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ORCIDJournal of Computational Biology, Volume 11
Volume 11, Number 1, February 2004
- Haiyan Huang, Ming-Chih J. Kao, Xianghong Jasmine Zhou, Jun S. Liu
, Wing Hung Wong:
Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification. 1-14 - Alberto Apostolico, Laxmi Parida:
Incremental Paradigms of Motif Discovery. 15-25 - Alberto Caprara, Robert D. Carr, Sorin Istrail, Giuseppe Lancia, Brian Walenz:
1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap. 27-52 - Andreas Wagner:
Reconstructing Pathways in Large Genetic Networks from Genetic Perturbations. 53-60 - Peter A. Spiro, Natasa Macura:
A Local Alignment Metric for Accelerating Biosequence Database Search. 61-82 - Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson:
FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions. 83-106 - Leo Wang-Kit Cheung:
Use of Runs Statistics for Pattern Recognition in Genomic DNA Sequences. 107-124 - Myong-Hee Sung, Richard Simon:
Genomewide Conserved Epitope Profiles of HIV-1 Predicted by Biophysical Properties of MHC Binding Peptides. 125-145 - Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty, Daniel E. Russ, Edward Suh:
Gene Clustering Based on Clusterwide Mutual Information. 147-161 - Ryszard W. Adamiak, Jacek Blazewicz, Piotr Formanowicz, Zofia Gdaniec, Marta Kasprzak, Mariusz Popenda, Marta Szachniuk:
An Algorithm for an Automatic NOE Pathways Analysis of 2D NMR Spectra of RNA Duplexes. 163-179 - Markus Wistrand, Erik L. L. Sonnhammer:
Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. 181-193 - Vladimir Makarenkov, Pierre Legendre:
From a Phylogenetic Tree to a Reticulated Network. 195-212
Volume 11, Number 2/3, March 2004
- Wentian Li, Fengzhu Sun, Ivo Grosse:
Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression. 215-226 - Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink:
Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data. 227-242 - Chen-Hsiang Yeang, Trey Ideker, Tommi S. Jaakkola:
Physical Network Models. 243-262 - Maáyan Fishelson, Dan Geiger:
Optimizing Exact Genetic Linkage Computations. 263-275 - Christopher James Langmead, Anthony K. Yan, Ryan H. Lilien, Lincong Wang, Bruce Randall Donald:
A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. 277-298 - Itay Lotan, Fabian Schwarzer:
Approximation of Protein Structure for Fast Similarity Measures. 299-317 - Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander:
Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. 319-355 - Amos Tanay, Ron Shamir:
Multilevel Modeling and Inference of Transcription Regulation. 357-375 - Gene W. Yeo, Christopher B. Burge:
Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals. 377-394 - Krishna M. Roskin, Mark Diekhans, David Haussler:
Score Functions for Determining Regional Conservation in Two-Species Local Alignments. 395-411 - Adam C. Siepel, David Haussler:
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. 413-428 - Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky:
Scalable Heuristics for Design of DNA Probe Arrays. 429-447 - Tatsuya Akutsu:
Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data. 449-462 - Minghua Deng, Ting Chen, Fengzhu Sun:
An Integrated Probabilistic Model for Functional Prediction of Proteins. 463-475 - Amir Ben-Dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini:
Towards Optimally Multiplexed Applications of Universal Arrays. 476-492 - Gideon Greenspan, Dan Geiger:
Model-Based Inference of Haplotype Block Variation. 493-504 - Lei M. Li, Jong Hyun Kim, Michael S. Waterman:
Haplotype Reconstruction from SNP Alignment. 505-516
Volume 11, Number 4, August 2004
- Craig J. Benham, Chengpeng Bi:
The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences. 519-543 - Kevin A. Janes, Jason R. Kelly, Suzanne Gaudet, John G. Albeck, Peter K. Sorger, Douglas A. Lauffenburger:
Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data. 544-561 - Rongling Wu, Chang-Xing Ma, George Casella:
A Mixed Polyploid Model for Linkage Analysis in Outcrossing Tetraploids Using a Pseudo-Test Backcross Design. 562-580 - Paul Helman, Robert Veroff, Susan R. Atlas, Cheryl Willman:
A Bayesian Network Classification Methodology for Gene Expression Data. 581-615 - Hilary S. Booth, John H. Maindonald, Susan R. Wilson, Jill E. Gready:
An Efficient Z-Score Algorithm for Assessing Sequence Alignments. 616-625 - Dan Levy, Mariel Vázquez, Michael Cornforth, Bradford Loucas, Rainer K. Sachs, Javier Arsuaga:
Comparing DNA Damage-Processing Pathways by Computer Analysis of Chromosome Painting Data. 626-641 - Jason Ku, Xiao-Jiang Feng, Herschel Rabitz:
Closed-Loop Learning Control of Bio-Networks. 642-659 - Ciprian Doru Giurcaneanu, Ioan Tabus, Jaakko Astola, Juha Ollila, Mauno Vihinen:
Fast Iterative Gene Clustering Based on Information Theoretic Criteria for Selecting the Cluster Structure. 660-682 - Zhihua Lin, Yuzhang Wu, Bo Zhu, Bing Ni, Li Wang:
Toward the Quantitative Prediction of T-Cell Epitopes: QSAR Studies on Peptides Having Affinity with the Class I MHC Molecular HLA-A*0201. 683-694 - Tracy L. Bergemann, Richard J. Laws, Filemon Quiaoit, Lue Ping Zhao:
A Statistically Driven Approach for Image Segmentation and Signal Extraction in cDNA Microarrays. 695-713 - Sue-Jane Wang, James J. Chen:
Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments. 714-726 - Nicolas Galtier, Alain Jean-Marie:
Markov-Modulated Markov Chains and the Covarion Process of Molecular Evolution. 727-733 - Michael Roberts, Brian R. Hunt, James A. Yorke, Randall A. Bolanos, Arthur L. Delcher:
A Preprocessor for Shotgun Assembly of Large Genomes. 734-752 - Franco P. Preparata, John S. Oliver:
DNA Sequencing by Hybridization Using Semi-Degenerate Bases. 753-765 - Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder:
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. 766-785
Volume 11, Number 5, October 2004
- Yuting Jia, T. Gregory Dewey, Ilya N. Shindyalov, Philip E. Bourne:
A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. 787-799 - Hagit Shatkay, Jason R. Miller, Clark M. Mobarry, Michael Flanigan, Shibu Yooseph, Granger G. Sutton:
ThurGood: Evaluating Assembly-to-Assembly Mapping. 800-811 - Joseph S. Oliveira, Janet B. Jones-Oliveira, David A. Dixon, Colin G. Bailey, Dean W. Gull:
Hyperdigraph-Theoretic Analysis of the EGFR Signaling Network: Initial Steps Leading to GTP: Ras Complex Formation. 812-842 - Andreas Heger, Michael Lappe, Liisa Holm:
Accurate Detection of Very Sparse Sequence Motifs. 843-857 - Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph:
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. 858-866 - Gill Bejerano, Nir Friedman, Naftali Tishby:
Efficient Exact p-Value Computation for Small Sample, Sparse, and Surprising Categorical Data. 867-886 - Andres Figueroa, James Borneman, Tao Jiang:
Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis. 887-901 - Itay Lotan, Fabian Schwarzer, Dan Halperin, Jean-Claude Latombe:
Algorithm and Data Structures for Efficient Energy Maintenance during Monte Carlo Simulation of Proteins. 902-932 - Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün:
The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. 933-944 - Kaleigh Smith, Michael T. Hallett:
Towards Quality Control for DNA Microarrays. 945-970 - Stephen D. Bay, Lonnie Chrisman, Andrew Pohorille, Jeff Shrager:
Temporal Aggregation Bias and Inference of Causal Regulatory Networks. 971-985 - Jieping Ye, Ravi Janardan:
Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance. 986-1000 - Miklós Csürös, Aleksandar Milosavljevic:
Pooled Genomic Indexing (PGI): Analysis and Design of Experiments. 1001-1021
Volume 11, Number 6, December 2004
- Grégory Nuel:
LD-SPatt: Large Deviations Statistics for Patterns on Markov Chains. 1023-1033 - Irit Gat-Viks, Amos Tanay, Ron Shamir:
Modeling and Analysis of Heterogeneous Regulation in Biological Networks. 1034-1049 - Revital Eres, Gad M. Landau, Laxmi Parida:
Permutation Pattern Discovery in Biosequences. 1050-1060 - Matteo Comin, Concettina Guerra, Giuseppe Zanotti:
PROuST: A Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques. 1061-1072 - Chiranjib Bhattacharyya, L. R. Grate, Michael I. Jordan, Laurent El Ghaoui, I. Saira Mian:
Robust Sparse Hyperplane Classifiers: Application to Uncertain Molecular Profiling Data. 1073-1089 - Pierre Chiappetta, Marie-Christine Roubaud, Bruno Torrésani:
Blind Source Separation and the Analysis of Microarray Data. 1090-1109 - Sebastian Böcker:
Sequencing from Compomers: Using Mass Spectrometry for DNA de novo Sequencing of 200+ nt. 1110-1134 - Mathäus Dejori, Martin Stetter:
Identifying Interventional and Pathogenic Mechanisms by Generative Inverse Modeling of Gene Expression Profiles. 1135-1148 - Ahmet Palazoglu, Attila Gürsoy, Yaman Arkun, Burak Erman:
Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis. 1149-1168 - Danny Barash:
Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. 1169-1174 - Nanxiang Ge, Charles B. Epstein:
An Empirical Bayesian Significance Test of cDNA Library Data. 1175-1188 - Darrell Conklin:
Recognition of the Helical Cytokine Fold. 1189-1200
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