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
Selected Papers from RECOMB 2001
- 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 Emilia 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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