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J. Comput. Biol.
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2024
1994
2024
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Publications
volume 31, number 1, 2024
Acknowledgment of Reviewers 2023.
J. Comput. Biol.
31 (1) (2024)
volume 30, number 4, 2023
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.
J. Comput. Biol.
30 (4) (2023)
Bikram Sahoo
,
Zandra Pinnix
,
Seth Sims
,
Alex Zelikovsky
Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer.
J. Comput. Biol.
30 (4) (2023)
Sarwan Ali
,
Babatunde Bello
,
Zahra Tayebi
,
Murray Patterson
Characterizing SARS-CoV-2 Spike Sequences Based on Geographical Location.
J. Comput. Biol.
30 (4) (2023)
David S. Campo
,
Alexander Mosa
,
Yury Khudyakov
A Novel Information-Theory-Based Genetic Distance That Approximates Phenotypic Differences.
J. Comput. Biol.
30 (4) (2023)
Prakash Chourasia
,
Sarwan Ali
,
Simone Ciccolella
,
Gianluca Della Vedova
,
Murray Patterson
Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data.
J. Comput. Biol.
30 (4) (2023)
Yi Li
,
Mandy Chen
,
Joshy George
,
Edison T. Liu
,
Radha Murthy-Karuturi
Adaptive Sentinel Testing in Workplace for COVID-19 Pandemic.
J. Comput. Biol.
30 (4) (2023)
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.
J. Comput. Biol.
30 (4) (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).
J. Comput. Biol.
30 (4) (2023)
Fiona Senchyna
,
Rahul Singh
Dynamic Epidemiological Networks: A Data Representation Framework for Modeling and Tracking of SARS-CoV-2 Variants.
J. Comput. Biol.
30 (4) (2023)
Jirí C. Moravec
,
Robert Lanfear
,
David L. Spector
,
Sarah D. Diermeier
,
Alex Gavryushkin
Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data.
J. Comput. Biol.
30 (4) (2023)
volume 30, number 5, 2023
Guo Mao
,
Zhengbin Pang
,
Ke Zuo
,
Jie Liu
Gene Regulatory Network Inference Using Convolutional Neural Networks from scRNA-seq Data.
J. Comput. Biol.
30 (5) (2023)
Zhijie Chen
,
Tianhao Yan
,
Zhanwen Yang
Numerical Analysis of Linearly Implicit Methods for Discontinuous Nonlinear Gurtin-MacCamy Model.
J. Comput. Biol.
30 (5) (2023)
Anna Pacínková
,
Vlad Popovici
IntOMICS: A Bayesian Framework for Reconstructing Regulatory Networks Using Multi-Omics Data.
J. Comput. Biol.
30 (5) (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.
J. Comput. Biol.
30 (5) (2023)
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.
J. Comput. Biol.
30 (5) (2023)
Donghui Son
,
Jaejik Kim
Estimation of Ordinary Differential Equation Models for Gene Regulatory Networks Through Data Cloning.
J. Comput. Biol.
30 (5) (2023)
volume 30, number 6, 2023
Zong Wang
,
Qimin Zhang
Positivity-Preserving Numerical Method and Relaxed Control for Stochastic Susceptible-Infected-Vaccinated Epidemic Model with Markov Switching.
J. Comput. Biol.
30 (6) (2023)
Nafiseh Sedaghat
,
Tamon Stephen
,
Leonid Chindelevitch
Speeding Up the Structural Analysis of Metabolic Network Models Using the Fredman-Khachiyan Algorithm B.
J. Comput. Biol.
30 (6) (2023)
Nozomi Hasegawa
,
Kana Shimizu
Efficient Colored de Bruijn Graph for Indexing Reads.
J. Comput. Biol.
30 (6) (2023)
Nathan P. Manes
,
Jian Song
,
Aleksandra Nita-lazar
EnsMOD: A Software Program for Omics Sample Outlier Detection.
J. Comput. Biol.
30 (6) (2023)
Yi Liu
,
Gang Li
Sure Joint Screening for High Dimensional Cox's Proportional Hazards Model Under the Case-Cohort Design.
J. Comput. Biol.
30 (6) (2023)
Margherita Cavattoni
,
Matteo Comin
ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs.
J. Comput. Biol.
30 (6) (2023)
volume 30, number 7, 2023
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.
J. Comput. Biol.
30 (7) (2023)
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.
J. Comput. Biol.
30 (7) (2023)
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.
J. Comput. Biol.
30 (7) (2023)
Tunç Basar Köse
,
Jiarong Li
,
Anna Ritz
Growing Directed Acyclic Graphs: Optimization Functions for Pathway Reconstruction Algorithms.
J. Comput. Biol.
30 (7) (2023)
Hyundoo Jeong
,
Jose Lugo-Martinez
,
Anna Ritz
,
Yijie Wang
,
Chi Zhang
Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC) Workshop (2022).
J. Comput. Biol.
30 (7) (2023)
Ziqi Ke
,
Haris Vikalo
Graph-Based Reconstruction and Analysis of Disease Transmission Networks Using Viral Genomic Data.
J. Comput. Biol.
30 (7) (2023)
Jhonatan Tavori
,
Hanoch Levy
On the Convexity of the Effective Reproduction Number.
J. Comput. Biol.
30 (7) (2023)
volume 30, number 8, 2023
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.
J. Comput. Biol.
30 (8) (2023)
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.
J. Comput. Biol.
30 (8) (2023)
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.
J. Comput. Biol.
30 (8) (2023)
Ying Yu
,
Tian Qiu
,
Junwen Duan
,
Jian-Xin Wang
Multigranularity Label Prediction Model for Automatic International Classification of Diseases Coding in Clinical Text.
J. Comput. Biol.
30 (8) (2023)
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.
J. Comput. Biol.
30 (8) (2023)
Arjun Srivatsa
,
Haoyun Lei
,
Russell Schwartz
A Clonal Evolution Simulator for Planning Somatic Evolution Studies.
J. Comput. Biol.
30 (8) (2023)
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.
J. Comput. Biol.
30 (8) (2023)
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.
J. Comput. Biol.
30 (8) (2023)
Alexsandro Oliveira Alexandrino
,
Andre Rodrigues Oliveira
,
Géraldine Jean
,
Guillaume Fertin
,
Ulisses Dias
,
Zanoni Dias
Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information.
J. Comput. Biol.
30 (8) (2023)
Zhipeng Cai
,
Pavel Skums
,
Alexander Zelikovsky
18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022).
J. Comput. Biol.
30 (8) (2023)
volume 30, number 9, 2023
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.
J. Comput. Biol.
30 (9) (2023)
Peixuan Zhou
,
Yi-Jia Zhang
,
Zeqian Li
,
Kuo Pang
,
Di Zhao
Protein Complex Identification Based on Heterogeneous Protein Information Network.
J. Comput. Biol.
30 (9) (2023)
An Huang
,
Xiaolan Xie
,
Xiaojun Yao
,
Huanxiang Liu
,
Xiaoqi Wang
,
Shaoliang Peng
HF-DDI: Predicting Drug-Drug Interaction Events Based on Multimodal Hybrid Fusion.
J. Comput. Biol.
30 (9) (2023)
Da Liu
,
Yi-Jia Zhang
,
Ming Yang
,
Jianyuan Yuan
,
Wen Qu
Extracting Mutant-Affected Protein-Protein Interactions via Gaussian-Enhanced Representation and Contrastive Learning.
J. Comput. Biol.
30 (9) (2023)
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.
J. Comput. Biol.
30 (9) (2023)
Akshay Juyal
,
Roya Hosseini
,
Daniel Novikov
,
Mark Grinshpon
,
Alex Zelikovsky
Reconstruction of Viral Variants via Monte Carlo Clustering.
J. Comput. Biol.
30 (9) (2023)
Jiancheng Zhong
,
Pan Cui
,
Yihong Zhu
,
Qiu Xiao
,
Zuohang Qu
DAHNGC: A Graph Convolution Model for Drug-Disease Association Prediction by Using Heterogeneous Network.
J. Comput. Biol.
30 (9) (2023)
Susanne Zabel
,
Jennifer Müller
,
Friedrich Götz
,
Kay Nieselt
BLASTphylo: An Interactive Web Tool for Taxonomic and Phylogenetic Analysis of Prokaryotic Genes.
J. Comput. Biol.
30 (9) (2023)
Zhipeng Cai
,
Pavel Skums
,
Alexander Zeilkovsky
18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022).
J. Comput. Biol.
30 (9) (2023)
Zhichao Wang
,
Xuelei Li
,
Jianping Fan
,
Jintao Meng
,
Zhenli Lin
,
Yi Pan
,
Yanjie Wei
SWsnn: A Novel Simulator for Spiking Neural Networks.
J. Comput. Biol.
30 (9) (2023)