7. 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 2007 
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 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 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 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 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 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 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
- Liu Siyuan, Liu Chao, Liu Yu, Zhao Chunzhe:
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 J. R. Vasconcelos, Ana C. 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
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
- Hua-Long 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
Microarray Gene Expression Analysis
- Vidya P. Kamath, Lawrence O. Hall, Timothy J. 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 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
- Joerg 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 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
