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ORCIDJournal 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 B. 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 S. 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
- Beatrijs Moerkerke, Els 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 S. Ribeiro, Rui Zhu, Stuart A. Kauffman:
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics. 1630-1639 - Peter 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, Christopher P. 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
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