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IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 8
Volume 8, Number 1, January 2011
- Marie-France Sagot:
EIC Editorial. 1 - Megan Owen, J. Scott Provan:
A Fast Algorithm for Computing Geodesic Distances in Tree Space. 2-13 - Mohak Shah, Jacques Corbeil
:
A General Framework for Analyzing Data from Two Short Time-Series Microarray Experiments. 14-26 - Sean Mauch, Mark A. Stalzer:
Efficient Formulations for Exact Stochastic Simulation of Chemical Systems. 27-35 - Dario Gasbarra, Sangita Kulathinal, Matti Pirinen
Estimating Haplotype Frequencies by Combining Data from Large DNA Pools with Database Information. 36-44 - Chandrajit L. Bajaj, Rezaul Alam Chowdhury, Vinay Siddahanavalli:
F2Dock: Fast Fourier Protein-Protein Docking. 45-58 - Joachim Giard, Patrice Rondao-Alface
Fast Surface-Based Travel Depth Estimation Algorithm for Macromolecule Surface Shape Description. 59-68 - Cinzia Pizzi, Pasi Rastas
Finding Significant Matches of Position Weight Matrices in Linear Time. 69-79 - Razvan Andonie
Fuzzy ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors Using a Small Molecular Data Set. 80-93 - Sushmita Mitra
Genetic Networks and Soft Computing. 94-107 - Wenxue Wang, Bijoy K. Ghosh, Himadri B. Pakrasi:
Identification and Modeling of Genes with Diurnal Oscillations from Microarray Time Series Data. 108-121 - Linkai Luo, Dengfeng Huang, Ling-Jun Ye, Qifeng Zhou, Guifang Shao, Hong Peng:
Improving the Computational Efficiency of Recursive Cluster Elimination for Gene Selection. 122-129 - Mehmet Tan
Influence of Prior Knowledge in Constraint-Based Learning of Gene Regulatory Networks. 130-142 - Liuling Gong, Nidhal Bouaynaya, Dan Schonfeld:
Information-Theoretic Model of Evolution over Protein Communication Channel. 143-151 - Nathan A. Barker, Chris J. Myers
Learning Genetic Regulatory Network Connectivity from Time Series Data. 152-165 - Delphine Ropers
Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli. 166-181 - Yufeng Wu:
New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations. 182-193 - Ankit Agrawal
Pairwise Statistical Significance of Local Sequence Alignment Using Sequence-Specific and Position-Specific Substitution Matrices. 194-205 - Rogier J. P. van Berlo, Dick de Ridder, Jean-Marc Daran
Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints. 206-216 - Leo Lahti
Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays. 217-225 - K. C. Dukka Bahadur, Dennis R. Livesay:
Topology Improves Phylogenetic Motif Functional Site Predictions. 226-233 - Tamjidul Hoque, Madhu Chetty
Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model. 234-245 - Joaquim F. Pinto da Costa, Hugo Alonso
A Weighted Principal Component Analysis and Its Application to Gene Expression Data. 246-252 - Ping Li, James Lam:
Disturbance Analysis of Nonlinear Differential Equation Models of Genetic SUM Regulatory Networks. 253-259 - Cheng-Wei Luo, Ming-Chiang Chen, Yi-Ching Chen, Roger W. L. Yang, Hsiao-Fei Liu, Kun-Mao Chao
Linear-Time Algorithms for the Multiple Gene Duplication Problems. 260-265 - Kezhi Mao
Recursive Mahalanobis Separability Measure for Gene Subset Selection. 266-272 - Vikram Krishnamurthy, Kai Yiu Luk:
Semi-Markov Models for Brownian Dynamics Permeation in Biological Ion Channels. 273-281
Volume 8, Number 2, March 2011
- Marie-France Sagot:
EIC Editorial. 289-291 - Fang-Xiang Wu
Guest Editorial: Special Focus on Bioinformatics and Systems Biology. 292-293 - Yanpeng Li, Xiaohua Hu, Hongfei Lin, Zhiahi Yang:
A Framework for Semisupervised Feature Generation and Its Applications in Biomedical Literature Mining. 294-307 - Jong Cheol Jeong, Xiaotong Lin, Xue-wen Chen:
On Position-Specific Scoring Matrix for Protein Function Prediction. 308-315 - Sangyoon Oh, Min Su Lee, Byoung-Tak Zhang:
Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification. 316-325 - Zina M. Ibrahim
Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks. 326-334 - Amit Sabnis, Robert W. Harrison
A Continuous-Time, Discrete-State Method for Simulating the Dynamics of Biochemical Systems. 335-341 - Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer:
A Genetic Optimization Approach for Isolating Translational Efficiency Bias. 342-352 - Ramesh Ram, Madhu Chetty
A Markov-Blanket-Based Model for Gene Regulatory Network Inference. 353-367 - Zengyou He
A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data. 368-380 - Yonghui Wu, Timothy J. Close, Stefano Lonardi
Accurate Construction of Consensus Genetic Maps via Integer Linear Programming. 381-394 - Zafer Aydin, Yucel Altunbasak, Hakan Erdogan:
Bayesian Models and Algorithms for Protein β-Sheet Prediction. 395-409 - Gabriel Cardona
Comparison of Galled Trees. 410-427 - Kwong-Sak Leung, Kin-Hong Lee, Jinfeng Wang, Eddie Y. T. Ng, Henry L. Y. Chan, Stephen Kwok-Wing Tsui
Data Mining on DNA Sequences of Hepatitis B Virus. 428-440 - Tien-ho Lin, Robert F. Murphy, Ziv Bar-Joseph
Discriminative Motif Finding for Predicting Protein Subcellular Localization. 441-451 - Saras Saraswathi, Suresh Sundaram
ICGA-PSO-ELM Approach for Accurate Multiclass Cancer Classification Resulting in Reduced Gene Sets in Which Genes Encoding Secreted Proteins Are Highly Represented. 452-463 - Itziar Irigoien
Microarray Time Course Experiments: Finding Profiles. 464-475 - Qiwen Dong, Shuigeng Zhou:
Novel Nonlinear Knowledge-Based Mean Force Potentials Based on Machine Learning. 476-486 - Sébastien Loriot, Sushant Sachdeva
On the Characterization and Selection of Diverse Conformational Ensembles with Applications to Flexible Docking. 487-498 - Robert Giegerich, Christian Höner zu Siederdissen
Semantics and Ambiguity of Stochastic RNA Family Models. 499-516 - Ali Tofigh, Michael T. Hallett
Simultaneous Identification of Duplications and Lateral Gene Transfers. 517-535 - Michael D. Lieberman, Sima Taheri, Huimin Guo, Fatemeh Mirrashed, Inbal Yahav, Aleks Aris, Ben Shneiderman:
Visual Exploration across Biomedical Databases. 536-550 - Glenn Hickey, Mathieu Blanchette, Paz Carmi, Anil Maheshwari, Norbert Zeh:
An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss. 551-556 - Juan Cortés, Sophie Barbe
Encoding Molecular Motions in Voxel Maps. 557-563 - Jairo Rocha
Graph Comparison by Log-Odds Score Matrices with Application to Protein Topology Analysis. 564-569 - André Fujita, João Ricardo Sato
Inferring Contagion in Regulatory Networks. 570-576
Volume 8, Number 3, May 2011
- Alfredo Benso
A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory. 577-591 - Erdem Yörük, Michael F. Ochs, Donald Geman, Laurent Younes
A Comprehensive Statistical Model for Cell Signaling. 592-606 - Jianxin Wang, Min Li, Jianer Chen, Yi Pan:
A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks. 607-620 - Jianxing Feng, Rui Jiang
A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data. 621-634 - Katharina T. Huber, Leo van Iersel, Steven Kelk, Radoslaw Suchecki
A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. 635-649 - James T. Murphy
A Theoretical Analysis of the Prodrug Delivery System for Treating Antibiotic-Resistant Bacteria. 650-658 - Santanu Ghorai
Cancer Classification from Gene Expression Data by NPPC Ensemble. 659-671 - Gregor Goessler:
Component-Based Modeling and Reachability Analysis of Genetic Networks. 672-682 - Yoshinori Tamada
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. 683-697 - Alexander K. Hudek, Daniel Gregory Brown:
FEAST: Sensitive Local Alignment with Multiple Rates of Evolution. 698-709 - Elizabeth S. Allman
Identifiability of Two-Tree Mixtures for Group-Based Models. 710-722 - Tianwei Yu
Incorporating Nonlinear Relationships in Microarray Missing Value Imputation. 723-731 - Bin Song, I. Esra Büyüktahtakin, Sanjay Ranka
Manipulating the Steady State of Metabolic Pathways. 732-747 - Qian Xu, Sinno Jialin Pan
Multitask Learning for Protein Subcellular Location Prediction. 748-759 - Rubén Armañanzas
Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms. 760-774 - Antonina Mitrofanova, Vladimir Pavlovic
Prediction of Protein Functions with Gene Ontology and Interspecies Protein Homology Data. 775-784 - Stephen J. Willson:
Regular Networks Can be Uniquely Constructed from Their Trees. 785-796 - Tilo Strutz:
3D Shape Reconstruction of Loop Objects in X-Ray Protein Crystallography. 797-807 - Banu Dost, Chunlei Wu, Andrew I. Su
TCLUST: A Fast Method for Clustering Genome-Scale Expression Data. 808-818 - Jayendra Venkateswaran, Bin Song, Tamer Kahveci, Chris Jermaine:
TRIAL: A Tool for Finding Distant Structural Similarities. 819-831 - Giorgio Valentini
True Path Rule Hierarchical Ensembles for Genome-Wide Gene Function Prediction. 832-847 - Mukul S. Bansal
A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. 848-850 - Aditya Kumar Sehgal, Sanmay Das, Keith Noto, Milton H. Saier Jr., Charles Elkan:
Identifying Relevant Data for a Biological Database: Handcrafted Rules versus Machine Learning. 851-857 - Minh Ngoc Nguyen, Jacek M. Zurada, Jagath C. Rajapakse
Toward Better Understanding of Protein Secondary Structure: Extracting Prediction Rules. 858-864
Volume 8, Number 4, July 2011
- Mark Borodovsky, Teresa M. Przytycka
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 865-866 - Yosi Shibberu, Allen Holder:
A Spectral Approach to Protein Structure Alignment. 867-875 - Nicola Ferraro, Luigi Palopoli
Asymmetric Comparison and Querying of Biological Networks. 876-889 - John Wiedenhoeft
The Plexus Model for the Inference of Ancestral Multidomain Proteins. 890-901 - Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis
Uncovering Hidden Phylogenetic Consensus in Large Data Sets. 902-911 - Rob Gysel, Dan Gusfield:
Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem. 912-917 - Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz
A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure. 918-928 - Sanghamitra Bandyopadhyay, Malay Bhattacharyya
A Biologically Inspired Measure for Coexpression Analysis. 929-942 - Nuno Tenazinha, Susana Vinga
A Survey on Methods for Modeling and Analyzing Integrated Biological Networks. 943-958 - Chao-Wen Huang, Wun-Shiun Lee, Sun-Yuan Hsieh:
An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences. 959-975 - Sebastian Böcker
Determination of Glycan Structure from Tandem Mass Spectra. 976-986 - Samuel S. Y. Wong, Weimin Luo, Keith C. C. Chan
EvoMD: An Algorithm for Evolutionary Molecular Design. 987-1003 - Ivan Merelli
Image-Based Surface Matching Algorithm Oriented to Structural Biology. 1004-1016 - Pietro di Lena
Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations? 1017-1028 - Katharina T. Huber, Andreas Spillner, Radoslaw Suchecki
Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds. 1029-1040 - Xin Zhao, Leo Wang-Kit Cheung:
Multiclass Kernel-Imbedded Gaussian Processes for Microarray Data Analysis. 1041-1053 - Peng Zhang, Houqiang Li, Honghui Wang, Stephen T. C. Wong, Xiaobo Zhou:
Peak Tree: A New Tool for Multiscale Hierarchical Representation and Peak Detection of Mass Spectrometry Data. 1054-1066 - Yasser El-Manzalawy, Drena Dobbs
Predicting MHC-II Binding Affinity Using Multiple Instance Regression. 1067-1079 - Feng Yang, Kezhi Mao
Robust Feature Selection for Microarray Data Based on Multicriterion Fusion. 1080-1092 - Peter Tiño, Hongya Zhao, Hong Yan
Searching for Coexpressed Genes in Three-Color cDNA Microarray Data Using a Probabilistic Model-Based Hough Transform. 1093-1107 - Li-San Wang, James H. Leebens-Mack
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. 1108-1119 - Bashir Sadjad, Zsolt Zsoldos:
Toward a Robust Search Method for the Protein-Drug Docking Problem. 1120-1133 - Yang Chen, Jinglu Hu:
Accurate Reconstruction for DNA Sequencing by Hybridization Based on a Constructive Heuristic. 1134-1140 - Sylvain Guillemot, Jesper Jansson
Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets. 1141-1147 - Tim Peters, David W. Bulger
Two-Step Cross-Entropy Feature Selection for Microarrays - Power Through Complementarity. 1148-1151
Volume 8, Number 5, September 2011
- Dongxiao Zhu, Lipi R. Acharya, Hui Zhang:
A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements. 1153-1169 - Rui Chang, Robert Shoemaker, Wei Wang:
A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention. 1170-1182 - Ekhine Irurozki
A Preprocessing Procedure for Haplotype Inference by Pure Parsimony. 1183-1195 - Simone Battagliero, Giuseppe Puglia
An Efficient Algorithm for Approximating Geodesic Distances in Tree Space. 1196-1207 - David J. John, Jacquelyn S. Fetrow
Continuous Cotemporal Probabilistic Modeling of Systems Biology Networks from Sparse Data. 1208-1222 - Carito Guziolowski
Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. 1223-1234 - Sitanshu Sekhar Sahu
Efficient Localization of Hot Spots in Proteins Using a Novel S-Transform Based Filtering Approach. 1235-1246 - Samuel Coulbourn Flores
Fast Flexible Modeling of RNA Structure Using Internal Coordinates. 1247-1257 - Biing-Feng Wang, Chien-Hsin Lin:
Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees. 1258-1272 - Chun-Hou Zheng, Lei Zhang
Metasample-Based Sparse Representation for Tumor Classification. 1273-1282 - Qian Peng, Andrew D. Smith
Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome. 1283-1295 - Nadja Betzler, René van Bevern, Michael R. Fellows
Parameterized Algorithmics for Finding Connected Motifs in Biological Networks. 1296-1308 - Jong Kyoung Kim
Probabilistic Models for Semisupervised Discriminative Motif Discovery in DNA Sequences. 1309-1317 - Pedro Feijão, João Meidanis:
SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems. 1318-1329 - Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier:
SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison. 1330-1343 - Peter Boyen, Dries Van Dyck, Frank Neven
SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks. 1344-1357 - Harry Buhrman, Peter T. S. van der Gulik, Steven Kelk, Wouter M. Koolen, Leen Stougie:
Some Mathematical Refinements Concerning Error Minimization in the Genetic Code. 1358-1372 - William W. L. Wong
Using Kernel Alignment to Select Features of Molecular Descriptors in a QSAR Study. 1373-1384 - Marco Muselli, Alberto Bertoni, Marco Frasca
A Mathematical Model for the Validation of Gene Selection Methods. 1385-1392 - Elena Dubrova, Maxim Teslenko:
A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks. 1393-1399 - Zhi-Zhong Chen, Lusheng Wang
Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L, d)-Motif Model. 1400-1410 - Simona Grusea:
On the Distribution of the Number of Cycles in the Breakpoint Graph of a Random Signed Permutation. 1411-1416 - Getachew K. Befekadu
Probabilistic Mixture Regression Models for Alignment of LC-MS Data. 1417-1424 - Paolo Magni
Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability. 1425-1430 - Ehud Aharoni, Hani Neuvirth, Saharon Rosset:
The Quality Preserving Database: A Computational Framework for Encouraging Collaboration, Enhancing Power and Controlling False Discovery. 1431-1437
Volume 8, Number 6, November 2011
- Apostolos Axenopoulos, Petros Daras
A Shape Descriptor for Fast Complementarity Matching in Molecular Docking. 1441-1457 - Wenqi Zhao, Guoliang Xu, Chandrajit L. Bajaj
An Algebraic Spline Model of Molecular Surfaces for Energetic Computations. 1458-1467 - Markus E. Nebel, Anika Scheid:
Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model. 1468-1482 - Liang Zhao, Limsoon Wong
Antibody-Specified B-Cell Epitope Prediction in Line with the Principle of Context-Awareness. 1483-1494 - Murat Can Cobanoglu, Yücel Saygin, Osman Ugur Sezerman
Classification of GPCRs Using Family Specific Motifs. 1495-1508 - Qi Li, Chandra Kambhamettu:
Contour Extraction of Drosophila Embryos. 1509-1521 - Jung Hun Oh
Fast Kernel Discriminant Analysis for Classification of Liver Cancer Mass Spectra. 1522-1534 - Qingfeng Chen, Yi-Ping Phoebe Chen
Function Annotation for Pseudoknot Using Structure Similarity. 1535-1544 - Georgios Chalkidis, Masao Nagasaki
High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA. 1545-1556 - Helong Li, Sam Kwong
Hilbert-Huang Transform for Analysis of Heart Rate Variability in Cardiac Health. 1557-1567 - Jinhua Sheng, Hong-Wen Deng
Integrated Analysis of Gene Expression and Copy Number Data on Gene Shaving Using Independent Component Analysis. 1568-1579 - Carla C. M. Chen
Methods for Identifying SNP Interactions: A Review on Variations of Logic Regression, Random Forest and Bayesian Logistic Regression. 1580-1591 - Chun-Hou Zheng, Lei Zhang
Molecular Pattern Discovery Based on Penalized Matrix Decomposition. 1592-1603 - Xavier Le Faucheur, Eli Hershkovitz, Rina Tannenbaum, Allen R. Tannenbaum:
Nonparametric Clustering for Studying RNA Conformations. 1604-1619 - Iván Dotú, Manuel Cebrián
On Lattice Protein Structure Prediction Revisited. 1620-1632 - Hong-Dong Li, Yi-Zeng Liang, Qing-Song Xu, Dong-Sheng Cao
Recipe for Uncovering Predictive Genes Using Support Vector Machines Based on Model Population Analysis. 1633-1641 - Christoph Hafemeister
Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential. 1642-1652 - Thomas Fober, Serghei Glinca, Gerhard Klebe, Eyke Hüllermeier:
Superposition and Alignment of Labeled Point Clouds. 1653-1666 - Tamir Tuller
Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics. 1667-1670 - Bing-Yu Sun, Zhi-Hua Zhu, Jiuyong Li
Combined Feature Selection and Cancer Prognosis Using Support Vector Machine Regression. 1671-1677 - Weiguo Liu, Bertil Schmidt
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. 1678-1684 - Louxin Zhang:
From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events. 1685-1691 - Michael R. Fellows
Haplotype Inference Constrained by Plausible Haplotype Data. 1692-1699 - Jérôme Ambroise, Joachim Giard, Jean-Luc Gala, Benoît Macq:
Identification of Relevant Properties for Epitopes Detection Using a Regression Model. 1700-1707 - Qingguo Wang
Improving a Consensus Approach for Protein Structure Selection by Removing Redundancy. 1708-1715 - Aleksandar Poleksic
Optimizing a Widely Used Protein Structure Alignment Measure in Expected Polynomial Time. 1716-1720 - Thiago de Souza Rodrigues, Fernanda Caldas Cardoso
Protein Classification with Extended-Sequence Coding by Sliding Window. 1721-1726
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