10. BIBE 2010: Philadelphia, Pennsylvania, USA

Regular Papers

• Lana X. Garmire, Shankar Subramaniam, David G. Garmire, Christopher K. Glass:
  A Clustering Approach to Identify Intergenic Non-coding RNA in Mouse Macrophages. 1-6
  
• Changyong Yu, Guoren Wang, Yuhai Zhao, Keming Mao:
  A Multi-stage Spectral Alignment Strategy for Unrestrictive PTM Peptide Identification. 7-13
  
• Petros Xanthopoulos, Steffen Rebennack, Chang-Chia Liu, Jicong Zhang, Gregory L. Holmes, Basim M. Uthman, Panos M. Pardalos:
  A Novel Wavelet Based Algorithm for Spike and Wave Detection in Absence Epilepsy. 14-19
  
• Fan Wang, Gagan Agrawal:
  A Self-Healing Approach for a Domain-Specific Deep Web Search Tool. 20-25
  
• Karthik Devarajan, Yan Zhou, Neeraj Chachra, Nader Ebrahimi:
  A Supervised Approach for Predicting Patient Survival with Gene Expression Data. 26-31
  
• Hiromi Arai, Naoya Tochio, Tsuyoshi Kato, Takanori Kigawa, Masayuki Yamamura:
  An Accurate Prediction Method for Protein Structural Class from Signal Patterns of NMR Spectra in the Absence of Chemical Shift Assignments. 32-37
  
• Alexandros Karargyris, Nikolaos G. Bourbakis:
  An Elastic Video Interpolation Methodology for Wireless Capsule Endoscopy Videos. 38-43
  
• Giovanni Stracquadanio, Renato Umeton, Alessio Papini, Pietro Liò, Giuseppe Nicosia:
  Analysis and Optimization of C3 Photosynthetic Carbon Metabolism. 44-51
  
• Sokratis Makrogiannis, Suraj Serai, Kenneth W. Fishbein, Willie Laney, Catherine Schreiber, William B. Ershler, Luigi Ferrucci, Richard G. S. Spencer:
  Automated Quantification of Muscle and Fat in the Thigh from Water-, Fat- and Non-suppressed MR Images. 52-57
  
• Stuart King, Yanni Sun, James R. Cole, Sakti Pramanik:
  BLAST Tree: Fast Filtering for Genomic Sequence Classification. 58-65
  
• Jia-wei Zhang, Li-ping Wang, Xia Liu, Hong-hai Zhu, Jun Dong:
  Chinese Cardiovascular Disease Database (CCDD) and Its Management Tool. 66-72
  
• Jiang Li, Ayyappa Vadlamudi, Shao-Hui Chuang, Xiaoyan Sun, Bo Sun, Frederic D. McKenzie, Lisa H. Cazares, Julius Nyalwidhe, Dean Troyer, O. John Semmes:
  Combining Prostate Cancer Region Predictions from MALDI Spectra Processing and Texture Analysis. 73-78
  
• Edward E. Allen, James L. Norris, David J. John, Stan J. Thomas, William H. Turkett Jr., Jacquelyn S. Fetrow:
  Comparison of Co-temporal Modeling Algorithms on Sparse Experimental Time Series Data Sets. 79-85
  
• Francisco Claude, Antonio Fariña, Miguel A. Martínez-Prieto, Gonzalo Navarro:
  Compressed q-Gram Indexing for Highly Repetitive Biological Sequences. 86-91
  
• Taehyong Kim, Woochang Hwang, Aidong Zhang, Murali Ramanathan:
  Computational Framework for Microstructural Bone Dynamics Model and Its Evaluation. 92-98
  
• Alan L. Kwan, Susan K. Dutcher, Gary D. Stormo:
  Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation. 99-105
  
• Lin Li, James Z. Wang, Dheeraj Chahal, Mark A. Eckert, Carl Lozar:
  Detection of Mild Cognitive Impairment Using Image Differences and Clinical Features. 106-111
  
• Tung T. Nguyen, Panagiota T. Foteinou, Ioannis P. Androulakis, Steve E. Calvano, Stephen F. Lowry:
  Dynamic Complexity of the Temporal Transcriptional Regulation Program in Human Endotoxemia. 112-117
  
• Vidya V. Iyer, Ioannis P. Androulakis, Charles M. Roth, Marianthi G. Ierapetritou:
  Effects of Triadimefon on the Metabolism of Cultured Hepatocytes. 118-123
  
• Yang Chen, Jinglu Hu:
  eSBH: An Accurate Constructive Heuristic Algorithm for DNA Sequencing by Hybridization. 124-129
  
• Forrest Sheng Bao, Zhixin Xie, Yuanlin Zhang:
  Fast Phased Small RNA Cycle Counting Algorithms. 130-135
  
• Ferhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci:
  Finding Dynamic Modules of Biological Regulatory Networks. 136-143
  
• Lei Shi, Young-Rae Cho, Aidong Zhang:
  Functional Flow Simulation Based Analysis of Protein Interaction Network. 144-149
  
• Omar Gaci:
  How to Fold Amino Acid Interaction Networks by Computational Intelligence Methods. 150-155
  
• Yang Pu, Saangho Lee, David C. Samuels, Layne T. Watson, Yang Cao:
  Hybrid Modeling and Simulation of Insulin Secretion Pathway in Pancreatic Islets. 156-161
  
• Chuang Wu, Andrew S. Walsh, Roni Rosenfeld:
  Identification of Viral Protein Genotypic Determinants Using Combinatorial Filtering and Active Learning. 162-167
  
• Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano:
  Identifying Hidden Confounders in Gene Networks by Bayesian Networks. 168-173
  
• Hamid Ravaee, Ali Masoudi-Nejad, Saeed Omidi, Ali Moeini:
  Improved Immune Genetic Algorithm for Clustering Protein-Protein Interaction Network. 174-179
  
• Marylens Hernandez, Alexander Lachmann, Shan Zhao, Kunhong Xiao, Avi Ma'ayan:
  Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. 180-184
  
• Haiyun Lu, Shamima Banu Bte Sm Rashid, Hao Li, Wee Kheng Leow, Yih-Cherng Liou:
  Knowledge-Guided Docking of Flexible Ligands to SH2 Domain Proteins. 185-190
  
• Dong-Chul Kim, Jean Gao, Chin-Rang Yang:
  Learning Proteomic Network Structure by a New Hill Climbing Algorithm. 191-196
  
• Jeremy D. Scheff, Ioannis P. Androulakis, Steve E. Calvano, Stephen F. Lowry:
  Modeling Circadian Rhythms in Inflammation. 197-202
  
• Ivan Buzurovic, Tarun Kanti Podder, Lei Fu, Yan Yu:
  Modular Software Design for Brachytherapy Image-Guided Robotic Systems. 203-208
  
• Tarun Kanti Podder, Ivan Buzurovic, Yan Yu:
  Multichannel Robot for Image-Guided Brachytherapy. 209-213
  
• W. Garrett Jenkinson, John Goutsias:
  On Constructing Thermodynamically Consistent Parametrizations of Kinetic Models. 214-219
  
• Wei Li, Paul M. Ruegger, James Borneman, Tao Jiang:
  Polony Identification Using the EM Algorithm Based on a Gaussian Mixture Model. 220-225
  
• Natalia V. Petrova, Cathy H. Wu:
  Prediction of Catalytic Residues in Proteins Using a Consensus of Prediction (CoP) Approach. 226-231
  
• Sohei Ito, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki:
  Qualitative Analysis of Gene Regulatory Networks by Satisfiability Checking of Linear Temporal Logic. 232-237
  
• Zeynep H. Gümüs, Fernando Siso-Nadal, Ada Gjrezi, Paul McDonagh, Iya Khalil, Paraskevi Giannakakou, Harel Weinstein:
  Quantification and Analysis of Combination Drug Synergy in High-Throughput Transcriptome Studies. 238-243
  
• Gandhi Arpit, Raghavendra Adiga, Kuruvilla Varghese:
  Space Efficient Diagonal Linear Space Sequence Alignment. 244-249
  
• Qian Cong, Bong-Hyun Kim, Lisa N. Kinch, Nick V. Grishin:
  Structural Differences between Proteins with Similar Sequences. 250-256
  
• Steven D. Essinger, Gail L. Rosen:
  The Effect of Sequence Error and Partial Training Data on BLAST Accuracy. 257-262
  
• Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga:
  Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. 263-266
  
• Lei Shi, Marko Srdanovic, Thijs Beuming, Lucy Skrabanek, Jonathan A. Javitch, Harel Weinstein:
  TRAC: A Platform for Structure-Function Studies of NSS-Proteins Integrates Information from Bioinformatics and Biomedical Literature. 267-272
  
• Ivan Buzurovic, Tarun Kanti Podder, Ke Huang, Yan Yu:
  Tumor Motion Prediction and Tracking in Adaptive Radiotherapy. 273-278
  

Poster Papers

• Alexandros Karargyris, Orestis Karargyris, Nikolaos G. Bourbakis:
  3D Representation of the Digestive Tract Surface in Wireless Capsule Endoscopy Videos. 279-280
  
• Ke Huang, Ivan Buzurovic, Yan Yu, Tarun Kanti Podder:
  A Comparative Study of a Novel AE-nLMS Filter and Two Traditional Filters in Predicting Respiration Induced Motion of the Tumor. 281-282
  
• Changhui Yan, Jingru Luo:
  A Comparison between Transmembrane Helices and Reentrant Loops. 283-284
  
• Kai Guo Yan, Tarun Kanti Podder, Ke Huang, Yan Yu, Lydia Liao:
  A Noninvasive Multimodal Sono-contrast NIR Spectroscopy System for Breast Cancer Diagnosis. 285-286
  
• Hao Zheng, Hongwei Wu:
  Analysis on the Correlation Relationships between the Temperature Range Condition and the Genic GC Content Levels of Prokaryotes. 287-288
  
• Norbert Nwankwo, Huseyin Seker:
  Assessment of the Binding Characteristics of Human Immunodeficiency Virus Type 1 Glycoprotein120 and Host Cluster of Differentiation4 Using Digital Signal Processing. 289-290
  
• Non Yok, Gail Rosen:
  Comparison of Gene Prediction Programs for Metagenomic Data. 291-292
  
• Foued Derraz, Abdelmalik Taleb-Ahmed, Laurent Peyrodie, Antonio Pinti, Azeddine Chikh, Fethi Bereksi-Reguig:
  Corpus Callosum Shape Deformation Analysis for Multiple Sclerosis. 293
  
• Marco Masseroli, Giorgio Ghisalberti, Luca Tettamanti:
  Detection of Errors and Inconsistencies in Biomolecular Databases through Integrative Approaches and Quality Controls. 294-295
  
• Hyunsoo Kim, Yingtao Bi, Ramana V. Davuluri:
  Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares. 296-297
  
• Rajanikanth Vadigepalli, Joshua Ogony, Helen Anni:
  Ethanol Effects on Transcription Factor Network Regulating Stem Cell Differentiation. 298-299
  
• Ionut Bebu, Françoise Seillier-Moiseiwitsch, Jing Wu, Thomas Mathew:
  Gene Set Analysis with Covariates. 300-301
  
• Hsiang-Yuan Yeh, Yi-Yu Liu, Cheng-Yu Yeh, Von-Wun Soo:
  Identifying Prostate Cancer-Related Networks from Microarray Data Based on Genotype-Phenotype Networks Using Markov Blanket Search. 302-303
  
• Tantan Liu, Fan Wang, Gagan Agrawal:
  Instance Discovery and Schema Matching with Applications to Biological Deep Web Data Integration. 304-305
  
• Michele Lombardi, Luca Benini, Abhishek Garg, Giovanni De Micheli:
  Methods for Designing Reliable Probe Arrays. 306-307
  
• Fotis E. Psomopoulos, Pericles A. Mitkas:
  Multi Level Clustering of Phylogenetic Profiles. 308-309
  
• Zhenqiu Liu, Terry Hyslop:
  Partial AUC for Differentiated Gene Detection. 310-311
  
• Marco Tagliasacchi, Roberto Sarati, Marco Masseroli:
  Prediction of Gene Ontology Annotations Based on Gene Functional Clustering. 312-313
  
• Kemal Aydin, Murat Demirer, Coskun Bayrak:
  Use of Hilbert Huang Transform in Uterine Contraction Analysis. 314-315
  
• Jack W. London, Devjani Chatterjee:
  Using the Semantically Interoperable Biospecimen Repository Application, caTissue: End User Deployment Lessons Learned. 316-317
  

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