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BIBM 2010: Hong Kong, China
- Taesung Park, Stephen Kwok-Wing Tsui, Luonan Chen, Michael K. Ng, Limsoon Wong, Xiaohua Hu:
2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, Hong Kong, China, December 18-21, 2010, Proceedings. IEEE Computer Society 2010, ISBN 978-1-4244-8306-8
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
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
Unsupervised integration of multiple protein disorder predictors. 49-52 - M. Michael Gromiha, N. Saranya, Samuel Selvaraj, B. Jayaram
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
Enhanced reference guided assembly. 77-80 - Chinh T. T. Su, Stephanus Daniel Handoko, Chee Keong Kwoh, Christian Schönbach
A possible mutation that enables H1N1 influenza a virus to escape antibody recognition. 81-84 - Zhengkui Wang
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
Truncation of protein sequences for fast profile alignment with application to subcellular localization. 115-120 - Michal Wozniak, Limsoon Wong
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-2Kb-peptide-TCR complexes. 127-132 - Tomás Flouri
An algorithm for mapping short reads to a dynamically changing genomic sequence. 133-136 - David Becerra, Angelica Sandoval
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
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
Overcoming drug resistance by co-targeting. 198-202 - Trupti Joshi, Qiuming Yao, D. Franklin Levi, Laurent Brechenmacher, Babu Valliyodan
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, F. 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
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, Kam M. Hui
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
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
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
Unsupervised discovery of fuzzy patterns in gene expression data. 269-273 - Wei Zhang, Scott J. Emrich
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
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
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. 314-318 - 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
A supervised learning approach to the unsupervised clustering of genes. 322-328 - Li-Zhi Liu, Fang-Xiang Wu
Structure identification and parameter estimation of biological s-systems. 329-334 - Jia Meng
An Iterated Conditional Modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks. 335-340 - Meeta Pradhan, Lakenvia Ledford, Yogesh Pandit
Global analysis of miRNA target genes in colon rectal cancer. 341-345 - Zhiqun Tang, Lihua Zhang, Amrita K. Cheema
A new method for alignment of LC-MALDI-TOF data. 346-351 - Yuji Zhang
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
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
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
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 - Eladio 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, Ke Zhi 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
Semi-supervised feature learning from clinical text. 462-466 - Qinghua Jiang, Guohua Wang, Tianjiao Zhang
Predicting human microRNA-disease associations based on support vector machine. 467-472 - Yinyin Yuan, Christina Curtis
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
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
Metabolomic profiling for biomarker discovery in pancreatic cancer. 505-509 - Wenan Chen, Charles Cockrell, Kevin Ward
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
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
seGOsa: Software environment for gene ontology-driven similarity assessment. 539-542 - Cagri Ozcaglar, Amina Shabbeer, Scott L. Vandenberg, Bülent Yener, Kristin P. Bennett:
Examining the sublineage structure of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors. 543-548 - Ping Xuan
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
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
Exploratory analysis of the BioAssay Network with implications to therapeutic discovery. 569-572 - Natthakan Iam-on
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
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
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
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
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
PSI-RA: A parallel sparse index for read alignment on genomes. 663-668 - Qinmin Vivian Hu, Jimmy Xiangji Huang
Exploring a multi-source fusion approach for genomics information retrieval. 669-672 - Sérgio Dias
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 G. 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
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
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