Journal of Computational Biology, Volume 13

Volume 13, Number 1, January 2006

• Joseph West, John Healy, Michael Wigler, William Casey, Bud Mishra:
  Validation of S. Pombe Sequence Assembly by Microarray Hybridization. 1-20
  
• David Chiang, Aravind K. Joshi, Ken A. Dill:
  A Grammatical Theory for the Conformational Changes of Simple Helix Bundles. 21-42
  
• Jakob Vesterstrøm, William R. Taylor:
  Flexible Secondary Structure Based Protein Structure Comparison Applied to the Detection of Circular Permutation. 43-63
  
• Moshe Havilio:
  Signal Deconvolution Based Expression-Detection and Background Adjustment for Microarray Data. 63-80
  
• Anna Gambin, Jerzy Tiuryn, Jerzy Tyszkiewicz:
  Alignment with Context Dependent Scoring Function. 81-101
  
• Manoj Bhasin, Ellis L. Reinherz, Pedro A. Reche:
  Recognition and Classification of Histones Using Support Vector Machine. 102-112
  
• Tim Hohm, Philipp Limbourg, Daniel Hoffmann:
  A Multiobjective Evolutionary Method for the Design of Peptidic Mimotopes. 113-125
  
• Joanne I. Yeh, Lisong Mao:
  Prediction of Membrane Proteins in Mycobacterium tuberculosis Using a Support Vector Machine Algorithm. 126-129
  

Volume 13, Number 2, March 2006

• Satoru Miyano:
  Preface: Special RECOMB 2005 Issue. 131-132
  
• Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan:
  Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. 133-144
  
• Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman:
  Towards an Integrated Protein-Protein Interaction Network: A Relational Markov Network Approach. 145-164
  
• Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir:
  A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks. 165-181
  
• Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
  Pairwise Alignment of Protein Interaction Networks. 182-199
  
• Brendan J. Frey, Quaid Morris, Timothy R. Hughes:
  GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data. 200-214
  
• Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini:
  Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis. 215-228
  
• Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung, Wen-Lian Hsu:
  RIBRA - An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem. 229-244
  
• Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini:
  A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions. 245-266
  
• Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang:
  RNA-RNA Interaction Prediction and Antisense RNA Target Search. 267-282
  
• Vineet Bafna, Haixu Tang, Shaojie Zhang:
  Consensus Folding of Unaligned RNA Sequences Revisited. 283-295
  
• Kim R. Rasmussen, Jens Stoye, Eugene W. Myers:
  Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. 296-308
  
• Sing-Hoi Sze, Yue Lu, Qingwu Yang:
  A Polynomial Time Solvable Formulation of Multiple Sequence Alignment. 309-319
  
• Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot:
  A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. 320-335
  
• Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor:
  The Average Common Substring Approach to Phylogenomic Reconstruction. 336-350
  
• Teresa M. Przytycka, George Davis, Nan Song, Dannie Durand:
  Graph Theoretical Insights into Evolution of Multidomain Proteins. 351-363
  
• Marshall W. Bern, David Goldberg:
  De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. 364-378
  
• Samuel S. Gross, Michael R. Brent:
  Using Multiple Alignments to Improve Gene Prediction. 379-393
  
• Yan Liu, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan:
  Protein Fold Recognition Using Segmentation Conditional Random Fields (SCRFs). 394-406
  
• Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson:
  The Multiple Common Point Set Problem and Its Application to Molecule Binding Pattern Detection. 407-428
  
• Nicholas Chia, Ralf Bundschuh:
  A Practical Approach to Significance Assessment in Alignment with Gaps. 429-441
  
• Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman:
  Alignment of Optical Maps. 442-462
  
• Chen-Hsiang Yeang, Tommi Jaakkola:
  Modeling the Combinatorial Functions of Multiple Transcription Factors. 463-480
  
• Eran Halperin, Elad Hazan:
  HAPLOFREQ-Estimating Haplotype Frequencies Efficiently. 481-500
  
• Vineet Bafna, Vikas Bansal:
  Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots. 501-521
  
• Zhihong Ding, Vladimir Filkov, Dan Gusfield:
  A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. 522-553
  
• Matthew Mazowita, Lani Haque, David Sankoff:
  Stability of Rearrangement Measures in the Comparison of Genome Sequences. 554-566
  
• Anne Bergeron, Julia Mixtacki, Jens Stoye:
  On Sorting by Translocations. 567-578
  

Volume 13, Number 3, April 2006

• Sündüz Keles, Mark J. van der Laan, Sandrine Dudoit, Simon E. Cawley:
  Multiple Testing Methods For ChIP - Chip High Density Oligonucleotide Array Data. 579-613
  
• Florian A. Potra, Xing Liu, Françoise Seillier-Moiseiwitsch, Anindya Roy, Yaming Hang, Mark R. Marten, Babu Raman, Carol Whisnant:
  Protein Image Alignment via Piecewise Affine Transformations. 614-630
  
• Gianluca Pollastri, Alessandro Vullo, Paolo Frasconi, Pierre Baldi:
  Modular DAG-RNN Architectures for Assembling Coarse Protein Structures. 631-650
  
• Pierre Nicolas, Anne-Sophie Tocquet, Vincent Miele, Florence Muri:
  A Reversible Jump Markov Chain Monte Carlo Algorithm for Bacterial Promoter Motifs Discovery. 651-667
  
• Arun Siddharth Konagurthu, Peter J. Stuckey:
  Optimal Sum-of-Pairs Multiple Sequence Alignment Using Incremental Carrillo and Lipman Bounds. 668-685
  
• Jonathan M. Carlson, Arijit Chakravarty, Robert H. Gross:
  BEAM: A Beam Search Algorithm for the Identification of Cis-Regulatory Elements in Groups of Genes. 686-701
  
• Jesper Jansson, Ngo Trung Hieu, Wing-Kin Sung:
  Local Gapped Subforest Alignment and Its Application in Finding RNA Structural Motifs. 702-718
  
• Sébastien Ferré, Ross D. King:
  Finding Motifs in Protein Secondary Structure for Use in Function Prediction. 719-731
  
• Ion I. Mandoiu, Dragos Trinca:
  Exact and Approximation Algorithms for DNA Tag Set Design. 732-744
  
• Chandan K. Reddy, Hsiao-Dong Chiang:
  A Stability Boundary Based Method for Finding Saddle Points on Potential Energy Surfaces. 745-766
  
• Kristin L. Ayers, Chiara Sabatti, Kenneth Lange:
  Reconstructing Ancestral Haplotypes with a Dictionary Model. 767-785
  
• Shuguang Huang, Yongming Qu:
  The Loss in Power When the Test of Differential Expression Is Performed under a Wrong Scale. 786-797
  
• Nandini Raghavan, Dhammika Amaratunga, Javier Cabrera, A. Nie, J. Qin, M. McMillian:
  On Methods for Gene Function Scoring as a Means of Facilitating the Interpretation of Microarray Results. 798-809
  
• Raya Khanin, Ernst Wit:
  How Scale-Free Are Biological Networks. 810-818
  
• Benny Chor, Amit Khetan, Sagi Snir:
  Maximum Likelihood Molecular Clock Comb: Analytic Solutions. 819-837
  
• Andrew Golightly, Darren J. Wilkinson:
  Bayesian Sequential Inference for Stochastic Kinetic Biochemical Network Models. 838-851
  

Volume 13, Number 4, May 2006

• Marcus Hjelm, Mattias Höglund, Jens Lagergren:
  New Probabilistic Network Models and Algorithms for Oncogenesis. 853-865
  
• Arkadii G. D'yachkov, Anthony J. Macula, Wendy K. Pogozelski, Thomas E. Renz, Vyacheslav V. Rykov, David C. Torney:
  New t-Gap Insertion-Deletion-Like Metrics for DNA Hybridization Thermodynamic Modeling. 866-881
  
• Dirk Metzler:
  Robust E-Values for Gapped Local Alignments. 882-896
  
• Ravi Vijaya Satya, Amar Mukherjee:
  An Optimal Algorithm for Perfect Phylogeny Haplotyping. 897-928
  
• Sumedha Gunewardena, Peter Jeavons, Zhaolei Zhang:
  Enhancing the Prediction of Transcription Factor Binding Sites by Incorporating Structural Properties and Nucleotide Covariations. 929-945
  
• Vera P. Turutina, Andrew A. Laskin, Nikolay A. Kudryashov, Konstantin G. Skryabin, Eugene V. Korotkov:
  Identification of Amino Acid Latent Periodicity within 94 Protein Families. 946-964
  
• Michael Cameron, Hugh E. Williams, Adam Cannane:
  A Deterministic Finite Automaton for Faster Protein Hit Detection in BLAST. 965-978
  
• Justin Colannino, Mirela Damian, Ferran Hurtado, John Iacono, Henk Meijer, Suneeta Ramaswami, Godfried T. Toussaint:
  An O(n log n)-Time Algorithm for the Restriction Scaffold Assignment Problem. 979-989
  
• Ding-Zhu Du, Frank K. Hwang, Weili Wu, Taieb Znati:
  New Construction for Transversal Design. 990-995
  
• E. Chudin, S. Kruglyak, S. C. Baker, S. Oeser, D. Barker, T. K. McDaniel:
  A Model of Technical Variation of Microarray Signals. 996-1003
  

Volume 13, Number 5, June 2006

• David Sankoff, Lani Haque:
  The Distribution of Genomic Distance between Random Genomes. 1005-1012
  
• Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson:
  On the Complexity of Sparse Exon Assembly. 1013-1027
  
• Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala:
  A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. 1028-1040
  
• Tatiana Maximova, Chen Keasar:
  A Novel Algorithm for Non-Bonded-List Updating in Molecular Simulations. 1041-1048
  
• John Goutsias, Seungchan Kim:
  Stochastic Transcriptional Regulatory Systems with Time Delays: A Mean-Field Approximation. 1049-1076
  
• David Chiang, Aravind K. Joshi, David B. Searls:
  Grammatical Representations of Macromolecular Structure. 1077-1100
  
• Elizabeth S. Allman, John A. Rhodes:
  The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models. 1101-1113
  
• Bradley J. Beattie, Peter N. Robinson:
  Binary State Pattern Clustering: A Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer. 1114-1130
  

Volume 13, Number 6, July 2006

• Angela P. Presson, Eric M. Sobel, Kenneth Lange, Jeanette C. Papp:
  Merging Microsatellite Data. 1131-1147
  
• Jing Wu, David Haussler:
  Coding Exon Detection Using Comparative Sequences. 1148-1164
  
• Yair Horesh, Ramit Mehr, Ron Unger:
  Designing an A* Algorithm for Calculating Edit Distance between Rooted-Unordered Trees. 1165-1176
  
• Michael C. Wendl:
  A General Coverage Theory for Shotgun DNA Sequencing. 1177-1196
  
• Einar Andreas Rødland:
  Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence. 1197-1213
  
• Manolis Christodoulakis, Costas S. Iliopoulos, Laurent Mouchard, Katerina Perdikuri, Athanasios K. Tsakalidis, Kostas Tsichlas:
  Computation of Repetitions and Regularities of Biologically Weighted Sequences. 1214-1231
  
• Meera Sitharam, Mavis Agbandje-Mckenna:
  Modeling Virus Self-Assembly Pathways: Avoiding Dynamics Using Geometric Constraint Decomposition. 1232-1265
  

Volume 13, Number 7, September 2006

• Lincong Wang, Ramgopal R. Mettu, Bruce Randall Donald:
  A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data. 1267-1288
  
• Adrian D. Haimovich, Bruce Byrne, Ramakrishna Ramaswamy, William J. Welsh:
  Wavelet Analysis of DNA Walks. 1289-1298
  
• Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
  Detecting Conserved Interaction Patterns in Biological Networks. 1299-1322
  
• Isaac Elias:
  Settling the Intractability of Multiple Alignment. 1323-1339
  
• Anne Bergeron, Jens Stoye:
  On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. 1340-1354
  
• Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma:
  Optimizing Multiple Spaced Seeds for Homology Search. 1355-1368
  
• Jonathan M. Keith:
  Segmenting Eukaryotic Genomes with the Generalized Gibbs Sampler. 1369-1383
  
• Florian A. Potra, Xing Liu:
  Aligning Families of Two-Dimensional Gels by a Combined Multiresolution Forward-Inverse Transformation Approach. 1384-1395
  

Volume 13, Number 8, October 2006

• Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter:
  On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. 1397-1418
  
• Maria Luisa Bonet, Katherine St. John, Ruchi Mahindru, Nina Amenta:
  Approximating Subtree Distances Between Phylogenies. 1419-1434
  
• Winfried Just:
  Reverse Engineering Discrete Dynamical Systems from Data Sets with Random Input Vectors. 1435-1456
  
• Joel E. Richardson:
  fjoin: Simple and Efficient Computation of Feature Overlaps. 1457-1464
  
• Gilles Didier, Ivan Laprevotte, Maude Pupin, Alain Hénaut:
  Local Decoding of Sequences and Alignment-Free Comparison. 1465-1476
  
• Giulia Menconi, Roberto Marangoni:
  A Compression-Based Approach for Coding Sequences Identification. I. Application to Prokaryotic Genomes. 1477-1488
  
• Catherine Mooney, Alessandro Vullo, Gianluca Pollastri:
  Protein Structural Motif Prediction in Multidimensional ø-Psi Space Leads to Improved Secondary Structure Prediction. 1489-1502
  
• Frank Emmert-Streib:
  Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins. 1503-1512
  

Volume 13, Number 9, November 2006

• B. Moerkerke, E. Goetghebeur:
  Selecting "Significant" Differentially Expressed Genes from the Combined Perspective of the Null and the Alternative. 1513-1531
  
• Peter C. Y. Chen:
  A Discrete-Event Approach to Transcription Control with Dynamic Event-Controllability. 1532-1545
  
• Derek A. Ruths, Luay Nakhleh, M. Sriram Iyengar, Shrikanth A. G. Reddy, Prahlad T. Ram:
  Hypothesis Generation in Signaling Networks. 1546-1557
  
• Gasper Jaklic, Tomaz Pisanski, Milan Randic:
  Characterization of Complex Biological Systems by Matrix Invariants. 1558-1564
  
• Yu Chen, Gordon M. Crippen:
  Fold Recognition via a Tree. 1565-1573
  
• William J. Bruno, John E. Pearson:
  Transformations that Preserve Detailed Balance in Markov Models. 1574-1578
  
• Pengfei Han, Xiuzhen Zhang, Raymond S. Norton, Zhi-Ping Feng:
  Predicting Disordered Regions in Proteins Based on Decision Trees of Reduced Amino Acid Composition. 1579-1590
  
• Bart J. A. Mertens, M. E. De Noo, Rob A. E. M. Tollenaar, André M. Deelder:
  Mass Spectrometry Proteomic Diagnosis: Enacting the Double Cross-Validatory Paradigm. 1591-1605
  
• Zhenqiu Liu, Shili Lin, Ming Tan:
  Genome-Wide Tagging SNPs with Entropy-Based Monte Carlo Method. 1606-1614
  
• Nak-Kyeong Kim, Jun Xie:
  Protein Multiple Alignment Incorporating Primary and Secondary Structure Information. 1615-1629
  
• Andre Ribeiro, Rui Zhu, Stuart A. Kauffman:
  A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics. 1630-1639
  
• P. Clote:
  Combinatorics of Saturated Secondary Structures of RNA. 1640-1657
  

Volume 13, Number 10, December 2006

• Noga Alon, Vera Asodi, Charles Cantor, Simon Kasif, John Rachlin:
  Multi-Node Graphs: A Framework for Multiplexed Biological Assays. 1659-1672
  
• Lu-Yong Wang, Dorin Comaniciu, Daniel P. Fasulo:
  Exploiting Interactions among Polymorphisms Contributing to Complex Disease Traits with Boosted Generative Modeling. 1673-1684
  
• Laxmi Parida:
  Using PQ Structures for Genomic Rearrangement Phylogeny. 1685-1700
  
• Nicolas Lartillot:
  Conjugate Gibbs Sampling for Bayesian Phylogenetic Models. 1701-1722
  
• Pengfei Han, Xiuzhen Zhang, Raymond S. Norton, Zhi-Ping Feng:
  Predicting Disordered Regions in Proteins Based on Decision Trees of Reduced Amino Acid Composition. 1723-1734
  
• Nak-Kyeong Kim, Jun Xie:
  Protein Multiple Alignment Incorporating Primary and Secondary Structure Information. 1735-1748
  
• Sushmita Roy, Terran Lane, Chris Allen, Anthony D. Aragon, Margaret Werner-Washburne:
  A Hidden-State Markov Model for Cell Population Deconvolution. 1749-1774
  
• Chun-Min Hung, Yueh-Min Huang, Ming-Shi Chang:
  CSAM: Using Clustering-Hashing-Signal Anchoring Method to Explore Human Novel Genes. 1775-1789