Journal of Computational Biology, Volume 24 (original) (raw)

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Volume 24, Number 1, January 2017

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    Jing He, Nurit Haspel, Brian Chen:
    Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop. 1
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    Hu Cao, Yonggang Lu:
    Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment. 2-12
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    Jin Seob Kim, Bijan Afsari, Gregory S. Chirikjian:
    Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy. 13-30
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    Wen Cheng, Changhui Yan:
    A Graph Approach to Mining Biological Patterns in the Binding Interfaces. 31-39
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    Roshanak Farhoodi, Bahar Akbal-Delibas, Nurit Haspel:
    Machine Learning Approaches for Predicting Protein Complex Similarity. 40-51
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    Stephanie Zeil, Julio A. Kovacs, Willy Wriggers, Jing He:
    Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix. 52-67
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    Bridget E. Nolan, Emily Levenson, Brian Y. Chen:
    Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity. 68-78
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    Anastasia Novinskaya, Didier Devaurs, Mark Moll, Lydia E. Kavraki:
    Defining Low-Dimensional Projections to Guide Protein Conformational Sampling. 79-89

Volume 24, Number 2, February 2017

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    Adrian-Horia Dediu, Carlos Martín-Vide:
    Preface: Selected Articles of the Second International Conference on Algorithms for Computational Biology (AlCoB 2015). 91-92
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    Nikita Alexeev, Anna Pologova, Max A. Alekseyev:
    Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs. 93-105
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    Jesper Jansson, Ramesh Rajaby:
    A More Practical Algorithm for the Rooted Triplet Distance. 106-126
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    Ron Zeira, Ron Shamir:
    Sorting by Cuts, Joins, and Whole Chromosome Duplications. 127-137
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    Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano:
    Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level. 138-152
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    Elizabeth S. Allman, John A. Rhodes, Seth Sullivant:
    Statistically Consistent _k_-mer Methods for Phylogenetic Tree Reconstruction. 153-171
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    Xin Tian, Ming-Yuan Xin, Jian Luo, Mingyao Liu, Zhen-Ran Jiang:
    Identification of Genes Involved in Breast Cancer Metastasis by Integrating Protein-Protein Interaction Information with Expression Data. 172-182
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    Jie Zhou:
    Effect of Protein Repetitiveness on Protein-Protein Interaction Prediction Results Using Support Vector Machines. 183-192

Volume 24, Number 3, March 2017

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    Bartek Wilczynski, Jerzy Tiuryn:
    FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules. 193-199
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    Celine Prakash, Arndt von Haeseler:
    An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile. 200-212
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    David M. Budden, Mitchell Jones:
    Cautionary Tales of Inapproximability. 213-216
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    Li Zhang, Han Wang, Lun Yan, Lingtao Su, Dong Xu:
    OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method. 217-228
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    Marc Cole, Steffen E. Eikenberry, Takahide Kato, Roman A. Sandler, Stanley M. Yamashiro, Vasilis Z. Marmarelis:
    Nonparametric Model of Smooth Muscle Force Production During Electrical Stimulation. 229-237
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    James Gigrich, Shahryar Sarkani, Thomas H. Holzer:
    A New Approach in Applying Systems Engineering Tools and Analysis to Determine Hepatocyte Toxicogenomics Risk Levels to Human Health. 238-254
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    Bruno Borguesan, Mario Inostroza-Ponta, Márcio Dorn:
    NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins. 255-265

Volume 24, Number 4, April 2017

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    Serge Sverdlov, Elizabeth Thompson:
    Combinatorial Methods for Epistasis and Dominance. 267-279
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    Anas Al-Okaily, Badar Almarri, Sultan Al Yami, Chun-Hsi Huang:
    Toward a Better Compression for DNA Sequences Using Huffman Encoding. 280-288
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    Doo Yang, Ilya Ioshikhes:
    Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns. 289-298
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    Lianping Yang, Weilin Zhang:
    A Multiresolution Graphical Representation for Similarity Relationship and Multiresolution Clustering for Biological Sequences. 299-310
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    Viktor Jonsson, Tobias Österlund, Olle Nerman, Erik Kristiansson:
    Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes. 311-326
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    Priya S. Venkat, Krishna R. Narayanan, Aniruddha Datta:
    A Bayesian Network-Based Approach to Selection of Intervention Points in the Mitogen-Activated Protein Kinase Plant Defense Response Pathway. 327-339
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    Grigoriy Gogoshin, Eric Boerwinkle, Andrei S. Rodin:
    New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data. 340-356
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    Audrone Jakaitiene, Mariano Avino, Mario Rosario Guarracino:
    Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments. 357-367
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    Ying Wang, Haiyan Hu, Xiaoman Li:
    rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database. 368-375

Volume 24, Number 5, May 2017

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    Amrit Dhar, Vladimir N. Minin:
    Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time. 377-399
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    Gira Lee, Hokeun Sun:
    Selection Probability for Rare Variant Association Studies. 400-411
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    Nicola Yanev, Metodi Traykov, Peter Milanov, Borislav Yurukov:
    Protein Folding Prediction in a Cubic Lattice in Hydrophobic-Polar Model. 412-421
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    Damian Bogdanowicz, Krzysztof Giaro:
    Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions. 422-435
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    Sihai Yang, Xian-Hua Han, Yukako Tohsato, Koji Kyoda, Shuichi Onami, Ikuko Nishikawa, Yen-Wei Chen:
    Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of Caenorhabditis elegans. 436-446
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    David Barrios, Carlos Prieto:
    D3GB: An Interactive Genome Browser for R, Python, and WordPress. 447-449
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    Ngoc Tam L. Tran, Chun-Hsi Huang:
    Cloud-based MOTIFSIM: Detecting Similarity in Large DNA Motif Data Sets. 450-459
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    Rajat Anand, Samrat Chatterjee:
    Extracting Genes Involved in Disease from a Connected Network of Perturbed Biological Processes. 460-469

Volume 24, Number 6, June 2017

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    Preface: Selected Papers from RECOMB 2016. 471
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    Chandler Zuo, Kailei Chen, Sündüz Keles:
    A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets. 472-485
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    Hao Wang, Joel McManus, Carl Kingsford:
    Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. 486-500
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    Meghana Kshirsagar, Keerthiram Murugesan, Jaime G. Carbonell, Judith Klein-Seetharaman:
    Multitask Matrix Completion for Learning Protein Interactions Across Diseases. 501-514
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    Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp:
    Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. 515-523
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    Nicoló Fusi, Jennifer Listgarten:
    Flexible Modeling of Genetic Effects on Function-Valued Traits. 524-535
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    Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald:
    LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. 536-546
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    David Pellow, Darya Filippova, Carl Kingsford:
    Improving Bloom Filter Performance on Sequence Data Using _k_-mer Bloom Filters. 547-557
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    Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky:
    Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. 558-570
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    Mingfu Shao, Bernard M. E. Moret:
    On Computing Breakpoint Distances for Genomes with Duplicate Genes. 571-580
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    Kristoffer Sahlin, Mattias Frånberg, Lars Arvestad:
    Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias. 581-589
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    Alexandru I. Tomescu, Paul Medvedev:
    Safe and Complete Contig Assembly Through Omnitigs. 590-602
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    Simona Cristea, Jack Kuipers, Niko Beerenwinkel:
    pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. 603-615
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    Daniel Doerr, Luis Antonio Brasil Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye:
    New Genome Similarity Measures based on Conserved Gene Adjacencies. 616-634

Volume 24, Number 7, July 2017

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    Haiyan Huang, Hua Tang, Jing Huang, Bin Chen, Ruixiao Liu, Rui (Sammi) Tang, Ying Lu, Peng Yang:
    Special Issue: Selected Papers of the Inaugural DahShu Data Science Symposium: Computational Precision Health (CPH 2017). 635-636
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    Yangyang Hao, Xiaoling Xuei, Lang Li, Harikrishna Nakshatri, Howard J. Edenberg, Yunlong Liu:
    RareVar: A Framework for Detecting Low-Frequency Single-Nucleotide Variants. 637-646
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    Tianzhou Ma, Faming Liang, Steffi Oesterreich, George C. Tseng:
    A Joint Bayesian Model for Integrating Microarray and RNA Sequencing Transcriptomic Data. 647-662
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    Funan Shi, Haiyan Huang:
    Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach. 663-674
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    Sara M. Clifton, Chaeryon Kang, Jingyi Jessica Li, Qi Long, Nirmish Shah, Daniel M. Abrams:
    Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain. 675-688
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    Hu Yang, Xiaoqin Liu:
    Studies on the Clustering Algorithm for Analyzing Gene Expression Data with a Bidirectional Penalty. 689-698
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    Huaying Fang, Chengcheng Huang, Hongyu Zhao, Minghua Deng:
    gCoda: Conditional Dependence Network Inference for Compositional Data. 699-708
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    Minhyeok Lee, Junhee Seok, Donghyun Tae, Hua Zhong, Sung Won Han:
    A Comparison of Two-Stage Approaches Based on Penalized Regression for Estimating Gene Networks. 709-720
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    Yoonha Choi, Marc Coram, Jie Peng, Hua Tang:
    A Poisson Log-Normal Model for Constructing Gene Covariation Network Using RNA-seq Data. 721-731

Volume 24, Number 8, August 2017

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    Abdoulaye Baniré Diallo, Engelbert Mephu Nguifo, Mohammed J. Zaki:
    Preface: Selected Papers from the Workshop Bioinformatics and Artificial Intelligence Joined with the International Joint Conference on Artificial Intelligence. 733
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    Vincent Picard, Anne Siegel, Jérémie Bourdon:
    A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. 734-745
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    Abedalrhman Alkhateeb, Luis Rueda:
    Zseq: An Approach for Preprocessing Next-Generation Sequencing Data. 746-755
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    Forough Firoozbakht, Iman Rezaeian, Michele D'agnillo, Lisa A. Porter, Luis Rueda, Alioune Ngom:
    An Integrative Approach for Identifying Network Biomarkers of Breast Cancer Subtypes Using Genomic, Interactomic, and Transcriptomic Data. 756-766
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    Ieva Vasiljeva, Ognjen Arandjelovic:
    Diagnosis Prediction from Electronic Health Records Using the Binary Diagnosis History Vector Representation. 767-786
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    Ham Ching Lam, Xuan Bi, Srinand Sreevatsan, Daniel Boley:
    Evolution and Vaccination of Influenza Virus. 787-798
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    Ahmed Halioui, Petko Valtchev, Abdoulaye Baniré Diallo:
    T-GOWler: Discovering Generalized Process Models Within Texts. 799-808
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    Ricardo de Souza Jacomini, David Correa Martins Jr., Felipe Leno da Silva, Anna Helena Reali Costa:
    GeNICE: A Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis. 809-830

Volume 24, Number 9, September 2017

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    Filippo Disanto, Noah A. Rosenberg:
    Enumeration of Ancestral Configurations for Matching Gene Trees and Species Trees. 831-850
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    Zheng Dai, David Becerra, Jérôme Waldispühl:
    On Stable States in a Topologically Driven Protein Folding Model. 851-862
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    Doaa Altarawy, Fatma-Elzahraa Eid, Lenwood S. Heath:
    PEAK: Integrating Curated and Noisy Prior Knowledge in Gene Regulatory Network Inference. 863-873
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    Daniel J. White, Jing Wang, Richard J. Hall:
    Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline. 874-881
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    Radhika Khanna, Sangeeta Mittal, Sujata Mohanty:
    Development of Computer Algorithm for Editing of Next Generation Sequencing Metagenome Data. 882-894
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    Ngoc Tam L. Tran, Chun-Hsi Huang:
    MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets. 895-905
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    Noa Godin, Jerry Eichler:
    The Mitochondrial Protein Atlas: A Database of Experimentally Verified Information on the Human Mitochondrial Proteome. 906-916
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    Byeonghyeok Park, Min-Jeong Baek, Byoungnam Min, In-Geol Choi:
    Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package. 917-922
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    Xiuli Ma, Guangyu Zhou, Jingbo Shang, Jingjing Wang, Jian Peng, Jiawei Han:
    Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining. 923-941
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    Yu Zheng, Xiaoyang Li, Lydia C. Manor, Hongbao Cao, Qiusheng Chen:
    An Integrative Computational Approach to Evaluate Genetic Markers for Chronic Lymphocytic Leukemia. 942-952

Volume 24, Number 10, October 2017

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    Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
    FSG: Fast String Graph Construction for De Novo Assembly. 953-968
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    Irina Balaur, Mansoor A. S. Saqi, Ana Barat, Artem Lysenko, Alexander Mazein, Christopher J. Rawlings, Heather J. Ruskin, Charles Auffray:
    EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. 969-980
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    Cheng-Hong Yang, Yu-Shiun Lin, Li-Yeh Chuang, Hsueh-Wei Chang:
    A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding. 981-994
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    Pedro Pablo González Pérez, Daniel J. Orta, Irving Peña, Eduardo C. Flores, José U. Ramírez, Hiram Isaac Beltrán, Salomón de Jesús Alas:
    A Computational Approach to Studying Protein Folding Problems Considering the Crucial Role of the Intracellular Environment. 995-1013
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    Marek C. Milewski, Karol Kamel, Anna Kurzynska-Kokorniak, Marcin K. Chmielewski, Marek Figlerowicz:
    EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments. 1014-1028
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    Lebin Thomas, Hari Ram, Ved Pal Singh:
    Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya. 1029-1042
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    Rajashekar Varma Kadumuri, Ramakrishna Vadrevu:
    LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures. 1043-1049
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    Haixin Ai, Runlin Wu, Li Zhang, Xuewei Wu, Junchao Ma, Huan Hu, Liangchao Huang, Wen Chen, Jian Zhao, Hongsheng Liu:
    pSuc-PseRat: Predicting Lysine Succinylation in Proteins by Exploiting the Ratios of Sequence Coupling and Properties. 1050-1059
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    Feilong Deng, Shi-Yi Chen, Zhou-Lin Wu, Yongsong Hu, Xianbo Jia, Song-Jia Lai:
    GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome. 1060-1064
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    Aldona Krupska:
    Influence of Oscillatory Enzyme Activity on the Reaction Kinetics: Mathematical Model. 1065-1070

Volume 24, Number 11, November 2017

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    Christina J. Castro, Terry Fei Fan Ng:
    U50: A New Metric for Measuring Assembly Output Based on Non-Overlapping, Target-Specific Contigs. 1071-1080
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    Mahmut Samil Sagiroglu, M. Oguzhan Külekci:
    A System Architecture for Efficient Transmission of Massive DNA Sequencing Data. 1081-1088
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    Pawel Blazej, Malgorzata Wnetrzak, Malgorzata Grabinska, Pawel Mackiewicz:
    Representations of Search Spaces in the Problem of Mutational Pressure Optimization According to Protein-Coding Sequences. 1089-1098
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    Yan Zhou, Baoxue Zhang, Gaorong Li, Tiejun Tong, Xiang Wan:
    GD-RDA: A New Regularized Discriminant Analysis for High-Dimensional Data. 1099-1111
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    Shengqing Lv, Yimin Chen, Zeyu Li, Jiahui Lu, Ming-ke Gao, Rongrong Lu:
    Application of Time-Frequency Domain Transform to Three-Dimensional Interpolation of Medical Images. 1112-1124
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    Gesiele Almeida Barros-Carvalho, Marie-Anne Van Sluys, Fabrício Martins Lopes:
    An Efficient Approach to Explore and Discriminate Anomalous Regions in Bacterial Genomes Based on Maximum Entropy. 1125-1133
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    Natacha Cerisier, Leslie Regad, Dhoha Triki, Anne-Claude Camproux, Michel Petitjean:
    Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets. 1134-1137
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    Andrey Kechin, Uljana Boyarskikh, Alexander E. Kel, Maxim Filipenko:
    cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. 1138-1143
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    Álvaro Rubio-Largo, Leonardo Vanneschi, Mauro Castelli, Miguel A. Vega-Rodríguez:
    Reducing Alignment Time Complexity of Ultra-Large Sets of Sequences. 1144-1154

Volume 24, Number 12, December 2017

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    Nikita A. Sakhanenko, James Kunert-Graf, David J. Galas:
    The Information Content of Discrete Functions and Their Application in Genetic Data Analysis. 1153-1178
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    Ron Zeira, Meirav Zehavi, Ron Shamir:
    A Linear-Time Algorithm for the Copy Number Transformation Problem. 1179-1194
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    Wenbin Chen, William Hendrix, Nagiza F. Samatova:
    The Application of the Weighted _k_-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways. 1195-1211
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    Cheng-Hong Yang, Yu-Da Lin, Li-Yeh Chuang, Jin-Bor Chen, Hsueh-Wei Chang:
    Joint Analysis of SNP-SNP-Environment Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm. 1212-1225
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    Haitham Elmarakeby, Mostafa Arefiyan, Elijah Myers, Song Li, Ruth Grene, Lenwood S. Heath:
    Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language. 1226-1229
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    Wenhe Su, Xiangke Liao, Yutong Lu, Quan Zou, Shaoliang Peng:
    Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework. 1230-1242
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    Chao Pei, Shu-Lin Wang, Jianwen Fang, Wei Zhang:
    GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif. 1243-1253
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    Shin-Fu Tsai, Chih-Wei Tung, Chen-An Tsai, Chen-Tuo Liao:
    An Exhaustive Scan Method for SNP Main Effects and SNP × SNP Interactions Over Highly Homozygous Genomes. 1254-1264
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    Samana Shrestha, Adam Vanasse, Leon N. Cooper, Michael Antosh:
    Gene Expression as a Dosimeter in Irradiated Drosophila melanogaster. 1265-1274
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    MD Shahinuzzaman, Dipak Barua:
    A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein-Protein Interaction. 1275-1283

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