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ORCID7th BIBE 2007: Boston, MA, USA
- Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2007, October 14-17, 2007, Harvard Medical School, Boston, MA, USA. IEEE Computer Society 2007, ISBN 978-1-4244-1509-0
IEEE BIBE Plenary Keynote Lecture Notes (Part I)
- A. Keith Dunker, Christopher J. Oldfield, Jingwei Meng, Pedro Romero, Jack Y. Yang, Zoran Obradovic, Vladimir N. Uversky:
Intrinsically Disordered Proteins: Predictions and Applications. 1 - John Quackenbush:
Stochasticity and Networks in Genomic Data. 2 - Mark Borodovsky:
Decoding Novel Genomes: From Microbiomes to the Eukaryota. 3 - Mary Qu Yang, Laura Elnitski
:
Promoter studies in the human genome: one perspective on an unfinished story. 4-6 - Yi Pan:
Protein Structure Prediction and Its Understanding Based on Machine Learning Methods. 7 - Guo-Cheng Yuan, Jun S. Liu:
Statistial Analysis of nucleosome occupancy and histone modification data. 8 - Mary Qu Yang, Jack Y. Yang:
An Investigation into the Feasibility of Detecting Microscopic Disease Using Machine Learning. 9-10 - Linda K. Molnar:
Nanobioinformatics: The Enabling Technology of Personalized Medicine. 11 - Vladimir N. Uversky, Christopher J. Oldfield, A. Keith Dunker:
Intrinsically Disordered Proteins in Human Diseases. 12 - Xudong Huang:
Metallobiochemistry of Alzheimer's Disease and Its Theranostic Agent Development. 13
Protein Structure and Function
- Suk Hoon Jung, Hee-Young Hur, Desok Kim, Dong-Soo Han:
Identification of Conserved Domain Combinations in S.cerevisiae Proteins. 14-20 - Wei Zhong, Jieyue He, Yi Pan:
Multiclass Fuzzy Clustering Support Vector Machines for Protein Local Structure Prediction. 21-26 - Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski:
A New Alignment-Independent Algorithm for Clustering Protein Sequences. 27-34 - David J. John, Jacquelyn S. Fetrow, James L. Norris:
Metropolis-Hastings Algorithm and Continuous Regression for finding Next-State Models of Protein Modification using Information Scores. 35-41 - Valerio Freschi:
Protein function prediction from interaction networks using a random walk ranking algorithm. 42-48 - A. Keith Dunker, Christopher J. Oldfield, Jingwei Meng, Pedro Romero, Jack Y. Yang, Zoran Obradovic, Vladimir N. Uversky:
Intrinsically Disordered Proteins: An Update. 49-58 - Gil Alterovitz, Eugenia Lyashenko, Michael Xiang, Marco Ramoni:
Linking Protein Mass with Function via Organismal Massome Networks. 59-65 - Yuehui Chen, Xueqin Zhang, Mary Qu Yang, Jack Y. Yang:
Ensemble of Probabilistic Neural Networks for Protein Fold Recognition. 66-70
Microarray Data and Applications (Part A)
- Qiankun Zhao, Prasenjit Mitra, Dongwon Lee, Jaewoo Kang:
HICCUP: Hierarchical Clustering Based Value Imputation using Heterogeneous Gene Expression Microarray Datasets. 71-78 - Erliang Zeng, Chengyong Yang, Tao Li, Giri Narasimhan:
On the Effectiveness of Constraints Sets in Clustering Genes. 79-86 - Song Li:
Integrate Qualitative Biological Knowledge to Build Gene Networks by Parallel Dynamic Bayesian Network Structure Learning. 87-92 - Kerstin Koch, Stefan Schönauer, Ivy Jansen, Jan Van den Bussche, Tomasz Burzykowski:
Finding Clusters of Positive and Negative Coregulated Genes in Gene Expression Data. 93-99 - Noha A. Yousri, Mohamed S. Kamel, Mohamed A. Ismail:
Pattern Cores And Connectedness in Cancer Gene Expression. 100-107 - Peter Warren, Deanne M. Taylor, Paolo G. V. Martini, Jennifer Jackson, Jadwiga R. Bienkowska:
PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays. 108-115
Microarray Data and Applications (Part B)
- Rasha F. Kashef, Mohamed S. Kamel:
Cooperative Partitional-Divisive Clustering and Its Application in Gene Expression Analysis. 116-122 - Chris Thachuk, Anne Condon:
On the Design of Oligos for Gene Synthesis. 123-130 - Kenneth A. Marx, John Sharko, Georges G. Grinstein, Shannon Odelberg, Hans-Georg Simon:
Evidence for Proximal to Distal Appendage Amputation Site Effects from Global Gene Expression Correlations Found in Newt Microarrays. 131-136 - Nha Nguyen, Heng Huang, Soontorn Oraintara, Yuhang Wang:
Denoising of Array-Based DNA Copy Number Data Using The Dual-tree Complex Wavelet Transform. 137-144 - Brian E. Howard, Beate Sick, Imara Perera, Yang Ju Im, Heike Winter-Sederoff, Steffen Heber:
Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier. 145-150 - Yu-Chun Lin, Hsiang-Yuan Yeh, Shih-Wu Cheng, Von-Wun Soo:
Comparing Cancer and Normal Gene Regulatory Networks Based on Microarray Data and Transcription Factor Analysis. 151-157
Microarray Data and Applications (Part C)
- Chan-Hoon Park, Soo-Jin Kim, Sun Kim, Dong-Yeon Cho, Byoung-Tak Zhang:
Finding Cancer-Related Gene Combinations Using a Molecular Evolutionary Algorithm. 158-163 - Yi Zhang, Chris H. Q. Ding, Tao Li:
A Two-Stage Gene Selection Algorithm by Combining ReliefF and mRMR. 164-171 - John H. Phan, May D. Wang:
Estimating Classification Error to Identify Biomarkers in Time Series Expression Data. 172-179 - Minseo Park, Deane L. Falcone, Kil-Young Yun, Karen M. Daniels:
Detection and Prediction of Alternative Splicing within Acceptor/Donor Sites in pre-mRNA of Arabidopsis thaliana. 180-186 - Mehdi Pirooznia, Arun Rawat, Jack Y. Yang, Mary Qu Yang, Ping Gong, Edward J. Perkins, Youping Deng:
An Effective Interwoven Loop Design Application for Two-Channel Microarray Experiments. 187-191 - Fan Wang, Gagan Agrawal, Ruoming Jin, Helen Piontkivska:
SNPMiner: A Domain-Specific Deep Web Mining Tool. 192-199
Biomedical Engineering
- Iman Veisi, Naser Pariz, Ali Karimpour:
Fast and Robust Detection of Epilepsy in Noisy EEG Signals Using Permutation Entropy. 200-203 - Vishnu Mallapragada, Nilanjan Sarkar, Tarun Kanti Podder:
A Robotic System for Real-time Tumor Manipulation During Image guided Breast Biopsy. 204-210 - Li Shen, Andrew J. Saykin, Moo K. Chung, Heng Huang:
Morphometric Analysis of Hippocampal Shape in Mild Cognitive Impairment: An Imaging Genetics Study. 211-217 - Serdar Bozdag, Timothy J. Close, Stefano Lonardi:
A Compartmentalized Approach to the Assembly of Physical Maps. 218-225 - Lelin Zhang, Hongkai Xiong, Kai Zhang, Xiaobo Zhou:
Graph Theory Application in Cell Nuleus Segmentation, Tracking and Identification. 226-232 - Walker H. Land Jr., Daniel W. McKee, Tatyana Zhukov, Dansheng Song, Wei Qian:
An End-to-End Process for Cancer Identification from Images of Lung Tissue. 233-239 - Bin Wang, Jianhua Xuan, Matthew T. Freedman, Peter G. Shields, Yue Joseph Wang:
Rat Mammary Fat Pad Segmentation and Growth Rate Evaluation in T1 Weighted MR Images. 240-245 - Kai Zhang, Hongkai Xiong, Xiaobo Zhou:
A Simulation-Based 3D Axon Axis Extraction in Confocal Fluorescence Microscopy Images. 246-250 - Walker H. Land Jr., Alda Mizaku, Thomas Raway, John J. Heine, Claudia Berman, Nataliya Kovalchuk:
Advancements in Automated Diagnostic Mammography. 251-256 - Zhuangli Liang, W. Clem Karl, Synho Do, Udo Hoffmann, Thomas J. Brady, Homer H. Pien:
Calcium De-blooming in Coronary CT Image. 257-262
Computational Methods in Bioinformatics
- Hyunsoo Kim, Haesun Park, Hongyuan Zha:
Distance Preserving Dimension Reduction Using the QR Factorization or the Cholesky Factorization. 263-269 - Dumitru Brinza, Alexander Zelikovsky:
Discrete Methods for Association Search and Status Prediction in Genotype Case-Control Studies. 270-277 - Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer:
A Multi-Objective Genetic Algorithm that Employs a Hybrid Approach for Isolating Codon Usage Bias Indicative of Translational Efficiency. 278-285 - Wamiq Manzoor Ahmed, Bulent Bayraktar, Arun K. Bhunia, E. Daniel Hirleman, J. Paul Robinson, Bartek Rajwa:
Rapid Detection and Classification of Bacterial Contamination Using Grid Computing. 286-293 - Sadaf R. Alam, Nikhil Bhatia, Jeffrey S. Vetter:
Sensitivity Analysis of Biomolecular Simulations using Symbolic Models. 294-300
Sequence Analysis
- Xiaoyong Fang, Zhigang Luo, Bo Yuan, Zhenghua Wang:
Detecting and Assessing Conserved Stems for Accurate Structural Alignment of RNA Sequences. 301-306 - Shibin Qiu, Terran Lane:
The RNA String Kernel for siRNA Efficacy Prediction. 307-314 - Stephanie Jimenez Irausquin, Liangjiang Wang:
A Machine Learning Approach for Prediction of Lipid-Interacting Residues in Amino Acid Sequences. 315-319 - Cornelia Caragea, Jivko Sinapov, Vasant G. Honavar, Drena Dobbs:
Assessing the Performance of Macromolecular Sequence Classifiers. 320-326 - Marina Barsky, Ulrike Stege, Alex Thomo, Chris Upton:
Shortest Path Approaches for the Longest Common Subsequence of a Set of Strings. 327-333 - Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Vandanaben Patel, Marvin K. Nakayama:
Constrained RNA Structural Alignment: Algorithms and Application to Motif Detection in the Untranslated Regions of Trypanosoma brucei mRNAs. 334-341
Systems Biology
- Young-Rae Cho, Woochang Hwang, Aidong Zhang:
Optimizing Flow-based Modularization by Iterative Centroid Search in Protein Interaction Networks. 342-349 - Qiong Cheng, Robert W. Harrison, Alexander Zelikovsky:
Homomorphisms of Multisource Trees into Networks with Applications to Metabolic Pathways. 350-357 - Melissa Freedenberg, Chanchala Kaddi, Chang F. Quo, May D. Wang:
Review of Systems Biology Simulation Tools for Translational Research. 358-365 - Juliette Blanchet, Matthieu Vignes:
Combined expression data with missing values and gene interaction network analysis: a Markovian integrated approach. 366-373 - Gil Alterovitz, Taro Muso, Paresh Malalur, Marco Ramoni:
A Systematic Approach to Quantifying Evolutionary Functional Trends Across the Universal Tree of Life. 374-378
Sequence and Structure
- Bernard Chen, Stephen Pellicer, Phang C. Tai, Robert W. Harrison, Yi Pan:
Super Granular Shrink-SVM Feature Elimination (Super GS-SVM-FE) Model for Protein Sequence Motif Information Extraction. 379-386 - Osman Abul, Geir Kjetil Sandve, Finn Drabløs:
False Discovery Rates in Identifying Functional DNA Motifs. 387-394 - Gaofeng Huang, Peter Jeavons:
A Geometrical Model for the SNP Motif Identification Problem. 395-402 - Fei Xiong, Chris Bailey-Kellogg:
A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure. 403-410 - Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, Wen Gao:
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots. 411-417 - Yu-Feng Huang, Yu-Shin Lin, Tian-Wei Hsu, Chien-Kang Huang:
Mining Conserved Structures of Enzymes from Functional Hierarchical Classification. 418-424 - Kreshna Gopal, James C. Sacchettini, Thomas R. Ioerger:
Database Approaches and Data Representation in Structural Bioinformatics. 425-432
Bioinformatics Applications
- Jung Hoon Woo, Tian Zheng, Ju Han Kim:
Identifying Genomic Regulators of Set-Wise Co-Expression. 433-439 - Mingwu Zhang, Daisuke Kihara, Sunil Prabhakar:
Tracing Lineage in Multi-version Scientific Databases. 440-447 - Nadia Yacoubi Ayadi, Zoé Lacroix:
Resolving Scientific Service Interoperability With Schema Mapping. 448-455 - M. L. Ujwal, Patrick Hoffman, Kenneth A. Marx:
A Machine Learning Approach to Pharmacological Profiling of the Quinone Scaffold in the NCI Database: A Compound Class Enriched in Those Effective Against Melanoma and Leukemia Cell Lines. 456-463 - Jung Hun Oh, Young Bun Kim, Prem Gurnani, Kevin P. Rosenblatt, Jean Gao:
Biomarker Selection for Predicting Alzheimer Disease Using High-Resolution MALDI-TOF Data. 464-471 - E. R. Muir, I. J. Ndiour, N. A. LeGoasduff, Richard A. Moffitt, Ying Liu, M. Cameron Sullards, Alfred H. Merrill, Yanfeng Chen, May D. Wang:
Multivariate Analysis of Imaging Mass Spectrometry Data. 472-479 - Jiaxing Xue, Jean Gao, Liping Tang:
Phagocyte Transmigration Modeling Using System Dynamic Controls. 480-485
WORKSHOP on Bio-Nano-Info Integration for Personalized Medicine
- David S. Paik:
Toward a Nanobioinformatics Infrastructure for Nanotechnology-based Prostate Cancer Therapeutic Response Tracking. 486 - Chenxi Shao, Hongli Deng:
A Novel Approach for Signal Transduction Networks Simulation at a Mesoscopic Level. 487-494 - Christopher Alberti, Jean-Philippe Villaréal, Delano Billingsley, Koon Yin Kong, Adam I. Marcus, Paraskevi Giannakakou, May D. Wang:
Microtubule Dynamics Classification Using a Statistical Model of the Movement of Outer Tips. 495-502 - Sohaib Waheed, Richard A. Moffitt, Qaiser Chaudry, Andrew N. Young, May D. Wang:
Computer Aided Histopathological Classification of Cancer Subtypes. 503-508 - John H. Phan, Richard A. Moffitt, Todd H. Stokes, May D. Wang:
Evolving Biological Behavior in Gene-Based Cellular Simulations. 509-516 - Mark Chen, Brian Huang, Eric Shin, Erik Robinson, Erik Pierstorff, Houjin Huang, Dean Ho:
Engineering Multifunctional Biologically-Amenable Nanomaterials for Interfacial Therapeutic Delivery and Substrate-Based Cellular Interrogation. 517-523 - Jack Y. Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng:
Non-Monotonic Radio-Sensitivity over Tumor Volumes on Adjuvant Radio Therapy A New Insight on Cell Killing and Modeling. 524-531
WORKSHOP on Joint Research in the Southern Illinois University, University of Illinois, and Oak Ridge National Labortaroy, U.S. Department of Energy
- Lisa Furby, Ravinder Gupta, Ajay Mahajan, Jarlen Don, Tsuchin Chu, Bakul Dave, Brad Schwartz:
Novel Materials for the Direct Removal of Water and Ions from the Body for Patients with Dialysis Needs. 532-537 - Min Xu, Louxin Zhang, Pei Li Joe Zhou:
A Robust Method for Generating Discriminative Gene Clusters. 538-545 - John R. Shell, Yonglian Wang, Nazeih M. Botros:
Biological Mechanism on a Chip: Modeling and Realization of Growth Hormone Secretion Mechanism. 546-552 - Manish Paliwal, D. Gordon Allan, Peter Filip:
Retrieval Analysis of a Cementless Modular Total Hip Arthroplasty Prosthesis. 553-558 - D. Gordon Allan, Manish Paliwal, Peter Filip:
Trabecular Metal Patella Implanted into Soft-Tissue in a Post-Patellectomized Knee A Case Report. 559-562 - Ying Chen, Joseph Y. Lo, James T. Dobbins:
A comparison between traditional shift-and-add (SAA) and point-by-point back projection (BP) -- relevance to morphology of microcalcifications for isocentric motion in Digital Breast tomosynthesis (DBT). 563-569 - Benfano Soewito, Ning Weng:
Methodology for Evaluating DNA Pattern Searching Algorithms on Multiprocessor. 570-577 - Qiang Shawn Cheng, Mehdi R. Zargham:
An Efficient Compression Method for Multiplanar Reformulated Biomedical Images. 578-584 - Jiazheng Yuan, Mengxia Zhu, M. Javed Iqbal, Jack Y. Yang, David A. Lightfoot:
A Computational Approach to Understand Arabidopsis thaliana and Soybean Resistance to Fusarium solani (Fsg). 585-592 - Yunfeng Yang, Michelle M. Zhu, Liyou Wu, Jizhong Zhou:
Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays. 593-600 - Salahuddin Mohammad Masum, Mohammed Yeasin:
Dynamic Load Balancing for Mining of Molecular Structures using Genetic Algorithm. 601-608
WORKSHOP on Progress Toward Petascale Applications in Bioinformatics And Computational Biology
- Robert Henschel, Matthias S. Müller:
I/O Induced Scalability Limits of Bioinformatics Applications. 609-613 - Marek Freindorf, Matthew D. Jones, Yihan Shao, Jing Kong, Thomas R. Furlani:
Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein: Toward Petascale Level of Protein Calculations. 614-619 - Jeffrey L. Tilson, Gloria Rendon, Mao-Feng Ger, Eric Jakobsson:
MotifNetwork: A Grid-enabled Workflow for High-throughput Domain Analysis of Biological Sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation. 620-627 - Scott B. Baden, Terrence J. Sejnowski, Thomas M. Bartol, Joel R. Stiles:
Toward Petascale Simulation of Cellular Microphysiology. 628-634
Special Session on Computational Intelligence in Medical Informatics
- Jacqueline Signorini, Patrick Greussay:
Silent Killing: an Object-Oriented View of Hypertension and Kidney Failures Part I. 635-640 - Wei Liu, Weidong Xu, Lihua Li:
Medical Image Retrieval Based on Bidimensional Empirical Mode Decomposition. 641-646 - Jun Kong, Wenjing Lu, Jianzhong Wang, Na Che, Yinghua Lu:
A Modified Fuzzy Kohonen's Competitive Learning Algorithms Incorporating Local Information for MR Image Segmentation. 647-653 - Siyuan Liu, Chao Liu, Yu Liu, Chunzhe Zhao:
An Efficient Modeling and Simulation System on the Kidney Matching, Distribution and Exchange Problems. 654-661 - Klaus H. Ecker, Lonnie R. Welch, Dazhang Gu:
SiteSeeker - A Motif Discovery Tool. 662-664
Special Session on Evolutionary Systems Biology
- Wen Zhou, Tian Xia, Jiansong Tong, Julie A. Dickerson, Bo Su, Xun Gu:
Modeling protein interaction network and mechanisms in exocytosis. 665-672 - Wenhai Chen, Tianzi Jiang, Tian Xia, Xun Gu:
Toward a Realistic Model for Gene Network Evolution. 673-679 - Pan Du, Simon M. Lin, Warren A. Kibbe, Haihui Wang:
Application of Wavelet Transform to the MS-based Proteomics Data Preprocessing. 680-686 - Jennifer L. Neary, Maribel Sanchez, Yufeng Wang, Timothy G. Lilburn:
Pathway Complements of Four Yersinia. 687-692 - Yi Zhang, Zhi-Li Pei, Jinhui Yang, Yanchun Liang:
An Improved Ant Colony Optimization Algorithm Based on Route Optimization and Its Applications in Travelling Salesman Problem. 693-698 - James F. Courage, Saurabh Gupta, Yufeng Wang:
Characterization of MYC expression in gefitinib versus Acute Myeloid Leukemia reveals novel therapeutic targets. 699-706 - Misha L. Rajaram, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman:
Hot and Cold: Spatial Fluctuation in HIV-1 Recombination Rates. 707-714
Special Session 13: Speciall Sesssion on Research in Bioinformatics, Neuroinformatics, and Systems Biology in East Asia
- Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano:
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles. 715-722 - Tae Ho Kang, Jae Soo Yoo, Hak Yong Kim:
Mining Frequent Contiguous Sequence Patterns in Biological Sequences. 723-728 - Shing-Kit Chan, Wai Lam:
Efficient Methods for Biomedical Named Entity Recognition. 729-735 - Dong-Soo Kahng, Yoonkey Nam, Doheon Lee:
Stochastic Simulation Model for Patterned Neural Multi-Electrode Arrays. 736-740 - Bum Ju Lee, Heon Gyu Lee, Jong Yun Lee, Keun Ho Ryu:
Classification of Enzyme Function from Protein Sequence based on Feature Representation. 741-747 - Yunkyu Sohn, Jaeseung Jeong:
Inferring Behavioral-level Circuits of Caenorhabditis elegans from the Topology of its Wiring Diagram. 748-752 - Huitao Sheng, Kishan Mehrotra, Chilukuri K. Mohan, Ramesh Raina:
HAMMER Algorithm: Hashing with Arithmetic Modulo-4 for Motif Extraction of Regulatory Elements. 753-758 - Meena K. Sakharkar, Kishore R. Sakharkar:
A Tale of Intronless Genes in Eukaryotic Genomes. 759-765 - Kishore R. Sakharkar, Meena K. Sakharkar:
To fuse or not to fuse. 766-773
Special Session on Sequence Alignment and Phylogenetic Analysis
- Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll, Mark J. Clement, Quinn Snell:
Using Parsimony to Guide Maximum Likelihood Searches. 774-779 - Xu Zhang, Tamer Kahveci:
QOMA2: Optimizing the alignment of many sequences. 780-787 - Ken D. Nguyen, Yi Pan:
A Reliable Metric for Quantifying Multiple Sequence Alignment. 788-795 - Ahmet Sacan, Ismail Hakki Toroslu:
Amino Acid Substitution Matrices Based on 4-Body Delaunay Contact Profiles. 796-801 - Feng Yue, Meng Zhang, Jijun Tang:
A Heuristic for Phylogenetic Reconstruction Using Transposition. 802-808 - Abdullah N. Arslan, Peyman Bizargity:
Phylogeny By Top Down Clustering Using a Given Multiple Alignment. 809-814 - Patricia Buendia:
Reconstructing Mutational Pathways from Serial Evolutionary Trees. 815-820
Special Session on Development of Algorithms for Solving Problems in Molecular Biology
- Swapnoneel Roy, Ashok Kumar Thakur:
Towards Construction of Optimal Strip-Exchanging Moves. 821-827 - Ruizhi Wang, Duoqian Miao, Gang Li, Hongyun Zhang:
Rough Overlapping Biclustering of Gene Expression Data. 828-834 - Fa Zhang, Zhaoyun Ma, Zhiyong Liu, Bo Yuan:
Using Domain-Based Structural Ensemble to Improve Structure Modeling. 835-841 - Guo-Zheng Li, Hao-Hua Meng, Mary Qu Yang, Jack Y. Yang:
Support Vector Regression with Feature Selection for the Multivariate Calibration of Spectrofluorimetric Determination of Aromatic Amino Acids. 842-848
Special Session on High-Throughput Data Analysis for Genomics and Proteomics
- Hyung-Won Koh, Lars Hildebrand:
Bottom-Up Multiple Row Addition Algorithms for the Biclustering-Problem. 849-856 - Hongling Wang, Alberto Maria Segre, Yungui Huang, Jeffrey R. O'Connell, Veronica J. Vieland:
Fast Computation of Human Genetic Linkage. 857-863 - Afef Elloumi Oueslati, Noureddine Ellouze, Zied Lachiri:
3D Spectrum Analysis of DNA Sequence: Application to Caenorhabditis elegans Genome. 864-871 - Jeffrey L. Tilson, Alan Blatecky, Gloria Rendon, Mao-Feng Ger, Eric Jakobsson:
MotifNetwork: Genome-Wide Domain Analysis using Grid-enabled Workflows. 872-879 - Elton José R. Vasconcelos, Ana Carolina L. Pacheco, Joao J. S. Gouveia, Fabiana F. Araújo, Michely C. Diniz, Michel T. Kamimura, Marcilia P. Costa, Rodrigo Maggioni, Raimundo Araujo-Filho, Raimundo B. Costa, Diana Magalhaes de Oliveira:
Profilins, Formins and Katanins as Flagellar Proteins of Leishmania spp.: a Genome-based, Multi-step Bioinformatics-driven Description. 880-887
Special Session on Bio-Medical Soft Computing
- Jason D. Bakos, Panormitis E. Elenis, Jijun Tang:
FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data. 888-895 - Elham Khabiri:
A Preliminary Study of Correlation between Depth and Path Length of GO Nodes with Gene Sequence Similarity. 896-899 - Siyuan Liu, Chao Liu, Chunzhe Zhao, Yu Liu:
Mathematical Models and Optimization Discussion on EA System on AIDS/HIV Spread Estimating and Countermeasures Evaluating. 900-907
Special Session on Bio-Complexity
- Radu Dobrescu, Loretta Ichim:
Fractal Dimension of Mie Scattering Spectra for the Appraisal of Infected HeLa Cells in Cultures. 908-913 - Jiejun Kong, Xiaoyan Hong, Dapeng Wu, Mario Gerla:
Complexity-theoretic Modeling of Biological Cyanide Poisoning as Security Attack in Self-organizing Networks. 914-921 - Alessandro Abate, Yu Bai, Nathalie Sznajder, Carolyn L. Talcott, Ashish Tiwari:
Quantitative and Probabilistic Modeling in Pathway Logic. 922-929 - Dimitrios Dakopoulos, Sanjay K. Boddhu, Nikolaos G. Bourbakis:
A 2D Vibration Array as an Assistive Device for Visually Impaired. 930-937
Special Session on Machine Learning Methods in Structural and Functional Genomics
- Leonardo Bobadilla, Fernando Niño, Edilberto Cepeda, Manuel A. Patarroyo:
Characterizing and Predicting Catalytic Residues in Enzyme Active Sites Based on Local Properties: A Machine Learning Approach. 938-945 - Tapan Patel, Li Liao:
Predicting Protein-Protein Interaction Based on Fisher Scores Extracted from Domain Profiles. 946-951 - Majid Masso, Iosif I. Vaisman:
A Novel Sequence-Structure Approach for Accurate Prediction of Resistance to HIV-1 Protease Inhibitors. 952-958 - Tho Hoan Pham, Tu Bao Ho, Dang Hung Tran, Kenji Satou:
Prediction of Histone Modifications in DNA sequences. 959-966 - Hualong Bu, Guo-Zheng Li, Xue-Qiang Zeng, Jack Y. Yang, Mary Qu Yang:
Feature Selection and Partial Least Squares Based Dimension Reduction for Tumor Classification. 967-973 - Hossam S. Sharara, Mohamed A. Ismail:
aCORR: A novel algorithm for clustering gene expression data. 974-981 - Vandana Gummuluru, Su-Shing Chen:
An Intelligent System for Searching Genomic Sequences. 982-986 - Michael L. Blinov, Ion I. Moraru:
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes. 987-994
Special Session on DNA Microarray Data Analysis
- Kenneth Bryan, Padraig Cunningham:
BALBOA: Extending Bicluster Analysis to Classify ORFs using Expression Data. 995-1002 - Zhenyu Wang, Vasile Palade:
A Comprehensive Fuzzy-Based Framework for Cancer Microarray Data Gene Expression Analysis. 1003-1010 - Ángela Blanco, Manuel Martín-Merino, Javier De Las Rivas:
Ensemble of Kernel Based Classifiers to Improve the Human Cancer Prediction using DNA Microarrays. 1011-1018 - Li Teng, Laiwan Chan:
Mining Order Preserving Patterns in Microarray Data by Finding Frequent Orders. 1019-1026 - Nha Nguyen, Heng Huang, Soontorn Oraintara, An P. N. Vo:
A New Smoothing Model for Analyzing Array CGH Data. 1027-1034 - Sheehyun Kim, Dongsup Kim:
Inference of Gene Regulatory Networks Using Time Sliding Comparison and Transcriptional Lagging Time from Time Series Gene Expression Profiles. 1035-1040
Microarray Gene Expression Analysis
- Vidya P. Kamath, Lawrence O. Hall, Timothy Yeatman, Steven Eschrich:
Multivariate Feature Selection using Random Subspace Classifiers for Gene Expression Data. 1041-1045 - Fei Wang, Tao Li:
Gene Selection via Matrix Factorization. 1046-1050 - Fang Zhou, Jieyue He, Wei Zhong:
Mutual Information based Minimum Spanning Trees Model for Selecting Discriminative Genes. 1051-1055 - Elena Baralis, Elisa Ficarra, Alessandro Fiori, Enrico Macii:
Gene-Markers Representation for Microarray Data Integration. 1056-1060 - Yinyin Yuan, Chang-Tsun Li:
Partial Mixture Model for Tight Clustering in Exploratory Gene Expression Analysis. 1061-1065 - Yuhang Wang, Siling Wang, Andrew R. Zinn:
rSWTi: A Robust Stationary Wavelet Denoising Method for Array CGH Data. 1066-1070 - Jahangheer S. Shaik, E. Olusegun George, Mohammed Yeasin:
An Empirical CDF Approach to Estimate the Significance of Gene Ranking for Finding Differentially Expressed Genes. 1071-1075 - Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, G. Alexander Patterson, Weixiong Zhang:
Gene expression profiling and machine learning to understand and predict primary graft dysfunction. 1076-1080 - Jared Fox, Nik Brown:
Sensitivity and Consistency of Affymetrix GeneChip Normalization Methods. 1081-1086
Bioengineering (Part A) -- Deformable and 3D Modeling
- Qing He, Ye Duan, Judith H. Miles, Nicole Takahashi:
Statistical Shape Analysis of the Corpus Callosum in Subtypes of Autism. 1087-1091 - Ying Zhu:
Simulation and Visualization of Menisci-Femur Contact Using Patient-Specific Deformable Models. 1092-1096 - Foued Derraz, Abdelmalik Taleb-Ahmed, Azeddine Chikh, Fethi Bereksi-Reguig:
Improved edge map of geometrical active contour model based on coupling to anisotropic diffusion filtering. 1097-1101 - Soroor Behbahani, Keivan Magholi:
Analysis of cardiac wall motion estimation methods. 1102-1107 - Tarun Kanti Podder, Ivan Buzurovic, Yida Hu, James M. Galvin, Yan Yu:
Partial transmission high-speed continuous tracking multi-leaf collimator for 4D adaptive radiation therapy. 1108-1112 - Wamiq Manzoor Ahmed, Magdalena Jonczyk, Ali Shamsaie, Arif Ghafoor, J. Paul Robinson:
Quantitative Analysis of Inter-object Spatial Relationships in Biological Images. 1113-1117
Bioengineering (Part B) -- Biomedical Image Processing I
- Jörg Meyer:
Histogram Transformation for Inter-Modality Image Registration. 1118-1123 - Antonio Ruiz, Manuel Ujaldon, Jose Antonio Andrades, Jose Becerra, Kun Huang, Tony Pan, Joel H. Saltz:
The GPU on biomedical image processing for color and phenotype analysis. 1124-1128 - Santiago Aja-Fernández, Marcos Martín-Fernández, Carlos Alberola-López:
Tissue Identification in Ultrasound Images using Rayleigh Local Parameter Estimation. 1129-1133 - Amirali Shayan Arani, Yi Zhu, Yi-Ning Cheng, Chung-Kuan Cheng, Shien-Fong Lin, Peng-Sheng Chen:
Exploring Cardioneural Signals from Noninvasive ECG Measurement. 1134-1138 - Akmal A. Younis, Ahmed T. Soliman, Mansur R. Kabuka, Nigel M. John:
MS Lesions Detection in MRI Using Grouping Artificial Immune Networks. 1139-1146 - Hyunsoo Kim, Haesun Park, Lars Eldén:
Non-negative Tensor Factorization Based on Alternating Large-scale Non-negativity-constrained Least Squares. 1147-1151
Bioengineering (Part C) -- Biomedical Image Processing II
- Henry Carrillo, Jorge Villarreal, Miguel Sotaquira, Alvaro Goelkel, Ricardo Gutierrez:
A Computer Aided Tool for the Assessment of Human Sperm Morphology. 1152-1157 - Benedito G. Aguiar Neto, Joseana M. Fechine, Silvana Cunha Costa, Menaka Muppa:
Feature Estimation for Vocal Fold Edema Detection Using Short-Term Cepstral Analysis. 1158-1162 - Heng Huang, Paul R. Bergstresser:
A New Hybrid Technique for Dermatological Image Registration. 1163-1167 - Chengwei Li, Ruiqiang Hu:
PID Control based on BP Neural Network for the Regulation of Blood Glucose Level in Diabetes. 1168-1172 - César Pichardo-Almarza, Rod H. Smallwood, S. A. Billings:
Spatiotemporal Analysis of an Agent-Based Model of a Colony of Keratinocytes: A First Approach for the Development of Validation Methods. 1173-1177
Sequence Analysis and Sequence Alignment
- Hongwei Huo, Vojislav Stojkovic:
A Suffix Tree Construction Algorithm for DNA Sequences. 1178-1182 - Viktor Martyanov, Larkin Elderon, Amy Gladfelter, Dhanalakshmi R. Nair, Robert H. Gross:
Identifying Fungal Regulatory Motif Patterns Using SCOPE, an Ensemble Learning Method Motif Finder. 1183-1187 - Tieming Ji, Desh Ranjan, Jeanne Curry, Mary O'Connell:
Computational Identification of Cis-regulatory Elements Associated with Pungency of Chili Peppers. 1188-1192 - Yong Gao, Michael Henderson:
Speeding Up Pairwise Sequence Alignments: A Scoring Scheme Reweighting Based Approach. 1194-1198 - Dan He, Abdullah N. Arslan, Yu He, Xindong Wu:
Iterative Refinement of Repeat Sequence Specification Using Constrained Pattern Matching. 1199-1203 - Antonio E. de la Serna:
Differential Scoring for Systolic Sequence Alignment. 1204-1208 - Lisa M. Guntly, Jennifer L. Leopold, Anne M. Maglia:
Determining Domain Similarity and Domain-Protein Similarity Using Functional Similarity Measurements of Gene Ontology Terms. 1209-1213 - Paul Dan Cristea, Rodica Tuduce, Iulian Nastac, Jan Cornelis, Rudi Deklerck, Marius Andrei:
Signal Representation and Processing of Nucleotide Sequences. 1214-1219 - Huiru Zheng, Haiying Wang, Jinglu Hu:
Cluster Analysis of Regulatory Sequences with a Log Likelihood Ratio Statistics-based Similarity Measure. 1220-1224
Bioengineering (Part D) -- Biomedical Applications
- Yong-Jie Ni, Chan-Hyun Youn, Byoung-Jin Kim, Youngjoo Han, Peng Liu:
A PQRM-based PACS System for Advanced Medical Services under Grid Environment. 1225-1229 - Sung-Huai Hsieh, Sheau-Ling Hsieh, Yung-Ching Weng, Tzu-Hsiang Yang, Feipei Lai, Po-Hsun Cheng, Xiao-Ou Ping, Mao-yu Jan, Jen-Chiun Lin, Chin-Hung Peng, K. H. Huang, L. F. Ko, Chi-Huang Chen, Kai-Ping Hsu:
Middleware based Inpatient Healthcare Information System. 1230-1234 - Courtney D. Corley, Lindsey Brown, Armin R. Mikler, Diane J. Cook, Karan P. Singh:
Generating social networks of intimate contacts for the study of public health intervention strategies. 1235-1239 - Wen-Ran Zhang, Karl E. Peace:
Yin Yang Mental Squares - An Equilibrium-Based System For Bipolar Neurobiological Pattern Classification and Analysis. 1240-1244 - Jared Fox, Nik Brown:
Automatically Extracting Acronyms from Biomedical Text. 1245-1248 - Mingyuan Zhao, Mingtian Zhou, Qingxin Zhu, Ping Yang:
Feature Extraction and Parameters Selection of Classification Model on Brain-Computer Interface. 1249-1253
Biological Networks
- Rui Chang:
Consistent Modeling, Integration and Simulation of Molecular Interaction Networks in Space-Time Dimension. 1254-1259 - Mehmet Tan, Faruk Polat, Reda Alhajj:
Feature Reduction for Gene Regulatory Network Control. 1260-1264 - George Chin Jr., Grant C. Nakamura, Daniel G. Chavarría-Miranda, Heidi J. Sofia:
Graph Mining of Networks from Genome Biology. 1265-1269 - Martin S. R. Paradesi, Doina Caragea, William H. Hsu:
Structural Prediction of Protein-Protein Interactions in Saccharomyces cerevisiae. 1270-1274 - Mohieddine Missaoui, David R. C. Hill, Cécile Militon, Pierre Peyret:
Complete Backtranslation of Oligopeptides for Metabolic Pathways Exploration of Complex Environments using Functional Microarrays. 1275-1279 - Kazuyuki Numata, Seiya Imoto, Satoru Miyano:
A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks. 1280-1284
Algorithms in Bioinformatics
- Lei Zhang, Renhou Li:
An Algorithm for Mining Fuzzy Association Rules Based on Immune Principles. 1285-1289 - Juan Shan, Yuxuan Wang, Changhui Yan:
Toward The Recognition Code Of Protein-DNA Recognition. 1290-1293 - Dragos Trinca, Sanguthevar Rajasekaran:
Self-Optimizing Parallel Algorithms for Haplotype Reconstruction and Their Evaluation on the JPT and CHB Genotype Data. 1294-1298 - Xiaolu Huang, Hesham H. Ali:
Reducing Folding Scenario Candidates in Pseudoknots Detection Using PLMM_DPSS Algorithm Integrated With Energy Filters. 1299-1303 - Paulius Micikevicius, Narsingh Deo:
Exploring Topological Properties of NMR Graphs. 1304-1307 - Yu-Ting Huang, Shih-Fang Lin, Chung-Cheng Chiu, Hsiang-Yuan Yeh, Von-Wun Soo:
Probability Analysis on Associations of Adverse Drug Events with Drug-Drug Interactions. 1308-1312
Bioinformatics Tools
- Jay Urbain, Nazli Goharian, Ophir Frieder:
Combining Semantics, Context, and Statistical Evidence in Genomics Literature Search. 1313-1317 - Fan Wang, Ruoming Jin, Gagan Agrawal, Helen Piontkivska:
Graph and Topological Structure Mining on Scientific Articles. 1318-1322 - Ying Liu, Yongjing Lin:
Supervised HITS Algorithm for MEDLINE Citation Ranking. 1323-1327 - Michel A. Kinsy, Zoé Lacroix:
Storing Efficiently Bioinformatics Workflows. 1328-1332 - Chen Lin, Wayne Mak, Pengyu Hong, Katharine J. Sepp, Norbert Perrimon:
Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases. 1333-1337 - Neha Nahar, Lutz Hamel, Maria S. Poptsova, J. Peter Gogarten:
GPX: A Tool for the Exploration and Visualization of Genome Evolution. 1338-1342 - Tom Milledge, Gaolin Zheng, Tim Mullins, Giri Narasimhan:
SBLAST: Structural Basic Local Alignment Searching Tools using Geometric Hashing. 1343-1347
Protein Structural Prediction and Functional Analysis
- Mudassir Fayyaz, Adnan Mujahid, Asifullah Khan, Tae-Sun Choi, Nadeem Iqbal:
G-protein Coupled Receptor Subfamilies Prediction Based on Nearest Neighbor Approach. 1348-1354 - Anjum Reyaz-Ahmed, Yan-Qing Zhang:
Protein Secondary Structure Prediction Using Genetic Neural Support Vector Machines. 1355-1359 - Xiaoli Li, Jun-Xiang Lee, Bharadwaj Veeravalli, See-Kiong Ng:
An HV-SVM Classifier to Infer TF-TF Interactions Using Protein Domains and GO Annotations. 1360-1364 - Fiona Browne, Haiying Wang, Huiru Zheng, Francisco Azuaje:
Supervised Statistical and Machine Learning Approaches to Inferring Pairwise and Module-Based Protein Interaction Networks. 1365-1369 - Jing Hu, Changhui Yan:
Predicting Protein Subcelluar Localizations Using Weighted Euclidian Distance. 1370-1373 - Alireza Hadj Khodabakhshi, Mehdi Mirzazadeh, Arvind Gupta:
An efficient data structure for applying multiple seeds in homology search. 1374-1378 - Ian MacDonald, George Berg:
A Mixture of Experts Method for Predicting Domain Boundaries in Proteins. 1379-1383 - Woochang Hwang, Taehyong Kim, Young-Rae Cho, Aidong Zhang, Murali Ramanathan:
SIGN: reliable protein interaction identification by integrating the Similarity In GO and the similarity in protein interaction Networks. 1384-1388
Bioinformatics Applications
- Elizabeth Rossin, Saumyadipta Pyne, Florian Hahne, Philip L. De Jager:
Identification of Differential Flow Cytometry Expression. 1389-1393 - Enis Afgan, Purushotham V. Bangalore:
Performance Characterization of BLAST for the Grid. 1394-1398 - Sihui Zhao, Jihye Kim, Steffen Heber:
Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing. 1399-1403 - Ionut Bebu, Françoise Seillier-Moiseiwitsch, Hongfang Liu:
Semiparametric RMA Background-Correction for Oligonucleotide Arrays. 1404-1408 - Anuradha Roy, Jennifer L. Leopold, Anne M. Maglia:
Alternative Splicing: Associating Frequency with Isoforms. 1409-1413 - Benjamin J. Kelly, Paul E. Anderson, Nicholas V. Reo, Nicholas J. DelRaso, Travis E. Doom, Michael L. Raymer:
A Proposed Statistical Protocol for the Analysis of Metabolic Toxicological Data Derived from NMR Spectroscopy. 1414-1418 - Fang-Xiang Wu, Jiarui Ding, Guy G. Poirier:
A Framework for Mass Spectral Quality Assessment without Prior Information. 1419-1423 - Tapani Utriainen, Graham J. L. Kemp:
Using long fragments to reconstruct RNA backbones. 1424-1428 - Jingwei Zhang, Layne T. Watson:
A Modified Uniformization Method for the Chemical Master Equation. 1429-1433 - Jonathan L. Jesneck, Sayan Mukherjee, Loren W. Nolte, Anna E. Lokshin, Jeffrey R. Marks, Joseph Y. Lo:
Decision Fusion of Circulating Markers for Breast Cancer Detection in Premenopausal Women. 1434-1438
IEEE BIBE Plenary Keynote Lecture Notes (Part II)
- Guo-Zheng Li, Xue-Qiang Zeng, Jack Y. Yang, Mary Qu Yang:
Partial Least Squares Based Dimension Reduction with Gene Selection for Tumor Classification. 1439-1444 - Steven Seltzer:
Functional and Molecular Imaging: Key Components of Personalized Healthcare. 1445 - Xiaohua Hu:
Biomedical Literature Mining. 1446 - Mary Qu Yang, Laura Elnitski:
An Overview of Bidirectional Promoters. 1447 - Ruzena Bajcsy:
Distributed Wireless Sensors on the Human Body. 1448 - Andreas D. Baxevanis:
Transforming Medicine: Genomics, Bioinformatics, and Human Health. 1449 - Brian D. Athey:
Integrative Biomedical Informatics. 1450 - Eric Jakobsson, May D. Wang, Linda K. Molnar:
Bio-Nano-Info Integration for Personalized Medicine. 1452
Tutorial Lecture Notes
- David A. Lightfoot, Mengxia Michelle Zhu:
Using The Soybean Genome Database (SoyGD) To Display and Analyze a 1 Gbp Genome Sequence. 1453 - Patrick S. P. Wang:
Biometrics Intelligence Information Systems and Applications. 1454 - Arif Ghafoor, J. Paul Robinson:
Knowledge Modeling for High Content Screening of Multimedia Biological Data. 1455 - Igor B. Zhulin:
Reconstructing Signal Transduction from Raw Genomic Data. 1456 - Tian Zheng:
Studying Co-Regulation and Inter-Regulation of Genes via eQTL Mapping. 1457 - Craig A. Stewart, Malinda Lingwall, David A. Bader:
Lecture on Progress toward Petascale Applications in Bioinformatics and Computational Biology. 1458 - Sadaf R. Alam, Pratul K. Agarwal, Jeffery A. Kuehn:
Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System. 1459-1466
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