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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 7
Volume 7, Number 1, January 2010
- Ester Díaz, Guillermo Ayala
, Maria Diaz-Fernandez, Liang Gong, Derek Toomre:
Automatic Detection of Large Dense-Core Vesicles in Secretory Cells and Statistical Analysis of Their Intracellular Distribution. 2-11 - Carol Lushbough, Michael K. Bergman, Carolyn J. Lawrence, Douglas M. Jennewein, Volker Brendel:
BioExtract Server - An Integrated Workflow-Enabling System to Access and Analyze Heterogeneous, Distributed Biomolecular Data. 12-24 - Shenghuo Zhu, Dingding Wang, Kai Yu, Tao Li, Yihong Gong:
Feature Selection for Gene Expression Using Model-Based Entropy. 25-36 - Petri Pehkonen, Garry Wong, Petri Törönen:
Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions. 37-49 - Rafal Kustra, Adam Zagdanski:
Data-Fusion in Clustering Microarray Data: Balancing Discovery and Interpretability. 50-63 - Oliver Rübel, Gunther H. Weber, Min-Yu Huang, E. Wes Bethel, Mark D. Biggin, Charless C. Fowlkes, Cris L. Luengo Hendriks, Soile V. E. Keränen, Michael B. Eisen, David W. Knowles, Jitendra Malik, Hans Hagen, Bernd Hamann:
Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data. 64-79 - Ju Han, Hang Chang, Kumari L. Andarawewa, Paul Yaswen, Mary Helen Barcellos-Hoff, Bahram Parvin:
Multidimensional Profiling of Cell Surface Proteins and Nuclear Markers. 80-90 - Bogdan Done, Purvesh Khatri, Arina Done, Sorin Draghici:
Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis. 91-99 - Zhenqiu Liu, Shili Lin, Ming Tan:
Sparse Support Vector Machines with L_{p} Penalty for Biomarker Identification. 100-107 - Yukyee Leung, Yeung Sam Hung:
A Multiple-Filter-Multiple-Wrapper Approach to Gene Selection and Microarray Data Classification. 108-117 - Theodore J. Perkins, Michael T. Hallett:
A Trade-Off between Sample Complexity and Computational Complexity in Learning Boolean Networks from Time-Series Data. 118-125 - Richard Pelikan, Milos Hauskrecht:
Efficient Peak-Labeling Algorithms for Whole-Sample Mass Spectrometry Proteomics. 126-137 - Pritha Mahata:
Exploratory Consensus of Hierarchical Clusterings for Melanoma and Breast Cancer. 138-152 - Sara C. Madeira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira:
Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm. 153-165 - Elchanan Mossel, Sébastien Roch:
Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci. 166-171 - Alex Alves Freitas, Daniela Wieser, Rolf Apweiler:
On the Importance of Comprehensible Classification Models for Protein Function Prediction. 172-182 - Noga Alon, Benny Chor, Fabio Pardi, Anat Rapoport:
Approximate Maximum Parsimony and Ancestral Maximum Likelihood. 183-187
Volume 7, Number 2, April 2010
- Marie-France Sagot:
EIC Editorial. 193-194 - Stefano Lonardi, Jake Yue Chen:
Data Mining in Bioinformatics: Selected Papers from BIOKDD. 195-196 - Aaron M. Smalter, Jun Huan, Yi Jia, Gerald H. Lushington:
GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics. 197-207 - Petko Bogdanov, Ambuj K. Singh:
Molecular Function Prediction Using Neighborhood Features. 208-217 - Luay Nakhleh:
A Metric on the Space of Reduced Phylogenetic Networks. 218-222 - Gunjan Gupta, Alexander Liu, Joydeep Ghosh:
Automated Hierarchical Density Shaving: A Robust Automated Clustering and Visualization Framework for Large Biological Data Sets. 223-237 - Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer:
Automated Isolation of Translational Efficiency Bias That Resists the Confounding Effect of GC(AT)-Content. 238-250 - Arthur Tenenhaus, Vincent Guillemot, Xavier Gidrol, Vincent Frouin:
Gene Association Networks from Microarray Data Using a Regularized Estimation of Partial Correlation Based on PLS Regression. 251-262 - Zexuan Zhu, Yew-Soon Ong, Jacek M. Zurada:
Identification of Full and Partial Class Relevant Genes. 263-277 - Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson:
Model Composition for Macromolecular Regulatory Networks. 278-287 - Shahid H. Bokhari, Daniel Janies:
Reassortment Networks for Investigating the Evolution of Segmented Viruses. 288-298 - Tracy L. Bergemann, Lue Ping Zhao:
Signal Quality Measurements for cDNA Microarray Data. 299-308 - Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet:
Alignments of RNA Structures. 309-322 - Minghui Jiang:
Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots. 323-332 - Tetsuo Shibuya:
Fast Hinge Detection Algorithms for Flexible Protein Structures. 333-341 - Sylvain Guillemot, Vincent Berry:
Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem. 342-353 - Xiaowen Liu, Jinyan Li, Lusheng Wang:
Modeling Protein Interacting Groups by Quasi-Bicliques: Complexity, Algorithm, and Application. 354-364 - Xingqin Qi, Guojun Li, Shuguang Li, Ying Xu:
Sorting Genomes by Reciprocal Translocations, Insertions, and Deletions. 365-374 - Giora Unger, Benny Chor:
Linear Separability of Gene Expression Data Sets. 375-381
Volume 7, Number 3, July 2010
- Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia:
An Overview of BioCreative II.5. 385-399 - Artemy Kolchinsky, Alaa Abi-Haidar, Jasleen Kaur, Ahmed Abdeen Hamed, Luis Mateus Rocha:
Classification of Protein-Protein Interaction Full-Text Documents Using Text and Citation Network Features. 400-411 - Hong-Jie Dai, Po-Ting Lai, Richard Tzong-Han Tsai:
Multistage Gene Normalization and SVM-Based Ranking for Protein Interactor Extraction in Full-Text Articles. 412-420 - Man Lan, Jian Su:
Empirical Investigations into Full-Text Protein Interaction Article Categorization Task (ACT) in the BioCreative II.5 Challenge. 421-427 - Yifei Chen, Feng Liu, Bernard Manderick:
BioLMiner System: Interaction Normalization Task and Interaction Pair Task in the BioCreative II.5 Challenge. 428-441 - Rune Sætre, Kazuhiro Yoshida, Makoto Miwa, Takuya Matsuzaki, Yoshinobu Kano, Jun'ichi Tsujii:
Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System. 442-453 - Yonggang Cao, Zuofeng Li, Feifan Liu, Shashank Agarwal, Qing Zhang, Hong Yu:
An IR-Aided Machine Learning Framework for the BioCreative II.5 Challenge. 454-461 - Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter:
Exploring Species-Based Strategies for Gene Normalization. 462-471 - Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Simon Clematide, Thérèse Vachon, Martin Romacker:
OntoGene in BioCreative II.5. 472-480 - Jörg Hakenberg, Robert Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez:
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles. 481-494 - Rezaul Alam Chowdhury, Hai-Son Le, Vijaya Ramachandran:
Cache-Oblivious Dynamic Programming for Bioinformatics. 495-510 - Leonardo Tininini, Paola Bertolazzi, Alessandra Godi, Giuseppe Lancia:
CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony. 511-523 - Ronald Jackups Jr., Jie Liang:
Combinatorial Analysis for Sequence and Spatial Motif Discovery in Short Sequence Fragments. 524-536 - Xiaoxu Han:
Nonnegative Principal Component Analysis for Cancer Molecular Pattern Discovery. 537-549 - Jia Zeng, Xiaoyu Zhao, Xiao-Qin Cao, Hong Yan:
SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition. 550-562 - Arthur Zimek, Fabian Buchwald, Eibe Frank, Stefan Kramer:
A Study of Hierarchical and Flat Classification of Proteins. 563-571 - Maria Luisa Bonet, Katherine St. John:
On the Complexity of uSPR Distance. 572-576
Volume 7, Number 4, October 2010
- Ion I. Mandoiu, Giri Narasimhan, Yi Pan, Yanqing Zhang:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 577-578 - Adriana Muñoz, David Sankoff:
Rearrangement Phylogeny of Genomes in Contig Form. 579-587 - Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield:
Untangling Tanglegrams: Comparing Trees by Their Drawings. 588-597 - Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi:
Pure Parsimony Xor Haplotyping. 598-610 - Yufeng Wu:
Exact Computation of Coalescent Likelihood for Panmictic and Subdivided Populations under the Infinite Sites Model. 611-618 - Sanguthevar Rajasekaran, Sahar Al Seesi, Reda A. Ammar:
Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots. 619-627 - Guillaume Blin, Florian Sikora, Stéphane Vialette:
Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set. 628-635 - Qiang Cheng:
A Sparse Learning Machine for High-Dimensional Data with Application to Microarray Gene Analysis. 636-646 - William B. Langdon, Graham J. G. Upton, Renata da Silva Camargo, Andrew P. Harrison:
A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips. 647-653 - Gang Li, Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee:
A Cluster Refinement Algorithm for Motif Discovery. 654-668 - Jianjun Zhou, Jörg Sander, Zhipeng Cai, Lusheng Wang, Guohui Lin:
Finding the Nearest Neighbors in Biological Databases Using Less Distance Computations. 669-680 - Liang-Tsung Huang, Lien Fu Lai, M. Michael Gromiha:
Human-Readable Rule Generator for Integrating Amino Acid Sequence Information and Stability of Mutant Proteins. 681-687 - Christophe Godin, Pascal Ferraro:
Quantifying the Degree of Self-Nestedness of Trees: Application to the Structural Analysis of Plants. 688-703 - Sagi Snir, Satish Rao:
Quartets MaxCut: A Divide and Conquer Quartets Algorithm. 704-718 - Xin Lu, Anthony Gamst, Ronghui Xu:
RDCurve: A Nonparametric Method to Evaluate the Stability of Ranking Procedures. 719-726 - Herbert H. Tsang, Kay C. Wiese:
SARNA-Predict: Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-Based Simulated Annealing. 727-740 - Liwen You, Vladimir Brusic, Marcus Gallagher, Mikael Bodén:
Using Gaussian Process with Test Rejection to Detect T-Cell Epitopes in Pathogen Genomes. 741-751 - Alberto Apostolico, Matteo Comin, Laxmi Parida:
VARUN: Discovering Extensible Motifs under Saturation Constraints. 752-762 - István Miklós, Bence Mélykúti, Krister M. Swenson:
The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths. 763-767
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