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
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- David Chiang, Aravind K. Joshi, Ken A. Dill:
A Grammatical Theory for the Conformational Changes of Simple Helix Bundles.
21-42
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- Jakob Vesterstrøm, William R. Taylor:
Flexible Secondary Structure Based Protein Structure Comparison Applied to the Detection of Circular Permutation.
43-63
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- Moshe Havilio:
Signal Deconvolution Based Expression-Detection and Background Adjustment for Microarray Data.
63-80
Electronic Edition (link) BibTeX
- Anna Gambin, Jerzy Tiuryn, Jerzy Tyszkiewicz:
Alignment with Context Dependent Scoring Function.
81-101
Electronic Edition (link) BibTeX
- Manoj Bhasin, Ellis L. Reinherz, Pedro A. Reche:
Recognition and Classification of Histones Using Support Vector Machine.
102-112
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- Tim Hohm, Philipp Limbourg, Daniel Hoffmann:
A Multiobjective Evolutionary Method for the Design of Peptidic Mimotopes.
113-125
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- Joanne I. Yeh, Lisong Mao:
Prediction of Membrane Proteins in Mycobacterium tuberculosis Using a Support Vector Machine Algorithm.
126-129
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Volume 13,
Number 2,
March 2006
Selected Papers From RECOMB 2005
- Satoru Miyano:
Preface: Special RECOMB 2005 Issue.
131-132
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- Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.
133-144
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- Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman:
Towards an Integrated Protein-Protein Interaction Network: A Relational Markov Network Approach.
145-164
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- Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir:
A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks.
165-181
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- Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
Pairwise Alignment of Protein Interaction Networks.
182-199
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- Brendan J. Frey, Quaid Morris, Timothy R. Hughes:
GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data.
200-214
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- Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini:
Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis.
215-228
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
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- Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang:
RNA-RNA Interaction Prediction and Antisense RNA Target Search.
267-282
Electronic Edition (link) BibTeX
- Vineet Bafna, Haixu Tang, Shaojie Zhang:
Consensus Folding of Unaligned RNA Sequences Revisited.
283-295
Electronic Edition (link) BibTeX
- Kim R. Rasmussen, Jens Stoye, Eugene W. Myers:
Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length.
296-308
Electronic Edition (link) BibTeX
- Sing-Hoi Sze, Yue Lu, Qingwu Yang:
A Polynomial Time Solvable Formulation of Multiple Sequence Alignment.
309-319
Electronic Edition (link) BibTeX
- Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot:
A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction.
320-335
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- Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor:
The Average Common Substring Approach to Phylogenomic Reconstruction.
336-350
Electronic Edition (link) BibTeX
- Teresa M. Przytycka, George Davis, Nan Song, Dannie Durand:
Graph Theoretical Insights into Evolution of Multidomain Proteins.
351-363
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- Marshall W. Bern, David Goldberg:
De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning.
364-378
Electronic Edition (link) BibTeX
- Samuel S. Gross, Michael R. Brent:
Using Multiple Alignments to Improve Gene Prediction.
379-393
Electronic Edition (link) BibTeX
- Yan Liu, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan:
Protein Fold Recognition Using Segmentation Conditional Random Fields (SCRFs).
394-406
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Nicholas Chia, Ralf Bundschuh:
A Practical Approach to Significance Assessment in Alignment with Gaps.
429-441
Electronic Edition (link) BibTeX
- Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman:
Alignment of Optical Maps.
442-462
Electronic Edition (link) BibTeX
- Chen-Hsiang Yeang, Tommi Jaakkola:
Modeling the Combinatorial Functions of Multiple Transcription Factors.
463-480
Electronic Edition (link) BibTeX
- Eran Halperin, Elad Hazan:
HAPLOFREQ-Estimating Haplotype Frequencies Efficiently.
481-500
Electronic Edition (link) BibTeX
- Vineet Bafna, Vikas Bansal:
Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots.
501-521
Electronic Edition (link) BibTeX
- Zhihong Ding, Vladimir Filkov, Dan Gusfield:
A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem.
522-553
Electronic Edition (link) BibTeX
- Matthew Mazowita, Lani Haque, David Sankoff:
Stability of Rearrangement Measures in the Comparison of Genome Sequences.
554-566
Electronic Edition (link) BibTeX
- Anne Bergeron, Julia Mixtacki, Jens Stoye:
On Sorting by Translocations.
567-578
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Gianluca Pollastri, Alessandro Vullo, Paolo Frasconi, Pierre Baldi:
Modular DAG-RNN Architectures for Assembling Coarse Protein Structures.
631-650
Electronic Edition (link) BibTeX
- Pierre Nicolas, Anne-Sophie Tocquet, Vincent Miele, Florence Muri:
A Reversible Jump Markov Chain Monte Carlo Algorithm for Bacterial Promoter Motifs Discovery.
651-667
Electronic Edition (link) BibTeX
- Arun Siddharth Konagurthu, Peter J. Stuckey:
Optimal Sum-of-Pairs Multiple Sequence Alignment Using Incremental Carrillo and Lipman Bounds.
668-685
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jesper Jansson, Ngo Trung Hieu, Wing-Kin Sung:
Local Gapped Subforest Alignment and Its Application in Finding RNA Structural Motifs.
702-718
Electronic Edition (link) BibTeX
- Sébastien Ferré, Ross D. King:
Finding Motifs in Protein Secondary Structure for Use in Function Prediction.
719-731
Electronic Edition (link) BibTeX
- Ion I. Mandoiu, Dragos Trinca:
Exact and Approximation Algorithms for DNA Tag Set Design.
732-744
Electronic Edition (link) BibTeX
- Chandan K. Reddy, Hsiao-Dong Chiang:
A Stability Boundary Based Method for Finding Saddle Points on Potential Energy Surfaces.
745-766
Electronic Edition (link) BibTeX
- Kristin L. Ayers, Chiara Sabatti, Kenneth Lange:
Reconstructing Ancestral Haplotypes with a Dictionary Model.
767-785
Electronic Edition (link) BibTeX
- Shuguang Huang, Yongming Qu:
The Loss in Power When the Test of Differential Expression Is Performed under a Wrong Scale.
786-797
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Raya Khanin, Ernst Wit:
How Scale-Free Are Biological Networks.
810-818
Electronic Edition (link) BibTeX
- Benny Chor, Amit Khetan, Sagi Snir:
Maximum Likelihood Molecular Clock Comb: Analytic Solutions.
819-837
Electronic Edition (link) BibTeX
- Andrew Golightly, Darren J. Wilkinson:
Bayesian Sequential Inference for Stochastic Kinetic Biochemical Network Models.
838-851
Electronic Edition (link) BibTeX
Volume 13,
Number 4,
May 2006
- Marcus Hjelm, Mattias Höglund, Jens Lagergren:
New Probabilistic Network Models and Algorithms for Oncogenesis.
853-865
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- 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
Electronic Edition (link) BibTeX
- Dirk Metzler:
Robust E-Values for Gapped Local Alignments.
882-896
Electronic Edition (link) BibTeX
- Ravi Vijaya Satya, Amar Mukherjee:
An Optimal Algorithm for Perfect Phylogeny Haplotyping.
897-928
Electronic Edition (link) BibTeX
- Sumedha Gunewardena, Peter Jeavons, Zhaolei Zhang:
Enhancing the Prediction of Transcription Factor Binding Sites by Incorporating Structural Properties and Nucleotide Covariations.
929-945
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Michael Cameron, Hugh E. Williams, Adam Cannane:
A Deterministic Finite Automaton for Faster Protein Hit Detection in BLAST.
965-978
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Ding-Zhu Du, Frank K. Hwang, Weili Wu, Taieb Znati:
New Construction for Transversal Design.
990-995
Electronic Edition (link) BibTeX
- E. Chudin, S. Kruglyak, S. C. Baker, S. Oeser, D. Barker, T. K. McDaniel:
A Model of Technical Variation of Microarray Signals.
996-1003
Electronic Edition (link) BibTeX
Volume 13,
Number 5,
June 2006
- David Sankoff, Lani Haque:
The Distribution of Genomic Distance between Random Genomes.
1005-1012
Electronic Edition (link) BibTeX
- Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson:
On the Complexity of Sparse Exon Assembly.
1013-1027
Electronic Edition (link) BibTeX
- Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala:
A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences.
1028-1040
Electronic Edition (link) BibTeX
- Tatiana Maximova, Chen Keasar:
A Novel Algorithm for Non-Bonded-List Updating in Molecular Simulations.
1041-1048
Electronic Edition (link) BibTeX
- John Goutsias, Seungchan Kim:
Stochastic Transcriptional Regulatory Systems with Time Delays: A Mean-Field Approximation.
1049-1076
Electronic Edition (link) BibTeX
- David Chiang, Aravind K. Joshi, David B. Searls:
Grammatical Representations of Macromolecular Structure.
1077-1100
Electronic Edition (link) BibTeX
- Elizabeth S. Allman, John A. Rhodes:
The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models.
1101-1113
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Volume 13,
Number 6,
July 2006
- Angela P. Presson, Eric Sobel, Kenneth Lange, Jeanette C. Papp:
Merging Microsatellite Data.
1131-1147
Electronic Edition (link) BibTeX
- Jing Wu, David Haussler:
Coding Exon Detection Using Comparative Sequences.
1148-1164
Electronic Edition (link) BibTeX
- Yair Horesh, Ramit Mehr, Ron Unger:
Designing an A* Algorithm for Calculating Edit Distance between Rooted-Unordered Trees.
1165-1176
Electronic Edition (link) BibTeX
- Michael C. Wendl:
A General Coverage Theory for Shotgun DNA Sequencing.
1177-1196
Electronic Edition (link) BibTeX
- Einar Andreas Rødland:
Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence.
1197-1213
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Meera Sitharam, Mavis Agbandje-Mckenna:
Modeling Virus Self-Assembly Pathways: Avoiding Dynamics Using Geometric Constraint Decomposition.
1232-1265
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Adrian D. Haimovich, Bruce Byrne, Ramakrishna Ramaswamy, William J. Welsh:
Wavelet Analysis of DNA Walks.
1289-1298
Electronic Edition (link) BibTeX
- Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
Detecting Conserved Interaction Patterns in Biological Networks.
1299-1322
Electronic Edition (link) BibTeX
- Isaac Elias:
Settling the Intractability of Multiple Alignment.
1323-1339
Electronic Edition (link) BibTeX
- Anne Bergeron, Jens Stoye:
On the Similarity of Sets of Permutations and Its Applications to Genome Comparison.
1340-1354
Electronic Edition (link) BibTeX
- Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma:
Optimizing Multiple Spaced Seeds for Homology Search.
1355-1368
Electronic Edition (link) BibTeX
- Jonathan M. Keith:
Segmenting Eukaryotic Genomes with the Generalized Gibbs Sampler.
1369-1383
Electronic Edition (link) BibTeX
- Florian A. Potra, Xing Liu:
Aligning Families of Two-Dimensional Gels by a Combined Multiresolution Forward-Inverse Transformation Approach.
1384-1395
Electronic Edition (link) BibTeX
Volume 13,
Number 8,
October 2006
- Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter:
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem.
1397-1418
Electronic Edition (link) BibTeX
- Maria Luisa Bonet, Katherine St. John, Ruchi Mahindru, Nina Amenta:
Approximating Subtree Distances Between Phylogenies.
1419-1434
Electronic Edition (link) BibTeX
- Winfried Just:
Reverse Engineering Discrete Dynamical Systems from Data Sets with Random Input Vectors.
1435-1456
Electronic Edition (link) BibTeX
- Joel E. Richardson:
fjoin: Simple and Efficient Computation of Feature Overlaps.
1457-1464
Electronic Edition (link) BibTeX
- Gilles Didier, Ivan Laprevotte, Maude Pupin, Alain Hénaut:
Local Decoding of Sequences and Alignment-Free Comparison.
1465-1476
Electronic Edition (link) BibTeX
- Giulia Menconi, Roberto Marangoni:
A Compression-Based Approach for Coding Sequences Identification. I. Application to Prokaryotic Genomes.
1477-1488
Electronic Edition (link) BibTeX
- Catherine Mooney, Alessandro Vullo, Gianluca Pollastri:
Protein Structural Motif Prediction in Multidimensional ø-Psi Space Leads to Improved Secondary Structure Prediction.
1489-1502
Electronic Edition (link) BibTeX
- Frank Emmert-Streib:
Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins.
1503-1512
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Peter C. Y. Chen:
A Discrete-Event Approach to Transcription Control with Dynamic Event-Controllability.
1532-1545
Electronic Edition (link) BibTeX
- Derek A. Ruths, Luay Nakhleh, M. Sriram Iyengar, Shrikanth A. G. Reddy, Prahlad T. Ram:
Hypothesis Generation in Signaling Networks.
1546-1557
Electronic Edition (link) BibTeX
- Gasper Jaklic, Tomaz Pisanski, Milan Randic:
Characterization of Complex Biological Systems by Matrix Invariants.
1558-1564
Electronic Edition (link) BibTeX
- Yu Chen, Gordon M. Crippen:
Fold Recognition via a Tree.
1565-1573
Electronic Edition (link) BibTeX
- William J. Bruno, John E. Pearson:
Transformations that Preserve Detailed Balance in Markov Models.
1574-1578
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Bart J. A. Mertens, M. E. De Noo, R. A. E. M. Tollenaar, André M. Deelder:
Mass Spectrometry Proteomic Diagnosis: Enacting the Double Cross-Validatory Paradigm.
1591-1605
Electronic Edition (link) BibTeX
- Zhenqiu Liu, Shili Lin, Ming Tan:
Genome-Wide Tagging SNPs with Entropy-Based Monte Carlo Method.
1606-1614
Electronic Edition (link) BibTeX
- Nak-Kyeong Kim, Jun Xie:
Protein Multiple Alignment Incorporating Primary and Secondary Structure Information.
1615-1629
Electronic Edition (link) BibTeX
- Andre Ribeiro, Rui Zhu, Stuart A. Kauffman:
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics.
1630-1639
Electronic Edition (link) BibTeX
- P. Clote:
Combinatorics of Saturated Secondary Structures of RNA.
1640-1657
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Lu-Yong Wang, Dorin Comaniciu, Daniel P. Fasulo:
Exploiting Interactions among Polymorphisms Contributing to Complex Disease Traits with Boosted Generative Modeling.
1673-1684
Electronic Edition (link) BibTeX
- Laxmi Parida:
Using PQ Structures for Genomic Rearrangement Phylogeny.
1685-1700
Electronic Edition (link) BibTeX
- Nicolas Lartillot:
Conjugate Gibbs Sampling for Bayesian Phylogenetic Models.
1701-1722
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Nak-Kyeong Kim, Jun Xie:
Protein Multiple Alignment Incorporating Primary and Secondary Structure Information.
1735-1748
Electronic Edition (link) BibTeX
- Sushmita Roy, Terran Lane, Chris Allen, Anthony D. Aragon, Margaret Werner-Washburne:
A Hidden-State Markov Model for Cell Population Deconvolution.
1749-1774
Electronic Edition (link) BibTeX
- Chun-Min Hung, Yueh-Min Huang, Ming-Shi Chang:
CSAM: Using Clustering-Hashing-Signal Anchoring Method to Explore Human Novel Genes.
1775-1789
Electronic Edition (link) BibTeX
Copyright © Sun May 17 00:07:09 2009
by Michael Ley (ley@uni-trier.de)
