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ORCIDJournal of Computational Biology, Volume 28
Volume 28, Number 1, January 2021
- Jael Sanyanda Wekesa
, Yushi Luan, Jun Meng:
Predicting Protein Functions Based on Differential Co-expression and Neighborhood Analysis. 1-18 - Obiora Cornelius Collins, Kevin Jan Duffy:
Mathematical Analyses on the Effects of Control Measures for a Waterborne Disease Model with Socioeconomic Conditions. 19-32 - Buwen Cao, Shuguang Deng, Hua Qin, Jiawei Luo, Guanghui Li, Cheng Liang:
Inferring MicroRNA-Disease Associations Based on the Identification of a Functional Module. 33-42 - Vishnu Kumar Sharma, Prasad V. Bharatam:
Identification of Selective Inhibitors of LdDHFR Enzyme Using Pharmacoinformatic Methods. 43-59 - Yang Yin, Yang-Fan Zou, Yu Xiao, Tian-Xi Wang, Ya-Ni Wang, Zhicheng Dong, Yuhu Huo, Bochen Yao, Ling-Bing Meng, Shuang-Xia Du:
Identification of Potential Hub Genes of Atherosclerosis Through Bioinformatic Analysis. 60-78 - Enfa Zhao, Hang Xie, Yushun Zhang:
Identification of Differentially Expressed Genes Associated with Idiopathic Pulmonary Arterial Hypertension by Integrated Bioinformatics Approaches. 79-88 - (Withdrawn) Screening of Clinical Factors Related to Prognosis of Breast Cancer Based on the Cox Proportional Risk Model. 89-98
- Yanwei Chen, Keke Wang, Mengyuan Shang, Shuangshuang Zhao, Zheng Zhang, Haizhen Yang, Zheming Chen, Rui Du, Qilong Wang, Baoding Chen:
Exploration of DNA Methylation-Driven Genes in Papillary Thyroid Carcinoma Based on the Cancer Genome Atlas. 99-114
Volume 28, Number 2, February 2021
- Ion I. Mandoiu, T. M. Murali, Giri Narasimhan, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019). 115-116 - Mohammad Mohebbi, Liang Ding, Russell L. Malmberg, Liming Cai:
Human MicroRNA Target Prediction via Multi-Hypotheses Learning. 117-132 - Shuzhen Kuang, Liangjiang Wang:
Deep Learning of Sequence Patterns for CCCTC-Binding Factor-Mediated Chromatin Loop Formation. 133-145 - Wutao Yin, Sakib Mostafa, Fang-Xiang Wu:
Diagnosis of Autism Spectrum Disorder Based on Functional Brain Networks with Deep Learning. 146-165 - Khajamoinuddin Syed, William C. Sleeman IV, Payal Soni, Michael Hagan, Jatinder Palta, Rishabh Kapoor, Preetam Ghosh:
Machine-Learning Models for Multicenter Prostate Cancer Treatment Plans. 166-184 - Matthew Hayes, Derrick Mullins, Angela Nguyen:
Complex Variant Discovery Using Discordant Cluster Normalization. 185-194 - Hsin-Hao Chen, Chung-Chin Lu:
Optimized Fluorescence-Based Detection in Single Molecule Synthesis Process. 195-208 - Ishwor Thapa, Hesham Ali:
A Multiomics Graph Database System for Biological Data Integration and Cancer Informatics. 209-219 - Chu-Yu Cheng, Chung-Chin Lu:
The Agility of a Neuron: Phase Shift Between Sinusoidal Current Input and Firing Rate Curve. 220-234
Volume 28, Number 3, March 2021
- Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias:
Genome Rearrangement Distance with Reversals, Transpositions, and Indels. 235-247 - Christopher L. Barrett, Andrei C. Bura, Qijun He, Fenix W. D. Huang, Thomas J. X. Li, Michael S. Waterman, Christian M. Reidys:
Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution. 248-256 - Gastone C. Castellani, Leon N. Cooper, Luciana Renata de Oliveira, Brian S. Blais:
Energy Consumption and Entropy Production in a Stochastic Formulation of BCM Learning. 257-268 - Jiasong Wang, Changchuan Yin:
A Fast Algorithm for Computing the Fourier Spectrum of a Fractional Period. 269-282 - Concettina Guerra, Sarang Joshi, Yinquan Lu, Francesco Palini, Umberto Ferraro Petrillo, Jarek Rossignac:
Rank-Similarity Measures for Comparing Gene Prioritizations: A Case Study in Autism. 283-295 - Angela M. Taravella Oill, Anagha J. Deshpande, Heini M. Natri, Melissa A. Wilson:
PopInf: An Approach for Reproducibly Visualizing and Assigning Population Affiliation in Genomic Samples of Uncertain Origin. 296-303 - Xiao Wang, Dan Hao, Haja N. Kadarmideen:
GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis. 304-316 - Yijun Xia, Juan Xie, Jun Zhao, Yin Lou, Dongsheng Cao:
Screening and Identification of Key Biomarkers in Melanoma: Evidence from Bioinformatic Analyses. 317-329 - Jie Yang, Qingchun Xu, Zhenyu Wang, Xun Lu, Liukui Pan, Jun Wu, Chen Wang:
Integrated Analysis of an lncRNA-Associated ceRNA Network Reveals Potential Biomarkers for Hepatocellular Carcinoma. 330-344
Volume 28, Number 4, April 2021
- Russell Schwartz:
RECOMB 2020 Special Issue. 345 - Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang:
Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning. 346-361 - Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang:
EPTool: A New Enhancing PSSM Tool for Protein Secondary Structure Prediction. 362-364 - Gizem Caylak, Öznur Tastan, A. Ercüment Çiçek:
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. 365-377 - Gizem Caylak, Öznur Tastan, A. Ercüment Çiçek:
A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing. 378-380 - Amatur Rahman, Paul Medevedev:
Representation of k-Mer Sets Using Spectrum-Preserving String Sets. 381-394 - Hongyu Zheng, Carl Kingsford, Guillaume Marçais:
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. 395-409 - Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye:
Computing the Rearrangement Distance of Natural Genomes. 410-431
Volume 28, Number 5, May 2021
- Kamran Ghasedi Dizaji, Wei Chen, Heng Huang:
Deep Large-Scale Multitask Learning Network for Gene Expression Inference. 485-500 - Brooks Paige, James Bell, Aurélien Bellet, Adrià Gascón, Daphne Ezer:
Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores. 435-451 - Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sébastien Roch:
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. 452-468 - Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael:
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. 469-484 - Songwei Ge, Haohan Wang, Amir Alavi, Eric P. Xing, Ziv Bar-Joseph:
Supervised Adversarial Alignment of Single-Cell RNA-seq Data. 501-513
Volume 28, Number 6, June 2021
- David J. Galas, James Kunert-Graf, Lisa Uechi, Nikita A. Sakhanenko:
Toward an Information Theory of Quantitative Genetics. 527-559 - Philipp Benner:
Computing Leapfrog Regularization Paths with Applications to Large-Scale K-mer Logistic Regression. 560-569 - Samaneh Yourdkhani, Elizabeth S. Allman, John A. Rhodes:
Parameter Identifiability for a Profile Mixture Model of Protein Evolution. 570-586 - Shijia Wang, Shufei Ge, Caroline Colijn, Priscila Biller, Liangliang Wang, Lloyd T. Elliott:
Estimating Genetic Similarity Matrices Using Phylogenies. 587-600 - Carlos Soto, Darshan W. Bryner, Nicola Neretti, Anuj Srivastava:
Toward a Three-Dimensional Chromosome Shape Alphabet. 601-618 - Jinuk Jung, Hyunwhan Joe, Kyung-Sik Ha, Jin-Muk Lim, Hong-Gee Kim:
Biomedical Entity Explorer: A Web Server for Biomedical Entity Exploration. 619-628 - Sarah E. Innis, Kelsie Reinaltt, Mete Civelek, Warren D. Anderson:
GSEAplot: A Package for Customizing Gene Set Enrichment Analysis in R. 629-631
Volume 28, Number 7, July 2021
- JCB Call for Papers for the Special Issue on "40 Years of Computational Biology: In Honor of Professor Michael Waterman's 80th Birthday": Deadline for Intention to submit: August 1, 2021 Deadline for Manuscript Submission: December 1, 2021. 633-635
- Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky:
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020). 636 - Wei Dai, Bingxi Chen, Wei Peng, Xia Li, Jiancheng Zhong, Jianxin Wang:
A Novel Multi-Ensemble Method for Identifying Essential Proteins. 637-649 - Lingzhi Zhu, Cheng Yan, Guihua Duan:
Prediction of Virus-Receptor Interactions Based on Improving Similarities. 650-659 - Gaoyan Wu, Mengyun Yang, Yaohang Li, Jianxin Wang:
De Novo Prediction of Drug-Target Interactions Using Laplacian Regularized Schatten p-Norm Minimization. 660-673 - Chun-Cheng Liu, Tao-Chuan Shih, Tun-Wen Pai, Chin-Hwa Hu, Wen-Shyong Tzou:
Enhanced Over-Representation Analysis for the Differential Regulation of Birc5a and HIF2α-Knockdown Approaches. 674-686 - Nian Wang, Min Zeng, Yiming Li, Fang-Xiang Wu, Min Li:
Essential Protein Prediction Based on node2vec and XGBoost. 687-700 - Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth, Daniel Merkle:
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry. 701-715 - Kseniia Cheloshkina, Islam Bzhikhatlov, Maria Poptsova:
Randomness in Cancer Breakpoint Prediction. 716-731 - Zhineng Chen, Sai Wang, Caiyan Jia, Kai Hu, Xiongjun Ye, Xuanya Li, Xieping Gao:
CRDet: Improving Signet Ring Cell Detection by Reinforcing the Classification Branch. 732-743 - Retraction of: A Study of Potential SARS-CoV-2 Antiviral Drugs and Preliminary Research of Their Molecular Mechanism, Based on Anti-SARS-CoV Drug Screening and Molecular Dynamics Simulation (doi: 10.1089/cmb.2020.0112). 744
Volume 28, Number 8, August 2021
- Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky:
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020). 745-746 - Ekaterina M. Myasnikova, Marat A. Sabirov, Alexander V. Spirov:
Quantitative Analysis of the Dynamics of Maternal Gradients in the Early Drosophila Embryo. 747-757 - Jaroslaw Paszek, Alexey Markin, Pawel Górecki, Oliver Eulenstein:
Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming. 758-773 - Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu:
SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data. 774-788 - Wen Yang, Lusheng Wang:
Fast and Accurate Algorithms for Mapping and Aligning Long Reads. 789-803 - Qiuyue Huang, Jun Wang, Xiangliang Zhang, Maozu Guo, Guoxian Yu:
IsoDA: Isoform-Disease Association Prediction by Multiomics Data Fusion. 804-819 - Marmar Moussa, Ion I. Mandoiu:
SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis. 820-841 - Filipp Rondel, Roya Hosseini, Bikram Sahoo, Sergey Knyazev, Igor Mandric, Frank Stewart, Ion I. Mandoiu, Bogdan Pasaniuc, Yuri Porozov, Alexander Zelikovsky:
Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data. 842-855
Volume 28, Number 9, September 2021
- Salem Malikic, Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, Mohammad Haghir Ebrahim-Abadi, Süleyman Cenk Sahinalp:
Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices. 857-879 - Caesar Z. Li, Eric S. Kawaguchi, Gang Li:
A New ℓ0-Regularized Log-Linear Poisson Graphical Model with Applications to RNA Sequencing Data. 880-891 - Vo Hong Thanh, Dani Korpela, Pekka Orponen:
Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots. 892-908 - Sunil Thomas:
Mapping the Nonstructural Transmembrane Proteins of Severe Acute Respiratory Syndrome Coronavirus 2. 909-921 - Shisheng Wang, Yi Zhong, Jingqiu Cheng, Hao Yang:
EnrichVisBox: A Versatile and Powerful Web Toolbox for Visualizing Complex Functional Enrichment Results of Omics Data. 922-930 - Bruno César Feltes, Joice De Faria Poloni, Márcio Dorn:
Benchmarking and Testing Machine Learning Approaches with BARRA: CuRDa, a Curated RNA-Seq Database for Cancer Research. 931-944
Volume 28, Number 10, October 2021
- Yury L. Orlovich, Kirill Kukharenko, Volker Kaibel, Pavel Skums:
Scale-Free Spanning Trees and Their Application in Genomic Epidemiology. 945-960 - Junfeng Liu, Yi Wang, Hongyu Zhao:
Calculating Orthologous Protein-Coding Sequence Set Probability Using the Poisson Process. 961-974 - Jeyakodi Gopal, Vigneshwar Suriya Prakash Sinnarasan, Amouda Venkatesan:
Identification of Repurpose Drugs by Computational Analysis of Disease-Gene-Drug Associations. 975-984 - James B. Nation, Justin Cabot-Miller, Oren Segal, Robert Lucito, Kira V. Adaricheva:
Combining Algorithms to Find Signatures That Predict Risk in Early-Stage Stomach Cancer. 985-1006 - Wei Zhang, Shu-Lin Wang, Yue Liu:
Identification of Cancer Driver Modules Based on Graph Clustering from Multiomics Data. 1007-1020 - Rudolfs Petrovs, Egils Stalidzans, Agris Pentjuss:
IMFLer: A Web Application for Interactive Metabolic Flux Analysis and Visualization. 1021-1032
Volume 28, Number 11, November 2021
- Sumit Kumar Jha, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020). 1033-1034 - Xuecong Fu, Haoyun Lei, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Michael Dean, Thomas Ried, Russell Schwartz:
Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers. 1035-1051 - Francesco Andreace, Cinzia Pizzi, Matteo Comin:
MetaProb 2: Metagenomic Reads Binning Based on Assembly Using Minimizers and K-Mers Statistics. 1052-1062 - Gustavo A. Arango-Argoty, Lenwood S. Heath, Amy Pruden, Peter J. Vikesland, Liqing Zhang:
MetaMLP: A Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples. 1063-1074 - Abdur Rahman Mohd Abul Basher, Ryan J. McLaughlin, Steven J. Hallam:
Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision. 1075-1103 - Subrata Saha, Ahmed Soliman, Sanguthevar Rajasekaran:
A Novel Pathway Network Analytics Method Based on Graph Theory. 1104-1112 - Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson:
From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering. 1113-1129 - Daniel Novikov, Sergey Knyazev, Mark Grinshpon, Pelin B. Icer, Pavel Skums, Alex Zelikovsky:
Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations. 1130-1141 - Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson:
Simpler and Faster Development of Tumor Phylogeny Pipelines. 1142-1155 - Qiaoji Xu, Lingling Jin, Yue Zhang, Xiaomeng Zhang, Chunfang Zheng, James H. Leebens-Mack, David Sankoff:
Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences. 1156-1179
Volume 28, Number 12, December 2021
- Mercè Llabrés, Francesc Rosselló, Gabriel Valiente:
The Generalized Robinson-Foulds Distance for Phylogenetic Trees. 1181-1195 - Esmaeil Nourani:
GoVec: Gene Ontology Representation Learning Using Weighted Heterogeneous Graph and Meta-Path. 1196-1207 - Shaoxun Liu, Yi Kou, Lin Chen:
Novel Few-Shot Learning Neural Network for Predicting Carbohydrate-Active Enzyme Affinity Toward Fructo-Oligosaccharides. 1208-1218 - Xuejun Chen, Zhenran Jiang:
ISFMDA: Learning Interactions of Selected Features-Based Method for Predicting Potential MicroRNA-Disease Associations. 1219-1227 - Poonam Dhankhar, Vikram Dalal, Viney Kumar:
Screening of Severe Acute Respiratory Syndrome Coronavirus 2 RNA-Dependent RNA Polymerase Inhibitors Using Computational Approach. 1228-1247 - Dikscha Sapra, Harpreet Kaur, Anjali Dhall, Gajendra P. S. Raghava:
ProCanBio: A Database of Manually Curated Biomarkers for Prostate Cancer. 1248-1257
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