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ORCIDJournal of Computational Biology, Volume 25
Volume 25, Number 1, January 2018
- Jing He, Kamal Al-Nasr
, Weitao Sun, Yonggang Lu:
Special IssuePreface: The 9th Computational Structural Bioinformatics Workshop. 1-2 - Jayvee R. Abella, Mark Moll, Lydia E. Kavraki:
Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods. 3-20 - Kamal Al-Nasr, Christopher Jones, Feras Yousef, Ruba Jebril:
PEM-fitter: A Coarse-Grained Method to Validate Protein Candidate Models. 21-32 - Tatiana Maximova, Zijing Zhang, Daniel Carr, Erion Plaku, Amarda Shehu:
Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements. 33-50 - Nathan Clement, Muhibur Rasheed, Chandrajit L. Bajaj:
Viral Capsid Assembly: A Quantified Uncertainty Approach. 51-71 - Jin Seob Kim, Gregory S. Chirikjian:
Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures. 72-88 - Michael Siderius, Filip Jagodzinski:
Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach. 89-102 - Weitao Sun:
The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules. 103-113 - Tunazzina Islam, Michael Poteat, Jing He:
Quantification of Twist from the Central Lines of β-Strands. 114-120
Volume 25, Number 2, February 2018
- Stephen F. Altschul, Andrew F. Neuwald:
Initial Cluster Analysis. 121-129 - Heewon Park, Teppei Shimamura, Seiya Imoto, Satoru Miyano:
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks. 130-145 - Jin-Hua He, Ze-Ping Han, Mao-Xian Zou, Li Wang, Yu Bing Lv, Jia Bin Zhou, Ming-Rong Cao, Yu-Guang Li:
Analyzing the LncRNA, miRNA, and mRNA Regulatory Network in Prostate Cancer with Bioinformatics Software. 146-157 - Cheng-Hong Yang, Yi-Cheng Chiang, Li-Yeh Chuang, Yu-Da Lin:
A CpGCluster-Teaching-Learning-Based Optimization for Prediction of CpG Islands in the Human Genome. 158-169 - Fatima A. Morad, Omran M. Rashidi, Saida S. Sadath, Faisal A. Al-Allaf, Mohammad Athar, Mohamed N. Alama, Sherif E. Edris, Nabeel S. Bondagji, Noor Ahmad Shaik, Babajan Banaganapalli, Zuhier Awan:
In Silico Approach to Investigate the Structural and Functional Attributes of Familial Hypercholesterolemia Variants Reported in the Saudi Population. 170-181 - Mohammad S. Rahman, Ann E. Nicholson, Gholamreza Haffari:
HetFHMM: A Novel Approach to Infer Tumor Heterogeneity Using Factorial Hidden Markov Models. 182-193 - Evaldo Bezerra Costa:
MELC Genomics: A Framework for De Novo Genome Assembly. 194-199 - Jordi Vilaplana, Rui Alves, Francesc Solsona, Jordi Mateo, Ivan Teixido, Marc Pifarré:
MetReS, an Efficient Database for Genomic Applications. 200-213 - Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson:
A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands. 214-235 - Sawsan Kanj, Thomas Brüls, Stéphane Gazut:
Shared Nearest Neighbor Clustering in a Locality Sensitive Hashing Framework. 236-250
Volume 25, Number 3, March 2018
Preface
- Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
Special IssuePreface: 13th International Symposium on BioinformaticsResearch and Applications (ISBRA 2017). 251-252
- Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu, Wing-Kai Hon:
Reconstructing One-Articulated Networks with Distance Matrices. 253-269 - Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang:
ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer. 270-281 - Michal Aleksander Ciach, Mateusz Krzysztof Lacki, Blazej Miasojedow, Frederik Lermyte, Dirk Valkenborg, Frank Sobott, Anna Gambin:
Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry. 282-301 - Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang:
A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting. 302-312 - Rashika Mishra, Ovidiu Daescu, Patrick Leavey, Dinesh Rakheja, Anita Sengupta:
Convolutional Neural Network for Histopathological Analysis of Osteosarcoma. 313-325 - Albert Ng, Dong Si:
Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing. 326-336 - Xiuchun Xiao, Bing Liu, Jing Zhang, Xueli Xiao, Yi Pan:
An Optimized Method for Bayesian Connectivity Change Point Model. 337-347 - Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente:
Unbiased Taxonomic Annotation of Metagenomic Samples. 348-360 - Lei Wang, Zhu-Hong You, Xing Chen, Shixiong Xia, Feng Liu, Xin Yan, Yong Zhou, Kejian Song:
A Computational-Based Method for Predicting Drug-Target Interactions by Using Stacked Autoencoder Deep Neural Network. 361-373
Volume 25, Number 4, April 2018
- Ana M. Jelovic, Nenad S. Mitic, Samira Eshafah, Milos V. Beljanski:
Finding Statistically Significant Repeats in Nucleic Acids and Proteins. 375-387 - Hong Wang, Xiaolin Chen, Gang Li:
Survival Forests with R-Squared Splitting Rules. 388-395 - Lingling Li, Tianhai Tian, Xinan Zhang:
Mutation Mechanisms of Human Breast Cancer. 396-404 - Hsin-Hsiung Huang, Senthil B. Girimurugan:
A Novel Real-Time Genome Comparison Method Using Discrete Wavelet Transform. 405-416 - Jaeil Ahn, Brian Conkright, Simina M. Boca, Subha Madhavan:
POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations. 417-429 - Andreas M. Kist, Angelika Lampert, Andrias O. O'Reilly:
DIsulfide Mapping PLanner Software Tool. 430-434 - Jun Fan, Jing Yang, Zhenran Jiang:
Prediction of Central Nervous System Side Effects Through Drug Permeability to Blood-Brain Barrier and Recommendation Algorithm. 435-443 - Andrey Minarsky, Nadya Morozova, Robert Penner, Christophe Soulé:
Theory of Morphogenesis. 444-450 - Rodrigo Ligabue-Braun, Bruno Borguesan, Hugo Verli, Mathias J. Krause, Márcio Dorn:
Everyone Is a Protagonist: Residue Conformational Preferences in High-Resolution Protein Structures. 451-465
Volume 25, Number 5, May 2018
- Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev:
AllSome Sequence Bloom Trees. 467-479 - Néli J. Fonseca-Júnior, Marcelo Q. L. Afonso, Lucas Carrijo de Oliveira, Lucas Bleicher:
PFstats: A Network-Based Open Tool for Protein Family Analysis. 480-486 - Qiang-Hui Guo, Jian Wang, Zhao Xu:
Approximation Algorithms for Protein Folding in the Hydrophobic-Polar Model on 3D Hexagonal Prism Lattice. 487-498 - Yang Xu, Xiaochun Luo:
PyPathway: Python Package for Biological Network Analysis and Visualization. 499-504 - Miha Moskon, Nikolaj Zimic, Miha Mraz:
Grohar: Automated Visualization of Genome-Scale Metabolic Models and Their Pathways. 505-508 - Shuangyang Wu, Wanfei Liu, Hasan Awad Aljohi, Sarah A. Alromaih, Ibrahim O. Alanazi, Qiang Lin, Jun Yu, Songnian Hu:
REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results. 509-516 - Carlos N. Fischer, Victor De A. Campos, Victor H. Barella:
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models. 517-527
Volume 25, Number 6, June 2018
- Yongan Zhao, Xiaofeng Wang, Haixu Tang:
A Secure Alignment Algorithm for Mapping Short Reads to Human Genome. 529-540 - Albert Vexler, Jihnhee Yu:
To t-Test or Not to t-Test? A p-Values-Based Point of View in the Receiver Operating Characteristic Curve Framework. 541-550 - Lu Zeng, Stephen M. Pederson, Danfeng Cao, Zhipeng Qu, Zhiqiang Hu, David L. Adelson, Chaochun Wei:
Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact. 551-562 - Xiaodong Wang, Lei Wang:
A Simple Linear Space Algorithm for Computing Nonoverlapping Inversion and Transposition Distance in Quadratic Average Time. 563-575 - Yan Dong, Hongbao Cao, Zhigang Liang:
A Curated Target Gene Pool Assisting Early Disease Prediction and Patient-Specific Treatment for Small Cell Lung Cancer. 576-585 - Lizhen Liu, Xiaowu Sun, Wei Song, Chao Du:
A Method for Predicting Protein Complexes from Dynamic Weighted Protein-Protein Interaction Networks. 586-605 - Chelsea M. Lawhorn, Rachel Schomaker, Jonathan T. Rowell, Olav Rueppell:
Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap. 606-612 - Markus Boenn:
ShRangeSim: Simulation of Single Nucleotide Polymorphism Clusters in Next-Generation Sequencing Data. 613-622
Volume 25, Number 7, July 2018
Preface
- S. Cenk Sahinalp:
Preface: Selected Articles from RECOMB 2017. 623
- Ashok Rajaraman, Jian Ma:
Toward Recovering Allele-specific Cancer Genome Graphs. 624-636 - Soyeon Ahn, Haris Vikalo:
aBayesQR: A Bayesian Method for Reconstruction of Viral Populations Characterized by Low Diversity. 637-648 - Benedict Paten, Jordan M. Eizenga, Yohei M. Rosen, Adam M. Novak, Erik Garrison, Glenn Hickey:
Superbubbles, Ultrabubbles, and Cacti. 649-663 - David Haussler, Maciej Smuga-Otto, Jordan M. Eizenga, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov:
A Flow Procedure for Linearization of Genome Sequence Graphs. 664-676 - Victoria Popic, Volodymyr Kuleshov, Michael P. Snyder, Serafim Batzoglou:
Fast Metagenomic Binning via Hashing and Bayesian Clustering. 677-688 - Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael:
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. 689-708 - Robert Osazuwa Ness, Karen Sachs, Parag Mallick, Olga Vitek:
A Bayesian Active Learning Experimental Design for Inferring Signaling Networks. 709-725 - Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald:
BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. 726-739 - Jesper Jansson, Andrzej Lingas, Ramesh Rajaby, Wing-Kin Sung:
Determining the Consistency of Resolved Triplets and Fan Triplets. 740-754 - Brad Solomon, Carl Kingsford:
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. 755-765 - Chirag Jain, Alexander T. Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy:
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. 766-779 - Dan F. DeBlasio, John D. Kececioglu:
Adaptive Local Realignment of Protein Sequences. 780-793 - Regev Schweiger, Eyal Fisher, Elior Rahmani, Liat Shenhav, Saharon Rosset, Eran Halperin:
Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability. 794-808 - Xiaoqian Wang, Jingwen Yan, Xiaohui Yao, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin, Li Shen, Heng Huang:
Longitudinal Genotype-Phenotype Association Study through Temporal Structure Auto-Learning Predictive Model. 809-824 - Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach:
Dynamic Alignment-Free and Reference-Free Read Compression. 825-836
Volume 25, Number 8, August 2018
- Miguel A. Vega-Rodríguez, José M. Granado Criado:
Preface to the Special Issue: Parallel Computing in Computational Biology: A Technological Point of View. 837-840 - Esteban Pérez-Wohlfeil, Oswaldo Trelles:
Precise and Parallel Pairwise Metagenomic Comparisons. 841-849 - Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco:
Large-Scale Simulations of Bacterial Populations Over Complex Networks. 850-861 - Héctor Martínez, Sergio Barrachina, Maribel Castillo, Enrique S. Quintana-Ortí, Jordi Rambla De Argila, Xavier Farré, Arcadi Navarro:
FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters. 862-870 - Marek Nowicki, Davit Bzhalava, Piotr Bala:
Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in Java Library. 871-881 - Juan José Escobar, Julio Ortega, Antonio Francisco Díaz, Jesús González, Miguel Damas:
A Power-Performance Perspective to Multiobjective Electroencephalogram Feature Selection on Heterogeneous Parallel Platforms. 882-893 - Jordi Lladós, Fernando Cores, Fernando Guirado:
Scalable Consistency in T-Coffee Through Apache Spark and Cassandra Database. 894-906
- Jian-Xin Wen, Xiaoqin Li, Yu Chang:
Signature Gene Identification of Cancer Occurrence and Pattern Recognition. 907-916 - Elise Rosati, Morgan Madec, Jean-Baptiste Kammerer, Luc Hébrard, Christophe Lallement, Jacques Haiech:
Efficient Modeling and Simulation of Space-Dependent Biological Systems. 917-933 - Fengqian Pang, Heng Li, Yonggang Shi, Zhiwen Liu:
Computational Analysis of Cell Dynamics in Videos with Hierarchical-Pooled Deep-Convolutional Features. 934-953 - Tatsuhiko Naito:
Human Splice-Site Prediction with Deep Neural Networks. 954-961
Volume 25, Number 9, September 2018
- Jian Zhao, Jiasong Wang, Hongmei Jiang:
Detecting Periodicities in Eukaryotic Genomes by Ramanujan Fourier Transform. 963-975 - Tsukasa Fukunaga, Michiaki Hamada:
A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs. 976-986 - Yoonji Kim, Jaejik Kim:
Estimation of Dynamic Systems for Gene Regulatory Networks from Dependent Time-Course Data. 987-996 - Bandana Kumari, Ravindra Kumar, Manish Kumar:
Prediction of Rare Palmitoylation Events in Proteins. 997-1008 - Álvaro Rubio-Largo, Mauro Castelli, Leonardo Vanneschi, Miguel A. Vega-Rodríguez:
A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment. 1009-1022 - Komlan Atitey, Pavel Loskot, Paul Rees:
Determining the Transcription Rates Yielding Steady-State Production of mRNA in the Lac Genetic Switch of Escherichia coli. 1023-1039 - Nicholas B. Larson, Chen Wang, Jie Na, Ross A. Rowsey, William Edward Highsmith, Nicole L. Hoppman, Jean-Pierre A. Kocher, Eric W. Klee:
Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. 1040-1049 - Xinrui Huang, Sha Li, Song Gao:
Applying a Modified Wavelet Shrinkage Filter to Improve Cryo-Electron Microscopy Imaging. 1050-1058 - Joonyeon Park, Myeongji Cho, Hyeon S. Son:
Simulation Model of Bacterial Resistance to Antibiotics Using Individual-Based Modeling. 1059-1070
Volume 25, Number 10, October 2018
- Yu Bao, Morihiro Hayashida, Pengyu Liu, Masayuki Ishitsuka, Jose C. Nacher, Tatsuya Akutsu:
Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets. 1071-1090 - Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Kel, Valentina Giansanti, Ivan Merelli:
Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution. 1091-1105 - Marek Palkowski, Wlodzimierz Bielecki:
Parallel Tiled Codes Implementing the Smith-Waterman Alignment Algorithm for Two and Three Sequences. 1106-1119 - Irfan Kösesoy, Murat Gök, Cemil Öz:
PROSES: A Web Server for Sequence-Based Protein Encoding. 1120-1122 - Shisheng Wang, Wen Zheng, Liqiang Hu, Meng Gong, Hao Yang:
MixProTool: A Powerful and Comprehensive Web Tool for Analyzing and Visualizing Multigroup Proteomics Data. 1123-1127 - Jie Chen, Shirong Deng:
Detection of Copy Number Variation Regions Using the DNA-Sequencing Data from Multiple Profiles with Correlated Structure. 1128-1140 - Jan Voges, Ali Fotouhi, Jörn Ostermann, Muhammed Oguzhan Külekci:
A Two-Level Scheme for Quality Score Compression. 1141-1151 - Qie Liu, Min Liu, Wenfa Wu:
Strong/Weak Feature Recognition of Promoters Based on Position Weight Matrix and Ensemble Set-Valued Models. 1152-1160 - Xuedong Wang, Wenhui Shang, Yu Chang, Xiaoqin Li:
Methylation Signature Genes Identification of the Lung Squamous Cell Carcinoma Occurrence and Recognition Research. 1161-1169
Volume 25, Number 11, November 2018
- Yaron Orenstein, Yun William Yu, Bonnie Berger:
Joker de Bruijn: Covering k-Mers Using Joker Characters. 1171-1178 - Christopher L. Barrett, Qijun He, Fenix W. D. Huang, Christian M. Reidys:
An Efficient Dual Sampling Algorithm with Hamming Distance Filtration. 1179-1192 - Xinrui Zhou, Amihood Amir, Concettina Guerra, Gad M. Landau, Jarek Rossignac:
EDoP Distance Between Sets of Incomplete Permutations: Application to Bacteria Classification Based on Gene Order. 1193-1202 - Nikita Alexeev, Max A. Alekseyev:
Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters. 1203-1219 - Theodore Alexandrov, Nina Golyandina, David M. Holloway, Alexander Shlemov, Alexander V. Spirov:
Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data. 1220-1230 - Siamak K. Sorooshyari, Matthew P. Taylor, H. Vincent Poor:
Probabilistic Modeling of Pseudorabies Virus Infection in a Neural Circuit. 1231-1246 - Ali Yousefian Jazi, Jinwook Choi:
Sequential Integration of Fuzzy Clustering and Expectation Maximization for Transcription Factor Binding Site Identification. 1247-1256 - Tiago Tambonis, Marcelo Boareto, Vitor B. P. Leite:
Differential Expression Analysis in RNA-seq Data Using a Geometric Approach. 1257-1265 - Hui Yang, Hao Lv, Hui Ding, Wei Chen, Hao Lin:
iRNA-2OM: A Sequence-Based Predictor for Identifying 2′-O-Methylation Sites in Homo sapiens. 1266-1277 - Dinko Osmankovic, Semir Doric, Naris Pojskic, Lada Lukic Bilela:
New Approach to Detect Coiled Coil and Leucine Zipper Motifs in Protein Sequences. 1278-1283
Volume 25, Number 12, December 2018
- Jose M. J. Costa, Helcio R. B. Orlande, Viviane O. F. Lione, Antonio G. F. Lima, Tayná C. S. Cardoso, Leonardo Antonio Bermeo Varón:
Simultaneous Model Selection and Model Calibration for the Proliferation of Tumor and Normal Cells During In Vitro Chemotherapy Experiments. 1285-1300 - Vijaya Raghavan Rangamaran, Bharathram Uppili, Dharani Gopal, Kirubagaran Ramalingam:
EasyQC: Tool with Interactive User Interface for Efficient Next-Generation Sequencing Data Quality Control. 1301-1311 - Xiaoping Yan, Yu Huang, Jiabin Wu:
Identify Cross Talk Between Circadian Rhythm and Coronary Heart Disease by Multiple Correlation Analysis. 1312-1327 - Caio R. N. Santiago, Vivian M. Y. Pereira, Luciano A. Digiampietri:
Homology Detection Using Multilayer Maximum Clustering Coefficient. 1328-1338 - Matthias Werner, Pascal Fieth, Alexander Hartmann:
Large-Deviation Properties of Sequence Alignment of Correlated Sequences. 1339-1346 - Hsin-Yao Wang, Shih-Cheng Chang, Wan-Ying Lin, Chun-Hsien Chen, Szu-Hsien Chiang, Kai-Yao Huang, Bo-Yu Chu, Jang-Jih Lu, Tzong-Yi Lee:
Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing. 1347-1360 - Ming Yang, Louis Z. Yang:
Determining a Reasonable Range of Relative Numerical Tolerance Values for Simulating Deterministic Models of Biochemical Reactions. 1361-1364 - Snehalika Lall, Debajyoti Sinha, Sanghamitra Bandyopadhyay, Debarka Sengupta:
Structure-Aware Principal Component Analysis for Single-Cell RNA-seq Data. 1365-1373 - Jeonifer M. Garren, Jaejik Kim:
Bootstrapping Time-Course Gene Expression Data for Gene Networks: Application to Gene Relevance Networks. 1374-1384 - Yue Liu, Shu-Lin Wang, Jun-Feng Zhang:
Prediction of Microbe-Disease Associations by Graph Regularized Non-Negative Matrix Factorization. 1385-1394
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