BIBM 2011: Atlanta, GA, USA
Fang-Xiang Wu, Mohammed Javeed Zaki, Shinichi Morishita, Yi Pan, Stephen Wong, Anastasia Christianson, Xiaohua Hu (Eds.): IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, GA, USA, 12-15 November, 2011. IEEE 2011 ISBN 978-1-4577-1799-4
Genomics and Molecular Structure, Function, and Evolution
Regular Papers
- Xin Chen, Tingting He, Xiaohua Hu, Yuan An, Xindong Wu: Inferring Functional Groups from Microbial Gene Catalogue with Probabilistic Topic Models. 3-9
- Qingyao Wu, Yunming Ye, Yang Liu, Michael K. Ng: Stratified Random Forest for Genome-wide Association Study. 10-15
- Jose Laborde, Anuj Srivastava, Jinfeng Zhang: Structure-based RNA Function Prediction Using Elastic Shape Analysis. 16-21
- Brian Y. Chen, Soutir Bandyopadhyay: VASP-S: A Volumetric Analysis and Statistical Model for Predicting Steric Influences on Protein-Ligand Binding Specificity. 22-29
- Jingfen Zhang, Dong Xu: Fast Algorithm for Clustering a Large Number of Protein Structural Decoys. 30-36
- Jianxin Wang, Xiaoqing Peng, Min Li, Yong Luo, Yi Pan: Active Protein Interaction Network and Its Application on Protein Complex Detection. 37-42
- Roberto Blanco: Simplification Methods for Maximum Parsimony: A Relational View. 49-56
- Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng: Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome. 57-62
- Min Li, Xuehong Wu, Jianxin Wang, Yi Pan: A New Measurement for Evaluating Clusters in Protein Interaction Networks. 63-68
- Ujwal R. Bagal, James Leebens-Mack, W. Walter Lorenz, Jeffrey F. D. Dean: Phylogenomic Analysis of the Phenylalanine Ammonia Lyase Gene Family in Loblolly Pine (Pinus Taeda L.). 69-74
- Cagri Ozcaglar, Amina Shabbeer, Natalia Kurepina, Bülent Yener, Kristin P. Bennett: Data-Driven Insights into Deletions of Mycobacterium tuberculosis Complex Chromosomal DR Region Using Spoligoforests. 75-82
- Sohee Oh, Jaehoon Lee, Min-Seok Kwon, Kyunga Kim, Taesung Park: Efficient and Fast Analysis for Detecting High Order Gene-by-Gene Interactions in a Genome-Wide Association Study. 83-88
- Pooya Shareghi, Yingfeng Wang, Russell L. Malmberg, Liming Cai: Simultaneous Prediction of RNA Secondary Structure and Helix Coaxial Stacking. 89-95
Short Papers
- Xiujuan Lei, Shuang Wu, Liang Ge, Aidong Zhang: Clustering PPI Data Based on Bacteria Foraging Optimization Algorithm. 96-99
- Jiandong Ding, Shusi Yu, Uwe Ohler, Jihong Guan, Shuigeng Zhou: imiRTP: An Integrated Method to Identifying miRNA-target Interactions in Arabidopsis thaliana. 100-104
- William Arndt, Jijun Tang: Emulating Insertion and Deletion Events in Genome Rearrangement Analysis. 105-108
- Andre J. Aberer, Alexandros Stamatakis: A Simple and Accurate Method for Rogue Taxon Identification. 118-122
- Bolin Chen, Yan Yan, Jin-Hong Shi, Shenggui Zhang, Fang-Xiang Wu: An Improved Graph Entropy-based Method for Identifying Protein Complexes. 123-126
- Weimin Luo, Keith C. C. Chan: Discovering Drug-Protein Interactions Based on their Fingerprints. 127-130
- Annie Chateau, Pierre Riou, Eric Rivals: Approximate Common Intervals in Multiple Genome Comparison. 131-134
- Jaeyoung Kim, Miyoung Shin: Employing Weighted Biological Network Structure for Finding Disease Genetic Markers in SNP Association Studies. 135-138
- Cristian Del Fabbro, Francesco Vezzi, Alberto Policriti: mrNA: The MPI Randomized Numerical Aligner. 139-142
- Vishal Bhola, Ajit S. Bopardikar, Rangavittal Narayanan, Kyusang Lee, TaeJin Ahn: No-Reference Compression of Genomic Data Stored in FASTQ Format. 147-150
- Brian E. Howard, Paola Veronese, Steffen Heber: Improved RNA-Seq Partitions in Linear Models for Isoform Quantification. 151-154
- Aldrin Montana, Alexander Dekhtyar, Emily Neal, Michael Black, Chris Kitts: Chronology-Sensitive Hierarchical Clustering of Pyrosequenced DNA Samples of E. coli: A Case Study. 155-159
- Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He: A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors. 160-163
Computational Systems Biology
Regular Papers
- Tianhai Tian: Stochastic Models for Studying the Degradation of mRNA Molecules. 167-172
- Zhenyu Yang, David Sankoff: Generalized Adjacency in Genetic Networks and the Conservation of Functional Gene Clusters. 173-178
- Bo Li, Yuehua Zhang, Pradip K. Srimani, Feng Luo: Predicing Yeast Synthetic Lethal Genetic Interactions Using Short Polypeptide Clusters. 185-190
- Jin-Hong Shi, Bolin Chen, Fang-Xiang Wu: Improve Accuracy of Peptide Identification with Consistency between Peptides. 191-196
- Haseong Kim, Erol Gelenbe: Reconstruction of Large-Scale Gene Regulatory Networks Using Bayesian Model Averaging. 202-207
- Xijun Liang, Zhonghang Xia, Li-Wei Zhang, Fang-Xiang Wu: Modeling Gene Regulatory Subnetworks from Time Course Gene Expression Data. 216-221
- Javad Safaei, Ján Manuch, Arvind Gupta, Ladislav Stacho, Steven Pelech: Evolutionary Conservation of Human Phosphorylation Sites. 222-227
- Damian Roqueiro, Lei Huang, Yang Dai: Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures. 228-233
Short Papers
- Utku Erdogdu, Mehmet Tan, Reda Alhajj, Faruk Polat, Douglas J. Demetrick, Jon G. Rokne: Employing Machine Learning Techniques for Data Enrichment: Increasing the Number of Samples for Effective Gene Expression Data Analysis. 238-242
- Karthik Tangirala, Doina Caragea: Semi-supervised Learning of Alternatively Spliced Exons Using Co-training. 243-246
- Bin Zhou, Jun Feng Xiao, Habtom W. Ressom: A Computational Pipeline for LC-MS/MS Based Metabolite Identification. 247-251
- David J. Dittman, Taghi M. Khoshgoftaar, Randall Wald, Huanjing Wang: Stability Analysis of Feature Ranking Techniques on Biological Datasets. 252-256
- Shan Gao, Jianwen Fang: Predicting Kinase-specific Phosphorylation Sites Using a Multitask Classification Framework. 257-260
- Tsung-Heng Tsai, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom: Bayesian Alignment Model for LC-MS Data. 261-264
- Chang F. Quo, May D. Wang: Biological Interpretation of Model-Reference Adaptive Control in a Mass Action Kinetics Metabolic Pathway Model. 265-268
- Pradipta Maji, Sushmita Paul: Microarray Time-Series Data Clustering Using Rough-Fuzzy C-Means Algorithm. 269-272
- Kevin McCormick, Li Liao: Prediction and Evaluation of miRNA - Target Gene Pairs Using K-means Clustering and Bipartite Graphs with Statistical Scoring. 273-277
- Liang-Chin Huang, Jake Yue Chen: A Network Biology Approach to Predicting Drug Cardiotoxicity. 278-281
- Xiao Wang, Guo-Zheng Li, Jia-Ming Liu, Rui-Wei Zhao: Multi-label Learning for Protein Subcellular Location Prediction. 282-285
- Wei Zhao, Justin Dauwels, Jacquin Niles, Jianshu Cao: Deconvolution of Microarray Data Predicts Transcriptionally Regulated Protein Kinases of Plasmodium falciparum. 286-289
- Julian Dymacek, Nancy Lan Guo: Systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data. 290-293
- Yan-E. Li, Juan Zhang, Bin Han, Lihua Li: Identifying Ovarian Cancer Chemotherapy Response Relevant Gene Cliques. 294-298
- Long Chen, Konstantinos Petritis, Tony Tegeler, Brianne Petritis, William E. Haskins, Jianqiu Michelle Zhang: Improved Quantification of Labeled LC-MS. 299-303
- Usman Rauf, Umair Siddique, Jamil Ahmad, Umar Khan Niazi: Formal Modeling and Analysis of Biological Regulatory Networks Using SPIN. 304-308
- Qiong Cheng, Mitsunori Ogihara, Vineet Gupta: Learning Condition-Dependent Dynamical PPI Networks from Conflict-Sensitive Phosphorylation Dynamics. 309-312
Medical Informatics and Translational Bioinformatics
Regular Papers
- Hong-Jun Yoon, Ching-Chung Li, Christhunesa Christudass, Robert Veltri, Jonathan I. Epstein, Zhen Zhang: Cardinal Multiridgelet-based Prostate Cancer Histological Image Classification for Gleason Grading. 315-320
- Ivanoe De Falco: A Differential Evolution-Based System Supporting Medical Diagnosis through Automatic Knowledge Extraction from Databases. 321-326
- Sarah Ostadabbas, Rasoul Yousefi, Mehrdad Nourani, Miad Faezipour, Lakshman Tamil, Matthew Pompeo: A Posture Scheduling Algorithm Using Constrained Shortest Path to Prevent Pressure Ulcers. 327-332
- Jun Kong, Michael J. Lee, Pelin Bagci, Puneet Sharma, Diego Martin, N. Volkan Adsay, Joel H. Saltz, Alton B. Farris: Computer-Based Image Analysis of Liver Steatosis with Large-Scale Microscopy Imagery and Correlation with Magnetic Resonance Imaging Lipid Analysis. 333-338
- Pedro Ferreira, Nuno A. Fonseca, Inês de Castro Dutra, Ryan W. Woods, Elizabeth S. Burnside: Predicting Malignancy from Mammography Findings and Surgical Biopsies. 339-344
- Garima Kushwaha, Gyan Prakash Srivastava, Dong Xu: PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design. 345-351
- Yanqiao Zhu, Fuhai Li, Derek Cridebring, Jinwen Ma, Stephen T. C. Wong, Tegy J. Vadakkan, Mei Zhang, John Landua, Wei Wei, Mary E. Dickinson, Jeffrey M. Rosen, Michael T. Lewis: Coupling Oriented Hidden Markov Random Field Model with Local Clustering for Segmenting Blood Vessels and Measuring Spatial Structures in Images of Tumor Microenvironment. 352-357
- Iyad Batal, Hamed Valizadegan, Gregory F. Cooper, Milos Hauskrecht: A Pattern Mining Approach for Classifying Multivariate Temporal Data. 358-365
- Min Liu, Hanchuan Peng, Amit K. Roy Chowdhury, Eugene W. Myers: 3D Neuron Tip Detection in Volumetric Microscopy Images. 366-371
- Rodney L. Summerscales, Shlomo Argamon, Shangda Bai, Jordan Hupert, Alan Schwartz: Automatic Summarization of Results from Clinical Trials. 372-377
- Anirban Chakraborty, Ram Kishor Yadav, G. Venugopala Reddy, Amit K. Roy Chowdhury: Cell Resolution 3D Reconstruction of Developing Multilayer Tissues from Sparsely Sampled Volumetric Microscopy Images. 378-383
- Erin K. Hamilton, Seonghye Jeon, Pepa Ramírez-Cobo, Kichun Sky Lee, Brani Vidakovic: Diagnostic Classification of Digital Mammograms by Wavelet-Based Spectral Tools: A Comparative Study. 384-389
Short Papers
- Te-Kang Jan, Hsuan-Tien Lin, Hsin-Pai Chen, Tsung-Chen Chern, Chung-Yueh Huang, Bing-Cheng Wen, Chia-Wen Chung, Yung-Jui Li, Ya-Ching Chuang, Li-Li Li, Yu-Jiun Chan, Juen-Kai Wang, Yuh-Lin Wang, Chi-Hung Lin, Da-Wei Wang: Cost-Sensitive Classification on Pathogen Species of Bacterial Meningitis by Surface Enhanced Raman Scattering. 390-393
- Dongdong Lin, Hongbao Cao, Yu-Ping Wang, Vince D. Calhoun: Classification of Schizophrenia Patients with Combined Analysis of SNP and fMRI Data Based on Sparse Representation. 394-397
- Phuong Pham, Li Yu, Minh Nguyen: A Novel Algorithm for Multi-class Cancer Diagnosis on MALDI-TOF Mass Spectra. 398-401
- Gang Chen, Jianxin Wang, Yi Pan, Jianer Chen: Identification of Breast Cancer Gene Signature in Protein Interaction Network Using Graph Centrality. 402-405
- Maciej Sykulski, Tomasz Gambin, Magdalena Bartnik, Katarzyna Derwinska, Barbara Wisniowiecka-Kowalnik, Pawel Stankiewicz, Anna Gambin: Efficient Multiple Samples aCGH Analysis for Rare CNVs Detection. 406-409
- Santa Di Cataldo, Elisa Ficarra, Andrea Acquaviva, Enrico Macii: Motion Artifact Correction in ASL images: An Improved Automated Procedure. 410-413
- Muhammad Hameed Siddiqi, Sungyoung Lee, Young-Koo Lee: Object Segmentation by Comparison of Active Contour Snake and Level Set in Biomedical Applications. 414-417
- Vineeth Nair, Milind Kaduskar, Pratibha Bhaskaran, Sandip Bhaumik, Hodong Lee: Preserving Narratives in Electronic Health Records. 418-421
- Sonal Kothari, John H. Phan, Andrew N. Young, May D. Wang: Histological Image Feature Mining Reveals Emergent Diagnostic Properties for Renal Cancer. 422-425
- Dong-Chul Kim, Jean Gao, Xiaoyu Wang, Chin-Rang Yang: A Framework for Personalized Medicine with Reverse Phase Protein Array and Drug Sensitivity. 426-429
- Fania Mokhayeri, M.-R. Akbarzadeh-T: Mental Stress Detection Based on Soft Computing Techniques. 430-433
Cross-Cutting Computational Methods and Bioinformatics Infrastructure
Regular Papers
- Heng Yang, Rehman Qureshi, Ahmet Sacan: Protein Structure Visualization by Dimension Reduction and Texture Mapping. 437-442
- Kevin A. Wilson, Andrea M. Rocha, Kanchana Padmanabhan, Kuangyu Wang, Zhengzhang Chen, Ye Jin, James R. Mihelcic, Nagiza F. Samatova: Detecting Pathway Cross-Talks by Analyzing Conserved Functional Modules across Multiple Phenotype-Expressing Organisms. 443-449
- Kristopher L. Patton, David J. John, James L. Norris: Probabilistic Signal Network Models from Multiple Replicates of Sparse Time-Course Data. 450-455
- Yan Chen, Xiaoshi Yin, Zhoujun Li, Xiaohua Hu, Jimmy Xiangji Huang: Promoting Ranking Diversity for Biomedical Information Retrieval Based on LDA. 456-461
- Katherine V. Wendelsdorf, Josep Bassaganya-Riera, Keith R. Bisset, Stephen Eubank, Raquel Hontecillas, Madhav V. Marathe: ENteric Immunity SImulator: A Tool for in silico Study of Gut Immunopathologies. 462-469
- Wooyoung Kim, Min Li, Jianxin Wang, Yi Pan: Essential Protein Discovery Based on Network Motif and Gene Ontology. 470-475
- Sheng Liu, Ronak Y. Patel, Pankaj R. Daga, Haining Liu, Gang Fu, Robert J. Doerksen, Yixin Chen, Dawn Wilkins: Multi-class Joint Rule Extraction and Feature Selection for Biological Data. 476-481
- Bo Hong, Jiadong Wu, Jun-tao Guo: Improving Prediction Accuracy of Protein-DNA Docking with GPU Computing. 482-487
- Liang Dong, Pradip K. Srimani, James Z. Wang: Ontology Graph Based Query Expansion for Biomedical Information Retrieval. 488-493
- Hyungro Lee, Youngik Yang, Heejoon Chae, Seungyoon Nam, Donghoon Choi, Patanachai Tangchaisin, Chathura Herath, Suresh Marru, Kenneth P. Nephew, Sun Kim: BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis. 494-499
- Timothy Matthew Fawcett, Stephanie Jimenez Irausquin, Mikhail Simin, Homayoun Valafar: An Artificial Neural Network Based Approach for Identification of Native Protein Structures Using an Extended Forcefield. 500-505
- Liang Ge, Nan Du, Aidong Zhang: Finding Informative Genes from Multiple Microarray Experiments: A Graph-based Consensus Maximization Model. 506-511
- Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo N. Mendes, Amit P. Sheth, Krishnaprasad Thirunarayan: Semantic Predications for Complex Information Needs in Biomedical Literature. 512-519
- Yul Kim, Bumki Min, Gwan-Su Yi: IDDI: The Integrated Domain-Domain Interaction Analysis System. 520-525
- Shuo Li, Jean Gao, James O. Nyagilo, Digant P. Dave: Probabilistic Partial Least Square Regression: A Robust Model for Quantitative Analysis of Raman Spectroscopy Data. 526-531
- Qinmin Hu, Jimmy Xiangji Huang, Xiaohua Hu: A Term Association Approach for Genomics Information Retrieval. 532-537
- Cornelia Caragea, Adrian Silvescu, Prasenjit Mitra: Protein Sequence Classification Using Feature Hashing. 538-543
- Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi, Akinori Yonezawa: Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering. 544-549
- Gurinder Pal Singh Gosal, Natarajan Kannan, Krys J. Kochut: ProKinO: A Framework for Protein Kinase Ontology. 550-555
- Hasan M. Jamil: Toward a Cooperative Natural Language Query Interface for Biological Databases. 556-561
- Jayasimha Reddy Katukuri, Ying Xie, Vijay V. Raghavan, Ashish Gupta: Supervised Link Discovery on Large-Scale Biomedical Concept Networks. 562-568
Short Papers
- Nicholas Soltau, Young-Rae Cho: Assessment of Cluster Overlaps to Improve Accuracy of Module Detection from PPI Networks. 569-573
- Milan Vukicevic, Boris Delibasic, Milos Jovanovic, Milija Suknovic, Zoran Obradovic: Internal Evaluation Measures as Proxies for External Indices in Clustering Gene Expression Data. 574-577
- Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Hongzhan Huang, Hagit Shatkay, Cathy H. Wu: An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents. 578-581
- Jian Wang, Dong Xie, Hongfei Lin, Zhihao Yang, Yijia Zhang: Identifying Protein Complexes from PPI Networks Using GO Semantic Similarity. 582-585
- Min-Yu Huang, Lester W. Mackey, Soile V. E. Keränen, Gunther H. Weber, Michael I. Jordan, David W. Knowles, Mark D. Biggin, Bernd Hamann: Visually Relating Gene Expression and in vivo DNA Binding Data. 586-589
- Apurva Mohan, Douglas M. Blough, Tahsin M. Kurç, Andrew R. Post, Joel H. Saltz: Detection of Conflicts and Inconsistencies in Taxonomy-Based Authorization Policies. 590-594
- Meenakshi Mishra, Brian Potetz, Jun Huan: Bayesian Classifiers for Chemical Toxicity Prediction. 595-599
- Vincent Yip, Sinan Kockara, Chenyi Hu: Efficient Calculation of Structural Similarity Threshold for the SCAN Network Clustering Algorithm. 600-603
- Chanchala Kaddi, R. Mitchell Parry, May D. Wang: Hypergeometric Similarity Measure for Spatial Analysis in Tissue Imaging Mass Spectrometry. 604-607
- Nicholas A. Furlotte, Lijing Xu, Robert W. Williams, Ramin Homayouni: Literature-based Evaluation of Microarray Normalization Procedures. 608-612
- Weijia Xu, Ame Wongsa, Jung Lee, Lei Shang, Jamie J. Cannone, Robin Ray Gutell: RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure. 613-617
- Yanan Jiang, Weijia Xu, Lee Parnell Thompson, Robin Ray Gutell, Daniel P. Miranker: R-PASS: A Fast Structure-Based RNA Sequence Alignment Algorithm. 618-622
- Pengfei Sun, Songmao Zhang: Using Rules to Investigate the Differences in Partonomy between Biomedical Ontologies. 623-626
- Hossam M. Ashtawy, Nihar R. Mahapatra: A Comparative Assessment of Conventional and Machine-Learning-Based Scoring Functions in Predicting Binding Affinities of Protein-Ligand Complexes. 627-630
Industry Track
- Luis Tari, Jan Küntzer, Jagruti Patel, Ying Li, Zhengwei Peng, Yuan Wang, Laura Aguiar, James Cai: Mining Gene-centric Relationships from Literature to Support Drug Discovery. 639-644
- Michael N. Liebman, Sabrina Molinaro: Hypothesis Generation and Evaluation in Clinical Trial Design. 645-651
- Kaushal Desai, David Brott, Xiaohua Hu, Anastasia Christianson: Mining Protein Interactions and Gene Expression Data to Gain Insights into Drug-induced Toxicity Mechanisms. 652-657
- Jian Wang: Data Exploration in Secondary Use of Healthcare Data. 658
- Michael Farnum, Victor S. Lobanov, Frank Defalco, Soledad Cepeda: Opening the Door to Electronic Medical Records: Using Informatics to Overcome Terabytes. 659
- Michael Farnum, Victor S. Lobanov, Eric Yang, Tim Schultz, Rudi Verbeeck: Uniting Data for Memory: Building Informatics against Alzheimer's. 660
- Sherri Matis, Matt Clark, Marcus Bjareland, Brian Takasaki, Nina Mian, Sorel Muresan, Sorona Popa: Decision Support in Safety Intelligence Using Pharmaconnect Knowledgebase. 661
- Anastasia M. Khoury Christianson: Generating More Knowledge from Our Data and More Value from Our Studies: The Value of Expert Information Science Skills. 662
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last updated on 2013-06-19T201401 by the dblp team