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ORCIDJournal of Computational Biology, Volume 17
Volume 17, Number 1, January 2010
- Alexander Schönhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp:
Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length. 1-20 - Lan Liu, Yonghui Wu, Stefano Lonardi
, Tao Jiang:
Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion. 21-37 - Regina Samaga, Axel von Kamp, Steffen Klamt:
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. 39-53 - Vladimir Vacic, Lilia M. Iakoucheva, Stefano Lonardi, Predrag Radivojac:
Graphlet Kernels for Prediction of Functional Residues in Protein Structures. 55-72 - Nirmalya Bandyopadhyay, Tamer Kahveci:
GBA Manager: An Online Tool for Querying Low-Complexity Regions in Proteins. 73-77 - Scott Mann, Jinyan Li, Yi-Ping Phoebe Chen:
Insights into Bacterial Genome Composition through Variable Target GC Content Profiling. 79-96 - Juhyun Jung, Taewoo Ryu, Yongdeuk Hwang, Eunjung Lee, Doheon Lee:
Prediction of Extracellular Matrix Proteins Based on Distinctive Sequence and Domain Characteristics. 97-105
Volume 17, Number 2, February 2010
- Dimitrije Jevremovic, Cong T. Trinh, Friedrich Srienc, Daniel Boley:
On Algebraic Properties of Extreme Pathways in Metabolic Networks. 107-119 - Hyungwon Choi, Zhaohui S. Qin, Debashis Ghosh:
A Double-Layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expression Data. 121-137 - Nha Nguyen, Heng Huang, Soontorn Oraintara, An P. N. Vo:
Stationary Wavelet Packet Transform and Dependent Laplacian Bivariate Shrinkage Estimator for Array-CGH Data Smoothing. 139-152 - Mert Karakas, Nils Woetzel, Jens Meiler:
BCL: : Contact-Low Confidence Fold Recognition Hits Boost Protein Contact Prediction and De Novo Structure Determination. 153-168 - Peng Qiu, Andrew J. Gentles, Sylvia K. Plevritis:
Reducing the Computational Complexity of Information Theoretic Approaches for Reconstructing Gene Regulatory Networks. 169-176 - Shuo Jiao, Shunpu Zhang:
Estimating the Proportion of Equivalently Expressed Genes in Microarray Data Based on Transformed Test Statistics. 177-187 - Marvin N. Steijaert, J. H. K. Van Den Brink, Anthony M. L. Liekens, Peter A. J. Hilbers, Huub M. M. ten Eikelder:
Computing the Stochastic Dynamics of Phosphorylation Networks. 189-199
Volume 17, Number 3, March 2010
- RECOMB Main Conference 2009. 201
- Tetsuo Shibuya:
Searching Protein 3-D Structures in Linear Time. 203-219 - Zengyou He, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, Weichuan Yu:
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. 221-235 - Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
Topology-Free Querying of Protein Interaction Networks. 237-252 - Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph:
Cross Species Expression Analysis of Innate Immune Response. 253-268 - Bonnie Kirkpatrick, Eran Halperin, Richard M. Karp:
Haplotype Inference in Complex Pedigrees. 269-280 - Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki:
Storage and Retrieval of Highly Repetitive Sequence Collections. 281-308 - Arvind Ramanathan, Pratul K. Agarwal, Maria G. Kurnikova, Christopher James Langmead:
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. 309-324 - Alexandre Donzé, Gilles Clermont, Christopher James Langmead:
Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology. 325-336 - Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis:
How Many Bootstrap Replicates Are Necessary? 337-354 - Oliver Stegle, Katherine J. Denby, Emma J. Cooke, David L. Wild, Zoubin Ghahramani, Karsten M. Borgwardt:
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. 355-367 - Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna:
Optimizing PCR Assays for DNA-Based Cancer Diagnostics. 369-381 - Dan Gusfield:
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. 383-399 - Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang:
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study. 401-415 - Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel:
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. 417-428 - Mathias Möhl, Sebastian Will, Rolf Backofen:
Lifting Prediction to Alignment of RNA Pseudoknots. 429-442 - Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette:
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. 443-457 - Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg:
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. 459-475 - Benjamin J. Hescott, Mark D. M. Leiserson, Lenore J. Cowen, Donna K. Slonim:
Evaluating Between-Pathway Models with Expression Data. 477-487 - Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret:
Sorting Signed Permutations by Inversions in O(nlogn) Time. 489-501 - Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford:
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. 503-516 - Suzanne S. Sindi, Benjamin J. Raphael:
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. 517-531 - Eun Yong Kang, Chun Ye, Ilya Shpitser, Eleazar Eskin:
Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples. 533-546 - Hyun Min Kang, Noah Zaitlen, Eleazar Eskin:
EMINIM: An Adaptive and Memory-Efficient Algorithm for Genotype Imputation. 547-560 - John D. Kececioglu, Eagu Kim, Travis J. Wheeler:
Aligning Protein Sequences with Predicted Secondary Structure. 561-580
Volume 17, Number 4, April 2010
- Zhiyuan Zhai, Shih-Yen Ku, Yihui Luan, Gesine Reinert, Michael S. Waterman, Fengzhu Sun:
The Power of Detecting Enriched Patterns: An HMM Approach. 581-592 - Tetsuo Shibuya:
Searching Protein Three-Dimensional Structures in Faster Than Linear Time. 593-602 - Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig:
A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. 603-615 - Mikael Bodén, Graham Dellaire, Kevin Burrage, Timothy L. Bailey:
A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies. 617-630 - Gang Wu, Ying Zhang, Yimin Wei:
Krylov Subspace Algorithms for Computing GeneRank for the Analysis of Microarray Data Mining. 631-646 - Namsu Ahn, Sungsoo Park:
Finding an Upper Bound for the Number of Contacts in Hydrophobic-Hydrophilic Protein Structure Prediction Model. 647-656
Volume 17, Number 5, May 2010
- Qingwu Yang, Gangman Yi, Fenghui Zhang, Michael R. Thon, Sing-Hoi Sze:
Identifying Gene Clusters within Localized Regions in Multiple Genomes. 657-668 - Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp:
Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. 669-684 - Yen-Lin Huang, Chin Lung Lu:
Sorting by Reversals, Generalized Transpositions, and Translocations Using Permutation Groups. 685-705 - Antonio Cardone, R. Wayne Albers, Ram D. Sriram, Harish C. Pant:
Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor CIP. 707-721 - Claude Berge, Nicolas Froloff, Ravi Kiran Reddy Kalathur, Myriam Maumy, Olivier Poch, Wolfgang Raffelsberger, Nicolas Wicker:
Multidimensional Fitting for Multivariate Data Analysis. 723-732 - Patrick C. H. Ma, Keith C. C. Chan:
Discovering Interesting Motif-Sets for Multi-Class Protein Sequence Classification. 733-743 - Myung-Hoon Chung, Chul Koo Kim:
Non-Random Mating Involving Inheritance of Social Status. 745-754 - Ivan Molineris, Gabriele Sales, Federico Bianchi, Ferdinando Di Cunto, Michele Caselle:
A New Approach for the Identification of Processed Pseudogenes. 755-765
Volume 17, Number 6, June 2010
- Fumei Lam, Ryan Tarpine, Sorin Istrail:
The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. 767-781 - Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu:
A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling. 783-798 - Frederick A. Matsen IV:
constNJ: An Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints. 799-818 - Mats Aspnäs, Kimmo Mattila, Kristoffer Osowski, Jan Westerholm:
Code Optimization of the Subroutine to Remove Near Identical Matches in the Sequence Database Homology Search Tool PSI-BLAST. 819-823 - Howsun Jow, Madhuchhanda Bhattacharjee, Richard J. Boys, Darren J. Wilkinson:
The Integration of Genetic Maps Using Bayesian Inference. 825-840 - Ján Manuch, Ladislav Stacho, Christine Stoll:
Two Lower Bounds for Self-Assemblies at Temperature 1. 841-852 - Elena S. Dimitrova, Paola Vera-Licona, John McGee, Reinhard C. Laubenbacher:
Discretization of Time Series Data. 853-868
Volume 17, Number 7, July 2010
- Adrián López García de Lomana, Qasim K. Beg, Gianni De Fabritiis, Jordi Villà-Freixa:
Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks. 869-878 - Shuguang Huang:
Statistical Issues in Subpopulation Analysis of High Content Imaging Data. 879-894 - Scott C. James, Varun Boriah:
Modeling Algae Growth in an Open-Channel Raceway. 895-906 - Lusheng Wang, Binhai Zhu:
On the Tractability of Maximal Strip Recovery. 907-914 - Minghui Jiang, Pedro J. Tejada, Ramoni O. Lasisi, Shanhong Cheng, D. Scott Fechser:
K-Partite RNA Secondary Structures. 915-925 - Huilan Chang, Hong-Bin Chen, Hung-Lin Fu:
Identification and Classification Problems on Pooling Designs for Inhibitor Models. 927-941 - Marcos R. Betancourt:
Comparison between Molecular Dynamic Based and Knowledge Based Potentials for Protein Side Chains. 943-952
Volume 17, Number 8, August 2010
- Ewa Szczurek, Przemyslaw Biecek, Jerzy Tiuryn, Martin Vingron:
Introducing Knowledge into Differential Expression Analysis. 953-967 - Ana Graça, Inês Lynce, João Marques-Silva, Arlindo L. Oliveira:
Haplotype Inference by Pure Parsimony: A Survey. 969-992 - Peter Minary, Michael Levitt:
Conformational Optimization with Natural Degrees of Freedom: A Novel Stochastic Chain Closure Algorithm. 993-1010 - Alberto Apostolico, Fabio Cunial:
The Subsequence Composition of Polypeptides. 1011-1049 - Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir:
A Faster Algorithm for Simultaneous Alignment and Folding of RNA. 1051-1065 - Bong-Rae Kim, Timothy McMurry, Wei Zhao, Rongling Wu, Arthur Berg:
Wavelet-Based Functional Clustering for Patterns of High-Dimensional Dynamic Gene Expression. 1067-1080 - Xiaodong Pang, Linxiang Zhou, Mingjun Zhang, Fang Xie, Long Yu, Lili Zhang, Lina Xu, Xinyi Zhang:
A Mathematical Model for Peptide Inhibitor Design. 1081-1093
Volume 17, Number 9, September 2010
- Preface. J. Comput. Biol. 17(9): 1095-1096 (2010)
- Cédric Chauve, Haris Gavranovic, Aïda Ouangraoua, Eric Tannier:
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II. 1097-1112 - Zhenyu Yang, David Sankoff:
Natural Parameter Values for Generalized Gene Adjacency. 1113-1128 - Aïda Ouangraoua, Anne Bergeron:
Combinatorial Structure of Genome Rearrangements Scenarios. 1129-1144 - Marília D. V. Braga, Jens Stoye:
The Solution Space of Sorting by DCJ. 1145-1165 - Cédric Chauve, Utz-Uwe Haus, Tamon Stephen, Vivija P. You:
Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction. 1167-1181 - Guillaume Blin, David C. Faye, Jens Stoye:
Finding Nested Common Intervals Efficiently. 1183-1194 - Andrew Wei Xu:
The Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions. 1195-1211 - Anne Bergeron, Paul Medvedev, Jens Stoye:
Rearrangement Models and Single-Cut Operations. 1213-1225 - Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller:
CAGE: Combinatorial Analysis of Gene-Cluster Evolution. 1227-1242 - João Delgado, Inês Lynce, Vasco Manquinho:
Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes. 1243-1265 - Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel:
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. 1267-1279 - Chih-Hao Hsu, Yu Zhang, Ross C. Hardison, Eric D. Green, Webb Miller:
An Effective Method for Detecting Gene Conversion Events in Whole Genomes. 1281-1297 - Zaky Adam, David Sankoff:
A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances. 1299-1314 - Mahdi Belcaid, Anne Bergeron, Guylaine Poisson:
Mosaic Graphs and Comparative Genomics in Phage Communities. 1315-1326 - Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin:
Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples. 1327-1344
Volume 17, Number 10, October 2010
- Laxmi Parida:
Ancestral Recombinations Graph: A Reconstructability Perspective Using Random-Graphs Framework. 1345-1370 - Ben Grainger, Michael I. Sadowski, William R. Taylor:
Re-Evaluating the "Rules" of Protein Topology. 1371-1384 - Zhijin Wu, Martin J. Aryee:
Subset Quantile Normalization Using Negative Control Features. 1385-1395 - Eldar Giladi, John Healy, Gene Myers, Chris Hart, Philipp Kapranov, Doron Lipson, Steve Roels, Edward C. Thayer, Stan Letovsky:
Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families. 1397-1411 - Zengti Li, Suogang Gao, Hongjie Du, Feng Zou, Weili Wu:
Efficient Error-Correcting Pooling Designs Constructed from Pseudo-Symplectic Spaces Over a Finite Field. 1413-1423 - Haiying Zhang, Bing Zhou:
On the Maximal Interval Subgraph of a Tree. 1425-1433 - Arvind Gupta, Mohammad M. Karimi, Ján Manuch, Ladislav Stacho, Xiaohong Zhao:
Haplotype Inferring via Galled-Tree Networks Is NP-Complete. 1435-1449 - Duong Dai Doan, Patricia A. Evans, Joseph D. Horton:
A Near-Linear Time Algorithm for Haplotype Determination on General Pedigrees. 1451-1465
Volume 17, Number 11, November 2010
- Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman:
Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. 1467-1490 - Nikita A. Sakhanenko, David J. Galas:
Markov Logic Networks in the Analysis of Genetic Data. 1491-1508 - Ilan Gronau, Shlomo Moran, Irad Yavneh:
Adaptive Distance Measures for Resolving K2P Quartets: Metric Separation versus Stochastic Noise. 1509-1518 - Sébastien Boisvert, François Laviolette, Jacques Corbeil:
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies. 1519-1533 - Sagi Snir, Edward N. Trifonov:
A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. 1535-1548 - Xiaohong Zhao, Lance E. Palmer, Randall A. Bolanos, Cristian Mircean, Daniel P. Fasulo, Gayle M. Wittenberg:
EDAR: An Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data. 1549-1560 - Xin Chen, Jianyi Yang:
Constructing Consensus Genetic Maps in Comparative Analysis. 1561-1573 - Christian M. Reidys, Rita R. Wang:
Shapes of RNA Pseudoknot Structures. 1575-1590
Volume 17, Number 12, December 2010
- Sarah Behrens, Martin Vingron:
Studying the Evolution of Promoter Sequences: A Waiting Time Problem. 1591-1606 - Xugang Ye, Yi-Kuo Yu, Stephen F. Altschul:
Compositional Adjustment of Dirichlet Mixture Priors. 1607-1620 - Qing Zhou:
On Weight Matrix and Free Energy Models for Sequence Motif Detection. 1621-1638 - Marc Herant, Micah Dembo:
Cytopede: A Three-Dimensional Tool for Modeling Cell Motility on a Flat Surface. 1639-1677 - Xin Liu, Ya-Pu Zhao:
Substitution Matrices of Residue Triplets Derived from Protein Blocks. 1679-1687 - Xinan Zhang, Yingdong Zhao, Avidan U. Neumann:
Partial Immunity and Vaccination for Influenza. 1689-1696 - Hock Peng Chan, Nancy Ruonan Zhang, Louis H. Y. Chen:
Importance Sampling of Word Patterns in DNA and Protein Sequences. 1697-1709 - Oscar Luaces, José Ramón Quevedo, Miguel Pérez-Enciso, Jorge Díez, Juan José del Coz, Antonio Bahamonde:
Explaining the Genetic Basis of Complex Quantitative Traits through Prediction Models. 1711-1723
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