Volume 15,
Number 1,
January 2008
- Franck Picard, Jean-Jacques Daudin, Michel Koskas, Sophie Schbath, Stéphane Robin:
Assessing the Exceptionality of Network Motifs.
1-20
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- M. Andrecut, Stuart A. Kauffman:
On the Sparse Reconstruction of Gene Networks.
21-30
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- W. A. Lorenz, Yann Ponty, Peter Clote:
Asymptotics of RNA Shapes.
31-63
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- Rosemarie Swanson, Ioannis Kagiampakis, Jerry W. Tsai:
An Information Measure of the Quality of Protein Secondary Structure Prediction.
65-79
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- Dumitru Brinza, Alexander Zelikovsky:
Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies.
81-90
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- Sagi Snir, Tandy Warnow, Satish Rao:
Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm.
91-103
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- C. Bidot, F. Gruy, C.-S. Haudin, F. El Hentati, B. Guy, C. Lambert:
Mathematical Modeling of T-Cell Activation Kinetic.
105-128
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Volume 15,
Number 2,
March 2008
- Xiaoqiu Huang:
Sequence Alignment with an Appropriate Substitution Matrix.
129-138
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- Hosna Jabbari, Anne Condon, Shelly Zhao:
Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding.
139-163
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- Ramu Anandakrishnan, Alexey Onufriev:
Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules.
165-184
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- Jutta Gebert, Susanne Motameny, Ulrich Faigle, Christian V. Forst, Rainer Schrader:
Identifying Genes of Gene Regulatory Networks Using Formal Concept Analysis.
185-194
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- Yongxi Cheng, Ding-Zhu Du:
New Constructions of One- and Two-Stage Pooling Designs.
195-205
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- Guzmán Santafé, José Antonio Lozano, Pedro Larrañaga:
Inference of Population Structure Using Genetic Markers and a Bayesian Model Averaging Approach for Clustering.
207-220
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- Thomas Stolte, Volker Hösel, Johannes Müller, Michael Speicher:
Modeling Clonal Expansion from M-FISH Experiments.
221-230
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Volume 15,
Number 3,
April 2008
- George Nicola, Colin A. Smith, Ruben Abagyan:
New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome.
231-240
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- Jing Li:
Prioritize and Select SNPs for Association Studies with Multi-Stage Designs.
241-257
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- Utz-Uwe Haus, Steffen Klamt, Tamon Stephen:
Computing Knock-Out Strategies in Metabolic Networks.
259-268
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- A. J. Adewale, I. Dinu, J. D. Potter, Q. Liu, Y. Yasui:
Pathway Analysis of Microarray Data via Regression.
269-277
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- Jing Wu, Jun Xie:
Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model.
279-290
Electronic Edition (link) BibTeX
- Mikael Bodén, Rohan D. Teasdale:
Determining Nucleolar Association from Sequence by Leveraging Protein-Protein Interactions.
291-304
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- Raya Khanin, Veronica Vinciotti:
Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs.
305-316
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- James O. Wrabl, Nick V. Grishin:
Statistics of Random Protein Superpositions: p-Values for Pairwise Structure Alignment.
317-355
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Volume 15,
Number 4,
May 2008
- Enno Ohlebusch, Stefan Kurtz:
Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences.
357-377
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- Valery Polyanovsky, Mikhail A. Roytberg, Vladimir G. Tumanyan:
Reconstruction of Genuine Pair-Wise Sequence Alignment.
379-391
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- Vladimir Filkov, Nameeta Shah:
A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast.
393-405
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- Jonathan M. Keith, Peter Adams, Stuart Stephen, John S. Mattick:
Delineating Slowly and Rapidly Evolving Fractions of the Drosophila Genome.
407-430
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- Patrick C. H. Ma, Keith C. C. Chan:
UPSEC: An Algorithm for Classifying Unaligned Protein Sequences into Functional Families.
431-443
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- Olga Tcheremenskaia, Alessandro Giuliani, Maurizio Tomasi:
PROFALIGN Algorithm Identifies the Regions Containing Folding Determinants by Scoring Pairs of Hydrophobic Profiles of Remotely Related Proteins.
445-455
Electronic Edition (link) BibTeX
- Jian Feng, Daniel Q. Naiman, Bret Cooper:
Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data.
457-468
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Volume 15,
Number 5,
June 2008
- Huy Hoang Do, Kwok Pui Choi, Franco P. Preparata, Wing-Kin Sung, Louxin Zhang:
Spectrum-Based De Novo Repeat Detection in Genomic Sequences.
469-488
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- Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang:
Structural Alignment of Pseudoknotted RNA.
489-504
Electronic Edition (link) BibTeX
- Zhiyu Zhao, Bin Fu, Francisco J. Alanis, Christopher M. Summa:
Feedback Algorithm and Web-Server for Protein Structure Alignment.
505-524
Electronic Edition (link) BibTeX
- Anthony J. Macula, Alexander Schliep, Morgan A. Bishop, Thomas E. Renz:
New, Improved, and Practical k-Stem Sequence Similarity Measures for Probe Design.
525-534
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- Zhixiang Chen, Bin Fu, Robert T. Schweller, Boting Yang, Zhiyu Zhao, Binhai Zhu:
Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments.
535-546
Electronic Edition (link) BibTeX
Volume 15,
Number 6,
July 2008
- Utz J. Pape, Sven Rahmann, Fengzhu Sun, Martin Vingron:
Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands.
547-564
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- Torsten Blum, Oliver Kohlbacher:
Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks.
565-576
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- Anne Kupczok, Arndt von Haeseler, Steffen Klaere:
An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.
577-591
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- Xu Ling, Xin He, Dong Xin, Jiawei Han:
Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison.
593-609
Electronic Edition (link) BibTeX
- David L. Gold, Bani K. Mallick, Kevin R. Coombes:
Real-Time Gene Expression: Statistical Challenges in Design and Inference.
611-623
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- Andrew K. C. Wong, Wai-Ho Au, Keith C. C. Chan:
Discovering High-Order Patterns of Gene Expression Levels.
625-637
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- Katharina T. Huber, Martin Lott, Vincent Moulton, Andreas Spillner:
The Complexity of Deriving Multi-Labeled Trees from Bipartitions.
639-651
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Volume 15,
Number 7,
September 2008
- Terry Speed:
Preface.
653-653
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- Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk:
Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments.
655-665
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- Yufeng Wu:
Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms.
667-684
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- Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Leinenbach, Andreas Hildebrandt, Christian G. Huber, Knut Reinert:
Computational Quantification of Peptides from LC-MS Data.
685-704
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- Marshall W. Bern, David Goldberg:
Improved Ranking Functions for Protein and Modification-Site Identifications.
705-719
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- Ydo Wexler, Dan Geiger:
Variational Upper and Lower Bounds for Probabilistic Graphical Models.
721-735
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- Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson:
Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules.
737-754
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- Hetunandan Kamisetty, Eric P. Xing, Christopher James Langmead:
Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation.
755-766
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- Yue Lu, Sing-Hoi Sze:
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences.
767-777
Electronic Edition (link) BibTeX
- Hiroyuki Kuwahara, Chris J. Myers:
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions.
779-792
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- Michal Ozery-Flato, Ron Shamir:
Sorting Genomes with Centromeres by Translocations.
793-812
Electronic Edition (link) BibTeX
- Anshul Nigham, David Hsu:
Protein Conformational Flexibility Analysis with Noisy Data.
813-828
Electronic Edition (link) BibTeX
- T. M. Murali, Corban G. Rivera:
Network Legos: Building Blocks of Cellular Wiring Diagrams.
829-844
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- Antonio Piccolboni:
Multivariate Segmentation in the Analysis of Transcription Tiling Array Data.
845-856
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- Wenyi Wang, Benilton Carvalho, Nathaniel D. Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry:
Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models.
857-866
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- Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy:
Support Vector Training of Protein Alignment Models.
867-880
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- Wah-Heng Lee, Wing-Kin Sung:
RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints.
881-898
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- Chen Yanover, Ora Schueler-Furman, Yair Weiss:
Minimizing and Learning Energy Functions for Side-Chain Prediction.
899-911
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- Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan:
QNet: A Tool for Querying Protein Interaction Networks.
913-925
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- Noah Zaitlen, Manuel Reyes-Gomez, David Heckerman, Nebojsa Jojic:
Shift-Invariant Adaptive Double Threading: Learning MHC II-Peptide Binding.
927-942
Electronic Edition (link) BibTeX
Volume 15,
Number 8,
October 2008
- Glenn Tesler, Dannie Durand:
Preface.
943-946
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- Chunfang Zheng, Qian Zhu, David Sankoff:
Descendants of Whole Genome Duplication within Gene Order Phylogeny.
947-964
Electronic Edition (link) BibTeX
- Ai Xia, Maria V. Sharakhova, Igor V. Sharakhov:
Reconstructing Ancestral Autosomal Arrangements in the Anopheles gambiae Complex.
965-980
Electronic Edition (link) BibTeX
- Benjamin Vernot, Maureen Stolzer, Aiton Goldman, Dannie Durand:
Reconciliation with Non-Binary Species Trees.
981-1006
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- Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler:
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications.
1007-1027
Electronic Edition (link) BibTeX
- Simon Gog, Martin Bader:
Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation.
1029-1041
Electronic Edition (link) BibTeX
- Cedric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk:
Gene Family Evolution by Duplication, Speciation, and Loss.
1043-1062
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- Denis Bertrand, Mathieu Lajoie, Nadia El-Mabrouk:
Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes.
1063-1077
Electronic Edition (link) BibTeX
- William Arndt, Jijun Tang:
Improving Reversal Median Computation Using Commuting Reversals and Cycle Information.
1079-1092
Electronic Edition (link) BibTeX
- Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thévenin, Stéphane Vialette:
Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between Two Genomes with Duplicate Genes.
1093-1115
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- Max A. Alekseyev:
Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes.
1117-1131
Electronic Edition (link) BibTeX
- Correction.
1132
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Volume 15,
Number 9,
November 2008
- Laxmi Parida, Marta Melé, Francesc Calafell, Jaume Bertranpetit:
Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns.
1133-1153
Electronic Edition (link) BibTeX
- Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc:
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity.
1155-1171
Electronic Edition (link) BibTeX
- M. Andrecut, S. Huang, Stuart A. Kauffman:
Heuristic Approach to Sparse Approximation of Gene Regulatory Networks.
1173-1186
Electronic Edition (link) BibTeX
- Lee Aaron Newberg:
Significance of Gapped Sequence Alignments.
1187-1194
Electronic Edition (link) BibTeX
- Hillary S. W. Han, Christian M. Reidys:
Pseudoknot RNA Structures with Arc-Length >= 4.
1195-1208
Electronic Edition (link) BibTeX
- Kanti V. Mardia, Vysaul B. Nyirongo:
Simulating Virtual Protein Calpha Traces with Applications.
1209-1220
Electronic Edition (link) BibTeX
- María Elena Díaz, Guillermo Ayala, Teresa León, Roberto Zoncu, Derek Toomre:
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets.
1221-1236
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Volume 15,
Number 10,
December 2008
- Xianyang Jiang, Dominique Lavenier, Stephen S.-T. Yau:
Coding Region Prediction Based on a Universal DNA Sequence Representation Method.
1237-1256
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- Gang Ma, Christian M. Reidys:
Canonical RNA Pseudoknot Structures.
1257-1273
Electronic Edition (link) BibTeX
- Jing Xiao, Lusheng Wang, Xiaowen Liu, Tao Jiang:
An Efficient Voting Algorithm for Finding Additive Biclusters with Random Background.
1275-1293
Electronic Edition (link) BibTeX
- Jialiang Yang, Louxin Zhang:
Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds.
1295-1313
Electronic Edition (link) BibTeX
- Antonio Lijoi, Ramsés H. Mena, Igor Prünster:
A Bayesian Nonparametric Approach for Comparing Clustering Structures in EST Libraries.
1315-1327
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- Miranda van Uitert, Wouter Meuleman, Lodewyk F. A. Wessels:
Biclustering Sparse Binary Genomic Data.
1329-1345
Electronic Edition (link) BibTeX
- Man-Hung Eric Tang, Anders Krogh, Ole Winther:
BayesMD: Flexible Biological Modeling for Motif Discovery.
1347-1363
Electronic Edition (link) BibTeX
- Riccardo Porreca, Samuel Drulhe, Hidde de Jong, Giancarlo Ferrari-Trecate:
Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks.
1365-1380
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Copyright © Sun May 17 00:07:09 2009
by Michael Ley (ley@uni-trier.de)