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ORCIDBIBM Workshops 2011: Atlanta, GA, USA
- 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, USA, November 12-15, 2011. IEEE Computer Society 2011, ISBN 978-1-4577-1612-6
Workshop on Next-generation Sequencing Analysis
- Junbo Duan, Ji-Gang Zhang, John Lefante, Hong-Wen Deng, Yu-Ping Wang:
Detection of copy number variation from next generation sequencing data with total variation penalized least square optimization. 3-12 - Ruben Cruz Huacarpuma, Maristela Holanda
, Maria Emília M. T. Walter:
A conceptual data model for transcriptome project pipeline. 13-18 - (Zhou) Bryan Bai, Stefan C. Kremer:
Regularization of sequence data for machine learning. 19-25 - Zhiyu Zhao, Tin Chi Nguyen, Nan Deng, Kristen Marie Johnson, Dongxiao Zhu:
SPATA: A seeding and patching algorithm for de novo transcriptome assembly. 26-33 - Francesco Abate, Andrea Acquaviva, Elisa Ficarra, Giulia Paciello, Enrico Macii, Alberto Ferrarini, Massimo Delledonne, Simona Soverini, Giovanni Martinelli:
A novel framework for chimeric transcript detection based on accurate gene fusion model. 34-41 - Jan Mendonca Correa, Alba Cristina Magalhaes Alves de Melo, Ricardo P. Jacobi, Azzedine Boukerche:
A fragment based alignment in linear space. 42-49 - Po-Yen Wu, John H. Phan, Fengfeng Zhou, May D. Wang:
Evaluation of normalization methods for RNA-Seq gene expression estimation. 50-57
Workshop on Computational Advances in Molecular Epidemiology (CAME 2011)
- Sergei L. Kosakovsky Pond:
Computational analysis of HIV-1 evolution and epidemiology. 60-63 - David S. Campo, Zoya Dimitrova, James Lara, Mike Purdy, Hong Thai, Sumathi Ramachandran, Lilia Ganova-Raeva, X. Zhai, Joseph C. Forbi, Chong-Gee Teo, Yuri Khudyakov:
Network of coordinated substitutions in the Hepatitis B virus polymerase. 64-71 - Irina V. Astrakhantseva, David S. Campo, Aufra Araujo, Chong-Gee Teo, Yuri Khudyakov, Saleem Kamili:
Variation in physicochemical properties of the hypervariable region 1 during acute and chronic stages of hepatitis C virus infection. 72-78 - Zoya Dimitrova, David S. Campo, Sumathi Ramachandran, Gilberto Vaughan, Lilia Ganova-Raeva, Yulin Lin, Joseph C. Forbi, Guo-liang Xia, Pavel Skums, Brian L. Pearlman, Yuri Khudyakov:
Assessments of intra- and inter-host diversity of hepatitis C virus using Next Generation Sequencing and Mass spectrometry. 79-86 - Arthi Ramachandran, Mariann Micsinai, Itsik Pe'er:
CONDEX: Copy number detection in exome sequences. 87-93 - Nicholas Mancuso, Bassam Tork, Pavel Skums, Ion I. Mandoiu, Alexander Zelikovsky:
Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads. 94-101 - James Lara, John E. Tavis, Maureen J. Donlin, William M. Lee, He-Jun Yuan, Brian L. Pearlman, Gilberto Vaughan, Joseph C. Forbi, Guo-liang Xia, Yuri Khudyakov:
Host-specific HCV evolution and response to the combined interferon and ribavirin therapy. 102-109 - James Lara, Yuri Khudyakov:
Modeling antigenic property of the hepatitis C virus NS3 protein. 110-117 - Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky:
RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. 118-123 - Kristin P. Bennett, Cagri Ozcaglar, Janani Ranganathan, Srivatsan Raghavan, Jacob Katz, Dan Croft, Bülent Yener, Amina Shabbeer:
Visualization of tuberculosis patient and Mycobacterium tuberculosis complex genotype data via host-pathogen maps. 124-129 - Austin Huang, Rami Kantor, Allison DeLong, Leeann Schreier, Sorin Istrail:
QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads. 130-136 - Yufeng Shen, Yee Him Cheung, Shuang Wang, Itsik Pe'er:
A parametric Bayesian method to test the association of rare variants. 137-143 - Pavel Skums, David S. Campo, Zoya Dimitrova, Gilberto Vaughan, Daryl T. Lau, Yuri Khudyakov:
Modelling differential interferon resistance of HCV quasispecies. 144-148
3rd Workshop on Data Mining for Biomarker Discovery (DMBD)
- Junwan Liu, Xiaohua Hu, Zhoujun Li, Yiming Chen:
Multiobjective optizition shuffled frog-leaping biclustering. 151-156 - Rency S. Varghese, Bin Zhou, Habtom W. Ressom:
Meta-analysis of LC-MS based metabolomic experiments. 157-164 - Ruifei Xie, Bin Han, Lihua Li, Juan Zhang, Lei Zhu:
Professional tennis player ranking strategy based Monte Carlo feature selection. 165-172 - Wayne E. Clarke, Christine Sidebottom, Isobel A. P. Parkin, Andrew Sharpe:
saskPrimer - An automated pipeline for design of intron-spanning PCR primers in non-model organisms. 173-177 - En-Shiun Annie Lee, Andrew K. C. Wong:
Synthesizing Aligned Random Pattern Digraphs from protein sequence patterns. 178-185 - E. M. Rivera, Z. Irizarry, Matilde Luz Sánchez Peña, C. E. Isaza, J. Seguel, Mauricio Cabrera-Ríos:
Consistent detection of cancer biomarkers with linear models. 186-192 - Lenka Vyslouzilova, Vojtech Adam, Andrea Szabóová, Olga Stepánková, René Kizek, Jiri Anyz:
Brdicka curve - A new source of biomarkers. 193-198
2nd Workshop on Integrative data analysis in systems biology (IDASB)
- Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch:
Ontology-based functional classification of genes: Evaluation with reference sets and overlap analysis. 201-208 - Koon Yin Kong, Adam I. Marcus, Paraskevi Giannakakou, May D. Wang:
A web interface for the quantification of microtubule dynamics. 209-214 - Neil Moore, Jerzy W. Jaromczyk:
Finding a longest open reading frame of an alternatively spliced gene. 215-222 - Piyaphol Phoungphol, Yanqing Zhang:
Multi-source kernel k-means for clustering heterogeneous biomedical data. 223-228 - Sudipto Saha, Rob M. Ewing:
Systematic discovery of condition specific Wnt signaling subnetworks. 229-234 - Xiaodong Zhou, E. Olusegun George:
An improved data integration methodology for system biology. 235-240 - Noha A. Yousri, Dalal M. Elkaffash:
Associating gene functional groups with multiple clinical conditions using Jaccard similarity. 241-246 - Hui Li, Chunmei Liu, Mugizi Robert Rwebangira, Legand Burge, William M. Southerland:
Rapid identification of multi-PTMs peptide sequence tags with a graph search approach. 247-250 - Hui Li, Chunmei Liu, Mugizi Robert Rwebangira, Legand Burge, William M. Southerland:
Rapid generation of peptide sequence tags with a graph search algorithm. 251-254 - Kathryn Dempsey, Ishwor Thapa, Dhundy Bastola, Hesham H. Ali:
Identifying modular function via edge annotation in gene correlation networks using Gene Ontology search. 255-261 - Rui Jiang, Jiaxin Wu:
Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs. 262-267 - Haiying Wang, Huiru Zheng:
Correlation of genomics features with the date and party hub distinction: A view from three dimensional protein structures. 268-273 - Jingchun Sun, Paul Hart, Zhongming Zhao:
Development and implementation of a novel computational tool for an efficient construction of drug-target interactome. 274-279
Workshop on Cancer Informatics
- Wenlong Tang, Hongbao Cao, Ji-Gang Zhang, Junbo Duan, Dongdong Lin, Yu-Ping Wang:
Classifying six glioma subtypes from combined gene expression and CNVs data based on compressive sensing approach. 282-288 - David J. Dittman, Taghi M. Khoshgoftaar, Randall Wald, Amri Napolitano:
Random forest: A reliable tool for patient response prediction. 289-296 - Sairam Behera, Ovidiu Daescu, Lech Papiez:
Optimal delivery of volumetric modulated arc therapy (VMAT) for moving target. 297-304 - Sabrina Rashid, Golam Morshed Maruf:
An adaptive feature reduction algorithm for cancer classification using wavelet decomposition of serum proteomic and DNA microarray data. 305-312
Workshop on Computational Structural Bioinformatics
- Jyh-Jong Tsay, Shih-Chieh Su:
Ab initio protein structure prediction based on memetic algorithm and 3D FCC lattice model. 315-318 - Marko Zivanic, Ovidiu Daescu, Anastasia Kurdia:
Rigid region pairwise sequence alignment. 319-326 - Masood Zamani, Stefan C. Kremer:
Amino acid encoding schemes for machine learning methods. 327-333 - Sajal Dash, Jack Snoeyink:
On the energy of bifurcated hydrogen bonds for protein structure prediction. 334-337 - Promita Bose, Xiaxia Yu, Robert W. Harrison:
Encoding protein structure with functions on graphs. 338-344 - Mina Maleki, Md. Mominul Aziz, Luis Rueda:
Analysis of relevant physicochemical properties in obligate and non-obligate protein-protein interactions. 345-351 - Jianlin Cheng, Zheng Wang, Jesse Eickholt, Xin Deng:
Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9. 352-357 - Irina Hashmi, Bahar Akbal-Delibas, Nurit Haspel, Amarda Shehu:
Protein docking with information on evolutionary conserved interfaces. 358-365 - Brian S. Olson, S. Farid Hendi, Amarda Shehu:
Protein conformational search with geometric projections. 366-373 - Kyung Dae Ko, Chunmei Liu, Mugizi Robert Rwebangira, Legand Burge, William M. Southerland:
The development of a proteomic analyzing pipeline to identify proteins with multiple RRMs and predict their domain boundaries. 374-381 - Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu:
P.R.E.S.S. - An R-package for exploring residual-level protein structural statistics. 382-389 - Antonio Mucherino, Carlile Lavor, Leo Liberti:
A symmetry-driven BP algorithm for the Discretizable Molecular Distance Geometry Problem. 390-395 - Jorge E. Duarte, Jaime Velasco-Medina, Pedro A. Moreno:
Hardware simulation of yeast glycolytic oscillations. 396-399 - Bahar Akbal-Delibas, Irina Hashmi, Amarda Shehu, Nurit Haspel:
Refinement of docked protein complex structures using evolutionary traces. 400-404 - Lin Chen, Jing He:
A distance and orientation dependent potential energy function with cluster energy. 405-409 - Weitao Sun:
Normal mode analysis of protein structure dynamics based on residue contact energy. 410-415 - Alberto Casagrande, Francesco Fabris:
SCOP family fingerprints: An information theoretic approach to structural classification of protein domains. 416-423 - Brian Yuan Chen, Soutir Bandyopadhyay:
A statistical model of overlapping volume in ligand binding cavities. 424-431 - Filip Jagodzinski, Jeanne Hardy, Ileana Streinu:
Using rigidity analysis to probe mutation-induced structural changes in proteins. 432-437
Workshop on Bioinformatics for microRNA and Disease
- Dachuang Liu, Cuihong Dai, Dechang Xu:
Cluster analysis of MiRNAs microarray data and prediction of lupeol's anti-cancer path. 440-445 - Xiaofeng Song, Minghao Wang, Yi-Ping Phoebe Chen, Ping Han:
Identifying multiple stem-loops pre-miRNA using support vector machine. 446-448 - Tzu-Hung Hsiao, Hung-I Harry Chen, Patricia C. Sanchez-Diaz, Jaclyn Y. Hung, Yidong Chen, Yufei Huang:
Gene sets enrichment analysis of miRNA expression profile. 449-454
4th Workshop on Biomolecular Network Analysis (IWBNA)
- Shouguo Gao, Xujing Wang:
Topology-based scoring method for identification of responsive protein-protein interaction subnetwork. 457-464 - Hongwei Wu, Yaming Lin, Fun Choi Chan, Rocío Alba-Flores:
Module detection for bacteria based on spectral clustering of protein-protein functional association networks. 465-472 - M. Mondal Ananda, Jhih-rong Lin, Jianjun Hu:
Network based subcellular localization prediction for multi-label proteins. 473-480 - Pietro Hiram Guzzi, Pierangelo Veltri, Mario Cannataro:
VeNet: A framework for the analysis of protein interaction networks through vector space embedding. 481-487 - Mingming Liu, Yanwei Huang, Liqing Zhang, David R. Bevan:
A new functional association-based protein complex prediction. 488-494 - Pietro Hiram Guzzi, Marianna Milano, Pierangelo Veltri, Mario Cannataro:
Using semantic similarity to detect features in yeast protein complexes. 495-502 - Yinhai Liu, Yang Yu, Chengjie Sun, Lei Lin, Xiaolong Wang:
A hierarchical link clustering based approach for identifying protein complexes by incorporating core-attachment structure. 503-508 - Kathryn Dempsey, Hesham H. Ali:
Evaluation of essential genes in correlation networks using measures of centrality. 509-515
Workshop on Biomedical and Health Informatics
- Shuihua Wang, Yingli Tian:
Indoor signage detection based on saliency map and bipartite graph matching. 518-525 - Ricardo Chincha, Yingli Tian:
Finding objects for blind people based on SURF features. 526-527 - Faiz M. Hasanuzzaman, Yingli Tian, Qingshan Liu:
Identifying medicine bottles by incorporating RFID and video analysis. 528-529 - Yang Chen, Manabu Torii, Chang-Tien Lu, Hongfang Liu:
Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts. 530-537 - Shameem Fathima, Nisar Hundewale:
Comparison of classification techniques-SVM and naives bayes to predict the Arboviral disease-Dengue. 538-539 - Sardar Ansari, Ashwin Belle, Kevin Ward, Rosalyn S. Hobson, Kayvan Najarian:
Reduction of periodic motion artifacts from impedance plethysmography. 540-547 - Pavani Davuluri, Jie Wu, Ashwin Belle, Charles H. Cockrell, Yang Tang, Kevin Ward, Kayvan Najarian, Rosalyn Hobson Hargraves:
A hybrid approach for hemorrhage segmentation in pelvic CT scans. 548-554 - Ashwin Belle, Rosalyn S. Hobson, Kayvan Najarian:
A physiological signal processing system for optimal engagement and attention detection. 555-561 - Saejoon Kim:
Margin-maximized redundancy-minimized SVM-RFE for diagnostic classification of mammograms. 562-569 - Dennis Wegener, Simona Rossi, Francesca Buffa, Mauro Delorenzi, Stefan Riiping:
Towards an environment for data mining based analysis processes in bioinformatics & personalized medicine. 570-577 - Meng-Han Yang, Yen-Jen Oyang, Jong-Ling Fuh:
Application of density estimation algorithms in analyzing co-morbidities of migraine. 578-585 - Min Song, Said Bleik, Hwanjo Yu, Wook-Shin Han:
Extracting biomedical concepts from fulltext by relative importance in a graph model. 586-593 - Patrizia Vizza, Pierangelo Veltri, Giuseppe Lucio Cascini:
A ROI-based algorithm for the classification of PET neuroimages. 594-595 - Alessio Pierluigi Placitelli, Luigi Gallo:
3D point cloud sensors for low-cost medical in-situ visualization. 596-597 - Siddharth Pandey, Michael D. Kane, John A. Springer:
GLASS: Genomic Literature Area Sequence Search. 598-599 - Jie Wu, Pavani Davuluri, Ashwin Belle, Charles H. Cockrell, Yang Tang, Kevin Ward, Rosalyn S. Hobson, Kayvan Najarian:
Fracture detection and quantitative measure of displacement in pelvic CT images. 600-606 - Hua Xu, Samir AbdelRahman, Min Jiang, Jung-Wei Fan, Yang Huang:
An initial study of full parsing of clinical text using the Stanford Parser. 607-614 - Arash Shaban-Nejad, Volker Haarslev:
An enhanced graph-oriented approach for change management in distributed biomedical ontologies and linked data. 615-622 - Sujin Kim, Desok Kim, Hyun-Joo Choi, Hee Jae Joo:
Detection of lobular carcinoma in situ(LCIS) by image analysis. 623-624 - Sérgio Lifschitz, Luciana S. A. Gomes, Stevens K. Rehen:
Dealing with reusability and reproducibility for scientific workflows. 625-632 - Jörg W. Schlundt, Stefan Jablonski:
A framework for designing compliance conform processes in clinical trials. 633-634 - Zainab Haydari, Yanqing Zhang, Hamid Soltanian-Zadeh:
Semi-automatic epilepsy spike detection from EEG signal using Genetic Algorithm and Wavelet transform. 635-638 - Zakiyeh Shojaei Estabragh, Mohammad Mansour Riahi Kashani, Farnaz Jeddi Moghaddam, Simin Sari, Koosha Sadeghi Oskooyee:
Bayesian network model for diagnosis of Social Anxiety Disorder. 639-640 - Ilma Andayana, Desok Kim, William J. Howat, Hayley C. Whitaker, Mark Gregson:
Development of glandular shape analysis for computer aided detection of prostatic cancer in hematoxylin-stained histologic slides. 641-642 - Yang Huang, Daniel Zisook, Yunan Chen, Michael Selter, Paul Minardi, John E. Mattison:
Lessons learned in improving the adoption of a real-time NLP decision support system. 643-648 - King-Ip (David) Lin, Vivek V. Datla, Linda Morrison, Max M. Louwerse:
Using a feedback system to enhance chart note quality in Electronic Health Records. 649-654 - Giovanna Sannino, Giuseppe De Pietro:
A smart context-aware mobile monitoring system for heart patients. 655-695
Workshop on Informatics Applications in Therapeutics
- Zhiping Zhang, Honghuang Lin:
Genomic profiling by machine learning. 662-668 - Arpita Das, Partha P. Goswami, Susanta Sen, Mahua Bhattacharya:
Classification of poor contrast mammograms using a novel and fast boundary detection technique. 669-676 - Guanglan Zhang, Ellis L. Reinherz, Derin B. Keskin, Vladimir Brusic:
A cDNA microarray for rapid and economical identification of HLA profiles of individuals. 677-679 - Esma Dilek, Tanya Zlateva, Guanglan Zhang, Lubomir T. Chitkushev, Jae Young Lee, Vladimir Brusic:
Probe design optimization of HLA microarray: Data cleaning of probe signals from cDNA tiling microarray: Outlier detection, noise reduction, and identification of uninformative probes in HLA typing application. 680-682 - Suresh Kalathur, Vladimir Brusic, Guanglan Zhang, Lubomir T. Chitkushev, Tanya Zlateva:
Visualization tools for presenting and analysis of global landscapes of vaccine targets. 683-688
Workshop on Data mining for genome-wide association studies
- Sungyoung Lee, Min-Seok Kwon, Ik-Soo Huh, Taesung Park:
CUDA-LR: CUDA-accelerated logistic regression analysis tool for gene-gene interaction for genome-wide association study. 691-695 - Christine W. Duarte, Yann C. Klimentidis, Jacqueline J. Harris, Michelle Cardel, José R. Fernández:
A hybrid Bayesian Network/Structural Equation Modeling (BN/SEM) approach for detecting physiological networks for obesity-related genetic variants. 696-702 - Min-Seok Kwon, Kyunga Kim, Sungyoung Lee, Wonil Chung, Sung-Gon Yi, Junghyun Namkung, Taesung Park:
GWAS-GMDR: A program package for genome-wide scan of gene-gene interactions with covariate adjustment based on multifactor dimensionality reduction. 703-707 - Ik-Soo Huh, Sohee Oh, Taesung Park:
A chi-square test for detecting multiple joint genetic variants in genome-wide association studies. 708-713 - Sungkyoung Choi, Sungho Won:
Robust analysis of related samples under the presence of population substructure. 714-720 - Rauf Ahmed Shams Malick, Nasir Touheed:
Variations in edge betweenness measure for gene regulatory networks. 721-724