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ORCIDJournal of Computational Biology, Volume 22
Volume 22, Number 1, January 2015
- Sunita Yadav, D. Swati, Hariharan Chandrasekharan:
Thiamine Pyrophosphate Riboswitch in Some Representative Plant Species: A Bioinformatics Study. 1-9 - Adam Persing, Ajay Jasra, Alexandros Beskos
, David J. Balding, Maria De Iorio:
A Simulation Approach for Change-Points on Phylogenetic Trees. 10-24 - Frédéric Y. Bois, Ghislaine Gayraud:
Probabilistic Generation of Random Networks Taking into Account Information on Motifs Occurrence. 25-36 - Derek E. Chen, Darryl L. Willick, Joseph B. Ruckel, Wely B. Floriano:
Principal Component Analysis of Binding Energies for Single-Point Mutants of hT2R16 Bound to an Agonist Correlate with Experimental Mutant Cell Response. 37-53 - Dhammika Amaratunga, Javier Cabrera, Yung-Seop Lee:
Resampling-Based Similarity Measures for High-Dimensional Data. 54-62 - Tuantuan Gui, Xiao Dong, Ru-Dong Li, Yixue Li, Zhen Wang:
Identification of Hepatocellular Carcinoma-Related Genes with a Machine Learning and Network Analysis. 63-71
Volume 22, Number 2, February 2015
- Heewon Park, Atsushi Niida, Satoru Miyano, Seiya Imoto:
Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis. 73-84 - Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu:
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. 85-110 - Quan Chen, Xianghong Jasmine Zhou, Fengzhu Sun:
Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists. 111-123 - Evan Senter, Peter Clote:
Fast, Approximate Kinetics of RNA Folding. 124-144 - Aditya Rao, Deepthi P., C. H. Renumadhavi, M. Girish Chandra, Rajgopal Srinivasan:
Compressed Sensing Methods for DNA Microarrays, RNA Interference, and Metagenomics. 145-158 - Xuan Guo, Ning Yu, Xiaojun Ding, Jianxin Wang, Yi Pan:
DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly. 159-177 - Fatemeh Zamanzad Ghavidel, Jürgen Claesen, Tomasz Burzykowski:
A Nonhomogeneous Hidden Markov Model for Gene Mapping Based on Next-Generation Sequencing Data. 178-188
Volume 22, Number 3, March 2015
- Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl:
Preface. 189 - Azadeh Saffarian, Mathieu Giraud, Hélène Touzet:
Modeling Alternate RNA Structures in Genomic Sequences. 190-204 - Laetitia Bourgeade, Cédric Chauve, Julien Allali:
Chaining Sequence/Structure Seeds for Computing RNA Similarity. 205-217 - Mattia Petroni, Nikolaj Zimic, Miha Mraz, Miha Moskon:
Stochastic Simulation Algorithm for Gene Regulatory Networks with Multiple Binding Sites. 218-226 - Meltem Gölgeli Matur, Johannes Müller, Christina Kuttler, Burkhard A. Hense:
An Approximative Approach for Single Cell Spatial Modeling of Quorum Sensing. 227-235 - Nha Nguyen, An P. N. Vo, Inchan Choi, Kyoung-Jae Won:
A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression. 236-249
Volume 22, Number 4, April 2015
- Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue. 251-252 - Anagha Joshi, Yvonne Beck, Tom Michoel:
Multi-Species Network Inference Improves Gene Regulatory Network Reconstruction for Early Embryonic Development in Drosophila. 253-265 - Edison Ong, Anthony Szedlak, Yunyi Kang, Peyton Smith, Nicholas Smith, Madison McBride, Darren Finlay, Kristiina Vuori, James Mason, Edward D. Ball, Carlo Piermarocchi, Giovanni Paternostro:
A Scalable Method for Molecular Network Reconstruction Identifies Properties of Targets and Mutations in Acute Myeloid Leukemia. 266-288 - Brittany A. Baur, Serdar Bozdag:
A Canonical Correlation Analysis-Based Dynamic Bayesian Network Prior to Infer Gene Regulatory Networks from Multiple Types of Biological Data. 289-299 - Xueling Li, Min Zhu, Allan R. Brasier, Andrzej S. Kudlicki:
Inferring Genome-Wide Functional Modulatory Network: A Case Study on NF-κB/RelA Transcription Factor. 300-312 - Bingqing Xie, Gady Agam, Sandhya Balasubramanian, Jinbo Xu, T. Conrad Gilliam, Natalia Maltsev, Daniela Börnigen:
Disease Gene Prioritization Using Network and Feature. 313-323 - Aaron Wise, Ziv Bar-Joseph:
cDREM: Inferring Dynamic Combinatorial Gene Regulation. 324-333
Volume 22, Number 5, May 2015
- Roded Sharan:
Preface. 335 - Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev:
On the Representation of De Bruijn Graphs. 336-352 - Adrian Guthals, Christina Boucher, Nuno Bandeira:
The Generating Function Approach for Peptide Identification in Spectral Networks. 353-366 - Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin:
IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. 367-376 - Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy J. Warnow:
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. 377-386 - Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, W. James Kent, David Haussler, Benedict Paten:
Building a Pan-Genome Reference for a Population. 387-401 - Keith Noto, Saeed Majidi, Andrea G. Edlow, Heather C. Wick, Diana W. Bianchi, Donna K. Slonim:
CSAX: Characterizing Systematic Anomalies in eXpression Data. 402-413 - Arne C. Reimers, Frank J. Bruggeman, Brett G. Olivier, Leen Stougie:
Fast Flux Module Detection Using Matroid Theory. 414-424 - Mingfu Shao, Yu Lin, Bernard M. E. Moret:
An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. 425-435 - Shutan Xu, Shuxue Zou, Lincong Wang:
A Geometric Clustering Algorithm with Applications to Structural Data. 436-450 - Wen-Yun Yang, Farhad Hormozdiari, Eleazar Eskin, Bogdan Pasaniuc:
A Spatial Haplotype Copying Model with Applications to Genotype Imputation. 451-462
Volume 22, Number 6, June 2015
- Hamidreza Chitsaz, Mohammad Aminisharifabad:
Exact Learning of RNA Energy Parameters From Structure. 463-473 - Hetunandan Kamisetty, Bornika Ghosh, Christopher James Langmead, Chris Bailey-Kellogg:
Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models. 474-486 - Arun Siddharth Konagurthu, Parthan Kasarapu, Lloyd Allison, James H. Collier, Arthur M. Lesk:
On Sufficient Statistics of Least-Squares Superposition of Vector Sets. 487-497 - Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth:
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. 498-509 - Benjamin J. Raphael, Fabio Vandin:
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. 510-527 - Yana Safonova, Anton Bankevich, Pavel A. Pevzner:
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. 528-545 - Hua Wang, Heng Huang, Chris H. Q. Ding:
Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency. 546-562 - Zhanyong Wang, Jae Hoon Sul, Sagi Snir, José Antonio Lozano, Eleazar Eskin:
Gene-Gene Interactions Detection Using a Two-stage Model. 563-576 - Shay Zakov, Vineet Bafna:
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. 577-594 - Marinka Zitnik, Blaz Zupan:
Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion. 595-608
Volume 22, Number 7, July 2015
- Yuzhen Guo:
The Noncompacted Folding of Proteins by Modified Elastic Net Algorithm. 609-618 - Robert Müller, Markus E. Nebel:
Combinatorics of RNA Secondary Structures with Base Triples. 619-648 - Jose M. J. Costa, Helcio R. B. Orlande, Haroldo Fraga de Campos Velho, Suani Tavares Rubim de Pinho, George S. Dulikravich, Renato M. Cotta, Silvio H. da Cunha Neto:
Estimation of Tumor Size Evolution Using Particle Filters. 649-665 - Zhexue Wei, Daming Zhu, Lusheng Wang:
A Dynamic Programming Algorithm For (1, 2)-Exemplar Breakpoint Distance. 666-676 - Huilan Chang, Yi-Chang Chiu, Yi-Lin Tsai:
A Variation of Cover-Free Families and Its Applications. 677-686 - Alex Radu, Michael A. Charleston:
Node Handprinting: A Scalable and Accurate Algorithm for Aligning Multiple Biological Networks. 687-697 - Florian Kaiser, Alexander Eisold, Dirk Labudde:
A Novel Algorithm for Enhanced Structural Motif Matching in Proteins. 698-713
Volume 22, Number 8, August 2015
- Sean Simmons, Jian Peng, Jadwiga R. Bienkowska, Bonnie Berger:
Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. 715-728 - Peter Zörnig:
Reduced-Size Integer Linear Programming Models for String Selection Problems: Application to the Farthest String Problem. 729-742 - Kaisa Koskinen, Petri Auvinen, K. Johanna Björkroth, Jenni Hultman:
Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data. 743-751 - Chia-Hui Huang:
Medical Reasoning with Rough-Set Influence Diagrams. 752-764 - Miao Sun, Dejian Lai, Li Zhang, Xuelin Huang:
Modified SuperCurve Method for Analysis of Reverse-Phase Protein Array Data. 765-769 - Oliver Serang:
A Fast Numerical Method for Max-Convolution and the Application to Efficient Max-Product Inference in Bayesian Networks. 770-783
Volume 22, Number 9, September 2015
- Jing He, Amarda Shehu, Nurit Haspel, Brian Chen:
The 7th Computational Structural Bioinformatics Workshop. 785-786 - Hui Dong, Jin Seob Kim, Gregory S. Chirikjian:
Computational Analysis of SAXS Data Acquisition. 787-805 - Irina Hashmi, Amarda Shehu:
idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking. 806-822 - Hsin-Yi Cindy Yeh, Aaron Lindsey, Chih-Peng Wu, Shawna L. Thomas, Nancy M. Amato:
Decoy Database Improvement for Protein Folding. 823-836 - Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He:
A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data. 837-843 - Rudy Clausen, Amarda Shehu:
A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes. 844-860 - Ziyi Guo, Brian Yuan Chen:
Conformational Sampling Reveals Amino Acids with a Steric Influence on Specificity. 861-875 - Ping Zhou, Ning Zhang, Ruth Nussinov, Buyong Ma:
Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. 876-886 - Kelin Xia, Zhixiong Zhao, Guo-Wei Wei:
Multiresolution Topological Simplification. 887-891 - Bahar Akbal-Delibas, Marc Pomplun, Nurit Haspel:
Accurate Prediction of Docked Protein Structure Similarity. 892-904
Volume 22, Number 10, October 2015
- Yael Baran, Eran Halperin:
A Note on the Relations Between Spatio-Genetic Models. 905-917 - Filippo Disanto, Noah A. Rosenberg:
Coalescent Histories for Lodgepole Species Trees. 918-929 - Alexa Pragman, Richard Issacson, Christine Wendt, Cavan Reilly:
A Method for Determining Taxonomical Contributions to Group Differences in Microbiomic Investigations. 930-939 - Tim Wallace, Ali Sekmen, Xiaofei Wang:
Application of Subspace Clustering in DNA Sequence Analysis. 940-952 - Alexandre Wagner Chagas Faria, Alisson Marques da Silva, Thiago de Souza Rodrigues, Marcelo Azevedo Costa, Antônio de Pádua Braga:
A Ranking Approach for Probe Selection and Classification of Microarray Data with Artificial Neural Networks. 953-961 - Bo Li, Xianfang Zheng, Chuancui Hu, Yunxia Cao:
Human Papillomavirus Genome-Wide Identification of T-Cell Epitopes for Peptide Vaccine Development Against Cervical Cancer: An Integration of Computational Analysis and Experimental Assay. 962-974
Volume 22, Number 11, November 2015
- Chin Lung Lu:
An Efficient Algorithm for the Contig Ordering Problem under Algebraic Rearrangement Distance. 975-987 - Ping Chen, Xuelin Huang:
Comparison of Analytic Methods for Quantitative Real-Time Polymerase Chain Reaction Data. 988-996 - Anthony O'Hare:
Inference in High-Dimensional Parameter Space. 997-1004 - Nikita A. Sakhanenko, David J. Galas:
Biological Data Analysis as an Information Theory Problem: Multivariable Dependence Measures and the Shadows Algorithm. 1005-1024 - Ajay Jasra, Adam Persing, Alexandros Beskos, Kari Heine, Maria De Iorio:
Bayesian Inference for Duplication-Mutation with Complementarity Network Models. 1025-1033 - Sera Kim, Kyeongjun Lee, Hokeun Sun:
Statistical Selection Strategy for Risk and Protective Rare Variants Associated with Complex Traits. 1034-1043 - Luís Felipe I. Cunha, Luis Antonio Brasil Kowada, Rodrigo de A. Hausen, Celina M. H. de Figueiredo:
A Faster 1.375-Approximation Algorithm for Sorting by Transpositions*. 1044-1056
Volume 22, Number 12, December 2015
- Marco Frasca, Alberto Bertoni, Giorgio Valentini:
UNIPred: Unbalance-Aware Network Integration and Prediction of Protein Functions. 1057-1074 - Ahmed T. Soliman, Tao Meng, Shu-Ching Chen, S. S. Iyengar, Puneeth Iyengar, John S. Yordy, Mei-Ling Shyu:
Driver Missense Mutation Identification Using Feature Selection and Model Fusion. 1075-1085 - Tran Tuan Anh, Nam Tri Vo, Hoang Duc Nguyen, Pham The Bao:
A Novel Method to Predict Highly Expressed Genes Based on Radius Clustering and Relative Synonymous Codon Usage. 1086-1096 - Kyoung-Tak Kang, Sung-Hwan Kim, Ju-Hyun Son, Young Han Lee, Heoung-Jae Chun:
Probabilistic Approach for Determining the Material Properties of Meniscal Attachments In Vivo Using Magnetic Resonance Imaging and a Finite Element Model. 1097-1107 - Shu-Yuan Niu, Ming-Yuan Xin, Jian Luo, Mingyao Liu, Zhen-Ran Jiang:
DSEP: A Tool Implementing Novel Method to Predict Side Effects of Drugs. 1108-1117 - Anas Al-Okaily:
Error Tree: A Tree Structure for Hamming and Edit Distances and Wildcards Matching. 1118-1128 - Olga Chernomor, Bui Quang Minh, Arndt von Haeseler:
Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference. 1129-1142
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