4. CSB Workshops 2005: Stanford, CA, USA
Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts (CSB 2005 Workshops), 8-11 August 2005, Stanford, CA, USA. IEEE Computer Society 2005 ISBN 0-7695-2442-7
Cover
- Title Page.
- Copyright.
Poster Abstracts
Biomedical Research
- Günter Tusch: Sequential Classification for Microarray and Clinical Data. 5-6
- Mark A. Sheppard, Liwen Shih: Efficient Image Texture Analysis and Classification for Prostate Ultrasound Diagnosis. 7-8
- Lu-Yong Wang, Amit Chakraborty, Dorin Comaniciu: Diagnosis and Biomarker Identi.cation on SELDI proteomics data by ADTBoost. 9-10
- Shawn Martin, W. Michael Brown, Jean-Loup Faulon, Derick C. Weis, Donald P. Visco: Inverse Design of Large Molecules using Linear Diophantine Equations. 11-16
Cellular Multicelluar Systems
- Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. Das: A Diffusion Model to Estimate the Inter-arrival Time of Charged Molecules in Stochastic Event based Modeling of Complex Biological Networks. 19-22
Comporative Genomics
- Jake K. Byrnes, Wen-Hsiung Li: Patterns of Gene Deletion following Genome Duplication in Yeast. 25-26
- Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim: PLATCOM: a Platform for Computational Comparative Genomics on the Web. 27-30
Data Mining
- Mengjun Wang, Jialin Zheng, Zhengxin Chen, Yong Shi: Classification Methods for HIV-1 Medicated Neuronal Damage. 31-32
- Guojun Li, Jizhu Lu, Victor Olman, Ying Xu: PROMOCO: a New Program for Prediction of cis Regulatory Elements: From High-Information Content Analysis to Clique Identification. 35-36
- Donnie Qi, Judith A. Blake, James A. Kadin, Joel E. Richardson, Martin Ringwald, Janan T. Eppig, Carol J. Bult: Data Integration in the Mouse Genome Informatics (MGI) Database. 37-38
- Talapady N. Bhat, Yadu B. Tewari, Henry Rodriguez, Robert N. Goldberg: HIV Structural and Biothermodynamics Databases: a Resource for the Pharmaceutical and Biotechnology Industry. 39-40
- Huimin Geng, Hesham H. Ali: A New Clustering Strategy with Stochastic Merging and Removing Based on Kernel Functions. 41-42
- Eveleen Darby, Tezeswari Nettimi, Shilpa Kodali, Liwen Shih: Head and Neck Cancer Metastasis Prediction via Artificial Neural Networks. 43-44
- Eric G. Stephan, Kyle R. Klicker, Mudita Singhal, Heidi J. Sofia: Problem Solving Environment Approach to Integrating Diverse Biological Data Sources. 47-50
Evolution and Phylogenetics
- Daniel Barker, Mark Pagel: Predicting functional gene-links from phylogenetic-statistical analyses of whole genomes. 51-52
- Xiaomeng Wu, Guohui Lin, Xiu-Feng Wan, Dong Xu: Whole Genome Phylogeny Based on Clustered Signature String Composition. 53-54
- Gang Wu, Jia-Huai You, Guohui Lin: A Polynomial Algorithm for the Minimum Quartet Inconsistency Problem with O(n) Quartet Errors. 55-56
- Andreas Kramer, Daniel R. Richards, James O. Bowlby, Ramon M. Felciano: Consensus Methods Using Phylogenetic Databases. 61-62
- Noppadon Khiripet: Bacterial Whole Genome Phylogeny Using Proteome Comparison and Optimal Reversal Distance. 63-64
- Rogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders: Identifying Orthologs: Cycle Splitting on the Breakpoint Graph. 65-68
Functional Genomics
- Theo A. Knijnenburg, Marcel J. T. Reinders, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Lodewyk F. A. Wessels: Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae. 71-72
- Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik: Automatic Protein Function Annotation through Candidate Ortholog Clusters from Incomplete Genomes. 73-74
- Irene S. Gabashvili, Richard J. Carter, Peter W. Markstein, Anne B. S. Giersch: EST-Based Analysis of Gene Expression in the Human Cochea. 75-76
- Alexander Vaughan, Rahul Singh, Ilmi Yoon, Megumi Fuse: EigenPhenotypes: Towards an Algorithmic Framework for Phenotype Discovery. 77-78
- Emily Chia-Yu Su, Allan Lo, Chin-Chin Lin, Fu Chang, Wen-Lian Hsu: A Novel Approach for Prediction of Multi-Labeled Protein Subcellular Localization for Prokaryotic Bacteria. 79-82
High Performance Computing
- David A. Bader, Vipin Sachdeva: Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system. 83-84
- Gui Liang Feng, Yujiang Shan: A generic algorithm to find all common intervals of two permutations. 85-88
Microarray Analysis
- Nathalie Pochet, Frizo A. L. Janssens, Frank De Smet, Kathleen Marchal, Ignace Vergote, Johan A. K. Suykens, Bart De Moor: M@CBETH: Optimizing Clinical Microarray Classification. 89-90
- Jiaxiong Pi, Yong Shi, Zhengxin Chen: Similarity and cluster analysis algorithms for Microarrays using R trees. 91-92
- Dick de Ridder, Marcel J. T. Reinders, Frank J. T. Staal, Jacques J. M. van Dongen: Maximum signi.cance clustering of oligonucleotide microarrays. 93-94
- Ann E. Loraine, Mari L. Salmi, Stephen C. Stout, Stanley J. Roux: Gene-Ontology-based analysis of gene expression changes in early development of Ceratopteris spores. 95-96
- Lu-Yong Wang, Ammaiappan Balasubramanian, Amit Chakraborty, Dorin Comaniciu: Fractal Clustering for Microarray Data Analysis. 97-98
- Manohar Kollegal, Sudeshna Adak, Richard Shippy, Timothy Sendera: Considerations in Making Microarray Cross-Platform Correlations. 101-102
- Alberto D. Pascual-Montano, Francisco Tirado, Pedro Carmona-Saez, José María Carazo, Roberto D. Pascual-Marqui: Two-way clustering of gene expression profiles by sparse matrix factorization. 103-104
- Bernard Chen, Robert W. Harrison, Yi Pan, Phang C. Tai: Novel Hybrid Hierarchical-K-means Clustering Method (H-K-means) for Microarray Analysis. 105-108
- Curtis Huttenhower, Olga G. Troyanskaya: A General Methodology for Integration of Microarray Data. 109
- Heng Huang, Rong Zhang, Fei Xiong, Fillia Makedon, Li Shen, Bruce Hettleman, Justin D. Pearlman: K-means+ Method for Improving Gene Selection for Classification of Microarray Data. 110-111
- Roger Pique-Regi, Antonio Ortega, Shahab Asgharzadeh: Sequential Diagonal Linear Discriminant Analysis (SeqDLDA) for Microarray Classification and Gene Identification. 112-116
Other
- Robert John Coulier: A Storage, Processing, and Retrieval System for Microtubule Tracking Data. 117
- Zoé Lacroix, Sumedha Gholba, Hervé Ménager: BioMap: Discovering Schema Mapping Using Ontologies. 118-119
- Thomas C. Hudson, Ann E. Stapleton, Amy M. Curley: Minimal Marker Sets to Discriminate Among Seedlines. 120-121
- Camille Bodley Troup, Bill Martin, Carl E. McMillin, Robert M. Horton: Simulated Pharmacogenomics Exercises for the Cybertory Virtual Molecular Biology Laboratory. 124-125
- Weichuan Yu, Xiaoye Li, Hongyu Zhao: Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach. 126-127
- Reeti Tandon, Sudeshna Adak, Brion Sarachan, William FitzHugh, Jeremy Heil, Vaibhav A. Narayan: Predicting Continuous Epitopes in Proteins. 133-134
- Eugene P. van Someren, Marcel J. T. Reinders: Which normalization method is best? A platform-independent biologically inspired quantitative comparison of normalization methods. 135-136
- Zoé Lacroix, Kaushal Parekh, Maria-Esther Vidal, Marelis Cardenas, Natalia Marquez, Louiqa Raschid: BioNavigation: Using Ontologies to Express Meaningful Navigational Queries Over Biological Resources. 137-138
- Alexander Churkin, Ornit Elgad, Oshrat Petgho, Danny Barash: RNAMute: RNA Secondary Structure Mutation Analysis Tool. 139-141
- James P. Carson, Christina Thaller, Musodiq Bello, Wah Chiu, Tao Ju, Joe D. Warren, Ioannis A. Kakadiaris, Gregor Eichele: Data Mining in situ Gene Expression Patterns at Cellular Resolution. 141-142
- Rehan Akbani, Stephen Kwek: Adapting Support Vector Machines to Predict Translation Initiation Sites the Human Genome. 143-148
Pathways Networks System Biology
- Xiang Guo, Hai Hu, Michael N. Liebman, Craig D. Shriver: Semantic Similarity-based Validation of Human Protein-Protein Interactions. 149-150
- Min Su Lee, Seung-Soo Park, Min Kyung Kim: A Protein Interaction Verification System Based on a Neural Network Algorithm. 151-154
- Merrill Knapp, Linda Briesemeister, Steven Eker, Patrick Lincoln, Andy Poggio, Carolyn L. Talcott, Keith Laderoute: Pathway Logic Helping Biologists Understand and Organize Pathway Information. 155-156
- Wen-Ting Lin, Kuen-Pin Wu, Wei-Neng Hung, Yi-Hwa Yian, Yet-Ran Chen, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu: MassTRAQ: a Fully Automated Tool for iTRAQ-labeled Protein Quantification. 157-158
- Corey Powell, Joshua M. Stuart: Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating. 159-160
- Andreas Kramer, Daniel R. Richards, James O. Bowlby, Ramon M. Felciano: Functional Modularity in a Large-Scale Mammalian Molecular Interaction Network. 161-163
- K.-H. Chiam, Vipul Bhargava, Gunaretnam Rajagopal: Oscillatory dynamics in the mitogen-activated protein kinase cascade. 164-165
- Rogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders: Predicting gene function by combining expression and interaction data. 166-167
- Federico Fontana, Luca Bianco, Vincenzo Manca: A symbolic approach to the simulation of biochemical models: application to circadian rhythms. 168-169
- Samik Ghosh, Preetam Ghosh, Kalyan Basu, Sajal K. Das: iSimBioSys: An "In Silico" Discrete Event Simulation Framework for Modeling Biological Systems. 170-171
- Eugene P. van Someren, B. L. T. Vaes, W. T. Steegenga, A. M. Sijbers, Koen J. Dechering, Marcel J. T. Reinders: Unravelling the murine osteoblast differentiation pathway by network structure analysis using time-series microarray data. 172-173
- Qiaofeng Yang, Stefano Lonardi: A Parallel Algorithm for Clustering Protein-Protein Interaction Networks. 174-177
- Matthew T. Weirauch, Joshua M. Stuart: Discovering Functional Transcription Factor Binding from Superimposed Gene Networks. 178-179
- Andrey Y. Sivachenko, Anton Yuryev, Nikolai Daraselia, Ilya Mazo: Identifying Local Gene Expression Patterns in Biomolecular Networks. 180-184
Pattern Recognition
- Christian Beaudry, Michael E. Berens, Tarek A. El Doker, Anna M. Joy, Lina J. Karam, Zoé Lacroix, Jad A. Lutfi, Sai Motoru: Automated Characterization of cellular migration phenomena. 185-186
- Ramana M. Gosukonda, Masoud Naghedolfeizi, Johnny Carter: Artificial Neural Networks to Predict Daylily Hybrids. 187-188
- Eric Sakk, David J. Schneider, Samuel W. Cartinhour, Christopher R. Myers, Monica Vencato, Alan Collmer: Computational identification and characterization of Type III secretion substrates. 191-192
- Adaya N. Cohen, Klara Kedem, Michal Shapira, Danny Barash: Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes. 193-195
- Gary L. Jahns, Nicholas J. DelRaso, Mark P. Westrick, Victor Chan, Nicholas V. Reo, Timothy R. Zacharewski: Joint Genomic and Metabolomic Analysis of Toxic Dose-Response Experiments. 195-198
Promoter Analysis
- Raja Loganantharaj: Predicting a Transcription Start Site: Case Study with Different Genomes. 199-200
- Raja Loganantharaj: On Discriminating a TATA-box from putative TATA boxes: A Case Study Using Plant Genome. 201-203
- Asim S. Siddiqui, Gordon Robertson, Misha Bilenky, Tamara Astakhova, Obi L. Griffith, Maik Hassel, Keven Lin, Stephen Montgomery, Mehrdad Oveisi, Erin Pleasance, Neil Robertson, Monica C. Sleumer, Kevin Teague, Richard Varhol, Maggie Zhang, Steven J. M. Jones: cis-Regulatory Element Prediction in Mammalian Genomes. 203-206
Protiend Structure Analysis
- Zhenglin Hou, Cunxi Wang, Odd-Arne Olsen: TPR Packing Analysis and 3D Modeling for the HAT Domain of Human Crooked Neck Protein. 207-208
- Javier A. Velázquez-Muriel, José María Carazo: Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM. 209-210
- Jinhui Ding, Elizabeth Eskow, Nelson L. Max, Silvia N. Crivelli: Protein Structure Prediction Using Physical-Based Global Optimization and Knowledge-Guided Fragment Packing. 211-212
- Hae-Jin Hu, Phang C. Tai, Robert W. Harrison, Jieyue He, Yi Pan: Protein Secondary Structure Prediction Using Support Vector Machine With a PSSM Profile and an Advanced Tertiary Classifier. 213-214
- Wei Zhong, Gulsah Altun, Robert W. Harrison, Phang C. Tai, Yi Pan: Mining Protein Sequence Motifs Representing Common 3D Structures. 215-216
- Peng Wang, Bo Yan, Jun-tao Guo, Chindo Hicks, Ying Xu: Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants. 217-
- Hsin-Nan Lin, Kuen-Pin Wu, Jia-Ming Chang, Ting-Yi Sung, Wen-Lian Hsu: GANAA Genetic Algorithm for NMR Backbone Resonance Assignment. 218-219
- Yogesh A. Girdhar, Christopher Bystroff, Srinivas Akella: Efficient Sampling of Protein Folding Pathways using HMMSTR and Efficient Sampling of Protein Folding Pathways using HMMSTR and. 222-223
- Jieyue He, Bernard Chen, Hae-Jin Hu, Robert W. Harrison, Phang C. Tai, Yisheng Dong, Yi Pan: Rule Clustering and Super-rule Generation for Transmembrane Segments Prediction. 224-227
- Huseyin Seker, Parvez I. Haris: Analysis of four different sets of predictive features for metalloproteins. 228-232
RNAi Analysis
- Amanda Birmingham, Emily M. Anderson, William S. Marshall, Anastasia Khvorova: Maximum Sequence Alignment Fails to Predict Off-targeted Gene Regulation by RNAi. 233-234
- Assaf Avihoo, Danny Barash: Temperature and Mutation Switches in the Secondary Structure of Small RNAs. 235-238
Sequence Alignment
- Carla Correa Tavares dos Reis, Rubem P. Mondaini: Using Parallel Algorithms for Searching Molecular Sequence Databases. 239-240
- Hyon Chang Kim, Yong Beom Seo, Ji Hwan Song, Dong Soon Choi, Churl K. Min, Han Jip Kim: Massive Multiple Sequence Alignment of 16S Bacterial Ribosomal RNAs Using ClustalW-Message Passing Interface (MPI) Based on Beowulf Linux System. 241-242
- Yao-ming Huang, Christopher Bystroff: Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions. 243-246
SNPs and Haplotyping
- Yasuyuki Tomita, Hiroyuki Honda, Mitsuhiro Yokota: Classification method for prediction of multifactorial disease development using interaction between genetic and environmental factors. 247-248
- Takashi Kido, Masanori Baba, Guijin Ji, Hidenori Satoh, Masaaki Muramatsu: Mapping SNP association results into type 2 DM Pathways-Metabolic Syndrome as a robust system. 249-250
- Zemin Ning, Mario Cáccamo, James C. Mullikin: ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale. 251-254
Synthetic Biological Systems
- G. Sampath, James TenEyck: Non-occurring and rare quads in PDB and translated introns from XPro with possible applications in nanostructure design. 256-257
- Gang Wu, Nabila Bashir-Bello, Stephen J. Freeland: The Synthetic Gene Designer: a Flexible Web Platform to Explore Sequence Space of Synthetic Genes for Heterologous Expression. 258-259
- Christopher Bystroff, Sam DeLuca, Carl N. McDaniel: ECOME: A simple model for an evolving consumption web. 260-261
- Sairam Subramanian, Ihor Lemischka, Ron Weiss: Engineering a 1: 2 Bio-multiplexer for controlled stem cell differentiation. 262
- David Karig, Jerome Ku, Ron Weiss: Engineering Multi-signal Systems for Complex Pattern Formation. 263-266
Visualization
- Weiguo Fan, Xin Lin, Yu-Wei Hsieh, Johnnie W. Baker, Boren Lin, Chun Che Tsai: Chemical Structure-Activity Relationship Visualization Using Structure Activity Maps. 267-268
- Arthur Chun-Chieh Shih, D. T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao: SinicView: An Interactive Visualization Tool for Comparison of Multiple Sequence Alignment Results. 269-270
- Ting-Cheng Lu, Jinhui Ding, Silvia N. Crivelli: DockingShop: a Tool for Interactive Protein Docking. 271-272
- Ting-Cheng Lu, Silvia N. Crivelli, Nelson L. Max: ProteinShop and POSE: Bringing Robotics and Intelligent Systems into the Field of Molecular Modeling. 273-274
- Richard S. Gunasekera, Hari Damodaran, Yasantha Rajakarunanayake, Keith Hyland: The Significance of Linearity of Quantities in Electrophoresed and Blotted Materials Demonstrated by BandScan - an Analytical Program. 277-282
Workshop: Controlling Complexity
- Denis Gracanin: An Approach to Distributed Interactive Simulation and Visualization of Complex Systems using Cluster Computing. 292-298
- Björn Olsson, Barbara Gawronska, Tom Ziemke, Sten F. Andler, Patric Nilsson, Anne Persson: An Information Fusion Approach to Controlling Complexity in Bioinformatics Research. 299-304
- James L. Rash, Michael G. Hinchey, Denis Gracanin: An Approach to Generating and Verifying Complex Scripts and Procedures. 305-313
- Adele H. Marshall, Roy Sterritt: Clustering Gene Expression Data using Continuous Markov Models. 314-321
- Walter Cedeño, Dimitris K. Agrafiotis: A Comparison of Particle Swarms Techniques for the Development of Quantitative Structure-Activity Relationship Models for Drug Design. 322-331
- J. Mikael Eklund, Ruzena Bajcsy, Jonathan Sprinkle, Gregory V. Simpson: Computing MEG Signal Sources. 332-338
Workshop: BioImage data Mining and Informatics
- Manfred Auer: Electron Microscope Tomography of Cells and Tissues: Studying the 3D Structure of Molecular Machines at Molecular Resolution. 339
- Michael Liebling, Scott E. Fraser, Mary E. Dickinson, Arian S. Forouhar, Morteza Gharib: Volume Measurements in the Embryonic Zebrafish Heart using 4D Confocal Microscopy. 350
- Richard M. Levenson, Clifford Hoyt, Jim Mansfield, Kirk Gossage: Multispectral Multidimensional Multiplexed Data: The More, the Merrier. 351
- Hanchuan Peng: Image Data Mining of Fruitfly Gene Expression Patterns. 352
- Jie Zhou, Hanchuan Peng: Toward Automatic Annotation of in situ mRNA Expression Patterns of Drosophila Embryos. 353
- Charless Fowlkes, Jitendra Malik, Cris L. Luengo Hendriks, Soile V. E. Keränen, Mark D. Biggin, David W. Knowles, Damir Sudar: Registering Drosophila Embryos at Cellular Resolution to Build a Quantitative 3D Atlas of Gene Expression Patterns and Morphology. 354-357
- James P. Carson, Tao Ju, Christina Thaller, Musodiq Bello, Joe D. Warren, Gregor Eichele, Wah Chiu: Data Mining in situ Gene Expression Patterns at Cellular Resolution. 358
- Abhi Gholap, Gauri Naik, Aparna Joshi, C. V. Kameswara Rao: Content-Based Tissue Image Mining. 359-363
- Luis Hernández, Paula Gothreaux, George Collins, Liwen Shih, Gerald Campbell: Digital Pathological Image Analysis and Cell Segmentation. 373
- Fuhui Long, Hanchuan Peng, Damir Sudar, David W. Knowles, Sophie Lelièvre: Cell Phenotype Classification Based on 3D Cell Image Analysis. 374
- Ambuj K. Singh, Arnab Bhattacharya, Vebjorn Ljosa: Current Challenges in Bioimage Database Design. 375-379
- Ilya G. Goldberg: Open Microscopy Environment. 380
- Harry Hochheiser, Ilya G. Goldberg: Towards Interactive Exploration of Images, Meta-Data, and Analytic Results in the Open Microscopy Environment. 381-377
- Chandrajit L. Bajaj: Structure Elucidation and Visualization of Reconstructed 3D Maps of Macromolecular Complexes. 388
Workshop: BioSpice and Use Case
- Ying Zhao, Charles Zhou, Ian Oglesby, Cliff Zhou: Large-scale Drug Function Prediction by Integrating QIS D2 and BioSpice. 391-394
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last updated on 2013-06-18T211851 by the dblp team