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ORCIDJournal of Computational Biology, Volume 10
Volume 10, Number 1, February 2003
- Bingwen Lu, Ting Chen:
A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry. 1-12 - Russell Schwartz
, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail:
Robustness of Inference of Haplotype Block Structure. 13-19 - Agatha H. Liu, Andrea Califano:
CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships. 21-45 - Xueliang Li, Zimao Li, Lusheng Wang:
The Inverse Problems for Some Topological Indices in Combinatorial Chemistry. 47-55 - Joseph S. Oliveira, Colin G. Bailey, Janet B. Jones-Oliveira, David A. Dixon, Dean W. Gull, Mary L. Chandler:
A Computational Model for the Identification of Biochemical Pathways in the Krebs Cycle. 57-82 - Sujay Chattopadhyay, Jayprokas Chakrabarti:
Temporal Changes in Phosphoglycerate Kinase Coding Sequences: A Quantitative Measure. 83-93 - Magnus Åstrand:
Contrast Normalization of Oligonucleotide Arrays. 95-102
Volume 10, Number 2, April 2003
- Gene Myers, Richard Durbin:
A Table-Driven, Full-Sensitivity Similarity Search Algorithm. 103-117 - Sayan Mukherjee, Pablo Tamayo, Simon Rogers, Ryan M. Rifkin, Anna Engle, Colin Campbell, Todd R. Golub, Jill P. Mesirov:
Estimating Dataset Size Requirements for Classifying DNA Microarray Data. 119-142 - Yinglei Lai, Deepali Shinde, Norman Arnheim, Fengzhu Sun:
The Mutation Process of Microsatellites During the Polymerase Chain Reaction. 143-155 - Yaning Yang, Josephine Hoh, Clemens Broger, Martin Neeb, Joanne Edington, Klaus Lindpaintner, Jürg Ott:
Statistical Methods for Analyzing Microarray Feature Data with Replications. 157-169 - Honghui Wan, Lugang Li, Scott Federhen, John C. Wootton:
Discovering Simple Regions in Biological Sequences Associated with Scoring Schemes. 171-185 - Eleazar Eskin, William Stafford Noble, Yoram Singer:
Protein Family Classification Using Sparse Markov Transducers. 187-213 - Robert Penchovsky, Jörg Ackermann:
DNA Library Design for Molecular Computation. 215-229 - Frank K. Hwang, Yu-Chi Liu:
Error-Tolerant Pooling Designs with Inhibitors. 231-236
Volume 10, Number 3/4, June 2003
- Nancy M. Amato, Ken A. Dill, Guang Song:
Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures. 239-255 - Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe, Chris Varma:
Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion. 257-281 - Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi:
Monotony of Surprise and Large-Scale Quest for Unusual Words. 283-311 - Peter F. Arndt, Christopher B. Burge, Terence Hwa:
DNA Sequence Evolution with Neighbor-Dependent Mutation. 313-322 - Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph:
Haplotyping as Perfect Phylogeny: A Direct Approach. 323-340 - Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon:
Continuous Representations of Time-Series Gene Expression Data. 341-356 - Sèverine Bérard, Eric Rivals:
Comparison of Minisatellites. 357-372 - Amir Ben-Dor, Benny Chor, Richard M. Karp, Zohar Yakhini:
Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem. 373-384 - Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir:
The Restriction Scaffold Problem. 385-398 - Jeremy Buhler:
Provably Sensitive Indexing Strategies for Biosequence Similarity Search. 399-417 - Barry Cohen, Steven Skiena:
Natural Selection and Algorithmic Design of mRNA. 419-432 - Ron O. Dror, Jonathan G. Murnick, Nicola J. Rinaldi, Voichita D. Marinescu, Ryan M. Rifkin, Richard A. Young:
Bayesian Estimation of Transcript Levels Using a General Model of Array Measurement Noise. 433-452 - Dannie Durand, David Sankoff:
Tests for Gene Clustering. 453-482 - Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir:
Handling Long Targets and Errors in Sequencing by Hybridization. 483-497 - Samuel A. Heath, Franco P. Preparata, Joel Young:
Sequencing by Hybridization by Cooperating Direct and Reverse Spectra. 499-508 - Fumei Lam, Marina Alexandersson, Lior Pachter:
Picking Alignments from (Steiner) Trees. 509-520 - Christopher James Langmead, Anthony K. Yan, C. Robertson McClung, Bruce Randall Donald:
Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns. 521-536 - Jia Li, Webb Miller:
Significance of Interspecies Matches when Evolutionary Rate Varies. 537-554 - Brendan Mumey, Brian W. Bailey, Bonnie Kirkpatrick, Algirdas J. Jesaitis, Thomas Angel, Edward A. Dratz:
A New Method for Mapping Discontinuous Antibody Epitopes to Reveal Structural Features of Proteins. 555-567 - Jürg Ott, Josephine Hoh:
Set Association Analysis of SNP Case-Control and Microarray Data. 569-574 - Adam C. Siepel:
An Algorithm to Enumerate Sorting Reversals for Signed Permutations. 575-597 - Saurabh Sinha:
Discriminative Motifs. 599-615 - Miguel L. Teodoro, George N. Phillips, Lydia E. Kavraki:
Understanding Protein Flexibility through Dimensionality Reduction. 617-634 - Andy Wildenberg, Steven Skiena, Pavel Sumazin:
Deconvolving Sequence Variation in Mixed DNA Populations. 635-652 - Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer:
Microarrays: How Many Do You Need? 653-667
Volume 10, Number 5, October 2003
- Elchanan Mossel:
On the Impossibility of Reconstructing Ancestral Data and Phylogenies. 669-676 - Fan R. K. Chung, Linyuan Lu, T. Gregory Dewey, David J. Galas:
Duplication Models for Biological Networks. 677-687 - George Michailidis, Kerby Shedden:
The Application of Rule-Based Methods to Class Prediction Problems in Genomics. 689-698 - Yonghong Wang, Hong-Yu Ou, Fengbiao Guo:
Recognition of Translation Initiation Sites of Eukaryotic Genes Based on an EM Algorithm. 699-708 - Wei-Fu Lu, Wen-Lian Hsu:
A Test for the Consecutive Ones Property on Noisy Data - Application to Physical Mapping and Sequence Assembly. 709-735 - Henrik Jönsson, Bo Söderberg:
An Approximate Maximum Likelihood Approach, Applied to Phylogenetic Trees. 737-749 - Daniel Faller, Henning U. Voss, Jens Timmer, Uwe Hobohm:
Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization. 751-762 - Antonio Piccolboni, Dan Gusfield:
On the Complexity of Fundamental Computational Problems in Pedigree Analysis. 763-773 - Lenwood S. Heath, John Paul C. Vergara:
Sorting by Short Swaps. 775-789 - Nadia Pisanti, Roberto Marangoni, Paolo Ferragina, Antonio Frangioni, A. Savona, C. Pisanelli, Fabrizio Luccio:
PaTre: A Method for Paralogy Trees Construction. 791-802
Volume 10, Number 6, December 2003
- Yu Zhang, Michael S. Waterman:
An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences. 803-819 - Hagit Shatkay, Ronen Feldman:
Mining the Biomedical Literature in the Genomic Era: An Overview. 821-855 - Li Liao, William Stafford Noble:
Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships. 857-868 - Gerton Lunter, István Miklós, Yun S. Song, Jotun Hein:
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. 869-889 - M. Kathleen Kerr:
Linear Models for Microarray Data Analysis: Hidden Similarities and Differences. 891-901 - Gonzalo Navarro, Mathieu Raffinot:
Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching. 903-923 - Ryan H. Lilien, Hany Farid, Bruce Randall Donald:
Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum. 925-946 - Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun:
Prediction of Protein Function Using Protein-Protein Interaction Data. 947-960 - Mark R. Segal, Kam D. Dahlquist, Bruce R. Conklin:
Regression Approaches for Microarray Data Analysis. 961-980 - Samuel Ieong, Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Siu-Ming Yiu:
Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs. 981-995 - Shalini Veerassamy, Andrew D. Smith, Elisabeth R. M. Tillier:
A Transition Probability Model for Amino Acid Substitutions from Blocks. 997-1010
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