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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