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TABLE OF CONTENTS
Issue No. 06 - Nov.-Dec. (vol. 9)
ISSN: 1545-5963
Front Covers

[Front inside cover] (Abstract)

pp. c2
Editorial

EIC Editorial (HTML)

pp. 1553-1557

A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees (Abstract)

J. H. Degnan , Dept. of Math. & Stat., Univ. of Canterbury, Christchurch, New Zealand
N. A. Rosenberg , Dept. of Biol., Stanford Univ., Stanford, CA, USA
T. Stadler , Inst. of Integrative Biol., ETH Zurich, Zurich, Switzerland
pp. 1558-1568

A Constrained Evolutionary Computation Method for Detecting Controlling Regions of Cortical Networks (Abstract)

Yang Tang , Res. Inst. of Intell. Control & Syst., Harbin Inst. of Technol., Harbin, China
Zidong Wang , Dept. of Inf. Syst. & Comput., Brunel Univ., Uxbridge, UK
Huijun Gao , Res. Inst. of Intell. Control & Syst., Harbin Inst. of Technol., Harbin, China
S. Swift , Dept. of Inf. Syst. & Comput., Brunel Univ., Uxbridge, UK
J. Kurths , Dept. of Transdisciplinary Concepts & Methods, Potsdam Inst. for Climate Impact Res., Potsdam, Germany
pp. 1569-1581

A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information (Abstract)

Y. Pirola , Dipt. di Inf. Sist. e Comun. (DISCo), Univ. degli Studi di Milano-Bicocca, Milan, Italy
G. D. Vedova , Dipt. di Statistica, Univ. degli Studi di Milano-Bicocca, Milan, Italy
S. Biffani , Centro Ric. e Studi Agroalimentari (CeRSA), Lodi, Italy
A. Stella , Centro Ric. e Studi Agroalimentari (CeRSA), Lodi, Italy
P. Bonizzoni , Dipt. di Inf. Sist. e Comun. (DISCo), Univ. degli Studi di Milano-Bicocca, Milan, Italy
pp. 1582-1594

A Hybrid Cellular Automaton Model of Solid Tumor Growth and Bioreductive Drug Transport (Abstract)

N. Kazmi , Sch. of Comput., Eng. & Inf. Sci., Northumbria Univ., Newcastle upon Tyne, UK
M. A. Hossain , Sch. of Comput., Eng. & Inf. Sci., Northumbria Univ., Newcastle upon Tyne, UK
R. M. Phillips , Inst. of Cancer Therapeutics, Univ. of Bradford, Bradford, UK
pp. 1595-1606

A Mathematical Model to Study the Dynamics of Epithelial Cellular Networks (Abstract)

A. Abate , Delft Center for Syst. & Control, Delft Univ. of Technol., Delft, Netherlands
S. Vincent , Ecole Normale Super. de Lyon, Lyon, France
R. Dobbe , Delft Center for Syst. & Control, Delft Univ. of Technol., Delft, Netherlands
A. Silletti , Dept. of Inf. Eng., Univ. of Padova, Padua, Italy
N. Master , Dept. of Electr. Eng. & Comput. Sci., Univ. of California at Berkeley, Berkeley, CA, USA
J. D. Axelrod , Dept. of Pathology, Stanford Univ., Stanford, CA, USA
C. J. Tomlin , Dept. of Electr. Eng. & Comput. Sci., Univ. of California at Berkeley, Berkeley, CA, USA
pp. 1607-1620

A Tabu Search Approach for the NMR Protein Structure-Based Assignment Problem (Abstract)

G. Cavuslar , Univ. of Wisconsin-Madison, Madison, WI, USA
B. Catay , Sabanci Univ., Istanbul, Turkey
M. S. Apaydin , Istanbul Sehir Univ., Istanbul, Turkey
pp. 1621-1628

An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence (Abstract)

C. Ma , Dept. of Comput. Sci., Univ. of Hong Kong, Hong Kong, China
T. K. F. Wong , Dept. of Comput. Sci., Univ. of Hong Kong, Hong Kong, China
T. W. Lam , Dept. of Comput. Sci., Univ. of Hong Kong, Hong Kong, China
W. K. Hon , Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan
K. Sadakane , Nat. Inst. of Inf., Tokyo, Japan
S. M. Yiu , Dept. of Comput. Sci., Univ. of Hong Kong, Hong Kong, China
pp. 1629-1638

Automatic Identification and Classification of Noun Argument Structures in Biomedical Literature (Abstract)

I. B. Ozyurt , Dept. of Psychiatry, Univ. of California, San Diego, La Jolla, CA, USA
pp. 1639-1648

Biomarker Identification and Cancer Classification Based on Microarray Data Using Laplace Naive Bayes Model with Mean Shrinkage (Abstract)

Meng-Yun Wu , Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
Dao-Qing Dai , Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
Yu Shi , Sch. of Math. & Stat., Zhengzhou Normal Univ., Zhengzhou, China
Hong Yan , Dept. of Electron. Eng., City Univ. of Hong Kong, Kowloon, China
Xiao-Fei Zhang , Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
pp. 1649-1662

Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies (Abstract)

O. Irsoy , Dept. of Comput. Eng., Bogazici Univ., Istanbul, Turkey
O. T. Yildiz , Dept. of Comput. Eng., Isik Univ., Istanbul, Turkey
E. Alpaydin , Dept. of Comput. Eng., Bogazici Univ., Istanbul, Turkey
pp. 1663-1675

Distinguishing Endogenous Retroviral LTRs from SINE Elements Using Features Extracted from Evolved Side Effect Machines (Abstract)

W. Ashlock , Dept. of Comput. Sci. & Eng., York Univ., Toronto, ON, Canada
S. Datta , Dept. of Comput. Sci. & Eng., York Univ., Toronto, ON, Canada
pp. 1676-1689

Improving Protein-Protein Interaction Pair Ranking with an Integrated Global Association Score (Abstract)

Richard Tzong-Han Tsai , Dept. of Comput. Sci. & Eng., Yuan Ze Univ., Chungli, Taiwan
pp. 1690-1695

Large-Scale Signaling Network Reconstruction (Abstract)

S. Hashemikhabir , Dept. of Comput. Eng., Middle East Tech. Univ., Ankara, Turkey
E. S. Ayaz , Dept. of Comput. & Inf. Sci. & Eng., Univ. of Florida, Gainesville, FL, USA
Y. Kavurucu , Dept. of Comput. & Inf. Sci. & Eng., Univ. of Florida, Gainesville, FL, USA
T. Can , Dept. of Comput. Eng., Middle East Tech. Univ., Ankara, Turkey
T. Kahveci , Dept. of Comput. & Inf. Sci. & Eng., Univ. of Florida, Gainesville, FL, USA
pp. 1696-1708

Multiparameter Spectral Representation of Noise-Induced Competence in Bacillus Subtilis (Abstract)

K. Sargsyan , Sandia Nat. Labs., Livermore, CA, USA
C. Safta , Sandia Nat. Labs., Livermore, CA, USA
B. Debusschere , Sandia Nat. Labs., Livermore, CA, USA
H. Najm , Sandia Nat. Labs., Livermore, CA, USA
pp. 1709-1723

On the Steady-State Distribution in the Homogeneous Ribosome Flow Model (Abstract)

M. Margaliot , Sch. of Electr. Eng.-Syst., Tel-Aviv Univ., Tel-Aviv, Israel
T. Tuller , Dept. of Biomed. Eng., Tel-Aviv Univ., Tel-Aviv, Israel
pp. 1724-1736

Probabilistic Arithmetic Automata and Their Applications (Abstract)

T. Marschall , Life Sci. Group, Centrum Wiskunde & Inf. (CWI), Amsterdam, Netherlands
I. Herms , Fac. of Technol., Bielefeld Univ., Bielefeld, Germany
H. Kaltenbach , Dept. of Biosyst. Sci.e & Eng., Swiss Fed. Inst. of Technol. (ETH), Basel, Switzerland
S. Rahmann , Inst. of Human Genetics, Univ. of Duisburg-Essen, Essen, Germany
pp. 1737-1750

SC³: Triple Spectral Clustering-Based Consensus Clustering Framework for Class Discovery from Cancer Gene Expression Profiles (Abstract)

Zhiwen Yu , Higher Educ. Megacenter, South China Univ. of Technol., Guangzhou, China
Le Li , Higher Educ. Megacenter, South China Univ. of Technol., Guangzhou, China
J. You , Dept. of Comput., Hong Kong Polytech. Univ., Kowloon, China
Hau-San Wong , Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
Guoqiang Han , Higher Educ. Megacenter, South China Univ. of Technol., Guangzhou, China
pp. 1751-1765

Sequence-Based Prediction of DNA-Binding Residues in Proteins with Conservation and Correlation Information (Abstract)

Xin Ma , State Key Lab. of Bioelectronics, Southeast Univ., Nanjing, China
Jing Guo , State Key Lab. of Bioelectronics, Southeast Univ., Nanjing, China
Hong-De Liu , State Key Lab. of Bioelectronics, Southeast Univ., Nanjing, China
Jian-Ming Xie , State Key Lab. of Bioelectronics, Southeast Univ., Nanjing, China
Xiao Sun , State Key Lab. of Bioelectronics, Southeast Univ., Nanjing, China
pp. 1766-1775

Symmetry Compression Method for Discovering Network Motifs (Abstract)

Jianxin Wang , Sch. of Inf. Eng. & Sci., Central South Univ., Changsha, China
Yuannan Huang , Sch. of Inf. Eng. & Sci., Central South Univ., Changsha, China
Fang-Xiang Wu , Dept. of Mech. Eng., Univ. of Saskatchewan, Saskatoon, SK, Canada
Yi Pan , Dept. of Comput. Sci., Georgia State Univ., Atlanta, GA, USA
pp. 1776-1789

Top-k Similar Graph Matching Using TraM in Biological Networks (Abstract)

M. S. Amin , Dept. of Comput. Sci., Wayne State Univ., Sunnyvale, CA, USA
R. L. Finley , Center for Mol. Med. & Genetics, Wayne State Univ., Detroit, MI, USA
H. M. Jamil , Dept. of Comput. Sci., Univ. of Idaho, Moscow, ID, USA
pp. 1790-1804

uAnalyze: Web-Based High-Resolution DNA Melting Analysis with Comparison to Thermodynamic Predictions (Abstract)

Z. L. Dwight , Dept. of Pathology, Univ. of Utah, Salt Lake City, UT, USA
R. Palais , Dept. of Math., Utah Valley Univ., Orem, UT, USA
C. T. Wittwer , Dept. of Pathology, Univ. of Utah, Salt Lake City, UT, USA
pp. 1805-1811

A Fast Ranking Algorithm for Predicting Gene Functions in Biomolecular Networks (Abstract)

M. Re , Dipt. di Inf., Univ. degli Studi di Milano, Milan, Italy
M. Mesiti , Dipt. di Inf., Univ. degli Studi di Milano, Milan, Italy
G. Valentini , Dipt. di Inf., Univ. degli Studi di Milano, Milan, Italy
pp. 1812-1818

Fuzzy Intervention in Biological Phenomena (Abstract)

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
N. Meskin , Dept. of Electr. Eng., Qatar Univ., Doha, Qatar
A. Datta , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
E. R. Dougherty , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
pp. 1819-1825

In Silico Search of DNA Drugs Targeting Oncogenes (Abstract)

G. Papadakis , Dept. of Biol., Univ. of Crete, Heraklion, Greece
E. Gizeli , Dept. of Biol., Univ. of Crete, Heraklion, Greece
pp. 1826-1830

Investigating Topic Models' Capabilities in Expression Microarray Data Classification (Abstract)

M. Bicego , Dipt. di Inf., Univ. degli Studi di Verona, Verona, Italy
P. Lovato , Dipt. di Inf., Univ. degli Studi di Verona, Verona, Italy
A. Perina , Microsoft Res., Redmond, WA, USA
M. Fasoli , Dipt. di Biotecnologie, Univ. degli Studi di Verona, Verona, Italy
M. Delledonne , Dipt. di Biotecnologie, Univ. degli Studi di Verona, Verona, Italy
M. Pezzotti , Dipt. di Biotecnologie, Univ. degli Studi di Verona, Verona, Italy
A. Polverari , Dipt. di Biotecnologie, Univ. degli Studi di Verona, Verona, Italy
V. Murino , Anal. & Comput. Vision (PAVIS), Ist. Italiano di Tecnol. (IIT), Genoa, Italy
pp. 1831-1836

KungFQ: A Simple and Powerful Approach to Compress fastq Files (Abstract)

E. Grassi , Dept. of Genetics, Biol. & Biochem., Mol. Biotechnol. Center, Turin, Italy
F. D. Gregorio , DNDG srl, Turin, Italy
I. Molineris , Dept. of Genetics, Biol. & Biochem., Mol. Biotechnol. Center, Turin, Italy
pp. 1837-1842

On the Hardness of Counting and Sampling Center Strings (Abstract)

C. Boucher , Dept. of Comput. Sci., Colorado State Univ., Fort Collins, CO, USA
M. Omar , Dept. of Math., California Inst. of Technol., Pasadena, CA, USA
pp. 1843-1846

"Pull Moves" for Rectangular Lattice Polymer Models Are Not Fully Reversible (Abstract)

D. Györffy , Res. Centre for Natural Sci., Inst. of Enzymology, Budapest, Hungary
P. Zavodszky , Res. Centre for Natural Sci., Inst. of Enzymology, Budapest, Hungary
A. Szilágyi , Res. Centre for Natural Sci., Inst. of Enzymology, Budapest, Hungary
pp. 1847-1849

A Simpler and More Accurate AUTO-HDS Framework for Clustering and Visualization of Biological Data (Abstract)

R. J. G. B. Campello , Dept. of Comput. Sci., Univ. of Alberta, Edmonton, AB, Canada
D. Moulavi , Dept. of Comput. Sci., Univ. of Alberta, Edmonton, AB, Canada
J. Sander , Dept. of Comput. Sci., Univ. of Alberta, Edmonton, AB, Canada
pp. 1850-1852
Errata
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