The Community for Technology Leaders
Green Image
TABLE OF CONTENTS
Issue No. 05 - Sept.-Oct. (vol. 9)
ISSN: 1545-5963
Front Covers

Cover1 (PDF)

pp. c1

Cover2 (PDF)

pp. c2
Special Section on the 10th Asia Pacific Bioinformatics Conference

QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization (Abstract)

Chee Keong Kwoh , Sch. of Comput. Eng., Nanyang Technol. Univ., Singapore, Singapore
Xuchang Ouyang , Bioinf. Res. Centre, Nanyang Technol. Univ., Singapore, Singapore
Chinh Tran To Su , Bioinf. Res. Centre, Nanyang Technol. Univ., Singapore, Singapore
Stephanus Daniel Handoko , Centre for Comput. Intell., Nanyang Technol. Univ., Singapore, Singapore
Yew Soon Ong , Sch. of Comput. Eng., Nanyang Technol. Univ., Singapore, Singapore
pp. 1266-1272

Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator (Abstract)

Yunping Zhu , State Key Lab. of Proteomics, Beijing Inst. of Radiat. Med., Beijing, China
Penghao Wang , Sch. of Stat. & Math., Univ. of Sydney, Sydney, NSW, Australia
Jie Ma , State Key Lab. of Proteomics, Beijing Inst. of Radiat. Med., Beijing, China
Pengyi Yang , Sch. of Inf. Technol., Univ. of Sydney, Sydney, NSW, Australia
Bing B. Zhou , Sch. of Inf. Technol., Univ. of Sydney, Sydney, NSW, Australia
Yee Hwa Yang , Sch. of Stat. & Math., Univ. of Sydney, Sydney, NSW, Australia
pp. 1273-1280

CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq (Abstract)

Lin Wan , Mol. & Comput. Biol. Program, Univ. of Southern California, Los Angeles, CA, USA
Fengzhu Sun , Mol. & Comput. Biol. Program, Univ. of Southern California, Los Angeles, CA, USA
pp. 1281-1292

How Little Do We Actually Know? On the Size of Gene Regulatory Networks (Abstract)

Jan Taubert , Dept. of Comput. & Syst. Biol., Rothamsted Res., Harpenden, UK
Ulrich Ruckert , Dept. of Electr. Eng. & Comput. Sci., Univ. of California, Berkeley, CA, USA
Jan Baumbach , Comput. Syst. Biol. Group, Max Planck Institutefor Inf., Saarbrucken, Germany
Richard Rottger , Comput. Syst. Biol. Group, Max Planck Institutefor Inf., Saarbrucken, Germany
pp. 1293-1300
Special Section on the Ninth International Conference on COmputational Methods in Systems Biology

Evaluation of Design Strategies for Time Course Experiments in Genetic Networks: Case Study of the XlnR Regulon in Aspergillus niger (Abstract)

Gerrit van Straten , Syst. & Control Group, Wageningen Univ., Wageningen, Netherlands
Leo H. de Graaff , Lab. of Syst. & Synthetic Biol., Wageningen, Netherlands
Astrid R. Mach-Aigner , Res. Div. Biotechnol. & Microbiol., Tech. Univ. Vienna, Vienna, Austria
Jimmy Omony , Syst. & Control Group, Wageningen Univ., Wageningen, Netherlands
Anton J. B. van Boxtel , Syst. & Control Group, Wageningen Univ., Wageningen, Netherlands
pp. 1316-1325

The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response (Abstract)

Vladimir Rogojin , Fac. of Med., Helsinki Univ., Helsinki, Finland
Eugen Czeizler , Dept. of Inf. & Comput. Sci., Aalto Univ., Aalto, Finland
Ion Petre , Dept. of Inf. Technol., Abo Akademi Univ., Turku, Finland
pp. 1326-1337

Time Series Dependent Analysis of Unparametrized Thomas Networks (Abstract)

Alexander Bockmayr , DFG Res. Center Matheon, Freie Univ. Berlin, Berlin, Germany
Hannes Klarner , DFG Res. Center Matheon, Freie Univ. Berlin, Berlin, Germany
Heike Siebert , DFG Res. Center Matheon, Freie Univ. Berlin, Berlin, Germany
pp. 1338-1351

A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application (Abstract)

Blaise Genest , IRISA, Rennes, France
Bing Liu , Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
S. Akshay , IRISA, ENS Cachan Bretagne, Rennes, France
Sucheendra K. Palaniappan , Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
P. S. Thiagarajan , Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
pp. 1352-1365

Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling (Abstract)

Pietro Lio , Comput. Lab., Univ. of Cambridge, Cambridge, UK
Nicola Paoletti , Sch. of Sci. & Technol., Univ. of Camerino, Camerino, Italy
Emanuela Merelli , Sch. of Sci. & Technol., Univ. of Camerino, Camerino, Italy
Marco Viceconti , Dept. of Mech. Eng., Univ. of Sheffield, Sheffield, UK
pp. 1366-1378
Regular Papers

A New Measure of Classifier Performance for Gene Expression Data (Abstract)

Blaise Hanczar , LIPADE, Univ. Paris Descartes, Paris, France
Avner Bar-Hen , MAP5, Univ. Paris Descartes, Paris, France
pp. 1379-1386

An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction (Abstract)

Amarda Shehu , Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
Kenneth A. De Jong , Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
Jack Compton , Barquin Int., Alexandria, VA, USA
Rezarta Islamaj-Dogan , Nat. Center for Biotechnol. Inf. (NCBI), Nat. Inst. of Health (NIH), Bethesda, MD, USA
Uday Kamath , Dept. of Comput. Sci., George Mason Univ., Ashburn, VA, USA
pp. 1387-1398

Detecting Phenotype-Specific Interactions between Biological Processes from Microarray Data and Annotations (Abstract)

Calin Voichita , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
Riyue Bao , Dept. of Biol. Sci., Wayne State Univ., Detroit, MI, USA
Nadeem A. Ansari , Microsoft Corp., Redmond, WA, USA
Sorin Draghici , Dept. of Obstetrics & Gynecology, Wayne State Univ., Detroit, MI, USA
pp. 1399-1409

Finding a Periodic Attractor of a Boolean Network (Abstract)

Avraham A. Melkman , Dept. of Comput. Sci., Ben-Gurion Univ. of the Negev, Beer-Sheva, Israel
Sven Kosub , Dept. of Comput. & Inf. Sci., Univ. of Konstanz, Konstanz, Germany
Tatsuya Akutsu , Inst. for Chem. Res., Kyoto Univ., Kyoto, Japan
Takeyuki Tamura , Inst. for Chem. Res., Kyoto Univ., Kyoto, Japan
pp. 1410-1421

Gene Selection Using Iterative Feature Elimination Random Forests for Survival Outcomes (Abstract)

Ken Hui , Sch. of Med., Dept. of Internal Med., Yale Univ., New Haven, CT, USA
Stephen L. George , Sch. of Med., Dept. of Biostat. & Bioinf., Duke Univ., Durham, NC, USA
Herbert Pang , Sch. of Med., Dept. of Biostat. & Bioinf., Duke Univ., Durham, NC, USA
Tiejun Tong , Dept. of Math., Hong Kong Baptist Univ., Kowloon Tong, China
pp. 1422-1431

Hierarchical Motif Vectors for Prediction of Functional Sites in Amino Acid Sequences Using Quasi-Supervised Learning (Abstract)

Bilge Karacali , Dept. of Electr. & Electron. Eng., Izmir Inst. of Technol., Urla Izmir, Turkey
pp. 1432-1441

Improving the Prediction of Clinical Outcomes from Genomic Data Using Multiresolution Analysis (Abstract)

Gregory F. Cooper , Dept. of Biomed. Inf., Univ. of Pittsburgh, Pittsburgh, PA, USA
Pablo H. Hennings-Yeomans , Dept. of Biomed. Inf., Univ. of Pittsburgh, Pittsburgh, PA, USA
pp. 1442-1450

LNA: Fast Protein Structural Comparison Using a Laplacian Characterization of Tertiary Structure (Abstract)

Pierre-Francois Marteau , IRISA, Universitede Bretagne Sud, Vannes, France
Nicolas Bonnel , IRISA, Universitede Bretagne Sud, Vannes, France
pp. 1451-1458

MORE: Mixed Optimization for Reverse Engineering—An Application to Modeling Biological Networks Response via Sparse Systems of Nonlinear Differential Equations (Abstract)

Gianna Toffolo , Dept. of Inf. Eng., Univ. of Padova, Padova, Italy
Barbara Di Camillo , Dept. of Inf. Eng., Univ. of Padova, Padova, Italy
Marco A. Montes de Oca , Dept. of Math. Sci., Univ. of Delaware, Newark, DE, USA
Francesco Sambo , Dept. of Inf. Eng., Univ. of Padova, Padova, Italy
Thomas Stutzle , IRIDIA-CoDE, Univ. Libre de Bruxelles, Brussels, Belgium
pp. 1459-1471

Noniterative Convex Optimization Methods for Network Component Analysis (Abstract)

Wei Chen , Dept. of Electr. & Electron. Eng., Univ. of Hong Kong, Hong Kong, China
Zhi Ding , Dept. of Electr. & Comput. Eng., Univ. of California, Davis, CA, USA
Neil Jacklin , Dept. of Electr. & Comput. Eng., Univ. of California, Davis, CA, USA
Chunqi Chang , State Key Lab. of Brain & Cognitive Sci., Univ. of Hong Kong, Hong Kong, China
pp. 1472-1481

Qualitative Reasoning for Biological Network Inference from Systematic Perturbation Experiments (Abstract)

Barbara Di Camillo , Dept. of Inf. Eng., Univ. of Padova, Padova, Italy
Silvana Badaloni , Dept. of Inf. Eng., Univ. of Padova, Padova, Italy
Francesco Sambo , Dept. of Inf. Eng., Univ. of Padova, Padova, Italy
pp. 1482-1491

Reduced False Positives in PDZ Binding Prediction Using Sequence and Structural Descriptors (Abstract)

M. Teresa Pisabarro , Struct. Bioinf., Tech. Univ. Dresden, Dresden, Germany
Hongbo Zhu , Struct. Bioinf., Tech. Univ. Dresden, Dresden, Germany
Joan Teyra , Struct. Bioinf., Tech. Univ. Dresden, Dresden, Germany
John C. Hawkins , Struct. Bioinf., Tech. Univ. Dresden, Dresden, Germany
pp. 1492-1503

Robust Bayesian Clustering for Replicated Gene Expression Data (Abstract)

Jianyong Sun , Centre for Plant Integrative Biol. (CPIB), Univ. of Nottingham, Nottingham, UK
Jonathan M. Garibaldi , Sch. of Comput. Sci., Univ. of Nottingham, Nottingham, UK
Kim Kenobi , Centre for Plant Integrative Biol. (CPIB), Univ. of Nottingham, Nottingham, UK
pp. 1504-1514

Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers (Abstract)

Fei Deng , Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
Lusheng Wang , Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
Zhi-Zhong Chen , Div. of Inf. Syst. Design, Tokyo Denki Univ., Saitama, Japan
pp. 1515-1528
Short Papers

A Novel Method to Select Informative SNPs and Their Application in Genetic Association Studies (Abstract)

Xiong Li , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Wen Zhu , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Bo Liao , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Zhi Cao , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
pp. 1529-1534

ClassAMP: A Prediction Tool for Classification of Antimicrobial Peptides (Abstract)

Pravin Nilawe , Biomed. Inf. Center of Indian Council of Med. Res., Nat. Inst. for Res. in Reproductive Health, Navi Mumbai, India
Shreyas Karnik , Sch. of Inf., Indiana Univ., Marshfield, WI, USA
V. K. Jayaraman , Center for Dev. of Adv. Comput., Pune Univ. Campus, Pune, India
Shaini Joseph , Biomed. Inf. Center of Indian Council of Med. Res., Nat. Inst. for Res. in Reproductive Health, Mumbai, India
Susan Idicula-Thomas , Biomed. Inf. Center of Indian Council of Med. Res., Nat. Inst. for Res. in Reproductive Health, Mumbai, India
pp. 1535-1538

Multiscale Denoising of Biological Data: A Comparative Analysis (Abstract)

A. Datta , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
N. Meskin , Dept. Electr. Eng., Qatar Univ., Doha, Qatar
H. N. Nounou , Electr. & Comput. Eng. Program, Texas A&M Univ. at Qatar, Doha, Qatar
M. N. Nounou , Chem. Eng. Program, Texas A&M Univ. at Qatar, Doha, Qatar
E. R. Dougherty , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
pp. 1539-1545

Stability Analysis of the Ribosome Flow Model (Abstract)

Tamir Tuller , Dept. of Biomed. Eng., Tel-Aviv Univ., Tel-Aviv, Israel
Michael Margaliot , Sch. of Electr. Eng., Tel-Aviv Univ., Tel-Aviv, Israel
pp. 1545-1552
Back Covers

Cover3 (PDF)

pp. c3

Cover4 (PDF)

pp. c4
110 ms
(Ver )