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ORCIDJournal of Computational Biology, Volume 9
Volume 9, Number 1, January 2002
- Rimli Sengupta, Martin Tompa:
Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach. 1-22 - Sanguthevar Rajasekaran, X. Jin, John L. Spouge:
The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform. 23-33 - Jon M. Sorenson
, Teresa Head-Gordon:
Protein Engineering Study of Protein L by Simulation. 35-54 - Charles L. Kooperberg, Thomas G. Fazzio, Jeffrey J. Delrow, Toshio Tsukiyama:
Improved Background Correction for Spotted DNA Microarrays. 55-66 - Hidde de Jong:
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. 67-103 - Edward R. Dougherty, Junior Barrera, Marcel Brun, Seungchan Kim, Roberto Marcondes Cesar Junior, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent:
Inference from Clustering with Application to Gene-Expression Microarrays. 105-126 - Seungchan Kim, Edward R. Dougherty, Junior Barrera, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent:
Strong Feature Sets from Small Samples. 127-146
Volume 9, Number 2, April 2002
- Thomas Lengauer:
Preface: Special RECOMB 2001 Issue. 147-148 - Nancy M. Amato, Guang Song:
Using Motion Planning to Study Protein Folding Pathways. 149-168 - Yoseph Barash, Nir Friedman:
Context-Specific Bayesian Clustering for Gene Expression Data. 169-191 - Yonatan Bilu, Michal Linial:
The Advantage of Functional Prediction Based on Clustering of Yeast Genes and Its Correlation with Non-Sequence Based Classifications. 193-210 - Mathieu Blanchette, Benno Schwikowski, Martin Tompa:
Algorithms for Phylogenetic Footprinting. 211-223 - Jeremy Buhler, Martin Tompa:
Finding Motifs Using Random Projections. 225-242 - Ralf Bundschuh:
Rapid Significance Estimation in Local Sequence Alignment with Gaps. 243-260 - Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger:
Predicting the Beta-Helix Fold from Protein Sequence Data. 261-276 - Miklós Csürös:
Fast Recovery of Evolutionary Trees with Thousands of Nodes. 277-297 - Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk:
Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels. 299-315 - Vladimir Filkov, Steven Skiena, Jizu Zhi:
Analysis Techniques for Microarray Time-Series Data. 317-330 - Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko:
A Structural EM Algorithm for Phylogenetic Inference. 331-353 - Alan M. Frieze, Bjarni V. Halldórsson:
Optimal Sequencing by Hybridization in Rounds. 355-369 - Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang:
A General Edit Distance between RNA Structures. 371-388 - Lior Pachter, Marina Alexandersson, Simon Cawley:
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems. 389-399 - Paul Pavlidis, Jason Weston, Jinsong Cai, William Stafford Noble:
Learning Gene Functional Classifications from Multiple Data Types. 401-411 - Ron Shamir, Dekel Tsur:
Large Scale Sequencing by Hybridization. 413-428 - Mengxiang Tang, Michael S. Waterman, Shibu Yooseph:
Zinc Finger Gene Clusters and Tandem Gene Duplication. 429-446 - Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau:
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes. 447-464
Volume 9, Number 3, June 2003
- Natalia Berloff, Markus Perola, Kenneth Lange:
Spline Methods for the Comparison of Physical and Genetic Maps. 465-475 - Shi-Yi Shen, Jun Yang, Adam Yao, Pei-Ing Hwang:
Super Pairwise Alignment (SPA): An Efficient Approach to Global Alignment for Homologous Sequences. 477-486 - Jian Zhang:
Analysis of Information Content for Biological Sequences. 487-503 - Michael D. Radmacher, Lisa M. McShane, Richard M. Simon:
A Paradigm for Class Prediction Using Gene Expression Profiles. 505-511 - Terry W. Clark, Sanggyu Lee, L. Ridgway Scott, San Ming Wang:
Computational Analysis of Gene Identification with SAGE. 513-526 - Myong-Hee Sung, Yingdong Zhao, Roland Martin, Richard M. Simon:
T-Cell Epitope Prediction with Combinatorial Peptide Libraries. 527-539 - Markus E. Nebel:
Combinatorial Properties of RNA Secondary Structures. 541-573 - Timothy L. Bailey, Michael Gribskov:
Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores. 575-593
Volume 9, Number 4, August 2002
- Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Müller:
A Combinatorial Approach to Protein Docking with Flexible Side Chains. 597-612 - Berrin A. Yanikoglu, Burak Erman:
Minimum Energy Configurations of the 2-Dimensional HP-Model of Proteins by Self-Organizing Networks. 613-620 - Jorng-Tzong Horng, Hsien-Da Huang, Ming-Hui Jin, Li-Cheng Wu, Shir-Ly Huang:
The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions. 621-640 - Alberto Mercatanti, Giuseppe Rainaldi, Laura Mariani, Roberto Marangoni, Lorenzo Citti:
A Method for Prediction of Accessible Sites on an mRNA Sequence for Target Selection of Hammerhead Ribozymes. 641-653 - Kevin R. Coombes, W. Edward Highsmith, Tammy A. Krogmann, Keith A. Baggerly, David N. Stivers, Lynne V. Abruzzo:
Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays. 655-669 - Philippe Broët, Sylvia Richardson, François Radvanyi:
Bayesian Hierarchical Model for Identifying Changes in Gene Expression from Microarray Experiments. 671-683
Volume 9, Number 5, October 2002
- Richard Desper, Olivier Gascuel:
Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle. 687-705 - Giri Narasimhan, Changsong Bu, Yuan Gao, Xuning Wang, Ning Xu, Kalai Mathee:
Mining Protein Sequences for Motifs. 707-720 - James Aspnes, Julia Hartling, Ming-Yang Kao, Junhyong Kim, Gauri Shah:
A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model. 721-741 - João Meidanis, Maria Emília Telles Walter, Zanoni Dias:
A Lower Bound on the Reversal and Transposition Diameter. 743-745 - Rainer Spang, Marc Rehmsmeier, Jens Stoye:
A Novel Approach to Remote Homology Detection: Jumping Alignments. 747-760
Volume 9, Number 6, December 2002
- Stéphane Robin, Jean-Jacques Daudin, Hugues Richard, Marie-France Sagot, Sophie Schbath:
Occurrence Probability of Structured Motifs in Random Sequences. 761-773 - Eleazar Eskin, William Stafford Noble, Yoram Singer:
Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences. 775-791 - Kajsa Ljungberg, Sverker Holmgren, Örjan Carlborg:
Efficient Algorithms for Quantitative Trait Loci Mapping Problems. 793-804 - Thomas L. York, Richard Durrett, Rasmus Nielsen:
Bayesian Estimation of the Number of Inversions in the History of Two Chromosomes. 805-818 - Dhananjay V. Raje, Hemant J. Purohit, R. N. Singh:
Distinguishing Features of 16S rDNA Gene for Five Dominating Bacterial Genus Observed in Bioremediation. 819-829 - Didier Piau:
Mutation-Replication Statistics of Polymerase Chain Reactions. 831-847 - Scott Doniger, Thomas Hofmann, Miao-Hui Joanne Yeh:
Predicting CNS Permeability of Drug Molecules: Comparison of Neural Network and Support Vector Machine Algorithms. 849-864
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