Journal 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 BibTeX
• Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail: Robustness of Inference of Haplotype Block Structure. 13-20 BibTeX
• Agatha H. Liu, Andrea Califano: CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships. 21-46 BibTeX
• Xueliang Li, Zimao Li, Lusheng Wang: The Inverse Problems for Some Topological Indices in Combinatorial Chemistry. 47-56 BibTeX
• 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 BibTeX
• Sujay Chattopadhyay, Jayprokas Chakrabarti: Temporal Changes in Phosphoglycerate Kinase Coding Sequences: A Quantitative Measure. 83-94 BibTeX
• Magnus Åstrand: Contrast Normalization of Oligonucleotide Arrays. 95-102 BibTeX

Volume 10, Number 2, April 2003

• Gene Myers, Richard Durbin: A Table-Driven, Full-Sensitivity Similarity Search Algorithm. 103-118 BibTeX
• 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 BibTeX
• Yinglei Lai, Deepali Shinde, Norman Arnheim, Fengzhu Sun: The Mutation Process of Microsatellites During the Polymerase Chain Reaction. 143-156 BibTeX
• Yaning Yang, Josephine Hoh, Clemens Broger, Martin Neeb, Joanne Edington, Klaus Lindpaintner, Jürg Ott: Statistical Methods for Analyzing Microarray Feature Data with Replications. 157-170 BibTeX
• Honghui Wan, Lugang Li, Scott Federhen, John C. Wootton: Discovering Simple Regions in Biological Sequences Associated with Scoring Schemes. 171-186 BibTeX
• Eleazar Eskin, William Stafford Noble, Yoram Singer: Protein Family Classification Using Sparse Markov Transducers. 187-214 BibTeX
• Robert Penchovsky, Jörg Ackermann: DNA Library Design for Molecular Computation. 215-230 BibTeX
• Frank K. Hwang, Y. C. Liu: Error-Tolerant Pooling Designs with Inhibitors. 231-236 BibTeX

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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi:
  Monotony of Surprise and Large-Scale Quest for Unusual Words. 283-311
  Electronic Edition (link) BibTeX
• Peter F. Arndt, Christopher B. Burge, Terence Hwa:
  DNA Sequence Evolution with Neighbor-Dependent Mutation. 313-322
  Electronic Edition (link) BibTeX
• Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph:
  Haplotyping as Perfect Phylogeny: A Direct Approach. 323-340
  Electronic Edition (link) BibTeX
• Ziv Bar-Joseph, Georg Gerber, David K. Gifford, Tommi Jaakkola, Itamar Simon:
  Continuous Representations of Time-Series Gene Expression Data. 341-356
  Electronic Edition (link) BibTeX
• Sèverine Bérard, Eric Rivals:
  Comparison of Minisatellites. 357-372
  Electronic Edition (link) BibTeX
• Amir Ben-Dor, Benny Chor, Richard M. Karp, Zohar Yakhini:
  Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem. 373-384
  Electronic Edition (link) BibTeX
• Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir:
  The Restriction Scaffold Problem. 385-398
  Electronic Edition (link) BibTeX
• Jeremy Buhler:
  Provably Sensitive Indexing Strategies for Biosequence Similarity Search. 399-417
  Electronic Edition (link) BibTeX
• Barry Cohen, Steven Skiena:
  Natural Selection and Algorithmic Design of mRNA. 419-432
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Dannie Durand, David Sankoff:
  Tests for Gene Clustering. 453-482
  Electronic Edition (link) BibTeX
• Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir:
  Handling Long Targets and Errors in Sequencing by Hybridization. 483-497
  Electronic Edition (link) BibTeX
• Samuel A. Heath, Franco P. Preparata, Joel Young:
  Sequencing by Hybridization by Cooperating Direct and Reverse Spectra. 499-508
  Electronic Edition (link) BibTeX
• Fumei Lam, Marina Alexandersson, Lior Pachter:
  Picking Alignments from (Steiner) Trees. 509-520
  Electronic Edition (link) BibTeX
• Christopher James Langmead, Anthony K. Yan, C. Robertson McClung, Bruce Randall Donald:
  Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns. 521-536
  Electronic Edition (link) BibTeX
• Jia Li, Webb Miller:
  Significance of Interspecies Matches when Evolutionary Rate Varies. 537-554
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Jürg Ott, Josephine Hoh:
  Set Association Analysis of SNP Case-Control and Microarray Data. 569-574
  Electronic Edition (link) BibTeX
• Adam C. Siepel:
  An Algorithm to Enumerate Sorting Reversals for Signed Permutations. 575-597
  Electronic Edition (link) BibTeX
• Saurabh Sinha:
  Discriminative Motifs. 599-615
  Electronic Edition (link) BibTeX
• Miguel L. Teodoro, George N. Phillips, Lydia E. Kavraki:
  Understanding Protein Flexibility through Dimensionality Reduction. 617-634
  Electronic Edition (link) BibTeX
• Andy Wildenberg, Steven Skiena, Pavel Sumazin:
  Deconvolving Sequence Variation in Mixed DNA Populations. 635-652
  Electronic Edition (link) BibTeX
• Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer:
  Microarrays: How Many Do You Need? 653-667
  Electronic Edition (link) BibTeX

Volume 10, Number 5, October 2003

• Elchanan Mossel:
  On the Impossibility of Reconstructing Ancestral Data and Phylogenies. 669-676
  Electronic Edition (link) BibTeX
• Fan R. K. Chung, Linyuan Lu, T. Gregory Dewey, David J. Galas:
  Duplication Models for Biological Networks. 677-687
  Electronic Edition (link) BibTeX
• George Michailidis, Kerby Shedden:
  The Application of Rule-Based Methods to Class Prediction Problems in Genomics. 689-698
  Electronic Edition (link) BibTeX
• Yonghong Wang, Hongyu Ou, Fengbiao Guo:
  Recognition of Translation Initiation Sites of Eukaryotic Genes Based on an EM Algorithm. 699-708
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Henrik Jönsson, Bo Söderberg:
  An Approximate Maximum Likelihood Approach, Applied to Phylogenetic Trees. 737-749
  Electronic Edition (link) BibTeX
• Daniel Faller, Henning U. Voss, Jens Timmer, Uwe Hobohm:
  Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization. 751-762
  Electronic Edition (link) BibTeX
• Antonio Piccolboni, Dan Gusfield:
  On the Complexity of Fundamental Computational Problems in Pedigree Analysis. 763-773
  Electronic Edition (link) BibTeX
• Lenwood S. Heath, John Paul C. Vergara:
  Sorting by Short Swaps. 775-789
  Electronic Edition (link) BibTeX
• Nadia Pisanti, Roberto Marangoni, Paolo Ferragina, Antonio Frangioni, A. Savona, C. Pisanelli, Fabrizio Luccio:
  PaTre: A Method for Paralogy Trees Construction. 791-802
  Electronic Edition (link) BibTeX

Volume 10, Number 6, December 2003

• Yu Zhang, Michael S. Waterman:
  An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences. 803-819
  Electronic Edition (link) BibTeX
• Hagit Shatkay, Ronen Feldman:
  Mining the Biomedical Literature in the Genomic Era: An Overview. 821-855
  Electronic Edition (link) BibTeX
• Li Liao, William Stafford Noble:
  Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships. 857-868
  Electronic Edition (link) BibTeX
• Gerton Lunter, István Miklós, Yun S. Song, Jotun Hein:
  An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. 869-889
  Electronic Edition (link) BibTeX
• M. Kathleen Kerr:
  Linear Models for Microarray Data Analysis: Hidden Similarities and Differences. 891-901
  Electronic Edition (link) BibTeX
• Gonzalo Navarro, Mathieu Raffinot:
  Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching. 903-923
  Electronic Edition (link) BibTeX
• Ryan H. Lilien, Hany Farid, Bruce Randall Donald:
  Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum. 925-946
  Electronic Edition (link) BibTeX
• Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun:
  Prediction of Protein Function Using Protein-Protein Interaction Data. 947-960
  Electronic Edition (link) BibTeX
• Mark R. Segal, Kam D. Dahlquist, Bruce R. Conklin:
  Regression Approaches for Microarray Data Analysis. 961-980
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Shalini Veerassamy, Andrew D. Smith, Elisabeth R. M. Tillier:
  A Transition Probability Model for Amino Acid Substitutions from Blocks. 997-1010
  Electronic Edition (link) BibTeX