default search action
4. CSB Workshops 2005: Stanford, CA, USA
- Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, CSB 2005 Workshops, Stanford, CA, USA, August 8-11, 2005. 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
- Luonan Chen, Ruiqi Wang, Kazuyuki Aihara:
Reducing Gene Regulatory Networks by Decomposition. 17-18 - Preetam Ghosh
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
- Natalia Khuri, Nikhila S. Rao:
Operon Prediction in Cyanobacteria using Comparative Genomics. 23-24 - 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 - Heather Trumbower, Jennifer Jackson:
Key Features of the UCSC Genome Site. 33-34 - 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
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 - Jason Lee, Sun Kim:
Cluster Utility: A New Metric for Clustering Biological Sequences. 45-46 - Eric G. Stephan
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 - Nicholas D. Pattengale, Bernard M. E. Moret
Phylogenetic Postprocessing. 57-58 - Corey Powell, Joshua M. Stuart:
A Novel Quartet-Based Method for Phylogenetic Inference. 59-60 - Mahesh M. Kulkarni, Bernard M. E. Moret
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
- PhuongAn Dam, Victor Olman, Ying Xu:
Improving Operon Prediction in E. coli. 69-70 - Theo A. Knijnenburg, Marcel J. T. Reinders, Jean-Marc Daran
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
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
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
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
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 - Carmen Lai, Marcel J. T. Reinders:
Multivariate gene selection: Does it help. 99-100 - Manohar Kollegal
Considerations in Making Microarray Cross-Platform Correlations. 101-102 - Alberto D. Pascual-Montano, Francisco Tirado
Two-way clustering of gene expression profiles by sparse matrix factorization. 103-104 - Bernard Chen, Robert W. Harrison
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
K-means+ Method for Improving Gene Selection for Classification of Microarray Data. 110-111 - Roger Pique-Regi
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 - Christopher Wilks, Sami Khuri:
A Fast Shotgun Assembly Heuristic. 122-123 - 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
Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach. 126-127 - Yong Zhang, Rahul Parthe, Donald A. Adjeroh:
Lossless Compression of DNA Microarray Images. 128-132 - 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
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
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
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 Krämer
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
A symbolic approach to the simulation of biochemical models: application to circadian rhythms. 168-169 - Samik Ghosh, Preetam Ghosh
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, Anneke 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
Automated Characterization of cellular migration phenomena. 185-186 - Ramana M. Gosukonda, Masoud Naghedolfeizi, Johnny Carter:
Artificial Neural Networks to Predict Daylily Hybrids. 187-188 - Alexander G. Churbanov, Hesham H. Ali:
Combinatorial method of splice sites prediction. 189-190 - Eric Sakk, David J. Schneider
Computational identification and characterization of Type III secretion substrates. 191-192 - Adaya N. Cohen, Klara Kedem, Michal Shapira
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
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
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
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
GANAA Genetic Algorithm for NMR Backbone Resonance Assignment. 218-219 - Amandeep S. Sidhu
Creating a Protein Ontology Resource. 220-221 - Yogesh A. Girdhar
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
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
ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale. 251-254
Synthetic Biological Systems
- Sara Hooshangi
Noise Propagation in Transcriptional Cascades. 255 - 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 K. Karig
Engineering Multi-signal Systems for Complex Pattern Formation. 263-266
Visualization
- Weiguo Fan, Xin Lin, Yu-Wei Hsieh, Johnnie W. Baker, Boren Lin
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 - Kay A. Robbins, Li Zhao:
Visualization of Logic Analysis of Phylogenetic Profiles (LAPP). 275-276 - 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
- Roy Sterritt
Autonomicity An Antidote for Complexity? 283-291 - Denis Gracanin
An Approach to Distributed Interactive Simulation and Visualization of Complex Systems using Cluster Computing. 292-298 - Björn Olsson
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
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
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 - Weibo Cai, Xiaoyuan Chen:
PET Imaging of Tumor Integrin Expression. 340-349 - Michael Liebling
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 C. Fowlkes, Jitendra Malik, Cris L. Luengo Hendriks
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 - Son Tran, Liwen Shih:
Efficient 3D Binary Image Skeletonization. 364-372 - Luis Hernández, Paula Gothreaux, George Collins, Liwen Shih, Gerald Campbell
Digital Pathological Image Analysis and Cell Segmentation. 373 - Fuhui Long, Hanchuan Peng, Damir Sudar
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 - Ying Zhao, Charles Zhou:
Drug Characteristics Prediction. 395-398
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-11-22 19:31 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by: