3. CSB 2004: Stanford, CA, USA

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 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 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 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, W. 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, Yoichi Takenaka, Hideo Matsuda:
  Inference of Gene Regulatory Network Based on Module Network Model with Gene Functional Classifications. 632-633
  
• Shoko Miyake, Yoichi Takenaka, Hideo Matsuda:
  A Graph Analysis Method to Detect Metabolic Sub-Networks Based on Phylogenetic Profile. 634-635
  
• Lie-Quan Lee, Jeff Varner, Kwok Ko:
  Parallel Extreme Pathway Computation for Metabolic Networks. 636-639
  
• Zhengchang Su, PhuongAn Dam, X. Chen, Victor Olman, Tao Jiang, Ying Xu:
  Computational Construction of Nitrogen Assimilation Pathway in Cyanobacteria Synechococcus sp. WH8102. 640-641
  
• Fenglou Mao, Zhengchang Su, Victor Olman, David Chuang, Ying Xu:
  Pathway Mapping with Operon Information: An Integer-Programming Method. 642-643
  
• Karen Sachs, Omar D. Perez, Dana Pe'er, Garry P. Nolan, David K. Gifford, Tommi Jaakkola, Douglas A. Lauffenburger:
  Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data. 644
  
• Wei Wang, Gregory F. Cooper:
  An Bayesian Method for Biological Pathway Discovery from High-Throughput Experimental Data. 645-646
  
• Tie Wang, Jeffrey W. Touchman, Guoliang Xue:
  Applying Two-Level Simulated Annealing on Bayesian Structure Learning to Infer Genetic Networks. 647-648
  

Pattern Recognition

• Hsiao Ping Lee, Tzu Fang Sheu, Yin-Te Tsai, Ching Hua Shih, Chuan Yi Tang:
  A Efficient Algorithm for Unique Signature Discovery on Whole-Genome EST Databases. 650-651
  
• Yan Ding, Hong Cao, Shu Wen:
  VirusFinder: A Web-Based Virus Identification System Using Viral Nucleotide Signatures. 652-653
  
• Jian Liu, Ming Li:
  Finding Cancer Biomarkers from Mass Spectrometry Data by Decision Lists. 654-655
  
• Hyunsoo Kim, Haesun Park:
  Incremental and Decremental Least Squares Support Vector Machine and Its Application to Drug Design. 656-657
  
• Eugene Lin, Dennis Chen, Yuchi Hwang, Ashely Chang, Z. John Gu:
  A Prediction Model for the Drug Efficacy of Interferon in CHC Patients Based on SNPs. 658-659
  
• Oriel Bergig, Danny Barash, Klara Kedem:
  RNA Motif Search Using the Structure to String (STR²) Method. 660-661
  
• Ravi Vijaya Satya, Amar Mukherjee:
  PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences. 662-665
  
• Victor Olman, Jizhu Lu, PhuongAn Dam, Zhengchang Su, Ying Xu:
  CUBIC: Search for Binding Sites. 666-667
  
• Kevin Crosby, Paula Gabbert:
  BioSPRINT: Classification of Intron and Exon Sequences Using the SPRINT Algorithm. 668-669
  
• Xutao Deng, Hesham H. Ali:
  A Hidden Markov Model for Gene Function Prediction from Sequential Expression Data. 670-671
  
• Alexandre Tchourbanov, Hesham H. Ali, Jitender S. Deogun:
  Using Enhancing Signals to Improve Specificity of ab initio Splice Site Sensors. 672-673
  
• Xiaolu Huang, Hesham H. Ali, Anguraj Sadanandam, Rakesh K. Singh:
  SRPVS: A New Motif Searching Algorithm for Protein Analysis. 674-675
  
• Donald A. Adjeroh, Jianan Feng:
  Locating All Tandem Repeat Families in a Sequence. 676-681
  

Promoter Analysis

• Youlian Pan, Brandon Smith, Hung Fang, A. Fazel Famili, Marianna Sikorska, P. Roy Walker:
  Selection of Putative Cis-Regulatory Motifs through Regional and Global Conservation. 684-685
  
• Yasuo Matsuyama, Ryo Kawamura:
  Promoter Recognition for E. coli DNA Segments by Independent Component Analysis. 686-691
  

Protein Structure Analysis

• Krishna Gopalakrishnan, R. H. Zadeh, Kayvan Najarian, Alireza Darvish:
  Computational Analysis and Classification of p53 Mutants According to Primary Structure. 694-695
  
• Gong-Xin Yu, Byung-Hoon Park, Praveen Chandramohan, Al Geist, Nagiza F. Samatova:
  In-Silico Prediction of Surface Residue Clusters for Enzyme-Substrate Specificity. 696-697
  
• Chenyang Cui, Donghui Wang, Jiaoying Shi:
  Comparing 3D Protein Structures Similarity by Using Fractal Features. 698-699
  
• Peng Wang, Zhengchang Su, Jun-tao Guo, Ying Xu:
  Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation. 700-701
  
• Jaspreet Singh Sodhi, Liam J. McGuffin, Kevin Bryson, Jonathan J. Ward, Lorenz Wernisch, David T. Jones:
  Automatic Prediction of Functional Site Regions in Low-Resolution Protein Structures. 702-703
  
• Barrett Abel, Martin Gollery:
  BPAP: A Computational Tool for Whole Genome Analysis and Annotation. 704-705
  
• Todd J. Taylor, Iosif I. Vaisman:
  A New Method of Secondary Structure Assignment Based on the Delaunay Tessellation of Protein Structures. 706-707
  
• Jun-tao Guo, Ying Xu:
  Molecular Modeling of Full-Length OxyR from Shewanella oneidensis MR-1 and Molecular Dynamics Studies of the Activation Domain. 708-709
  
• Sumeet Dua, Naveen Kandiraju:
  A Novel Computational Framework for Structural Classification of Proteins Using Local Geometric Parameter Matching. 710-711
  
• K. Arun, Christopher James Langmead:
  Large-Scale Testing of Chemical Shift Prediction Algorithms and Improved Machine Learning-Based Approaches to Shift Prediction. 712-713
  

RNAi Analysis

• Chris H. Q. Ding, Richard F. Meraz, Xiaofeng He, Stephen R. Holbrook:
  Contraction Graphs for Representation and Analysis of RNA Secondary Structure. 716-717
  
• Christopher Maher, Marja Timmermans, Lincoln Stein, Doreen Ware:
  Identifying MicroRNAs in Plant Genomes. 718-723
  
• Assaf Avihoo, Nir Dromi, Danny Barash:
  Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs. 724-725
  

Sequence Alignment

• Robert C. Edgar:
  MUSCLE: Multiple Sequence Alignment with Improved Accuracy and Speed. 728-729
  
• Greg Knowles, Paul Gardner-Stephen:
  A New Hardware Architecture for Genomic and Proteomic Sequence Alignment. 730-731
  
• Paul Gardner-Stephen, Greg Knowles:
  DASH: Localising Dynamic Programming for Order of Magnitude Faster, Accurate Sequence Alignment. 732-735
  
• Daniela Puiu:
  SUPERCONTIGS: A Contig Scaffolding Tool. 736-737
  
• Aaron E. Darling, Bob Mau, Mark Craven, Nicole T. Perna:
  Multiple Alignment of Rearranged Genomes. 738-739
  
• Maulik K. Shah, HoJoon Lee, Stephanie A. Rogers, Jeffrey W. Touchman:
  An Exhaustive Genome Assembly Algorithm Using K-Mers to Indirectly Perform N-Squared Comparisons in O(N). 740-741
  

SNPs and Haplotyping

• Shiori Furihata, Toshikazu Ito, Naoyuki Kamatani:
  Association Tests and Estimation of Haplotype Frequencies and of Penetrance-Related Parameters in a Case-Control Study. 744-745
  

Synthetic Biological Systems

• Ruiqi Wang, Junya Nakai, Mitsuyasu Seo, Luonan Chen:
  Designing Synthetic Biological Systems by Multiple Time Scale Networks. 748-749
  

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