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TABLE OF CONTENTS
Issue No. 05 - Sept.-Oct. (vol. 10)
ISSN: 1545-5963

[Front Cover] (PDF)

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[Front inside cover] (PDF)

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Nonoverlapping Clone Pooling for High-Throughput Sequencing (Abstract)

Reginaldo M. Kuroshu , Inst. de Cienc. e Tecnol., Univ. Fed. de Sao Paulo, Sao Josedos Campos, Brazil
pp. 1091-1097

Improved Multiple Sequence Alignments Using Coupled Pattern Mining (Abstract)

K. S. M. Tozammel Hossain , Dept. of Comput. Sci., Virginia Tech, Blacskburg, VA, USA
Debprakash Patnaik , Amazon Inc., Seattle, WA, USA
Srivatsan Laxman , Microsoft Res., Bangalore, India
Prateek Jain , Microsoft Res., Bangalore, India
Chris Bailey-Kellogg , Dept. of Comput. Sci., Dartmouth Coll., Hanover, NH, USA
Naren Ramakrishnan , Dept. of Comput. Sci., Virginia Tech, Blacskburg, VA, USA
pp. 1098-1112

Reverse Engineering Molecular Hypergraphs (Abstract)

Ahsanur Rahman , Dept. of Comput. Sci., Virginia Tech, Blacksburg, VA, USA
Christopher L. Poirel , Dept. of Comput. Sci., Virginia Tech, Blacksburg, VA, USA
David J. Badger , Dept. of Comput. Sci., Virginia Tech, Blacksburg, VA, USA
Craig Estep , Dept. of Comput. Sci., Virginia Tech, Blacksburg, VA, USA
T. M. Murali , Dept. of Comput. Sci., Virginia Tech, Blacksburg, VA, USA
pp. 1113-1124

Stochastic Model Simulation Using Kronecker Product Analysis and Zassenhaus Formula Approximation (Abstract)

Mehmet Umut Caglar , Dept. of Phys., Texas Tech Univ., Lubbock, TX, USA
Ranadip Pal , Dept. of Phys., Texas Tech Univ., Lubbock, TX, USA
pp. 1125-1136

Coalescent-Based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data (Abstract)

Ming-Chi Tsai , CMU-Pitt PhD Program in Computational Biology, Pittsburgh
Guy Blelloch , Carnegie Mellon University, Pittsburgh
R. Ravi , Carnegie-Mellon University, Pittsburgh
Russell Schwartz , Carnegie Mellon University, Pittsburgh
pp. 1137-1149

Quantitative Analysis of Live-Cell Growth at the Shoot Apex of Arabidopsis thaliana: Algorithms for Feature Measurement and Temporal Alignment (Abstract)

Oben M. Tataw , Univ. of California, Riverside, Riverside, CA, USA
G. Venugopala Reddy , Univ. of California, Riverside, Riverside, CA, USA
Eamonn J. Keogh , Univ. of California, Riverside, Riverside, CA, USA
Amit K. Roy-Chowdhury , Univ. of California, Riverside, Riverside, CA, USA
pp. 1150-1161

Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction (Abstract)

Kevin Molloy , Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
Sameh Saleh , Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
Amarda Shehu , Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
pp. 1162-1175

Expanded Explorations into the Optimization of an Energy Function for Protein Design (Abstract)

Yao-ming Huang , Dept. of Bioeng. & Therapeutive Sci., Univ. of California, San Francisco, San Francisco, CA, USA
Christopher Bystroff , Rensselaer Polytech. Inst., Troy, NY, USA
pp. 1176-1187

Biological Sequence Classification with Multivariate String Kernels (Abstract)

Pavel P. Kuksa , Machine Learning Dept., NEC Labs. America, Inc., Princeton, NJ, USA
pp. 1201-1210

Text Categorization of Biomedical Data Sets Using Graph Kernels and a Controlled Vocabulary (Abstract)

Said Bleik , Inf. Syst. Dept., Univ. Heights, Newark, NJ, USA
Meenakshi Mishra , Dept. of Electr. Eng. & Comput. Sci., Univ. of Kansas, Lawrence, KS, USA
Jun Huan , Dept. of Electr. Eng. & Comput. Sci., Univ. of Kansas, Lawrence, KS, USA
Min Song , Dept. of Libr. & Inf. Sci., Yonsei Univ., Seoul, South Korea
pp. 1211-1217

Chemical Name Extraction Based on Automatic Training Data Generation and Rich Feature Set (Abstract)

Su Yan , IBM Almaden Res. Center, San Jose, CA, USA
W. Scott Spangler , IBM Almaden Res. Center, San Jose, CA, USA
Ying Chen , IBM Almaden Res. Center, San Jose, CA, USA
pp. 1218-1233

Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing (Abstract)

Liliana D. Florea , Johns Hopkins University School of Medicine, Baltimore
Steven L. Salzberg , Johns Hopkins School of Medicine and Bloomberg School of Public Health, Baltimore
pp. 1234-1240

An Adaptive Window Length Strategy for Eukaryotic CDS Prediction (Abstract)

Devendra Kumar Shakya , Dept. of Biomed. Eng., Samrat Ashok Technol. Inst., Vidisha, India
Rajiv Saxena , Jaypee Univ. of Eng. & Technol., Guna, India
Sanjeev Narayan Sharma , Dept. of Biomed. Eng., Samrat Ashok Technol. Inst., Vidisha, India
pp. 1241-1252

Coalescent Histories for Caterpillar-Like Families (Abstract)

Noah A. Rosenberg , Stanford University, Stanford
pp. 1253-1262

Computing the Joint Distribution of Tree Shape and Tree Distance for Gene Tree Inference and Recombination Detection (Abstract)

Yujin Chung , Dept. of Stat., Univ. of Wisconsin, Madison, WI, USA
Nicole T. Perna , Dept. of Genetics, Univ. of Wisconsin, Madison, WI, USA
Cecile Ane , Dept. of Stat., Univ. of Wisconsin, Madison, WI, USA
pp. 1

FRESCO: Referential Compression of Highly Similar Sequences (Abstract)

Sebastian Wandelt , Humboldt-University of Berlin, Berlin
Ulf Leser , Humboldt-University of Berlin, Berlin
pp. 1275-1288

Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm (Abstract)

Kamal Al Nasr , Dept. of Comput. Sci., Tennessee State Univ., Nashville, TN, USA
Chunmei Liu , Dept. of Syst. & Comput. Sci., Howard Univ., Washington, DC, USA
Mugizi Rwebangira , Dept. of Syst. & Comput. Sci., Howard Univ., Washington, DC, USA
Legand Burge , Dept. of Syst. & Comput. Sci., Howard Univ., Washington, DC, USA
Jing He , Dept. of Comput. Sci., Old Dominion Univ., Norfolk, VA, USA
pp. 1289-1298

Operon Prediction Using Chaos Embedded Particle Swarm Optimization (Abstract)

Li-Yeh Chuang , Dept. of Chem. Eng., I-Shou Univ., Kaohsiung, Taiwan
Cheng-Huei Yang , Dept. of Electron. Commun. Eng., Nat. Kaohsiung Inst. of Marine Technol., Kaohsiung, Taiwan
Jui-Hung Tsai , Dept. of Electron. & Commun. Eng., Nat. Kaohsiung Marine Univ., Kaohsiung, Taiwan
Cheng-Hong Yang , Dept. of Electron. Eng., Nat. Kaohsiung Univ. of Appl. Sci., Kaohsiung, Taiwan
pp. 1299-1309

Statistical Detection of Boolean Regulatory Relationships (Abstract)

Ting Chen , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
Ulisses M. Braga-Neto , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
pp. 1

Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model (Abstract)

Yoram Zarai , Sch. of Electr. Eng., Tel-Aviv Univ., Tel-Aviv, Israel
Michael Margaliot , Sch. of Electr. Eng., Tel-Aviv Univ., Tel-Aviv, Israel
Tamir Tuller , Sch. of Electr. Eng., Tel-Aviv Univ., Tel-Aviv, Israel
pp. 1322-1328

Fast Computation of Minimal Cut Sets in Metabolic Networks with a Berge Algorithm that Utilizes Binary Bit Pattern Trees (HTML)

Christian Jungreuthmayer , University of Natural Resources and Life Sciences, Vienna and Austrian Centre of Industrial Biotechnology (ACIB), Vienna
Marie Beurton-Aimar , University of Bordeaux, Talence
Jurgen Zanghellini , University of Natural Resources and Life Sciences, Vienna and Austrian Centre of Industrial Biotechnology (ACIB), Vienna
pp. 1

Naïve Bayesian Classifiers with Multinomial Models for rRNA Taxonomic Assignment (Abstract)

Kuan-Liang Liu , Inst. of Inf. Manage., Nat. Cheng Kung Univ., Tainan, Taiwan
Tzu-Tsung Wong , Inst. of Inf. Manage., Nat. Cheng Kung Univ., Tainan, Taiwan
pp. 1

Strategy for Naturelike Designer Transcription Factors with Reduced Toxicity (Abstract)

Christian Bach , Dept. of Biomed. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
Prabir K. Patra , Dept. of Biomed. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
Jani M. Pallis , Dept. of Mech. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
William B. Sherman , Bard High Sch., Queens, NY, USA
Hassan Bajwa , Dept. of Electr. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
pp. 1340-1343

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