BIBM 2010: Hong Kong, China

Genomics and Molecular Structure, Function and Evolution

• Chien-Chih Wang, Chien-Yu Chen:
  Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties. 3-8
  
• Yang Liu, Yiu-Fai Lee, Michael K. Ng:
  Classification of genome-wide copy number variations and their associated SNP and gene networks analysis. 9-12
  
• Zejun Zheng, Bertil Schmidt, Guillaume Bourque:
  Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine. 13-16
  
• Luis Rueda, Sridip Banerjee, Md. Mominul Aziz, Mohammad Raza:
  Protein-protein interaction prediction using desolvation energies and interface properties. 17-22
  
• Weiqiang Zhou, Hong Yan:
  Prediction of DNA-binding protein based on alpha shape modeling. 23-28
  
• Vikas Rao Pejaver, Sun Kim:
  Gene cluster profile vectors: A novel method to infer functional coupling using both gene proximity and co-occurrence profiles. 29-34
  
• Yiwei Zhang, Fei Hu, Jijun Tang:
  Phylogenetic reconstruction with gene rearrangements and gene losses. 35-38
  
• Bing Han, Xue-wen Chen:
  Detecting SNPs-disease associations using Bayesian networks. 39-42
  
• Ke Chen, Marcin J. Mizianty, Lukasz A. Kurgan:
  Accurate prediction of ATP-binding residues using sequence and sequence-derived structural descriptors. 43-48
  
• Ping Zhang, Zoran Obradovic:
  Unsupervised integration of multiple protein disorder predictors. 49-52
  
• M. Michael Gromiha, N. Saranya, Samuel Selvaraj, B. Jayaram, Kazuhiko Fukui:
  Sequence and structural features of binding site residues in protein-protein complexes. 53-56
  
• Roberto Blanco:
  Structural parsimony: Reductions in sequence space. 57-61
  
• Qian Xu, Evan Wei Xiang, Qiang Yang:
  Protein-protein interaction prediction via Collective Matrix Factorization. 62-67
  
• Shu-Yun Le, Bruce A. Shapiro:
  Characterization of structural features for small regulatory RNAs in Escherichia coli genomes. 68-72
  
• Wei Chen, Shao-Wu Zhang, Yongmei Cheng, Quan Pan:
  Prediction of Protein-RNA interaction site using SVM-KNN algorithm with spatial information. 73-76
  
• Federica Cattonaro, Alberto Policriti, Francesco Vezzi:
  Enhanced reference guided assembly. 77-80
  
• T. T. Su Chinh, Stephanus Daniel Handoko, Chee Keong Kwoh, Christian Schönbach, Xiaoli Li:
  A possible mutation that enables H1N1 influenza a virus to escape antibody recognition. 81-84
  
• Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal:
  CEO a cloud epistasis computing model in GWAS. 85-90
  
• Junho Kim, Doheon Lee:
  A new perspective of integrative genome-wide association analysis considering trans eSNP effect. 91-94
  
• Bo Liu, Theodore Gibbons, Mohammadreza Ghodsi, Mihai Pop:
  MetaPhyler: Taxonomic profiling for metagenomic sequences. 95-100
  
• Qingqing Cai, Xiaoyan Zhang, Zuofeng Li:
  MiRNAs as promising phylogenetic markers for inferring deep metazoan phylogeny and in support of Olfactores hypothesis. 101-104
  
• Ross K. K. Leung, Stephen Kwok-Wing Tsui:
  alns - A searchable and filterable sequence alignment format. 105-108
  
• Zhiyong Wang, Feng Zhao, Jian Peng, Jinbo Xu:
  Protein 8-class secondary structure prediction using Conditional Neural Fields. 109-114
  
• Man-Wai Mak, Wei Wang, Sun-Yuan Kung:
  Truncation of protein sequences for fast profile alignment with application to subcellular localization. 115-120
  
• Michal Wozniak, Limsoon Wong, Jerzy Tiuryn:
  CAMBer: An approach to support comparative analysis of multiple bacterial strains. 121-126
  
• I.-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang:
  Template-based scoring functions for visualizing biological insights of H-2K^b-peptide-TCR complexes. 127-132
  
• Tomás Flouri, Jan Holub, Costas S. Iliopoulos, Solon P. Pissis:
  An algorithm for mapping short reads to a dynamically changing genomic sequence. 133-136
  
• David Becerra, Angelica Sandoval, Daniel Restrepo-Montoya, Luis F. Niño:
  A parallel multi-objective ab initio approach for protein structure prediction. 137-141
  
• M. Mondal Ananda, Jianjun Hu:
  NetLoc: Network based protein localization prediction using protein-protein interaction and co-expression networks. 142-148
  
• Xin Chen, Xiaohua Hu, Xiajiong Shen, Gail Rosen:
  Probabilistic topic modeling for genomic data interpretation. 149-152
  
• Yuzhen Ye:
  Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. 153-157
  
• Alvaro J. González, Li Liao, Cathy H. Wu:
  Predicting ligand binding residues using multi-positional correlations and kernel canonical correlation analysis. 158-163
  
• Shao-Ke Lou, Jing-Woei Li, Hao Qin, Aldrin Kay-Yuen Yim, Leung-Yau Lo, Bing Ni, Kwong-Sak Leung, Stephen Kwok-Wing Tsui, Ting-Fung Chan:
  Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length. 164-170
  
• Anveshi Charuvaka, Huzefa Rangwala:
  Evaluation of short read metagenomic assembly. 171-178
  
• Jian Ma:
  A probabilistic framework for inferring ancestral genomic orders. 179-184
  
• Nan Zhao, Bin Pang, Chi-Ren Shyu, Dmitry Korkin:
  An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches. 185-189
  

Computational Systems Biology

• Yan-Fei Wang, Zu-Guo Yu, Vo Anh:
  Fuzzy C-means method with empirical mode decomposition for clustering microarray data. 192-197
  
• Marzieh Ayati, Golnaz Taheri, Shahriar Arab, Limsoon Wong, Changiz Eslahchi:
  Overcoming drug resistance by co-targeting. 198-202
  
• Trupti Joshi, Qiuming Yao, D. Franklin Levi, Laurent Brechenmacher, Babu Valliyodan, Gary Stacey, Henry Nguyen, Dong Xu:
  SoyMetDB: The soybean metabolome database. 203-208
  
• Cen Gao, Jing Li:
  Machine learning approaches for the investigation of features beyond seed matches affecting miRNA binding. 209-213
  
• Xumeng Li, Frank Alex Feltus, Xiaoqian Sun, James Zijun Wang, Feng Luo:
  A non-parameter Ising model for network-based identification of differentially expressed genes in recurrent breast cancer patients. 214-217
  
• Jo-Yang Lu, Eric Y. Chuang, Chuhsing Kate Hsiao, Mong-Hsun Tsai, Liang-Chuan Lai, Pei-Chun Chen:
  Utilizing Cox regression model to assess the relations between predefined gene sets and the survival outcome of lung adenocarcinoma. 218-221
  
• Xuepo Ma, Travis J. Hestilow, Jian Cui, Jianqiu Zhang:
  Iterative correction of suppressed peptide profiles from FTMS measurements. 222-227
  
• N. Baskaran, Chee Keong Kwoh, M. Hui Kam:
  Outcomes of gene association analysis of cancer microarray data are impacted by pre-processing algorithms. 228-233
  
• Jin-Hong Shi, Fang-Xiang Wu:
  Peptide charge state determination of tandem mass spectra from low-resolution collision induced dissociation. 234-239
  
• Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching:
  Finding optimal control policy in Probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. 240-246
  
• Lei Shi, Aidong Zhang:
  Semi-supervised learning protein complexes from protein interaction networks. 247-252
  
• Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano:
  Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. 253-258
  
• Javad Safaei, Ján Manuch, Arvind Gupta, Ladislav Stacho, Steven Pelech:
  Prediction of human protein kinase substrate specificities. 259-264
  
• Weixiang Liu, Songfeng Zheng, Sen Jia, LinLin Shen, Xianghua Fu:
  Sparse nonnegative matrix factorization with the elastic net. 265-268
  
• Gene P. K. Wu, Keith C. C. Chan, Andrew K. C. Wong, Bin Wu:
  Unsupervised discovery of fuzzy patterns in gene expression data. 269-273
  
• Wei Zhang, Scott J. Emrich, Erliang Zeng:
  A two-stage machine learning approach for pathway analysis. 274-279
  
• Guimei Liu, Chern Han Yong, Limsoon Wong, Hon Nian Chua:
  Decomposing PPI networks for complex discovery. 280-283
  
• Tzu-Pin Lu, Liang-Chuan Lai, Chuhsing Kate Hsiao, Pei-Chun Chen, Mong-Hsun Tsai, Eric Y. Chuang:
  Concurrent analysis of copy number variations and expression profiles to identify genes associated with tumorigenesis and survival outcome in lung adenocarcinoma. 284-289
  
• Bo Xu, Hongfei Lin, Zhihao Yang:
  Ontology integration to identify protein complex in protein interaction networks. 290-295
  
• Shigeru Saito, Xinrong Zhou, Taejeong Bae, Sunghoon Kim, Katsuhisa Horimoto:
  A procedure for identifying master regulators in conjunction with network screening and inference. 296-301
  
• Haseong Kim, Erol Gelenbe:
  Stochastic gene expression modeling with hill function for switch-like gene responses. 302-307
  
• Zhenyu Wang, Vasile Palade:
  Multi-objective evolutionary algorithms based Interpretable Fuzzy models for microarray gene expression data analysis. 308-313
  
• Riet De Smet, Kathleen Marchal:
  An ensemble method for querying gene expression compendia with experimental lists. 3141-318
  
• Leah Spontaneo, Nick Cercone:
  Correlating CpG islands, motifs, and sequence variants in human chromosome 21. 319-322
  
• Andrew K. Rider, Geoffrey Siwo, Scott J. Emrich, Michael T. Ferdig, Nitesh V. Chawla:
  A supervised learning approach to the unsupervised clustering of genes. 322-328
  
• Li-Zhi Liu, Fang-Xiang Wu, Li-Li Han, Wen-Jun Zhang:
  Structure identification and parameter estimation of biological s-systems. 329-334
  
• Jia Meng, Jianqiu Zhang, Yidong Chen, Yufei Huang:
  An Iterated Conditional Modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks. 335-340
  
• Meeta Pradhan, Lakenvia Ledford, Yogesh Pandit, Mathew Palakal:
  Global analysis of miRNA target genes in colon rectal cancer. 341-345
  
• Zhiqun Tang, Lihua Zhang, Amrita K. Cheema, Habtom W. Ressom:
  A new method for alignment of LC-MALDI-TOF data. 346-351
  
• Yuji Zhang, Jianhua Jason Xuan, Robert Clarke, Habtom W. Ressom:
  Module-based biomarker discovery in breast cancer. 352-356
  
• Zheng Xia, Xiaobo Zhou, Wei Chen, Chunqi Chang:
  A graph-based elastic net for variable selection and module identification for genomic data analysis. 357-362
  
• Tias Guns, Hong Sun, Kathleen Marchal, Siegfried Nijssen:
  Cis-regulatory module detection using constraint programming. 363-368
  
• Bing Ni, Leung-Yau Lo, Kwong-Sak Leung:
  A generalized sequence pattern matching algorithm using complementary dual-seeding. 369-372
  
• Sung-Gon Yi, Taesung Park:
  Integrated analysis of the various types of microarray data using linear-mixed effects models. 373-379
  
• Zina M. Ibrahim, Alioune Ngom, Ahmed Y. Tawfik:
  A dynamic qualitative probabilistic network approach for extracting gene regulatory network motifs. 380-385
  

Medical Informatics and Translational Bioinformatics

• Iman Rezaeian, Luis Rueda:
  A parameterless automatic spot detection method for cDNA microarray images. 388-392
  
• Qi Chu, Fa Zhang, Kai Zhang, Xiaohua Wan, Mingwei Chen, Zhiyong Liu:
  An accurate, automatic method for markerless alignment of electron tomographic images. 393-396
  
• Jin Liu, Tuan D. Pham, Wei Wen, Perminder S. Sachdev:
  Spatially constrained fuzzy hyper-prototype clustering with application to brain tissue segmentation. 397-400
  
• Wei Kong, Xiaoyang Mou, Xiaohua Hu:
  Exploring matrix factorization techniques for significant genes identification of microarray dataset. 401-405
  
• Chung-Yueh Huang, Tsung-Heng Tsai, Bing-Cheng Wen, Chia-Wen Chung, Yung-Jui Li, Ya-Ching Chuang, Wen-Jie Lin, Li-Li Li, Juen-Kai Wang, Yuh-Lin Wang, Chi-Hung Lin, Da-Wei Wang:
  Hybrid SVM/CART classification of pathogenic species of bacterial meningitis with surface-enhanced Raman scattering. 406-409
  
• Wei Liu, Weidong Xu, Lihua Li, Shuang Li, Huanping Zhao, Juan Zhang:
  Improved mammographic mass retrieval performance using multi-view information. 410-415
  
• Arpit Srivastava, Abhinav Asati, Mahua Bhattacharya:
  A fast and noise-adaptive rough-fuzzy hybrid algorithm for medical image segmentation. 416-421
  
• David Boutte, Jingyu Liu:
  Sparse canonical correlation analysis applied to fMRI and genetic data fusion. 422-426
  
• E. Martin:
  Solving training issues in the application of the wavelet transform to precisely analyze human body acceleration signals. 427-432
  
• Long Qu, Victoria L. Vetter, Geoffrey L. Bird, Haijun Qiu, Peter S. White:
  A Naïve Bayes classifier for differential diagnosis of Long QT Syndrome in children. 433-437
  
• Yifeng Li, Alioune Ngom:
  Non-negative matrix and tensor factorization based classification of clinical microarray gene expression data. 438-443
  
• Feng Yang, K. Z. Mao:
  Improving robustness of gene ranking by resampling and permutation based score correction and normalization. 444-449
  
• Nancy Yu Song, Hong Yan:
  Autoregressive modeling of DNA features for short exon recognition. 450-455
  
• Klaus Drechsler, Cristina Oyarzun Laura:
  Hierarchical decomposition of vessel skeletons for graph creation and feature extraction. 456-461
  
• Zhuoran Wang, John Shawe-Taylor, Anoop Shah:
  Semi-supervised feature learning from clinical text. 462-466
  
• Qinghua Jiang, Guohua Wang, Tianjiao Zhang, Yadong Wang:
  Predicting human microRNA-disease associations based on support vector machine. 467-472
  
• Yinyin Yuan, Christina Curtis, Carlos Caldas, Florian Markowetz:
  A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes. 473-478
  
• Ying-Wooi Wan, Changchang Xiao, Nancy Lan Guo:
  Network-based identification of smoking-associated gene signature for lung cancer. 479-484
  
• Chao Zhang, Shunfu Xu, Dong Xu:
  Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori. 485-488
  
• Tao Zeng, Xuan Guo, Juan Liu:
  Discovering negative correlated gene sets from integrative gene expression data for cancer prognosis. 489-492
  
• Hyungmin Lee, Miyoung Shin, Munpyo Hong:
  A gene ranking method using text-mining for the identification of disease related genes. 493-498
  
• Shouyi Wang, Wanpracha Art Chaovalitwongse, Stephen Wong:
  A novel reinforcement learning framework for online adaptive seizure prediction. 499-504
  
• Prabhjit Kaur, Kathryn Sheikh, Alexander Kirilyuk, Ksenia Kirilyuk, Habtom W. Ressom, Amrita K. Cheema, Bhaskar Kallakury:
  Metabolomic profiling for biomarker discovery in pancreatic cancer. 505-509
  
• Wenan Chen, Charles Cockrell, Kevin Ward, Kayvan Najarian:
  Intracranial pressure level prediction in traumatic brain injury by extracting features from multiple sources and using machine learning methods. 510-515
  
• Murat Seckin Ayhan, Ryan G. Benton, Vijay V. Raghavan, Suresh K. Choubey:
  Exploitation of 3D Stereotactic Surface Projection for automated classification of Alzheimer's disease according to dementia levels. 516-519
  
• Xiaofei Nan, Nan Wang, Ping Gong, Chaoyang Zhang, Yixin Chen, Dawn Wilkins:
  Gene selection using 1-norm regularization for multi-class microarray data. 520-524
  
• Shuo Li, Jean Gao, James O. Nyagilo, Digant P. Dave:
  Eigenspectra, a robust regression method for multiplexed Raman spectra analysis. 525-530
  

Cross-Cutting Computational Methods and Bioinformatics Infrastructure

• Ying Shen, Shaohong Zhang, Hau-San Wong:
  A new method for measuring the semantic similarity on gene ontology. 533-538
  
• Huiru Zheng, Francisco Azuaje, Haiying Wang:
  seGOsa: Software environment for gene ontology-driven similarity assessment. 539-542
  
• Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bülent Yener, Kristin P. Bennett:
  Examining the sublineage structure of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors. 543-548
  
• Ping Xuan, Maozu Guo, Lei-lei Shi, Jun Wang, Xiaoyan Liu, Wenbin Li, Yingpeng Han:
  Two-stage clustering based effective sample selection for classification of pre-miRNAs. 549-552
  
• Said Bleik, Wei Xiong, Yiran Wang, Min Song:
  Biomedical concept extraction using concept graphs and ontology-based mapping. 553-556
  
• Taehyong Kim, Jaehan Koh, Kang Li, Murali Ramanathan, Aidong Zhang:
  Identification of critical location on a microstructural bone network. 557-562
  
• Qiwei Li, Tong Liang, Xiaodan Fan, Chunhui Xu, Weichang Yu, Shuo-Yen Robert Li:
  An automatic procedure to search highly repetitive sequences in genome as fluorescence in situ hybridization probes and its application on Brachypodium distachyon. 563-568
  
• Jintao Zhang, Gerald H. Lushington, Jun Huan:
  Exploratory analysis of the BioAssay Network with implications to therapeutic discovery. 569-572
  
• Natthakan Iam-on, Simon Garrett, Chris Price, Tossapon Boongoen:
  Link-based cluster ensembles for heterogeneous biological data analysis. 573-578
  
• Alisa Yurovsky, Bernard M. E. Moret:
  FluRF, an automated flu virus reassortment finder based on phylogenetic trees. 579-584
  
• Hao Lian, Chengsen Song, Young-Rae Cho:
  Decomposing protein interactome networks by graph entropy. 585-589
  
• Osamu Maruyama, Ayaka Chihara:
  NWE: Node-weighted expansion for protein complex prediction using random walk distances. 590-594
  
• Zhihao Yang, Yuan Lin, Jiajin Wu, Nan Tang, Hongfei Lin, Yanpeng Li:
  Ranking SVM for multiple kernels output combination in protein-protein interaction extraction from biomedical literature. 595-598
  
• Jung-Chih Chang, Tzu-Pin Lu, Eric Y. Chuang, Liang-Chuan Lai, Mong-Hsun Tsai, Chuhsing Kate Hsiao, Pei-Chun Chen:
  Concurrent analysis of copy number variation and gene expression: Application in paired non-smoking female lung cancer patients. 599-602
  
• Jiarui Ding, Sohrab P. Shah:
  Robust hidden semi-Markov modeling of array CGH data. 603-608
  
• Mingon Kang, Jean X. Gao, Liping Tang:
  Computational modeling of phagocyte transmigration during biomaterial-mediated foreign body responses. 609-612
  
• Somu Perianayagam, Gregory R. Andrews, John H. Hartman:
  Rex: A toolset for reproducing software experiments. 613-617
  
• Vladimir Nikulin, Tian-Hsiang Huang, Geoffrey J. McLachlan:
  A comparative study of two matrix factorization methods applied to the classification of gene expression data. 618-621
  
• M. Oguzhan Külekci, Jeffrey Scott Vitter, Bojian Xu:
  Time- and space-efficient maximal repeat finding using the burrows-wheeler transform and wavelet trees. 622-625
  
• Kazi Zakia Sultana, Anupam Bhattacharjee, Hasan M. Jamil:
  IsoKEGG: A logic based system for querying biological pathways in KEGG. 626-631
  
• Mehmet Tan, Faruk Polat, Reda Alhajj:
  Feature selection for graph kernels. 632-637
  
• Myungha Jang, Arang Rhie, Hyun Seok Park:
  Toward automatically drawn metabolic pathway atlas with peripheral node abstraction algorithm. 638-642
  
• Jin Xu, Qiwei Li, Xiaodan Fan, Victor O. K. Li, Shuo-Yen Robert Li:
  An Evolutionary Monte Carlo algorithm for identifying short adjacent repeats in multiple sequences. 643-648
  
• Ed Keedwell, Ajit Narayanan:
  Gene expression rule discovery with a multi-objective neural-genetic hybrid. 649-656
  
• Chih-Hsuan Wei, Hung-Yu Kao:
  Represented indicator measurement and corpus distillation on focus species detection. 657-662
  
• M. Oguzhan Külekci, Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter, Bojian Xu:
  PSI-RA: A parallel sparse index for read alignment on genomes. 663-668
  
• Qinmin Vivian Hu, Jimmy Xiangji Huang, Jun Miao:
  Exploring a multi-source fusion approach for genomics information retrieval. 669-672
  
• Sérgio Dias, Abel J. P. Gomes:
  GPU-based triangulation of the van der Waals surface. 673-676
  
• Songfeng Zheng, Weixiang Liu:
  Selecting informative genes by Lasso and Dantzig selector for linear classifiers. 677-680
  
• Neeraj Koul, Ngot Bui, Vasant Honavar:
  Scalable, updatable predictive models for sequence data. 681-685
  
• Meenakshi Mishra, Hongliang Fei, Jun Huan:
  Computational prediction of toxicity. 686-691
  
• Xiaoshi Yin, Zhoujun Li, Jimmy Xiangji Huang, Xiaohua Hu:
  A relevance-novelty combined model for genomics search result diversification. 692-695
  
• Lei Shi, Shikui Tu, Lei Xu:
  Gene clustering by structural prior based local factor analysis model under Bayesian Ying-Yang harmony learning. 696-699
  

Last update Tue May 21 16:16:59 2013 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page