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3. 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
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
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
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
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
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
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
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 S. 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
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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