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Journal of Computational Biology, Volume 14
Volume 14, Number 1, January 2007
- Ilan Gronau, Shlomo Moran:
Neighbor Joining Algorithms for Inferring Phylogenies via LCA Distances. 1-15 - Baharak Rastegari
, Anne Condon:
Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications. 16-32 - Sven Siebert, Rolf Backofen:
A Dynamic Programming Approach for Finding Common Patterns in RNAs. 33-44 - Laxmi Parida:
Gapped Permutation Pattern Discovery for Gene Order Comparisons. 45-55 - Qingwu Yang, Sing-Hoi Sze:
Path Matching and Graph Matching in Biological Networks. 56-67 - Karen Lees, Stephen J. Roberts, Pari Skamnioti, Sarah J. Gurr:
Gene Microarray Analysis Using Angular Distribution Decomposition. 68-83 - Morgan A. Bishop, Anthony J. Macula, Kayla Nimmo, Lauren Wood, Wendy K. Pogozelski, Thomas E. Renz:
Group Testing to Annihilate Pairs Applied to DNA Cross-Hybridization Elimination Using SYBR Green I. 84-96 - Nilanjan Saha, Layne T. Watson, Karen Kafadar, Naren Ramakrishnan
Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process. 97-112
Volume 14, Number 2, March 2007
- Leming Zhou
Designing Sensitive and Specific Spaced Seeds for Cross-Species mRNA-to-Genome Alignment. 113-130 - Pankaj K. Agarwal, Nabil H. Mustafa
Fast Molecular Shape Matching Using Contact Maps. 131-143 - Dan Levy, Christopher Reeder, Bradford Loucas, Lynn Hlatky, Allen M. Chen
Interpreting Chromosome Aberration Spectra. 144-155 - Daniel Stefankovic
Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-Identifiable Distributions. 156-189 - Jérôme Waldispühl
Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model. 190-215 - Isaac Elias, Tamir Tuller
Reconstruction of Ancestral Genomic Sequences Using Likelihood. 216-237 - Yong Kong
Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search. 238-254
Volume 14, Number 3, April 2007
- Haifeng Li, Anton Valouev, David C. Schwartz, Michael S. Waterman, Lei M. Li:
A Quantile Method for Sizing Optical Maps. 255-266 - Eric P. Xing, Michael I. Jordan
Bayesian Haplotype Inference via the Dirichlet Process. 267-284 - Mary Ellen Bock, Claudio Garutti, Concettina Guerra:
Discovery of Similar Regions on Protein Surfaces. 285-299 - Laxmi Parida:
Discovering Topological Motifs Using a Compact Notation. 300-323 - Naftali Kaminski
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. 324-338 - Grzegorz A. Rempala, Kenneth S. Ramos, Ted Kalbfleisch
Validation of a Mathematical Model of Gene Transcription in Aggregated Cellular Systems: Application to L1 Retrotransposition. 339-349 - Mariusz Lubomirski, Michael R. D'Andrea, Stanley M. Belkowski, Javier Cabrera, James M. Dixon, Dhammika Amaratunga:
A Consolidated Approach to Analyzing Data from High-Throughput Protein Microarrays with an Application to Immune Response Profiling in Humans. 350-359 - Noah A. Rosenberg
Counting Coalescent Histories. 360-377
Volume 14, Number 4, May 2007
- Sébastien Angibaud, Guillaume Fertin
A Pseudo-Boolean Framework for Computing Rearrangement Distances between Genomes with Duplicates. 379-393 - Guillaume Blin
Gene Maps Linearization Using Genomic Rearrangement Distances. 394-407 - Michal Ozery-Flato
Sorting by Reciprocal Translocations via Reversals Theory. 408-422 - Wei Xu, Chunfang Zheng, David Sankoff:
Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes. 423-435 - Zaky Adam, Monique Turmel
Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution. 436-445 - Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette:
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem. 446-461 - Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk, Olivier Gascuel:
Duplication and Inversion History of a Tandemly Repeated Genes Family. 462-478 - Damian Wójtowicz
Evolution of Gene Families Based on Gene Duplication, Loss, Accumulated Change, and Innovation. 479-495 - Nan Song, R. D. Sedgewick, Dannie Durand:
Domain Architecture Comparison for Multidomain Homology Identification. 496-516 - Cuong Than, Derek A. Ruths, Hideki Innan
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. 517-535
Volume 14, Number 5, June 2007
- Alberto Apostolico:
Preface. 537-538 - Teresa M. Przytycka
Stability of Characters and Construction of Phylogenetic Trees. 539-549 - Jim C. Huang, Quaid Morris
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. 550-563 - Jinbo Xu, Feng Jiao, Bonnie Berger:
A Parameterized Algorithm for Protein Structure Alignment. 564-577 - Tsung-Han Chiang, Mehmet Serkan Apaydin
Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values. 578-593 - Michael Cameron, Yaniv Bernstein, Hugh E. Williams:
Clustered Sequence Representation for Fast Homology Search. 594-614 - Martin Bader, Enno Ohlebusch:
Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. 615-636 - Wei Xie, Nikolaos V. Sahinidis
A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem. 637-654 - Philipp W. Messer
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics. 655-668 - Stefanie Scheid
Compensating for Unknown Confounders in Microarray Data Analysis Using Filtered Permutations. 669-681 - Samuel A. Andersson, Jens Lagergren
Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model. 682-697
Volume 14, Number 6, July 2007
- Alberto Apostolico:
Preface. 699-700 - Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim:
Efficient Enumeration of Phylogenetically Informative Substrings. 701-723 - Nicholas D. Pattengale, Eric J. Gottlieb, Bernard M. E. Moret
Efficiently Computing the Robinson-Foulds Metric. 724-735 - David Heckerman, Carl Myers Kadie, Jennifer Listgarten:
Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction. 736-746 - Mehmet Koyutürk
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. 747-764 - Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. 765-776 - Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg:
Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. 777-790 - Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. 791-816 - Benny Chor, Tamir Tuller
Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. 817-838 - Shawna L. Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato:
Simulating Protein Motions with Rigidity Analysis. 839-855 - Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
A Study of Accessible Motifs and RNA Folding Complexity. 856-872
Volume 14, Number 7, July 2007
- Nevzat Onur Domaniç
A Novel Approach to the Detection of Genomic Approximate Tandem Repeats in the Levenshtein Metric. 873-891 - Manikandan Narayanan
Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm. 892-907 - Isana Veksler-Lublinsky
A Structure-Based Flexible Search Method for Motifs in RNA. 908-926 - Réka Albert
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence. 927-949 - Liqing Zhang, Layne T. Watson:
Note on the Computation of Critical Effective Population Sizes. 950-960 - Frank Emmert-Streib
The Chronic Fatigue Syndrome: A Comparative Pathway Analysis. 961-972 - Mircea Andrecut, Stuart A. Kauffman:
A Physical Analogy of the Genetic Toggle Switch. 973-983 - Stefan Zeiser, Johannes Müller, Volkmar Liebscher
Modeling the Hes1 Oscillator. 984-1000 - Manolis Christodoulakis, Geoffrey Brian Golding, Costas S. Iliopoulos, Yoan José Pinzón Ardila, William F. Smyth:
Efficient Algorithms for Counting and Reporting Segregating Sites in Genomic Sequences. 1001-1010 - Yi Y. Shi, Gerald A. Miller, Oleg Denisenko, Hong Qian, Karol Bomsztyk:
Quantitative Model for Binary Measurements of Protein-Protein Interactions. 1011-1023
Volume 14, Number 8, October 2007
- Xue Wu, Chau-Wen Tseng, Nathan Edwards:
HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models. 1025-1043 - Zakharia M. Frenkel, Edward N. Trifonov:
Evolutionary Networks in the Formatted Protein Sequence Space. 1044-1057 - Beckett W. Sterner
Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. 1058-1073 - Rolf Backofen, Shihyen Chen, Danny Hermelin
Locality and Gaps in RNA Comparison. 1074-1087 - Morgan A. Bishop, Arkadii G. D'yachkov, Anthony J. Macula, Thomas E. Renz, Vyacheslav V. Rykov:
Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes. 1088-1104 - Koen Deforche, Ricardo Camacho
Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo. 1105-1114 - Aleksandar Stojmirovic
Information Flow in Interaction Networks. 1115-1143
Volume 14, Number 9, November 2007
- Laxmi Parida:
Statistical Significance of Large Gene Clusters. 1145-1159 - Zheng Fu, Xin Chen, Vladimir Vacic
MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement. 1160-1175 - Francis L. Martin
Identifying Variables Responsible for Clustering in Discriminant Analysis of Data from Infrared Microspectroscopy of a Biological Sample. 1176-1184 - Hendrik Fuß, Werner Dubitzky, C. Stephen Downes, Mary Jo Kurth:
Deactivation of Src Family Kinases: Hypothesis Testing Using a Monte Carlo Sensitivity Analysis of Systems-Level Properties. 1185-1200 - Tetsuo Shibuya:
Efficient Substructure RMSD Query Algorithms. 1201-1207 - Yongxi Cheng, Ding-Zhu Du:
Efficient Constructions of Disjunct Matrices with Applications to DNA Library Screening. 1208-1216 - Achim Tresch, Tim Beißbarth, Holger Sültmann
Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects. 1217-1228 - Ilkka Havukkala
On the Reliable Identification of Plant Sequences Containing a Polyadenylation Site. 1229-1245
Volume 14, Number 10, December 2007
- Dan Gusfield, Vikas Bansal, Vineet Bafna
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. 1247-1272 - Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu:
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. 1273-1286 - Scott C. Schmidler
Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction. 1287-1310 - Dongxiao Zhu, Alfred O. Hero III:
Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation. 1311-1326 - Michael Hirsch
Optimal Search Space for Clustering Gene Expression Data via Consensus. 1327-1341 - Binhai Zhu:
Protein Local Structure Alignment Under the Discrete Fréchet Distance. 1343-1351 - Magnus Åstrand, Petter Mostad
Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data. 1353-1367
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