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ORCIDJournal of Computational Biology, Volume 30
Volume 30, Number 1, January 2023
- Acknowledgment of Reviewers 2022. 1-2
- Sumaira Zaman, Samuel Sledzieski, Bonnie Berger, Yi-Chieh Wu, Mukul S. Bansal
:
virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. 3-20 - Soumitra Pal, Brian Oliver, Teresa M. Przytycka:
Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus. 21-40 - Biing-Feng Wang:
Fast Algorithms for the Simplified Partial Digest Problem. 41-51 - Ozgur E. Akman, Kevin Doherty, Benjamin J. Wareham:
BDEtools: A MATLAB Package for Boolean Delay Equation Modeling. 52-69 - Dennis R. Goulet, Yongqi Yan, Palak Agrawal, Andrew B. Waight, Amanda Nga-sze Mak, Yi Zhu:
Codon Optimization Using a Recurrent Neural Network. 70-81 - Chaochao Yan, Jinyu Yang, Hehuan Ma, Sheng Wang, Junzhou Huang:
Molecule Sequence Generation with Rebalanced Variational Autoencoder Loss. 82-94 - Ananthan Nambiar, Simon Liu, Maeve Heflin, John Malcolm Forsyth, Sergei Maslov, Mark Hopkins, Anna M. Ritz:
Transformer Neural Networks for Protein Family and Interaction Prediction Tasks. 95-111 - Jian Shao, Ziqing Liu, Shaoyun Li, Benrui Wu, Zedong Nie, Yuefei Li, Kaixin Zhou:
Continuous Glucose Monitoring Time Series Data Analysis: A Time Series Analysis Package for Continuous Glucose Monitoring Data. 112-116
Volume 30, Number 2, February 2023
- Mai Alzamel, Christopher Hampson, Costas S. Iliopoulos, Fatima Vayani:
Preface: MatBio 2021 Special Section. 117 - Mona Meghdari Miardan, Arash Jamshidpey, David Sankoff:
Escape from Parsimony of a Double-Cut-and-Join Genome Evolution Process. 118-130 - Jamie J. Alnasir, Hugh P. Shanahan:
Intra-Exon Motif Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in RNA-Seq. 131-148 - Geoffrey Brian Golding, Holly Koponen, Neerja Mhaskar, W. F. Smyth:
Computing Maximal Covers for Protein Sequences. 149-160 - Md. Shamsuzzoha Bayzid:
Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees. 161-175 - Akito Yamamoto, Tetsuo Shibuya:
Privacy-Preserving Statistical Analysis of Genomic Data Using Compressive Mechanism with Haar Wavelet Transform. 176-188 - Shijia Wang, Shufei Ge, Benjamin Sobkowiak, Liangliang Wang, Louis Grandjean, Caroline Colijn, Lloyd T. Elliott:
Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix. 189-203 - Akshara Pande, Sumeet Patiyal, Anjali Lathwal, Chakit Arora, Dilraj Kaur, Anjali Dhall, Gaurav Mishra, Harpreet Kaur, Neelam Sharma, Shipra Jain, Salman Sadullah Usmani, Piyush Agrawal, Rajesh Kumar, Vinod Kumar, Gajendra P. S. Raghava:
Pfeature: A Tool for Computing Wide Range of Protein Features and Building Prediction Models. 204-222 - Heewon Park, Seiya Imoto, Satoru Miyano:
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. 223-243
Volume 30, Number 3, March 2023
- Muhammad Ali Nayeem, Naser Anjum Samudro, Mohammad Saifur Rahman, M. Sohel Rahman:
MAMMLE: A Framework for Phylogeny Estimation Based on Multiobjective Application-aware Multiple Sequence Alignment and Maximum Likelihood Ensemble. 245-249 - DeAngelo Wilson, John D. Rogers:
Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting. 250-260 - Damian Bogdanowicz, Krzysztof Giaro:
Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages. 261-276 - Dakota Dragomir, Elizabeth S. Allman, John A. Rhodes:
Parameter Identifiability of a Multitype Pure-Birth Model of Speciation. 277-292 - Jie Ren, Huaimin Yuan, Qimin Zhang:
Positivity Preserving Truncated Euler-Maruyama Scheme for the Stochastic Age-Structured HIV/AIDS Model. 293-322 - Andrew Banman, Nikita A. Sakhanenko, James Kunert-Graf, David J. Galas:
ApoE Modifier Alleles for Alzheimer's Disease Discovered by Information Theory Dependency Measures: MIST Software Package. 323-336 - Shilong Zhang, Sufang Wang:
ATAC-DEA: A Web-Based ATAC-Seq Data Differential Peak and Annotation Analysis Application. 337-345 - Malvika Ashok, Abhishek Gupta:
Automatic Segmentation of Organs-at-Risk in Thoracic Computed Tomography Images Using Ensembled U-Net InceptionV3 Model. 346-362
Volume 30, Number 4, April 2023
- Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). 363-365 - Audrey Mitchell, Marco Ruiz, Soua Yang, Chen Wang, Jaime I. Dávila:
Excerno: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival. 366-375 - Yi Li, Mandy Chen, Joshy George, Edison T. Liu, Radha Murthy-Karuturi:
Adaptive Sentinel Testing in Workplace for COVID-19 Pandemic. 376-390 - Saima Sultana Tithi, Frank O. Aylward, Roderick V. Jensen, Liqing Zhang:
FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data. 391-408 - Jiahui Tan, Yutong Zhao, Cara Burns, Dechao Tian, Kun Zhao:
Novel Network Method Major Minor Variation Clustering Enables Identification of Poliovirus Clusters with High-Resolution Linkages. 409-419 - David S. Campo, Alexander Mosa, Yury Khudyakov:
A Novel Information-Theory-Based Genetic Distance That Approximates Phenotypic Differences. 420-431 - Sarwan Ali, Babatunde Bello, Zahra Tayebi, Murray Patterson:
Characterizing SARS-CoV-2 Spike Sequences Based on Geographical Location. 432-445 - Fiona Senchyna, Rahul Singh:
Dynamic Epidemiological Networks: A Data Representation Framework for Modeling and Tracking of SARS-CoV-2 Variants. 446-468 - Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson:
Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. 469-491 - Leonid Bunimovich, Athulya Ram:
Local Immunodeficiency: Combining Cross-Immunoreactivity Networks. 492-501 - Bikram Sahoo, Zandra Pinnix, Seth Sims, Alex Zelikovsky:
Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer. 502-517 - Jirí C. Moravec, Robert Lanfear, David L. Spector, Sarah D. Diermeier, Alex Gavryushkin:
Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data. 518-537 - Sahar Al Seesi, Anas Al-Okaily, Tatiana Shcheglova, Elham Sherafat, Fahad Alqahtani, Adam T. Hagymasi, Anupinder Kaur, Pramod Kumar Srivastava, Ion I. Mandoiu:
GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction. 538-551
Volume 30, Number 5, May 2023
- Takeyuki Tamura, Ai Muto-fujita, Yukako Tohsato, Tomoyuki Kosaka:
Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-Integer Linear Programming for Metabolite Production in Constraint-Based Models: gDel_minRN. 553-568 - Anna Pacínková, Vlad Popovici:
IntOMICS: A Bayesian Framework for Reconstructing Regulatory Networks Using Multi-Omics Data. 569-574 - Fang-Zhen Li, Xuefen Zhang, Hui-Ying Cai, Ling-Qiang Ran, Hai-Yan Zhou, Zhi-E. Liu:
Chromosome Three-Dimensional Structure Reconstruction: An Iterative ShRec3D Algorithm. 575-587 - Zhijie Chen, Tianhao Yan, Zhanwen Yang:
Numerical Analysis of Linearly Implicit Methods for Discontinuous Nonlinear Gurtin-MacCamy Model. 588-608 - Donghui Son, Jaejik Kim:
Estimation of Ordinary Differential Equation Models for Gene Regulatory Networks Through Data Cloning. 609-618 - Guo Mao, Zhengbin Pang, Ke Zuo, Jie Liu:
Gene Regulatory Network Inference Using Convolutional Neural Networks from scRNA-seq Data. 619-631
Volume 30, Number 6, May 2023
- Margherita Cavattoni, Matteo Comin:
ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs. 633-647 - Nozomi Hasegawa, Kana Shimizu:
Efficient Colored de Bruijn Graph for Indexing Reads. 648-662 - Yi Liu, Gang Li:
Sure Joint Screening for High Dimensional Cox's Proportional Hazards Model Under the Case-Cohort Design. 663-677 - Nafiseh Sedaghat, Tamon Stephen, Leonid Chindelevitch:
Speeding Up the Structural Analysis of Metabolic Network Models Using the Fredman-Khachiyan Algorithm B. 678-694 - Zong Wang, Qimin Zhang:
Positivity-Preserving Numerical Method and Relaxed Control for Stochastic Susceptible-Infected-Vaccinated Epidemic Model with Markov Switching. 695-725 - Nathan P. Manes, Jian Song, Aleksandra Nita-lazar:
EnsMOD: A Software Program for Omics Sample Outlier Detection. 726-735
Volume 30, Number 7, July 2023
- Hyundoo Jeong, Jose Lugo-Martinez, Anna M. Ritz, Yijie Wang, Chi Zhang:
Special Issue Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC) Workshop (2022). 737 - Hong Seo Lim, Peng Qiu:
Quantifying Cell-Type-Specific Differences of Single-Cell Datasets Using Uniform Manifold Approximation and Projection for Dimension Reduction and Shapley Additive exPlanations. 738-750 - Puhua Niu, Maria J. Soto, Shuai Huang, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian:
Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction. 751-765 - Michael Robben, Mohammad Sadegh Nasr, Avishek Das, Jai Prakash Veerla, Manfred Huber, Justyn Jaworski, Jon Weidanz, Jacob M. Luber:
Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology. 766-782 - Jhonatan Tavori, Hanoch Levy:
On the Convexity of the Effective Reproduction Number. 783-795 - Ziqi Ke, Haris Vikalo:
Graph-Based Reconstruction and Analysis of Disease Transmission Networks Using Viral Genomic Data. 796-813 - Tunç Basar Köse, Jiarong Li, Anna M. Ritz:
Growing Directed Acyclic Graphs: Optimization Functions for Pathway Reconstruction Algorithms. 814-828
Volume 30, Number 8, August 2023
- Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
Special Issue, Part I 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022). 829-830 - Arjun Srivatsa, Haoyun Lei, Russell Schwartz:
A Clonal Evolution Simulator for Planning Somatic Evolution Studies. 831-847 - Zhen-Chang Wang, Jin-Xing Liu, Junliang Shang, Ling-Yun Dai, Chun-Hou Zheng, Juan Wang:
ARGLRR: A Sparse Low-Rank Representation Single-Cell RNA-Sequencing Data Clustering Method Combined with a New Graph Regularization. 848-860 - Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias:
Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information. 861-876 - Xiaoshu Zhu, Liyuan Pang, Xiaojun Ding, Wei Lan, Shuang Meng, Xiaoqing Peng:
A Gene Correlation Measurement Method for Spatial Transcriptome Data Based on Partitioning and Distribution. 877-888 - Qian Qiao, Shasha Yuan, Junliang Shang, Jin-Xing Liu:
Multi-View Enhanced Tensor Nuclear Norm and Local Constraint Model for Cancer Clustering and Feature Gene Selection. 889-899 - Ying Yu, Tian Qiu, Junwen Duan, Jian-Xin Wang:
Multigranularity Label Prediction Model for Automatic International Classification of Diseases Coding in Clinical Text. 900-911 - Xiaobo Li, Yi-Jia Zhang, Xingwang Li, Xianwei Pan, Jian Wang, Mingyu Lu:
Automatic International Classification of Diseases Coding via Note-Code Interaction Network with Denoising Mechanism. 912-925 - Yi Shen, Ying-Lian Gao, Juan Wang, Boxin Guan, Jin-Xing Liu:
Identification of Disease-Associated MicroRNAs Via Locality-Constrained Linear Coding-Based Ensemble Learning. 926-936 - Ying Wang, Jin-Xing Liu, Juan Wang, Junliang Shang, Ying-Lian Gao:
A Graph Representation Approach Based on Light Gradient Boosting Machine for Predicting Drug-Disease Associations. 937-947
Volume 30, Number 9, September 2023
- Zhipeng Cai, Pavel Skums, Alexander Zeilkovsky:
Special Issue, Part 2 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022). 949-950 - Zhichao Wang, Xuelei Li, Jianping Fan, Jintao Meng, Zhenli Lin, Yi Pan, Yanjie Wei:
SWsnn: A Novel Simulator for Spiking Neural Networks. 951-960 - An Huang, Xiaolan Xie, Xiaojun Yao, Huanxiang Liu, Xiaoqi Wang, Shaoliang Peng:
HF-DDI: Predicting Drug-Drug Interaction Events Based on Multimodal Hybrid Fusion. 961-971 - Da Liu, Yi-Jia Zhang, Ming Yang, Jianyuan Yuan, Wen Qu:
Extracting Mutant-Affected Protein-Protein Interactions via Gaussian-Enhanced Representation and Contrastive Learning. 972-984 - Peixuan Zhou, Yi-Jia Zhang, Zeqian Li, Kuo Pang, Di Zhao:
Protein Complex Identification Based on Heterogeneous Protein Information Network. 985-998 - Susanne Zabel, Jennifer Müller, Friedrich Götz, Kay Nieselt:
BLASTphylo: An Interactive Web Tool for Taxonomic and Phylogenetic Analysis of Prokaryotic Genes. 999-1008 - Akshay Juyal, Roya Hosseini, Daniel Novikov, Mark Grinshpon, Alex Zelikovsky:
Reconstruction of Viral Variants via Monte Carlo Clustering. 1009-1018 - Jiancheng Zhong, Pan Cui, Yihong Zhu, Qiu Xiao, Zuohang Qu:
DAHNGC: A Graph Convolution Model for Drug-Disease Association Prediction by Using Heterogeneous Network. 1019-1033 - Liang Pan, Xia Xiao, Shengyun Liu, Shaoliang Peng:
An Integration Framework of Secure Multiparty Computation and Deep Neural Network for Improving Drug-Drug Interaction Predictions. 1034-1045 - Boyan Yordanov, Sara-Jane Dunn, Colin Gravill, Himanshu Arora, Hillel Kugler, Christoph M. Wintersteiger:
The Reasoning Engine: A Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models. 1046-1058
Volume 30, Number 10, October 2023
- Tom Wilson, Duong H. T. Vo, Thomas Thorne:
Identifying Subpopulations of Cells in Single-Cell Transcriptomic Data: A Bayesian Mixture Modeling Approach to Zero Inflation of Counts. 1059-1074 - Xianglong Liang, Hokeun Sun:
Weighted Selection Probability to Prioritize Susceptible Rare Variants in Multi-Phenotype Association Studies with Application to a Soybean Genetic Data Set. 1075-1088 - Masaru Nakajima, Andrew D. Smith:
Counting Distinguishable RNA Secondary Structures. 1089-1097 - Xiaochen Yang, Zhanwen Yang, Chiping Zhang:
Numerical Analysis of Split-Step Backward Euler Method with Truncated Wiener Process for a Stochastic Susceptible-Infected-Susceptible Model. 1098-1111 - Arunothai Kanlaya, Chakkrid Klin-Eam:
Constructing Double Cyclic Codes over F2+uF2 for DNA Codes. 1112-1130 - Hongliang Zou, Wanting Yu:
Integrating Low-Order and High-Order Correlation Information for Identifying Phage Virion Proteins. 1131-1143
Volume 30, Number 11, November 2023
- Haixu Tang:
Preface: RECOMB 2023 Special Issue. 1145 - Yasamin Tabatabaee, Sebastien Roch, Tandy J. Warnow:
QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. 1146-1181 - Ghanshyam Chandra, Chirag Jain:
Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs. 1182-1197 - Spencer Krieger, John D. Kececioglu:
Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference. 1198-1225 - Riza Özçelik, Alperen Bag, Berk Atil, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli:
A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. 1226-1239 - Melih Barsbey, Riza Özçelik, Alperen Bag, Berk Atil, Arzucan Özgür, Elif Ozkirimli:
A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta. 1240-1245 - Chihao Zhang, Shihua Zhang, Jingyi Jessica Li:
A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification. 1246-1249
Volume 30, Number 12, December 2023
- Hongyu Zheng, Guillaume Marçais, Carl Kingsford:
Creating and Using Minimizer Sketches in Computational Genomics. 1251-1276 - Luiz Augusto G. Silva, Luis Antonio Brasil Kowada, Maria Emília M. T. Walter:
A Barrier for Further Approximating Sorting by Transpositions. 1277-1288 - Rui Su, Jujuan Zhuang, Shuhan Liu, Di Liu, Kexin Feng:
EnILs: A General Ensemble Computational Approach for Predicting Inducing Peptides of Multiple Interleukins. 1289-1304 - Shipra Jain, Kawal Preet Kaur Malhotra, Sumeet Patiyal, Gajendra Pal Singh Raghava:
A Highly Accurate Model for Screening Prostate Cancer Using Propensity Index Panel of Ten Genes. 1305-1314 - Gladys M. Cavero Rozas, Jose M. Cisneros Mandujano, Yomali A. Ferreyra Chombo, Daniela V. Moreno Rencoret, Yerko M. Ortiz Mora, Martín Eduardo Gutiérrez Pescarmona, Alberto J. Donayre Torres:
pyBrick-DNA: A Python-Based Environment for Automated Genetic Component Assembly. 1315-1321 - Jan Pawel Jastrzebski, Stefano Pascarella, Aleksandra Lipka, Slawomir Dorocki:
IncRna: The R Package for Optimizing lncRNA Identification Processes. 1322-1326
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