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ORCID3. CSB 2004: Stanford, CA, USA
- 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, USA, August 16-19, 2004. IEEE Computer Society 2004, ISBN 0-7695-2194-0
Keynote Addresses
- Ron Shamir:
Computational Dissection of Regulatory Networks Using Diverse High-Throughput Data. 2-3 - Eugene W. Myers:
Whole Genome Sequencing, Comparative Genomics, and Systems Biology. 4
Invited Talks
- Paul S. Meltzer, Sean R. Davis, Kristin Baird, Yidong Chen:
Are We There Yet? Genomic Profiling and Mechanism in Cancer Research. 6 - Jim Kent:
Spaghetti Code, Soupy Logic, and the Expression of Genes. 7 - Stephen T. C. Wong:
High Content Cellular Analysis and Their Applications. 8 - Sandy Shaw, Paul Shapshak:
Fractal Genomics Modeling: A New Approach to Genomic Analysis and Biomarker Discovery. 9-17 - Hamid Bolouri:
From DNA Sequence to Network Behavior: Functional Properties of Genetic Regulatory Networks. 18
Genomics
- Chang-Heng Chang, Li-Ching Hsieh, Ta-Yuan Chen, Hong-Da Chen, Liaofu Luo, Hoong-Chien Lee:
Shannon Information in Complete Genomes. 20-30 - Hong Liu, Li Li, Asher Zilberstein, Chang S. Hahn:
Segmental Duplications Containing Tandem Repeated Genes Encoding Putative Deubiquitinating Enzymes. 31-39 - Yinhe Cao, Wen-wen Tung, Jianbo Gao:
Recurrence Time Statistics: Versatile Tools for Genomic DNA Sequence Analysis. 40-51 - Vineet Bafna, Shaojie Zhang
:
FastR: Fast Database Search Tool for Non-Coding RNA. 52-61 - Lei Chen, Shiyong Lu, Jeffrey L. Ram:
Compressed Pattern Matching in DNA Sequences. 62-68 - Michael Molla, Jude W. Shavlik, Thomas Albert, Todd Richmond, Steven Smith:
A Self-Tuning Method for One-Chip SNP Identification. 69-79 - Pang Ko, Mahesh Narayanan, Anantharaman Kalyanaraman, Srinivas Aluru:
Space-Conserving Optimal DNA-Protein Alignment . 80-88
Evolution and Phylogeny
- Russell Schwartz:
Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation. 90-97 - Usman Roshan, Bernard M. E. Moret, Tandy J. Warnow, Tiffani L. Williams:
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees. 98-109 - Patricia Buendia, Giri Narasimhan:
MinPD: Distance-Based Phylogenetic Analysis and Recombination Detection of Serially-Sampled HIV Quasispecies. 110-119
Transcriptomes
- Stefano Lonardi, Yu Luo:
Gridding and Compression of Microarray Images. 122-130 - Sach Mukherjee, Stephen J. Roberts:
A Theoretical Analysis of Gene Selection. 131-141 - Haifeng Li, Keshu Zhang, Tao Jiang:
Minimum Entropy Clustering and Applications to Gene Expression Analysis. 142-151 - Rui Kuang, Eugene Ie, Ke Wang, Kai Wang, Mahira Siddiqi, Yoav Freund, Christina S. Leslie:
Profile-Based String Kernels for Remote Homology Detection and Motif Extraction. 152-160 - Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto:
A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data. 161-172 - Zhaohui Sun, Jingyi Yang, Jitender S. Deogun:
MISAE: A New Approach for Regulatory Motif Extraction. 173-181 - Jinze Liu, Jiong Yang, Wei Wang:
Biclustering in Gene Expression Data by Tendency. 182-193 - Karuturi R. Krishna Murthy, Liu Jian Hua:
Improved Fourier Transform Method for Unsupervised Cell-Cycle Regulated Gene Prediction. 194-203
Proteomics
- Yonghua Han, Bin Ma, Kaizhong Zhang:
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error. 206-215 - Patrik D'haeseleer, George M. Church:
Estimating and Improving Protein Interaction Error Rates. 216-223 - Tolga Can, Orhan Çamoglu, Ambuj K. Singh, Yuan-Fang Wang:
Automated Protein Classification Using Consensus Decision. 224-235 - Bo Yan, Chongle Pan, Victor Olman, Robert L. Hettich, Ying Xu:
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation - A Graph-Theoretic Approach. 236-244
Structural Bioinformatics
- Zhuozhi Wang, Kaizhong Zhang:
Multiple RNA Structure Alignment. 246-254 - Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger:
Weighting Features to Recognize 3D Patterns of Electron Density in X-Ray Protein Crystallography. 255-265 - Rahul Singh:
Reasoning about Molecular Similarity and Properties. 266-277 - Christopher James Langmead, Bruce Randall Donald:
High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment. 278-289 - Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara:
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures. 290-299 - Shu-Yun Le, Jacob V. Maizel Jr., Kaizhong Zhang:
An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes. 300-310 - Arvind Gupta, Ján Manuch, Ladislav Stacho:
Inverse Protein Folding in 2D HP Mode (Extended Abstract). 311-318 - Lincong Wang, Bruce Randall Donald:
Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimum Number of Residual Dipolar Couplings. 319-330
Pathways & Networks
- Alon Kaufman, Martin Kupiec, Eytan Ruppin:
Multi-Knockout Genetic Network Analysis: The Rad6 Example. 332-340 - Hiroshi Mamitsuka, Yasushi Okuno:
A Hierarchical Mixture of Markov Models for Finding Biologically Active Metabolic Paths Using Gene Expression and Protein Classes. 341-352 - Zheng Yun, Kwoh Chee Keong:
Dynamic Algorithm for Inferring Qualitative Models of Gene Regulatory Networks. 353-362 - Victor Olman, Hanchuan Peng, Zhengchang Su, Ying Xu:
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes. 363-370
Applied Bioinformatics
- Sarah E. Boyd, Maria J. García de la Banda, Robert N. Pike, James C. Whisstock, George B. Rudy:
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity. 372-381 - Huiqing Liu, Jinyan Li, Limsoon Wong:
Selection of Patient Samples and Genes for Outcome Prediction. 382-392
Data Mining & Ontology
- Ying Liu, Brian J. Ciliax, Karin Borges, Venu Dasigi, Ashwin Ram, Shamkant B. Navathe, Ray Dingledine:
Comparison of Two Schemes for Automatic Keyword Extraction from MEDLINE for Functional Gene Clustering. 394-404 - Shiming Dong, Eileen T. Kraemer:
Calculation, Visualization, and Manipulation of MASTs (Maximum Agreement Subtrees). 405-414 - Raf M. Podowski, John G. Cleary, Nicholas T. Goncharoff, Gregory Amoutzias, William S. Hayes:
AZuRE, a Scalable System for Automated Term Disambiguation of Gene and Protein Names. 415-424 - Sheng Zhong, Lu Tian, Cheng Li, Kai-Florian Storch, Wing Hung Wong:
Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework. 425-435 - Jinze Liu, Wei Wang, Jiong Yang:
Gene Ontology Friendly Biclustering of Expression Profiles. 436-447
Biomedical Research
- Anguraj Sadanandam, Michelle L. Varney, Rakesh K. Singh:
High-Throughput Computational and Experimental Biology Strategy in Identifying Tumor Expressing CAMs. 450-451
Cellular Multicellular Systems
- Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik:
State-Space Model for Gene Regulatory Networks with Time Delays. 454-455 - Yingxin Li, Carol A. Heckman, Julie A. Barnes:
Nonlinear Modeling on Protein Kinase C(PKC)-Epsilon Inverse Regulation of Stress Fibers in Oncogenically Transformed Cells. 456-457 - Yizhou Xie, Xujing Wang:
Analysis of Population Dynamics in Beta-Cell Destruction Lead to Identification of Novel Candidate Genes for Type 1 Diabetes. 458-459
Comparative Genomics
- Heidi J. Sofia, Abigail L. Corrigan, Kyle R. Klicker, George Chin Jr., Eric G. Stephan:
Exploring Genomic Context Patterns for Rhodobacter Sphaeroides in the HERBE Knowledge Discovery Environment. 462-463 - Mark L. Farman, Joshua W. Gilkerson, Jerzy W. Jaromczyk, Chuck Staben:
RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes. 464-467
Data Mining
- Ian Shadforth, Daniel Crowther, Conrad Bessant:
Search-Space Reduction of a Non-Redundant Peptide Database. 470-471 - Samir V. Deshpande, Rabih E. Jabbour, Charles Wick, A. Peter Snyder:
Automated and Rapid Bacterial Identification Using LC-Mass Spectrometry with a Relational Database Management System. 472-473 - John H. Phan, Chang F. Quo, Kejiao Guo, Weimin Feng, Geoffrey Wang, May D. Wang:
Development of a Knowledge-Based Multi-Scheme Cancer Microarray Data Analysis System. 474-475 - Fang Liu, Tor-Kristian Jenssen, Vegard Nygaard, John Sack, Eivind Hovig:
FigSearch: Using Maximum Entropy Classifier to Categorize Biological Figures. 476-477 - Maxim Shklar, Orit Shmueli, Liora Strichman-Almashanu, Michael Shmoish, Doron Lancet, Marilyn Safran:
GeneTide: Terra Incognita Discovery Endeavor Mining ESTs and Expression Data to Elucidate Known and De-Novo GeneCards Genes. 478-479 - Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Biclustering Gene-Feature Matrices for Statistically Significant Dense Patterns. 480-484 - Xuanfu Wu, Zhengxin Chen:
Recognition of Exon/Intron Boundaries Using Dynamic Ensembles. 485-486 - Sach Mukherjee, Stephen J. Roberts:
Probabilistic Consistency Analysis for Gene Selection. 487-488 - Zoé Lacroix, Kaushal Parekh, Hasan Davulcu, I. V. Ramakrishnan, Nikeeta Julasana:
Automating the Biological Data Collection Process with Agents. 489-490 - Jeffrey Stone, Xindong Wu, Marc Greenblatt:
An Intelligent Digital Library System for Biologists. 491-492 - Huimin Geng, Dhundy Bastola, Hesham H. Ali:
A New Approach to Clustering Biological Data Using Message Passing. 493-494 - Daniel Quest, Hesham H. Ali:
Ontology Specific Data Mining Based on Dynamic Grammars. 495-496 - Yuhang Wang, Fillia Makedon:
Application of Relief-F Feature Filtering Algorithm to Selecting Informative Genes for Cancer Classification Using Microarray Data. 497-498 - Andrey Gorin, Robert M. Day, Andrey Borziak, Michael B. Strader, Gregory B. Hurst, Tema Fridman:
Probability Profile Method - New Approach to Data Analysis in Tandem Mass Spectrometry. 499-502 - Tomonori Izumitani, Hirotoshi Taira, Hideto Kazawa, Eisaku Maeda:
Assigning Gene Ontology Categories (GO) to Yeast Genes Using Text-Based Supervised Learning Methods. 503-504 - Robert M. Day, Andrey Borziak, Andrey Gorin:
PPM-Chain De novo Peptide Identification Program Comparable in Performance to Sequest. 505-508
Evolution and Phylogenetics
- Zhenhua Guo, John W. Stiller:
Comparative Genomics of Cyclin-Dependent Kinases Suggest Co-Evolution of the RNAP II C-Terminal Domain and CTD-Directed CDKs. 510-511 - Terrence S. T. Mak, Kai-Pui Lam:
Embedded Computation of Maximum-Likelihood Phylogeny Inference Using Platform FPGA. 512-514 - Boris Budagyan, Ann E. Loraine:
Gene Length and Alternative Transcription in Fruit Fly. 515-516 - Francisca Zanoguera, Massimo de Francesco:
Protein Classification into Domains of Life Using Markov Chain Models. 517-519 - Weihong Qi, David W. Lacher, Alyssa C. Bumbaugh, Katie E. Hyma, Lindsey M. Ouellette, Teresa M. Large, Cheryl L. Tarr, Thomas S. Whittam:
EcMLST: An Online Database for Multi Locus Sequence Typing of Pathogenic Escherichia coli. 520-521 - Fei Nan, Donald A. Adjeroh:
On Complexity Measures for Biological Sequences. 522-526
Functional Genomics
- Allison Griggs, Shuba Gopal:
A Markov Model Based Gene Discrimination Approach in Trypanosomes. 528 - Jonathan J. Ward, Jaspreet Singh Sodhi, Bernard F. Buxton, David T. Jones:
Predicting Gene Ontology Annotations from Sequence Data Using Kernel-Based Machine Learning Algorithms. 529-530 - Yan Qi, Jianbo Gao, Yinhe Cao, Wen-wen Tung:
Deriving a Novel Codon Index by Combining Period-3 and Fractal Features of DNA Sequences. 531-532 - Kirt M. Noël, Kay C. Wiese:
Exploring the Use of Stem-Loop Characteristics for Pinpointing Structural RNA Genes. 533-534 - Richard F. Meraz, Xiaofeng He, Chris H. Q. Ding, Stephen R. Holbrook:
Positive Sample Only Learning (PSOL) for Predicting RNA Genes in E. coli. 535-538
High Content Analysis
- Peter M. Kasson, Johannes B. Huppa, Mark M. Davis, Axel T. Brünger:
Quantitative Analysis of Membrane Protein Localization and Signaling. 540-541
High Performance Computing
- Zemin Ning, William Spooner, Adam Spargo, Steven Leonard, Mark Rae, Antony J. Cox:
The SSAHA Trace Server. 544-545 - Grace Steele, Vojislav Stojkovic:
Agent-Oriented Approach to DNA Computing. 546-551 - Jung-Yup Kang, Sandeep Gupta, Jean-Luc Gaudiot:
Accelerating the Kernels of BLAST with an Efficient PIM (Processor-In-Memory) Architecture. 552-553
Microarray Analysis
- Xiao Yang:
Qvalue Method May Not Always Control False Discovery Rate in Genomics Applications. 556-557 - Dongqing Liu, Ting Shi, Joseph A. DiDonato, John D. Carpten, Jianping Zhu, Zhong-Hui Duan:
Application of a Genetic Algorithm/K-Nearest Neighbor Method to the Classification of Renal Cell Carcinoma. 558-559 - Haili Jiao, Peixin Yang, Zhengxin Chen:
Mining Estrogen Microarray Data: An Approach Using Contrast Data Analysis. 560-561 - Weimin Feng, Gaurav Tuteja, May D. Wang:
EGOMinor: A Genomics and Proteomics Data Computation and Interpretation System for Biomedical Applications. 562-563 - Bill Martin, Robert M. Horton:
A Java Program to Create Simulated Microarray Images. 564-565 - Shawn Martin, George Davidson, Elebeoba E. May, Jean-Loup Faulon, Margaret Werner-Washburne:
Inferring Genetic Networks from Microarray Data. 566-569 - Nini Rao, Simon J. Shepherd:
Extracting Characteristic Patterns from Genome - Wide Expression Data by Non-Negative Matrix Factorization. 570-571 - Hyunsoo Kim, Gene H. Golub, Haesun Park:
Imputation of Missing Values in DNA Microarray Gene Expression Data. 572-573 - Qian Diao, Wei Hu, Hao Zhong, Juntao Li, Feng Xue, Tao Wang, Yimin Zhang:
Disease Gene Explorer: Display Disease Gene Dependency by Combining Bayesian Networks with Clustering. 574-575 - Yuan-Kai Wang, Cheng-Wei Huang:
DNA Microarray Image Analysis Using Active Contour Model. 576-577 - Danny Barash, Dorin Comaniciu:
Meanshift Clustering for DNA Microarray Analysis. 578-579 - Yizhou Xie, Soumitra Ghosh, Parthav Jailwalia, Xujing Wang:
The Dynamic Range of Gene Expressions Depend on Their Ontology. 580-581 - Hui Fang, ChengXiang Zhai, Lei Liu, Jiong Yang:
Subspace Clustering for Microarray Data Analysis: Multiple Criteria and Significance Assessment. 582-583 - John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra:
Comparative Analysis of Gene Expression and DNA Copy Number Data for Pancreatic and Breast Cancers Using an Orthogonal Decomposition. 584-585 - Geoffrey Yang, Ming-Hsiu Ho, Earl Hubbell:
High-Throughput Microarray-Based Genotyping. 586-587
Other
- Lawrence D'Antonio, Paramjeet Singh Bagga:
Computational Methods for Predicting Intramolecular G-Quadruplexes in Nucleotide Sequences. 590-591 - Xiequn Xu, William Bradley Barbazuk, Yucheng Feng, Karel Schubert, Agnes P. Chan, Geo Pertea, Li Zheng, Foo Cheung, Yuandan Lee:
Gene Recovery of Two Genome-Filtration Sequencing Techniques When Applied to the Maize Genome. 594-595 - Zoé Lacroix, Kaushal Parekh, Louiqa Raschid, Maria-Esther Vidal:
Navigating through the Biological Maze. 594-595 - Zoé Lacroix, Vidyadhari Edupuganti:
How Biological Source Capabilities May Affect the Data Collection Process. 596-597 - Stephan Heymann, Felix Naumann, Louiqa Raschid, Peter Rieger:
Labeling and Enhancing Life Sciences Links. 598-599
Pathways Networks Systems Biology
- Alireza Darvish, EunSang Bak, Krishna Gopalakrishnan, R. H. Zadeh, Kayvan Najarian:
A New Hierarchical Method for Identification of Dynamic Regulatory Pathways from Time-Series DNA Microarray Data. 602-603 - Pei Wang, Young Kim, Jonathan R. Pollack, Robert Tibshirani:
Boosted PRIM with Application to Searching for Oncogenic Pathway of Lung Cancer. 604-609 - Fang-Xiang Wu, Anthony J. Kusalik, Wen-Jun Zhang:
A. Genetic Algorithm for Inferring Time Delays in Gene Regulatory Networks. 610-611 - Peng Wang, Zhengchang Su, PhuongAn Dam, Ying Xu:
A Knowledge Base for Computational Pathway Reconstruction. 612-613 - PhuongAn Dam, Zhengchang Su, Victor Olman, Ying Xu:
In Silico Construction of the Carbon Fixation Pathway in Synechococcus sp. WH8102. 614-615 - Stephen A. Racunas, Christopher Griffin, Nigam Shah:
A Finite Model Theory for Biological Hypotheses. 616-620 - Hee Young Kang, Hak Yong Kim:
Functional Modules from Protein Networks of Kinome and Cell Cycle in Saccharomyces Cerevisiae. 621-622 - Olusola C. Idowu, Steven J. Lynden, Malcolm P. Young, Péter András:
Bacillus Subtilis Protein Interaction Network Analysis. 623-625 - Jean-Loup Faulon, Shawn Martin, Robert D. Carr:
Dynamical Robustness in Gene Regulatory Networks. 626-627 - Catalin C. Barbacioru, Daniel J. Cowden, Joel H. Saltz:
An Algorithm for Reconstruction of Markov Blankets in Bayesian Networks of Gene Expression Datasets. 628-629 - Jianbo Gao, Jesse S. A. Bridgewater, Vwani P. Roychowdhury:
Synchronized Oscillations and Chaos in Coupled Genetic Repressilators. 630-631 - Kohei Taki, Reiji Teramoto,