Table of Contents

• A Clustering Approach to Identify Intergenic Non-coding RNA in Mouse MacrophagesLana X. Garmire, Shankar Subramaniam, David G. Garmire, Christopher K. Glass. 1-6 [doi]
• A Multi-stage Spectral Alignment Strategy for Unrestrictive PTM Peptide IdentificationChangyong Yu, Guoren Wang, Yuhai Zhao, Keming Mao. 7-13 [doi]
• A Novel Wavelet Based Algorithm for Spike and Wave Detection in Absence EpilepsyPetros Xanthopoulos, Steffen Rebennack, Chang-Chia Liu, Jicong Zhang, Gregory L. Holmes, Basim M. Uthman, Panos M. Pardalos. 14-19 [doi]
• A Self-Healing Approach for a Domain-Specific Deep Web Search ToolFan Wang, Gagan Agrawal. 20-25 [doi]
• A Supervised Approach for Predicting Patient Survival with Gene Expression DataKarthik Devarajan, Yan Zhou, Neeraj Chachra, Nader Ebrahimi. 26-31 [doi]
• An Accurate Prediction Method for Protein Structural Class from Signal Patterns of NMR Spectra in the Absence of Chemical Shift AssignmentsHiromi Arai, Naoya Tochio, Tsuyoshi Kato, Takanori Kigawa, Masayuki Yamamura. 32-37 [doi]
• An Elastic Video Interpolation Methodology for Wireless Capsule Endoscopy VideosAlexandros Karargyris, Nikolaos G. Bourbakis. 38-43 [doi]
• Analysis and Optimization of C3 Photosynthetic Carbon MetabolismGiovanni Stracquadanio, Renato Umeton, Alessio Papini, Pietro Liò, Giuseppe Nicosia. 44-51 [doi]
• Automated Quantification of Muscle and Fat in the Thigh from Water-, Fat- and Non-suppressed MR ImagesSokratis Makrogiannis, Suraj Serai, Kenneth W. Fishbein, Willie Laney, Catherine Schreiber, William B. Ershler, Luigi Ferrucci, Richard G. Spencer. 52-57 [doi]
• BLAST Tree: Fast Filtering for Genomic Sequence ClassificationStuart King, Yanni Sun, James R. Cole, Sakti Pramanik. 58-65 [doi]
• Chinese Cardiovascular Disease Database (CCDD) and Its Management ToolJia-wei Zhang, Li-Ping Wang, Xia Liu, Hong-hai Zhu, Jun Dong. 66-72 [doi]
• Combining Prostate Cancer Region Predictions from MALDI Spectra Processing and Texture AnalysisJiang Li, Ayyappa Vadlamudi, Shao-Hui Chuang, Xiaoyan Sun, Bo Sun, Frederic D. McKenzie, Lisa H. Cazares, Julius Nyalwidhe, Dean Troyer, O. John Semmes. 73-78 [doi]
• Comparison of Co-temporal Modeling Algorithms on Sparse Experimental Time Series Data SetsEdward E. Allen, James L. Norris, David J. John, Stan J. Thomas, William H. Turkett Jr., Jacquelyn S. Fetrow. 79-85 [doi]
• Compressed q-Gram Indexing for Highly Repetitive Biological SequencesFrancisco Claude, Antonio Fariña, Miguel A. Martínez-Prieto, Gonzalo Navarro. 86-91 [doi]
• Computational Framework for Microstructural Bone Dynamics Model and Its EvaluationTaehyong Kim, Woochang Hwang, Aidong Zhang, Murali Ramanathan. 92-98 [doi]
• Detecting Coevolution of Functionally Related Proteins for Automated Protein AnnotationAlan L. Kwan, Susan K. Dutcher, Gary D. Stormo. 99-105 [doi]
• Detection of Mild Cognitive Impairment Using Image Differences and Clinical FeaturesLin Li, James Z. Wang, Dheeraj Chahal, Mark A. Eckert, Carl Lozar. 106-111 [doi]
• Dynamic Complexity of the Temporal Transcriptional Regulation Program in Human EndotoxemiaTung T. Nguyen, Panagiota T. Foteinou, Ioannis P. Androulakis, Steve E. Calvano, Stephen F. Lowry. 112-117 [doi]
• Effects of Triadimefon on the Metabolism of Cultured HepatocytesVidya V. Iyer, Ioannis P. Androulakis, Charles M. Roth, Marianthi G. Ierapetritou. 118-123 [doi]
• eSBH: An Accurate Constructive Heuristic Algorithm for DNA Sequencing by HybridizationYang Chen, Jinglu Hu. 124-129 [doi]
• Fast Phased Small RNA Cycle Counting AlgorithmsForrest Sheng Bao, Zhixin Xie, Yuanlin Zhang. 130-135 [doi]
• Finding Dynamic Modules of Biological Regulatory NetworksFerhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci. 136-143 [doi]
• Functional Flow Simulation Based Analysis of Protein Interaction NetworkLei Shi, Young-Rae Cho, Aidong Zhang. 144-149 [doi]
• How to Fold Amino Acid Interaction Networks by Computational Intelligence MethodsOmar Gaci. 150-155 [doi]
• Hybrid Modeling and Simulation of Insulin Secretion Pathway in Pancreatic IsletsYang Pu, Saangho Lee, David C. Samuels, Layne T. Watson, Yang Cao. 156-161 [doi]
• Identification of Viral Protein Genotypic Determinants Using Combinatorial Filtering and Active LearningChuang Wu, Andrew S. Walsh, Roni Rosenfeld. 162-167 [doi]
• Identifying Hidden Confounders in Gene Networks by Bayesian NetworksTomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano. 168-173 [doi]
• Improved Immune Genetic Algorithm for Clustering Protein-Protein Interaction NetworkHamid Ravaee, Ali Masoudi-Nejad, Saeed Omidi, Ali Moeini. 174-179 [doi]
• Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome NetworkMarylens Hernandez, Alexander Lachmann, Shan Zhao, Kunhong Xiao, Avi Ma ayan. 180-184 [doi]
• Knowledge-Guided Docking of Flexible Ligands to SH2 Domain ProteinsHaiyun Lu, Shamima Banu Bte Sm Rashid, Hao Li, Wee Kheng Leow, Yih-Cherng Liou. 185-190 [doi]
• Learning Proteomic Network Structure by a New Hill Climbing AlgorithmDong-Chul Kim, Jean Gao, Chin-Rang Yang. 191-196 [doi]
• Modeling Circadian Rhythms in InflammationJeremy D. Scheff, Ioannis P. Androulakis, Steve E. Calvano, Stephen F. Lowry. 197-202 [doi]
• Modular Software Design for Brachytherapy Image-Guided Robotic SystemsIvan Buzurovic, Tarun Kanti Podder, Lei Fu, Yan Yu. 203-208 [doi]
• Multichannel Robot for Image-Guided BrachytherapyTarun Kanti Podder, Ivan Buzurovic, Yan Yu. 209-213 [doi]
• On Constructing Thermodynamically Consistent Parametrizations of Kinetic ModelsW. Garrett Jenkinson, John Goutsias. 214-219 [doi]
• Polony Identification Using the EM Algorithm Based on a Gaussian Mixture ModelWei Li, Paul M. Ruegger, James Borneman, Tao Jiang. 220-225 [doi]
• Prediction of Catalytic Residues in Proteins Using a Consensus of Prediction (CoP) ApproachNatalia V. Petrova, Cathy H. Wu. 226-231 [doi]
• Qualitative Analysis of Gene Regulatory Networks by Satisfiability Checking of Linear Temporal LogicSohei Ito, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. 232-237 [doi]
• Quantification and Analysis of Combination Drug Synergy in High-Throughput Transcriptome StudiesZeynep H. Gümüs, Fernando Siso-Nadal, Ada Gjrezi, Paul McDonagh, Iya Khalil, Paraskevi Giannakakou, Harel Weinstein. 238-243 [doi]
• Space Efficient Diagonal Linear Space Sequence AlignmentGandhi Arpit, Raghavendra Adiga, Kuruvilla Varghese. 244-249 [doi]
• Structural Differences between Proteins with Similar SequencesQian Cong, Bong-Hyun Kim, Lisa N. Kinch, Nick V. Grishin. 250-256 [doi]
• The Effect of Sequence Error and Partial Training Data on BLAST AccuracySteven D. Essinger, Gail L. Rosen. 257-262 [doi]
• Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding SimulationsStanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga. 263-266 [doi]
• TRAC: A Platform for Structure-Function Studies of NSS-Proteins Integrates Information from Bioinformatics and Biomedical LiteratureLei Shi, Marko Srdanovic, Thijs Beuming, Lucy Skrabanek, Jonathan A. Javitch, Harel Weinstein. 267-272 [doi]
• Tumor Motion Prediction and Tracking in Adaptive RadiotherapyIvan Buzurovic, Tarun Kanti Podder, Ke Huang, Yan Yu. 273-278 [doi]
• 3D Representation of the Digestive Tract Surface in Wireless Capsule Endoscopy VideosAlexandros Karargyris, Orestis Karargyris, Nikolaos G. Bourbakis. 279-280 [doi]
• A Comparative Study of a Novel AE-nLMS Filter and Two Traditional Filters in Predicting Respiration Induced Motion of the TumorKe Huang, Ivan Buzurovic, Yan Yu, Tarun Kanti Podder. 281-282 [doi]
• A Comparison between Transmembrane Helices and Reentrant LoopsChanghui Yan, Jingru Luo. 283-284 [doi]
• A Noninvasive Multimodal Sono-contrast NIR Spectroscopy System for Breast Cancer DiagnosisKai Guo Yan, Tarun Kanti Podder, Ke Huang, Yan Yu, Lydia Liao. 285-286 [doi]
• Analysis on the Correlation Relationships between the Temperature Range Condition and the Genic GC Content Levels of ProkaryotesHao Zheng, Hongwei Wu. 287-288 [doi]
• Assessment of the Binding Characteristics of Human Immunodeficiency Virus Type 1 Glycoprotein120 and Host Cluster of Differentiation4 Using Digital Signal ProcessingNorbert Nwankwo, Huseyin Seker. 289-290 [doi]
• Comparison of Gene Prediction Programs for Metagenomic DataNon Yok, Gail Rosen. 291-292 [doi]
• Corpus Callosum Shape Deformation Analysis for Multiple SclerosisFoued Derraz, Abdelmalik Taleb-Ahmed, Laurent Peyrodie, Antonio Pinti, Azeddine Chikh, Fethi Bereksi-Reguig. 293 [doi]
• Detection of Errors and Inconsistencies in Biomolecular Databases through Integrative Approaches and Quality ControlsMarco Masseroli, Giorgio Ghisalberti, Luca Tettamanti. 294-295 [doi]
• Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least SquaresHyunsoo Kim, Yingtao Bi, Ramana V. Davuluri. 296-297 [doi]
• Ethanol Effects on Transcription Factor Network Regulating Stem Cell DifferentiationRajanikanth Vadigepalli, Joshua Ogony, Helen Anni. 298-299 [doi]
• Gene Set Analysis with CovariatesIonut Bebu, Françoise Seillier-Moiseiwitsch, Jing Wu, Thomas Mathew. 300-301 [doi]
• Identifying Prostate Cancer-Related Networks from Microarray Data Based on Genotype-Phenotype Networks Using Markov Blanket SearchHsiang-Yuan Yeh, Yi-Yu Liu, Cheng-Yu Yeh, Von-Wun Soo. 302-303 [doi]
• Instance Discovery and Schema Matching with Applications to Biological Deep Web Data IntegrationTantan Liu, Fan Wang, Gagan Agrawal. 304-305 [doi]
• Methods for Designing Reliable Probe ArraysMichele Lombardi, Luca Benini, Abhishek Garg, Giovanni De Micheli. 306-307 [doi]
• Multi Level Clustering of Phylogenetic ProfilesFotis E. Psomopoulos, Pericles A. Mitkas. 308-309 [doi]
• Partial AUC for Differentiated Gene DetectionZhenqiu Liu, Terry Hyslop. 310-311 [doi]
• Prediction of Gene Ontology Annotations Based on Gene Functional ClusteringMarco Tagliasacchi, Roberto Sarati, Marco Masseroli. 312-313 [doi]
• Use of Hilbert Huang Transform in Uterine Contraction AnalysisKemal Aydin, Murat Demirer, Coskun Bayrak. 314-315 [doi]
• Using the Semantically Interoperable Biospecimen Repository Application, caTissue: End User Deployment Lessons LearnedJack W. London, Devjani Chatterjee. 316-317 [doi]