univ. of Ireland Galway, Galway, Ireland
pp. 846-856

Exploiting Intrastructure Information for Secondary Structure Prediction with Multifaceted Pipelines (Abstract)

G. Armano , Dept. of Electr. & Electron. Eng., Univ. of Cagliari, Cagliari, Italy
F. Ledda , Dept. of Electr. & Electron. Eng., Univ. of Cagliari, Cagliari, Italy
pp. 799-808

A Biologically Inspired Validity Measure for Comparison of Clustering Methods over Metabolic Data Sets (Abstract)

L. Kamenetzky , Partner Group, Max-Planck Inst. for Mol. Plant Physiol., Castelar, Argentina
D. H. Milone , Res. Center for Signals, Syst. & Comput. Intell., FICH-UNL, Santa Fe, Argentina
G. Stegmayer , Center for R&D of Inf. Syst. (CIDISI, UTN-FRSF, Santa Fe, Argentina
M. G. Lopez , Partner Group, Max-Planck Inst. for Mol. Plant Physiol., Castelar, Argentina
F. Carrari , Partner Group, Max-Planck Inst. for Mol. Plant Physiol., Castelar, Argentina
pp. 706-716

Protein Complexes Discovery Based on Protein-Protein Interaction Data via a Regularized Sparse Generative Network Model (Abstract)

Dao-Qing Dai , Center for Comput. Vision & Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
Xiao-Fei Zhang , Center for Comput. Vision & Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
Xiao-Xin Li , Center for Comput. Vision & Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
pp. 857-870

Markov Invariants for Phylogenetic Rate Matrices Derived from Embedded Submodels (Abstract)

P. Jarvis , Sch. of Math. & Phys., Univ. of Tasmania, Hobart Tas, TAS, Australia
J. Sumner , Sch. of Math. & Phys., Univ. of Tasmania, Hobart Tas, TAS, Australia
pp. 828-836

The GA and the GWAS: Using Genetic Algorithms to Search for Multilocus Associations (Abstract)

Shannon K. McWeeney , Oregon Health & Science University, Portland
Michael A. Mooney , Oregon Health & Science University, Portland
Beth Wilmot , Oregon Clinical and Translational Research Institute, Portland
pp. 899-910

The Relevance of Topology in Parallel Simulation of Biological Networks (Abstract)

Rosita Guido , University of Calabria, Arcavacata de Rende
Davide Prandi , Laboratory of Computational Oncology, Mattarello
Tommaso Mazza , IRCCS Casa Sollievo della Sofferenza, Rome
Paolo Ballarini , Ecole Centrale de Paris, Chatenay-Malabry, France
pp. 911-923

Weighted Markov Chain Based Aggregation of Biomolecule Orderings (Abstract)

Sanghamitra Bandyopadhyay , Indian Statistical Institute, Kolkata
Ujjwal Maulik , Jadavpur University, Kolkata
Debarka Sengupta , Indian Statistical Institute, Kolkata
pp. 924-933

The GA and the GWAS: Using Genetic Algorithms to Search for Multilocus Associations (Abstract)

M. A. Mooney , Dept. of Med. Inf. & Clinical Epidemiology, Oregon Health & Sci. Univ., Portland, OR, USA
pp. 899-910
Regular Papers

Designing Filters for Fast-Known NcRNA Identification (Abstract)

J. Buhler , Dept. of Comput. Sci., Washington Univ., St. Louis, MO, USA
Yanni Sun , Dept. of Comput. Sci. & Eng., Michigan State Univ., East Lansing, MI, USA
Cheng Yuan , Dept. of Comput. Sci. & Eng., Michigan State Univ., East Lansing, MI, USA
pp. 774-787
EIC Search

Mutual Information Optimization for Mass Spectra Data Alignment (Abstract)

I. Zoppis , Dept. of Inf., Univ. of Milano-Bicocca, Milan, Italy
E. Gianazza , Dept. of Exp. Med., Univ. of Milano-Bicocca, Monza, Italy
M. Borsani , Dept. of Exp. Med., Univ. of Milano-Bicocca, Monza, Italy
C. Chinello , Dept. of Exp. Med., Univ. of Milano-Bicocca, Monza, Italy
V. Mainini , Dept. of Exp. Med., Univ. of Milano-Bicocca, Monza, Italy
C. Galbusera , Dept. of Neurosci. & Biomed. Technol., Univ. of Milano-Bicocca, Monza, Italy
C. Ferrarese , Dept. of Neurology, San Gerardo Hosp., Monza, Italy
G. Galimberti , Dept. of Neurology, San Gerardo Hosp., Monza, Italy
S. Sorbi , Dept. of Neurological & Psychiatric Sci., Univ. of Florence, Florence, Italy
B. Borroni , Dept. of Neurology, Univ. of Brescia, Brescia, Italy
F. Magni , Dept. of Exp. Med., Univ. of Milano-Bicocca, Monza, Italy
M. Antoniotti , Dept. of Inf., Univ. of Milano-Bicocca, Milan, Italy
G. Mauri , Dept. of Inf., Univ. of Milano-Bicocca, Milan, Italy
pp. 934-939

Comment on "SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition” (PDF)

D. Fagundes-Lima , Nupeb, Univ. Fed. de Ouro Preto, Ouro Preto, Brazil
G. Weber , Dept. de Fis., UFMG, Belo Horizonte, Brazil
pp. 940-941
Regular Papers

Empirical Evidence of the Applicability of Functional Clustering through Gene Expression Classification (Abstract)

J. Klema , Dept. of Cybern., Czech Tech. Univ. in Prague, Prague, Czech Republic
M. Krejnik , Dept. of Cybern., Czech Tech. Univ. in Prague, Prague, Czech Republic
pp. 788-798

A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms (Abstract)

Xiao-Fei Zhang , Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
Dao-Qing Dai , Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
pp. 740-753
Special Section on the Second International Workshop on High Performance Computational Systems Biology

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Computing on GPU with CUDA and ELLPACK-R Sparse Format (Abstract)

N. A. Hamilton , Inst. for Mol. Biosci., Univ. of Queensland, St. Lucia, QLD, Australia
K. Burrage , Comput. Lab., Oxford Univ., Oxford, UK
A. Bustamam , Dept. of Math., Univ. of Indonesia, Depok, Indonesia
pp. 679-692
Regular Papers

Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration (Abstract)

W. S. Noble , Dept. of Genome Sci., Univ. of Washington, Seattle, WA, USA
O. Serang , Dept. of Pathology, Children's Hosp. Boston, Boston, MA, USA
pp. 809-817
Special Section on the Second International Workshop on High Performance Computational Systems Biology

On Parameter Synthesis by Parallel Model Checking (Abstract)

A. Streck , Fac. of Inf., Masaryk Univ., Brno, Czech Republic
A. Krejci , Fac. of Inf., Masaryk Univ., Brno, Czech Republic
L. Brim , Fac. of Inf., Masaryk Univ., Brno, Czech Republic
J. Barnat , Fac. of Inf., Masaryk Univ., Brno, Czech Republic
D. Safranek , Fac. of Inf., Masaryk Univ., Brno, Czech Republic
M. Vejnar , Fac. of Inf., Masaryk Univ., Brno, Czech Republic
T. Vejpustek , Fac. of Inf., Masaryk Univ., Brno, Czech Republic
pp. 693-705
Regular Papers

Quantifying Dynamic Stability of Genetic Memory Circuits (Abstract)

Peng Li , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
Yong Zhang , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
Garng M. Huang , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
pp. 871-884

Gene Classification Using Parameter-Free Semi-Supervised Manifold Learning (Abstract)

Hong Huang , Key Lab. on Opto-Electron. Tech. & Syst., Chongqing Univ., Chongqing, China
Hailiang Feng , Key Lab. on Opto-Electron. Tech. & Syst., Chongqing Univ., Chongqing, China
pp. 818-827
Special Section on the Second International Workshop on High Performance Computational Systems Biology

Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing (Abstract)

Diego di Bernardo , Telethon Inst. of Genetics & Med. (TIGEM), Naples, Italy
G. D'Angelo , Telethon Inst. of Genetics & Med. (TIGEM), Naples, Italy
M. Santoro , Telethon Inst. of Genetics & Med. (TIGEM), Naples, Italy
V. Siciliano , Telethon Inst. of Genetics & Med. (TIGEM), Naples, Italy
F. Gregoretti , Inst. of High Performance Comput. & Networking ICAR-CNR, Naples, Italy
V. Belcastro , Telethon Inst. of Genetics & Med. (TIGEM), Naples, Italy
G. Oliva , Inst. of High Performance Comput. & Networking ICAR-CNR, Naples, Italy
pp. 668-678
Regular Papers

A Comparative Study on Filtering Protein Secondary Structure Prediction (Abstract)

G. Christodoulou , Dept. of Comput. Sci., Univ. of Cyprus, Nicosia, Cyprus
V. J. Promponas , Dept. of Biol. Sci., Univ. of Cyprus, Nicosia, Cyprus
M. Agathocleous , Dept. of Comput. Sci., Univ. of Cyprus, Nicosia, Cyprus
P. Kountouris , Dept. of Comput. Sci., Univ. of Cyprus, Nicosia, Cyprus
S. Hadjicostas , Dept. of Comput. Sci., Univ. of Cyprus, Nicosia, Cyprus
V. Vassiliades , Dept. of Comput. Sci., Univ. of Cyprus, Nicosia, Cyprus
C. Christodoulou , Dept. of Comput. Sci., Univ. of Cyprus, Nicosia, Cyprus
pp. 731-739

Mutagenic Primer Design for Mismatch PCR-RFLP SNP Genotyping Using a Genetic Algorithm (Abstract)

Cheng-Huei Yang , Dept. of Electron. Commun. Eng., Nat. Kaohsiung Marine Univ., Kaohsiung, Taiwan
Yu-Huei Cheng , Dept. of Network Syst., Toko Univ., Chiayi, Taiwan
Cheng-Hong Yang , Dept. of Network Syst., Toko Univ., Chiayi, Taiwan
Li-Yeh Chuang , Dept. of Chem. Eng., I-Shou Univ., Kaohsiung, Taiwan
pp. 837-845
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