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Journal of Computational Biology, Volume 18
Volume 18, Number 1, January 2011
- Cuong V. Than, Noah A. Rosenberg
:
Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences. 1-15 - Ryan Day, Xiaotao Qu, Rosemarie Swanson, Zach Bohannan, Robert Bliss, Jerry W. Tsai:
Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints. 17-26 - Rumen Andonov, Noël Malod-Dognin
Maximum Contact Map Overlap Revisited. 27-41 - Markus Heinonen, Sampsa Lappalainen, Taneli Mielikäinen, Juho Rousu:
Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism. 43-58 - Yaniv Ovadia, Daniel Fielder, Chris Conow, Ran Libeskind-Hadas:
The Cophylogeny Reconstruction Problem Is NP-Complete. 59-65 - Jia F. Weng, Doreen A. Thomas
Maximum Parsimony, Substitution Model, and Probability Phylogenetic Trees. 67-80 - Elisabetta Marras, Antonella Travaglione, Enrico Capobianco:
Manifold Learning in Protein Interactomes. 81-96 - Thomas K. F. Wong, Tak Wah Lam
Structural Alignment of RNA with Complex Pseudoknot Structure. 97-108 - Paul A. Jenkins
Inference from Samples of DNA Sequences Using a Two-Locus Model. 109-127 - Correction. 129
Volume 18, Number 2, February 2011
- Manolis Kellis, Andrea Califano
Preface. 131 - Liat Perlman, Assaf Gottlieb, Nir Atias, Eytan Ruppin, Roded Sharan:
Combining Drug and Gene Similarity Measures for Drug-Target Elucidation. 133-145 - Pradeep Bandaru, Mukesh Bansal, Ilya Nemenman
Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data. 147-154 - Patrick Ng, Uri Keich
Alignment Constrained Sampling. 155-168 - Chang F. Quo, Richard A. Moffitt, Alfred H. Merrill Jr., May D. Wang
Adaptive Control Model Reveals Systematic Feedback and Key Molecules in Metabolic Pathway Regulation. 169-182 - Alberto Corradin
Sensitivity Analysis of Retrovirus HTLV-1 Transactivation. 183-193 - Athanasios Polynikis, Giulia Cuccato, Stefania Criscuolo, Stephen John Hogan
Design and Construction of a Versatile Synthetic Network for Bistable Gene Expression in Mammalian Systems. 195-203
Volume 18, Number 3, March 2011
- Bonnie Berger:
Preface: 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010). 205
- Nir Atias, Roded Sharan:
An Algorithmic Framework for Predicting Side Effects of Drugs. 207-218 - Ferhat Ay
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. 219-235 - Sivan Bercovici, Dan Geiger:
Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA. 237-249 - José Caldas
Hierarchical Generative Biclustering for MicroRNA Expression Analysis. 251-261 - Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk
Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. 263-281 - Manfred Claassen
Proteome Coverage Prediction for Integrated Proteomics Datasets. 283-293 - Timothy Danford, Robin D. Dowell
Discovering Regulatory Overlapping RNA Transcripts. 295-303 - Jianxing Feng, Wei Li, Tao Jiang
Inference of Isoforms from Short Sequence Reads. 305-321 - Bjarni V. Halldórsson
The Clark Phaseable Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS. 323-333 - Michael Hirsch, Bernhard Schölkopf, Michael Habeck
A Blind Deconvolution Approach for Improving the Resolution of Cryo-EM Density Maps. 335-346 - Richard Jang, Xin Gao
Towards Fully Automated Structure-Based NMR Resonance Assignment of 15N-Labeled Proteins From Automatically Picked Peaks. 347-363 - Wei-Chun Kao, Yun S. Song:
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. 365-377 - David R. Kelley, Carl Kingsford:
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. 379-390 - Adam Kowalczyk, Justin Bedo
The Poisson Margin Test for Normalization-Free Significance Analysis of NGS Data. 391-400 - Christos Kozanitis, Christopher T. Saunders
Compressing Genomic Sequence Fragments Using SlimGene. 401-413 - Fumei Lam, Charles H. Langley, Yun S. Song:
On the Genealogy of Asexual Diploids. 415-428 - Jonathan Laserson, Vladimir Jojic, Daphne Koller:
Genovo: De Novo Assembly for Metagenomes. 429-443 - Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny. 445-457 - Bogdan Pasaniuc
Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. 459-468 - Benedict Paten, Mark Diekhans
Cactus Graphs for Genome Comparisons. 469-481 - Manu N. Setty, Alexander Gusev, Itsik Pe'er:
HLA Type Inference via Haplotypes Identical by Descent. 483-493 - Itai Sharon
Pathway-Based Functional Analysis of Metagenomes. 495-505 - Fabio Vandin, Eli Upfal
Algorithms for Detecting Significantly Mutated Pathways in Cancer. 507-522 - Yu-Wei Wu
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples. 523-534
Volume 18, Number 4, April 2011
- Roberto Grossi, Andrea Pietracaprina, Nadia Pisanti
MADMX: A Strategy for Maximal Dense Motif Extraction. 535-545 - Karin Noy, Fadi Towfic, Gayle M. Wittenberg, Daniel P. Fasulo:
Shape-Based Feature Matching Improves Protein Identification via LC-MS and Tandem MS. 547-557 - Alex Graudenzi
Robustness Analysis of a Boolean Model of Gene Regulatory Network with Memory. 559-577 - Simona Grusea, E. Pardoux, Olivier Chabrol, Pierre Pontarotti
Compound Poisson Approximation and Testing for Gene Clusters with Multigene Families. 579-594 - Valeria Fionda, Luigi Palopoli
Biological Network Querying Techniques: Analysis and Comparison. 595-625 - Shu-Bo Zhang, Song-Yu Zhou, Jianguo He, Jian-Huang Lai:
Phylogeny Inference Based on Spectral Graph Clustering. 627-637
- Sajid Marhon
Gene Prediction Based on DNA Spectral Analysis: A Literature Review. 639-676
Volume 18, Number 5, May 2011
- Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman:
Sequence Alignment as Hypothesis Testing. 677-691 - Shuai Cheng Li
Finding Nearly Optimal GDT Scores. 693-704 - Nahla A. Belal, Lenwood S. Heath:
A Theoretical Model for Whole Genome Alignment. 705-728 - Wessel N. van Wieringen
Exploratory Factor Analysis of Pathway Copy Number Data with an Application Towards the Integration with Gene Expression Data. 729-741 - Lavanya Kannan, Hua Li, Arcady R. Mushegian
A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance. 743-757 - Xiaoyan Zhao, Sing-Hoi Sze:
Motif Finding in DNA Sequences Based on Skipping Nonconserved Positions in Background Markov Chains. 759-770 - Gregory Kucherov
Regular Language Constrained Sequence Alignment Revisited. 771-781
Volume 18, Number 6, June 2011
- Alan Veliz-Cuba
Boolean Models Can Explain Bistability in the lac Operon. 783-794 - Tade Souaiaia, Zach Frazier, Ting Chen:
ComB: SNP Calling and Mapping Analysis for Color and Nucleotide Space Platforms. 795-807 - Norbert Dojer, Przemyslaw Biecek
Bi-Billboard: Symmetrization and Careful Choice of Informant Species Results in Higher Accuracy of Regulatory Element Prediction. 809-819 - Jacek Blazewicz
RNA Partial Degradation Problem: Motivation, Complexity, Algorithm. 821-834 - Frans E. S. Tan, Valéria Lima Passos
On the A-Optimality Criterion for Finding Two-Color Microarray Optimal Designs. 835-841 - Marcin Pacholczyk
Exploring the Landscape of Protein-Ligand Interaction Energy Using Probabilistic Approach. 843-850 - Hong-Bin Chen, Annalisa De Bonis:
An Almost Optimal Algorithm for Generalized Threshold Group Testing with Inhibitors. 851-864
Volume 18, Number 7, July 2011
- Pavel A. Pevzner, Ron Shamir
Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). 865
- Jeff Elhai:
Humans, Computers, and the Route to Biological Insights: Regaining Our Capacity for Surprise. 867-878
- Jian Ma
Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges. 879-893 - Seung-Jin Sul, Tiffani L. Williams:
Big Cat Phylogenies, Consensus Trees, and Computational Thinking. 895-906 - Bahar Taneri:
Is there Room for Ethics within Bioinformatics Education? 907-916 - Eugene V. Koonin, Pere Puigbò
Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life". 917-924
Volume 18, Number 8, August 2011
- Yi-Kuo Yu, Stephen F. Altschul:
The Complexity of the Dirichlet Model for Multiple Alignment Data. 925-939 - Xugang Ye, Yi-Kuo Yu, Stephen F. Altschul:
On the Inference of Dirichlet Mixture Priors for Protein Sequence Comparison. 941-954 - Bjarni V. Halldórsson
An Algorithm for Detecting High Frequency Copy Number Polymorphisms Using SNP Arrays. 955-966 - Sagi Snir, Lior Pachter
Tracing the Most Parsimonious Indel History. 967-986 - Valerio Freschi:
Improved Biological Network Reconstruction Using Graph Laplacian Regularization. 987-996 - Bernhard Knapp, Sophie Frantal, Michael Cibena, Wolfgang Schreiner, P. Bauer:
Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible? 997-1005 - Jesun Sahariar Firoz, Masud Hasan, Ashik Zinnat Khan, M. Sohel Rahman
The 1.375 Approximation Algorithm for Sorting by Transpositions Can Run in O(n log n) Time. 1007-1011 - Hsien-Chi Kuo, Po-Yu Lin, Ting-Chiun Chung, Chin-Mei Chao, Liang-Chuan Lai
DBCAT: Database of CpG Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells. 1013-1017
Volume 18, Number 9, September 2011
- Preface: Satellite Workshop on Comparative Genomics, Research in Computational Molecular Biology (RECOMB-CG 2010). 1019-1021
- Roland Wittler, Ján Manuch, Murray Patterson, Jens Stoye
Consistency of Sequence-Based Gene Clusters. 1023-1039 - Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve
A 2-Approximation for the Minimum Duplication Speciation Problem. 1041-1053 - Yu Lin
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes. 1055-1064 - Robert Warren, David Sankoff:
Genome Aliquoting Revisited. 1065-1075 - Minghui Jiang:
The Zero Exemplar Distance Problem. 1077-1086 - Mukul S. Bansal
Detecting Highways of Horizontal Gene Transfer. 1087-1114 - Emmanuel Mongin, Ken Dewar, Mathieu Blanchette:
Mapping Association between Long-Range cis-Regulatory Regions and Their Target Genes Using Synteny. 1115-1130 - Yu Lin
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. 1131-1139 - Raluca Uricaru, Alban Mancheron
Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps. 1141-1154 - Hugo Devillers, Hélène Chiapello, Sophie Schbath
Robustness Assessment of Whole Bacterial Genome Segmentations. 1155-1165 - Marília D. V. Braga, Eyla Willing, Jens Stoye
Double Cut and Join with Insertions and Deletions. 1167-1184 - Olivier Tremblay Savard, Yves Gagnon, Denis Bertrand, Nadia El-Mabrouk:
Genome Halving and Double Distance with Losses. 1185-1199 - Ghada Badr, Krister M. Swenson, David Sankoff:
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. 1201-1210 - Atheer A. Matroud, Christopher P. Tuffley
An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats in Biological Sequences. 1211-1218 - Aïda Ouangraoua, Anne Bergeron, Krister M. Swenson:
Theory and Practice of Ultra-Perfection. 1219-1230 - Jakub Kovác, Robert Warren, Marília D. V. Braga, Jens Stoye
Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. 1231-1241 - Ján Manuch, Murray Patterson:
The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree. 1243-1253 - Katharina Jahn:
Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences. 1255-1274
Volume 18, Number 10, October 2011
- Tatsuya Akutsu
Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions. 1275-1290 - Alex Graudenzi
Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory. 1291-1303 - Joshua Collins, Simone Linz
Quantifying Hybridization in Realistic Time. 1305-1318 - Emiliano Barreto-Hernandez
Pre-Processing Optimization of RNA Immunoprecipitation Microarray Data. 1319-1328 - Hoon Kim
Biomarker Discovery Using Statistically Significant Gene Sets. 1329-1338 - Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, Alain Denise:
Counting RNA Pseudoknotted Structures. 1339-1351 - Fabrício Martins Lopes, Roberto Marcondes Cesar Jr.
Gene Expression Complex Networks: Synthesis, Identification, and Analysis. 1353-1367
Volume 18, Number 11, November 2011
- Vineet Bafna
Preface: Research in Computational Molecular Biology (RECOMB 2011). 1369 - Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang
Multiplex De Novo Sequencing of Peptide Antibiotics. 1371-1381 - Kerstin Scheubert, Franziska Hufsky
Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. 1383-1397 - Mark D. M. Leiserson, Diana Tatar, Lenore J. Cowen, Benjamin J. Hescott:
Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut. 1399-1409 - Xin Li, Jing Li
Haplotype Reconstruction in Large Pedigrees with Untyped Individuals through IBD Inference. 1411-1421 - Tobias Petri, Robert Küffner, Ralf Zimmer
Experiment Specific Expression Patterns. 1423-1435 - Dana Silverbush, Michael Elberfeld, Roded Sharan:
Optimally Orienting Physical Networks. 1437-1448 - Glenn Hickey, Mathieu Blanchette:
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. 1449-1464 - Jérôme Waldispühl
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. 1465-1479 - Bonnie Kirkpatrick, Shuai Cheng Li
Pedigree Reconstruction Using Identity by Descent. 1481-1493 - Daniel Newkirk, Jacob Biesinger
AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization. 1495-1505 - Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs. 1507-1523 - Shay Zakov, Yoav Goldberg, Michael Elhadad
Rich Parameterization Improves RNA Structure Prediction. 1525-1542 - Yun Yu, Tandy J. Warnow, Luay Nakhleh:
Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. 1543-1559 - Sinan Erten, Gürkan Bebek, Mehmet Koyutürk
Vavien: An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks. 1561-1574 - Allison P. Heath, George N. Bennett, Lydia E. Kavraki
An Algorithm for Efficient Identification of Branched Metabolic Pathways. 1575-1597 - Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
An Optimization-Based Sampling Scheme for Phylogenetic Trees. 1599-1609 - Jae Hoon Sul, Buhm Han, Eleazar Eskin:
Increasing Power of Groupwise Association Test with Likelihood Ratio Test. 1611-1624 - Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner:
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. 1625-1634 - Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. 1635-1647 - Fabian L. Wauthier, Michael I. Jordan
Nonparametric Combinatorial Sequence Models. 1649-1660 - Jianyang Zeng, Kyle E. Roberts, Pei Zhou
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. 1661-1679 - Song Gao, Wing-Kin Sung
Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. 1681-1691 - Wei Li, Jianxing Feng, Tao Jiang
IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. 1693-1707 - Tien-ho Lin, Ziv Bar-Joseph
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. 1709-1722 - Amnon Amir, Or Zuk:
Bacterial Community Reconstruction Using Compressed Sensing. 1723-1741 - Andrew S. Parker, Karl E. Griswold
Optimization of Combinatorial Mutagenesis. 1743-1756
Volume 18, Number 12, December 2011
- Himanshu Chandola, Anthony K. Yan, Shobha Potluri, Bruce Randall Donald, Chris Bailey-Kellogg:
NMR Structural Inference of Symmetric Homo-Oligomers. 1757-1775 - Jiun-Rung Chen, Ye-In Chang:
An Up-Down Bit Pattern Approach to Coregulated and Negative-Coregulated Gene Clustering of Microarray Data. 1777-1791 - Markus E. Nebel, Christian M. Reidys, Rita R. Wang:
Loops in Canonical RNA Pseudoknot Structures. 1793-1806 - Rafal Adamczak, Jaroslaw Pillardy, Brinda K. Vallat, Jaroslaw Meller
Fast Geometric Consensus Approach for Protein Model Quality Assessment. 1807-1818 - Matteo Comin
The Irredundant Class Method for Remote Homology Detection of Protein Sequences. 1819-1829 - Meng-Rong Li, Yu-Ju Lin, Tzong-Hann Shieh:
The Flux Model of the Movement of Tumor Cells and Healthy Cells Using a System of Nonlinear Heat Equations. 1831-1839
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