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ORCIDBIBM 2011: Atlanta, GA, USA
- Fang-Xiang Wu, Mohammed Javeed Zaki, Shinichi Morishita, Yi Pan, Stephen Wong, Anastasia Christianson, Xiaohua Hu:
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, GA, USA, November 12-15, , 2011. IEEE Computer Society 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 Yuan 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 - Uros Midic, Zoran Obradovic:
Intrinsic Disorder in Putative Protein Sequences. 43-48 - 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 H. 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 - Ayat Hatem, Doruk Bozdag, Ümit V. Çatalyürek:
Benchmarking Short Sequence Mapping Tools. 109-113 - Brian S. Olson, Amarda Shehu:
Populating Local Minima in the Protein Conformational Space. 114-117 - 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 - Yi Xiong, Wen Zhang, Tao Zeng, Juan Liu:
Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties. 143-146 - 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 - Alexander Senf, Xue-wen Chen:
Functional Gene Detection and Clustering from Seed Gene Sets. 179-184 - 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 - Li-Ping Tian, Fang-Xiang Wu:
Delay-Dependent Stability for Genetic Regulatory Networks. 197-201 - Haseong Kim, Erol Gelenbe:
Reconstruction of Large-Scale Gene Regulatory Networks Using Bayesian Model Averaging. 202-207 - Yann Christinat, Bernard M. E. Moret:
Inferring Transcript Phylogenies. 208-215 - 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
- Bingbo Wang, Lin Gao:
Global Network Alignment Based on Multiple Hub Seeds. 234-237 - 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 R. Martín, 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 V. 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 G. 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