Volume 14,
Number 1,
January 2007
- Ilan Gronau, Shlomo Moran:
Neighbor Joining Algorithms for Inferring Phylogenies via LCA Distances.
1-15
Electronic Edition (link) BibTeX
- Baharak Rastegari, Anne Condon:
Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications.
16-32
Electronic Edition (link) BibTeX
- Sven Siebert, Rolf Backofen:
A Dynamic Programming Approach for Finding Common Patterns in RNAs.
33-44
Electronic Edition (link) BibTeX
- Laxmi Parida:
Gapped Permutation Pattern Discovery for Gene Order Comparisons.
45-55
Electronic Edition (link) BibTeX
- Qingwu Yang, Sing-Hoi Sze:
Path Matching and Graph Matching in Biological Networks.
56-67
Electronic Edition (link) BibTeX
- Karen Lees, Stephen Roberts, Pari Skamnioti, Sarah J. Gurr:
Gene Microarray Analysis Using Angular Distribution Decomposition.
68-83
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Nilanjan Saha, Layne T. Watson, Karen Kafadar, Naren Ramakrishnan, Alexey Onufriev, Shrinivasrao P. Mane, Cecilia Vasquez-Robinet:
Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process.
97-112
Electronic Edition (link) BibTeX
Volume 14,
Number 2,
March 2007
- Leming Zhou, Liliana Florea:
Designing Sensitive and Specific Spaced Seeds for Cross-Species mRNA-to-Genome Alignment.
113-130
Electronic Edition (link) BibTeX
- Pankaj K. Agarwal, Nabil H. Mustafa, Yusu Wang:
Fast Molecular Shape Matching Using Contact Maps.
131-143
Electronic Edition (link) BibTeX
- Dan Levy, Christopher Reeder, Bradford Loucas, Lynn Hlatky, Allen Chen, Michael Cornforth, Rainer K. Sachs:
Interpreting Chromosome Aberration Spectra.
144-155
Electronic Edition (link) BibTeX
- Daniel Stefankovic, Eric Vigoda:
Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-Identifiable Distributions.
156-189
Electronic Edition (link) BibTeX
- Jérôme Waldispühl, Peter Clote:
Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model.
190-215
Electronic Edition (link) BibTeX
- Isaac Elias, Tamir Tuller:
Reconstruction of Ancestral Genomic Sequences Using Likelihood.
216-237
Electronic Edition (link) BibTeX
- Yong Kong:
Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search.
238-254
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Eric P. Xing, Michael I. Jordan, Roded Sharan:
Bayesian Haplotype Inference via the Dirichlet Process.
267-284
Electronic Edition (link) BibTeX
- Mary Ellen Bock, Claudio Garutti, Concettina Guerra:
Discovery of Similar Regions on Protein Surfaces.
285-299
Electronic Edition (link) BibTeX
- Laxmi Parida:
Discovering Topological Motifs Using a Compact Notation.
300-323
Electronic Edition (link) BibTeX
- Naftali Kaminski, Ziv Bar-Joseph:
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies.
324-338
Electronic Edition (link) BibTeX
- Grzegorz A. Rempala, Kenneth S. Ramos, Ted Kalbfleisch, Ivo Teneng:
Validation of a Mathematical Model of Gene Transcription in Aggregated Cellular Systems: Application to L1 Retrotransposition.
339-349
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Noah A. Rosenberg:
Counting Coalescent Histories.
360-377
Electronic Edition (link) BibTeX
Volume 14,
Number 4,
May 2007
Special Issue on the RECOMB Satellite Workshop on Comparative Genomics
- Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette:
A Pseudo-Boolean Framework for Computing Rearrangement Distances between Genomes with Duplicates.
379-393
Electronic Edition (link) BibTeX
- Guillaume Blin, Eric Blais, Danny Hermelin, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk:
Gene Maps Linearization Using Genomic Rearrangement Distances.
394-407
Electronic Edition (link) BibTeX
- Michal Ozery-Flato, Ron Shamir:
Sorting by Reciprocal Translocations via Reversals Theory.
408-422
Electronic Edition (link) BibTeX
- Wei Xu, Chunfang Zheng, David Sankoff:
Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes.
423-435
Electronic Edition (link) BibTeX
- Zaky Adam, Monique Turmel, Claude Lemieux, David Sankoff:
Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution.
436-445
Electronic Edition (link) BibTeX
- Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette:
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem.
446-461
Electronic Edition (link) BibTeX
- Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk, Olivier Gascuel:
Duplication and Inversion History of a Tandemly Repeated Genes Family.
462-478
Electronic Edition (link) BibTeX
- Damian Wójtowicz, Jerzy Tiuryn:
Evolution of Gene Families Based on Gene Duplication, Loss, Accumulated Change, and Innovation.
479-495
Electronic Edition (link) BibTeX
- Nan Song, R. D. Sedgewick, Dannie Durand:
Domain Architecture Comparison for Multidomain Homology Identification.
496-516
Electronic Edition (link) BibTeX
- Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh:
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions.
517-535
Electronic Edition (link) BibTeX
Volume 14,
Number 5,
June 2007
Special Issue on RECOMB 2006,
Part I
- Alberto Apostolico:
Preface.
537-538
Electronic Edition (link) BibTeX
- Teresa M. Przytycka:
Stability of Characters and Construction of Phylogenetic Trees.
539-549
Electronic Edition (link) BibTeX
- Jim C. Huang, Quaid Morris, Brendan J. Frey:
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data.
550-563
Electronic Edition (link) BibTeX
- Jinbo Xu, Feng Jiao, Bonnie Berger:
A Parameterized Algorithm for Protein Structure Alignment.
564-577
Electronic Edition (link) BibTeX
- Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe:
Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values.
578-593
Electronic Edition (link) BibTeX
- Michael Cameron, Yaniv Bernstein, Hugh E. Williams:
Clustered Sequence Representation for Fast Homology Search.
594-614
Electronic Edition (link) BibTeX
- Martin Bader, Enno Ohlebusch:
Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions.
615-636
Electronic Edition (link) BibTeX
- Wei Xie, Nikolaos V. Sahinidis:
A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem.
637-654
Electronic Edition (link) BibTeX
- Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt:
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics.
655-668
Electronic Edition (link) BibTeX
- Stefanie Scheid, Rainer Spang:
Compensating for Unknown Confounders in Microarray Data Analysis Using Filtered Permutations.
669-681
Electronic Edition (link) BibTeX
- Samuel A. Andersson, Jens Lagergren:
Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model.
682-697
Electronic Edition (link) BibTeX
Volume 14,
Number 6,
July 2007
Special Issue RECOMB 2006,
Part II
- Alberto Apostolico:
Preface.
699-700
Electronic Edition (link) BibTeX
- Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim:
Efficient Enumeration of Phylogenetically Informative Substrings.
701-723
Electronic Edition (link) BibTeX
- Nicholas D. Pattengale, Eric J. Gottlieb, Bernard M. E. Moret:
Efficiently Computing the Robinson-Foulds Metric.
724-735
Electronic Edition (link) BibTeX
- David Heckerman, Carl Myers Kadie, Jennifer Listgarten:
Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction.
736-746
Electronic Edition (link) BibTeX
- Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks.
747-764
Electronic Edition (link) BibTeX
- Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics.
765-776
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Benny Chor, Tamir Tuller:
Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length.
817-838
Electronic Edition (link) BibTeX
- Shawna L. Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato:
Simulating Protein Motions with Rigidity Analysis.
839-855
Electronic Edition (link) BibTeX
- Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
A Study of Accessible Motifs and RNA Folding Complexity.
856-872
Electronic Edition (link) BibTeX
Volume 14,
Number 7,
July 2007
- Nevzat Onur Domaniç, Franco P. Preparata:
A Novel Approach to the Detection of Genomic Approximate Tandem Repeats in the Levenshtein Metric.
873-891
Electronic Edition (link) BibTeX
- Manikandan Narayanan, Richard M. Karp:
Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm.
892-907
Electronic Edition (link) BibTeX
- Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem:
A Structure-Based Flexible Search Method for Motifs in RNA.
908-926
Electronic Edition (link) BibTeX
- Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo D. Sontag, Alexander Zelikovsky, Kelly Westbrooks:
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence.
927-949
Electronic Edition (link) BibTeX
- Liqing Zhang, Layne T. Watson:
Note on the Computation of Critical Effective Population Sizes.
950-960
Electronic Edition (link) BibTeX
- Frank Emmert-Streib:
The Chronic Fatigue Syndrome: A Comparative Pathway Analysis.
961-972
Electronic Edition (link) BibTeX
- M. Andrecut, Stuart A. Kauffman:
A Physical Analogy of the Genetic Toggle Switch.
973-983
Electronic Edition (link) BibTeX
- Stefan Zeiser, Johannes Müller, Volkmar Liebscher:
Modeling the Hes1 Oscillator.
984-1000
Electronic Edition (link) BibTeX
- Manolis Christodoulakis, G. 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
Electronic Edition (link) BibTeX
- Yi Y. Shi, Gerald A. Miller, Oleg Denisenko, Hong Qian, Karol Bomsztyk:
Quantitative Model for Binary Measurements of Protein-Protein Interactions.
1011-1023
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Zakharia M. Frenkel, Edward N. Trifonov:
Evolutionary Networks in the Formatted Protein Sequence Space.
1044-1057
Electronic Edition (link) BibTeX
- Beckett Sterner, Rohit Singh, Bonnie Berger:
Predicting and Annotating Catalytic Residues: An Information Theoretic Approach.
1058-1073
Electronic Edition (link) BibTeX
- Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann, Kaizhong Zhang:
Locality and Gaps in RNA Comparison.
1074-1087
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Beth Shapiro, Yves Moreau, Andrew Rambaut, Anne-Mieke Vandamme, Philippe Lemey:
Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo.
1105-1114
Electronic Edition (link) BibTeX
- Aleksandar Stojmirovic, Yi-Kuo Yu:
Information Flow in Interaction Networks.
1115-1143
Electronic Edition (link) BibTeX
Volume 14,
Number 9,
November 2007
- Laxmi Parida:
Statistical Significance of Large Gene Clusters.
1145-1159
Electronic Edition (link) BibTeX
- Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang:
MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement.
1160-1175
Electronic Edition (link) BibTeX
- Francis L. Martin, Matthew J. German, Ernst Wit, Thomas Fearn, Narasimhan Ragavan, Hubert M. Pollock:
Identifying Variables Responsible for Clustering in Discriminant Analysis of Data from Infrared Microspectroscopy of a Biological Sample.
1176-1184
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Tetsuo Shibuya:
Efficient Substructure RMSD Query Algorithms.
1201-1207
Electronic Edition (link) BibTeX
- Yongxi Cheng, Ding-Zhu Du:
Efficient Constructions of Disjunct Matrices with Applications to DNA Library Screening.
1208-1216
Electronic Edition (link) BibTeX
- Achim Tresch, T. Beissbarth, Holger Sültmann, Ruprecht Kuner, Annemarie Poustka, Andreas Buness:
Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects.
1217-1228
Electronic Edition (link) BibTeX
- Ilkka Havukkala, Stijn Vanderlooy:
On the Reliable Identification of Plant Sequences Containing a Polyadenylation Site.
1229-1245
Electronic Edition (link) BibTeX
Volume 14,
Number 10,
December 2007
- Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song:
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters.
1247-1272
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Scott C. Schmidler, Joseph E. Lucas, Terrence G. Oas:
Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction.
1287-1310
Electronic Edition (link) BibTeX
- Dongxiao Zhu, Alfred O. Hero III:
Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation.
1311-1326
Electronic Edition (link) BibTeX
- Michael Hirsch, Stephen Swift, Xiaohui Liu:
Optimal Search Space for Clustering Gene Expression Data via Consensus.
1327-1341
Electronic Edition (link) BibTeX
- Binhai Zhu:
Protein Local Structure Alignment Under the Discrete Fréchet Distance.
1343-1351
Electronic Edition (link) BibTeX
- Magnus Åstrand, Petter Mostad, Mats Rudemo:
Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data.
1353-1367
Electronic Edition (link) BibTeX
Copyright © Sun May 17 00:07:09 2009
by Michael Ley (ley@uni-trier.de)