| 2057 | -- | 0 | Aidong Zhang. EIC Farewell and New EIC Introduction |
| 2058 | -- | 0 | Srinivas Aluru. Editorial: From the New Editor-in-Chief |
| 2059 | -- | 2060 | Carlos Martín-Vide, Miguel A. Vega-Rodríguez. Algorithms for Computational Biology: Seventh Edition |
| 2061 | -- | 2071 | Tathagata Debnath, Mingzhou Song 0001. Fast Optimal Circular Clustering and Applications on Round Genomes |
| 2072 | -- | 2079 | Shaoheng Liang, Qingnan Liang, Rui Chen 0013, Ken Chen. Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data |
| 2080 | -- | 2093 | Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Klairton Lima Brito, Ulisses Dias, Zanoni Dias. Sorting Permutations by Intergenic Operations |
| 2094 | -- | 2108 | Gabriel Siqueira, Klairton Lima Brito, Ulisses Dias, Zanoni Dias. Heuristics for Genome Rearrangement Distance With Replicated Genes |
| 2109 | -- | 2122 | Nickolas Steinauer, Kevin Zhang, Chun Guo, Jinsong Zhang. Computational Modeling of Gene-Specific Transcriptional Repression, Activation and Chromatin Interactions in Leukemogenesis by LASSO-Regularized Logistic Regression |
| 2123 | -- | 2124 | Louxin Zhang, Shaoliang Peng, Yi-Ping Phoebe Chen, David Sankoff, Guoliang Li, Hong-Yu Zhang. Guest Editorial for the 17th Asia Pacific Bioinformatics Conference |
| 2125 | -- | 2135 | Pawel Górecki 0001, Oliver Eulenstein, Jerzy Tiuryn. The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost |
| 2136 | -- | 2143 | Melissa Grueter, Kalani Duran, Ramya Ramalingam, Ran Libeskind-Hadas. Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model |
| 2144 | -- | 2156 | Haoxing Du, Yi Sheng Ong, Marina Knittel, Ross Mawhorter, Nuo Liu, Gianluca Gross, Reiko Tojo, Ran Libeskind-Hadas, Yi-Chieh Wu. Multiple Optimal Reconciliations Under the Duplication-Loss-Coalescence Model |
| 2157 | -- | 2166 | Hongzhe Guo, Yilei Fu, Yan Gao, Junyi Li, Yadong Wang, Bo Liu 0023. deGSM: Memory Scalable Construction Of Large Scale de Bruijn Graph |
| 2167 | -- | 2176 | Cui Su, Jun Pang 0001, Soumya Paul. Towards Optimal Decomposition of Boolean Networks |
| 2177 | -- | 2188 | Tom Hartmann, Max Bannach, Martin Middendorf. Sorting Signed Permutations by Inverse Tandem Duplication Random Losses |
| 2189 | -- | 2197 | Nguyen-Quoc-Khanh Le, Binh P. Nguyen. Prediction of FMN Binding Sites in Electron Transport Chains Based on 2-D CNN and PSSM Profiles |
| 2198 | -- | 2207 | Ozan Firat Özgül, Batuhan Bardak, Mehmet Tan. A Convolutional Deep Clustering Framework for Gene Expression Time Series |
| 2208 | -- | 2217 | Fuhao Zhang, Hong Song, Min Zeng, Fang-Xiang Wu, Yaohang Li, Yi Pan 0001, Min Li 0007. A Deep Learning Framework for Gene Ontology Annotations With Sequence- and Network-Based Information |
| 2218 | -- | 2229 | Zilu Wang, Qinghui Hong, Xiaoping Wang 0001. A Memristive Circuit Implementation of Eyes State Detection in Fatigue Driving Based on Biological Long Short-Term Memory Rule |
| 2230 | -- | 2238 | Pablo Nascimento da Silva, Alexandre Plastino 0001, Fabio Fabris, Alex Alves Freitas. A Novel Feature Selection Method for Uncertain Features: An Application to the Prediction of Pro-/Anti-Longevity Genes |
| 2239 | -- | 2248 | Dong Li 0002, Zhisong Pan, Guyu Hu, Graham Anderson, Shan He 0001. Active Module Identification From Multilayer Weighted Gene Co-Expression Networks: A Continuous Optimization Approach |
| 2249 | -- | 2260 | Qiong Fang, Dewei Su, Wilfred Ng, Jianlin Feng. An Effective Biclustering-Based Framework for Identifying Cell Subpopulations From scRNA-seq Data |
| 2261 | -- | 2270 | Junyi Chen, Junhui Hou, Ka Chun Wong. Categorical Matrix Completion With Active Learning for High-Throughput Screening |
| 2271 | -- | 2280 | Oyetunji E. Ogundijo, Kaiyi Zhu, Xiaodong Wang 0001, Dimitris Anastassiou. Characterizing Intra-Tumor Heterogeneity From Somatic Mutations Without Copy-Neutral Assumption |
| 2281 | -- | 2290 | Shaoxun Yuan, Haitao Li, Jiansheng Wu, Xiao Sun 0006. Classification of Mild Cognitive Impairment With Multimodal Data Using Both Labeled and Unlabeled Samples |
| 2291 | -- | 2301 | Anne-Marie Lyne, Leïla Perié. Comparing Phylogenetic Approaches to Reconstructing Cell Lineage From Microsatellites With Missing Data |
| 2302 | -- | 2313 | Guillermo Blanco, Borja Sánchez, Lorena Ruiz, Florentino Fdez-Riverola, Abelardo Margolles, Anália Lourenço. Computational Approach to the Systematic Prediction of Glycolytic Abilities: Looking Into Human Microbiota |
| 2314 | -- | 2326 | Eyla Willing, Jens Stoye, Marília D. V. Braga. Computing the Inversion-Indel Distance |
| 2327 | -- | 2338 | Junzhong Ji, Yao Yao. Convolutional Neural Network With Graphical Lasso to Extract Sparse Topological Features for Brain Disease Classification |
| 2339 | -- | 2352 | Annalisa Occhipinti, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger, Boyan Yordanov, Claudio Angione. Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism |
| 2353 | -- | 2363 | Min Zeng, Chengqian Lu, Zhihui Fei, Fang-Xiang Wu, Yaohang Li, Jianxin Wang 0001, Min Li 0007. DMFLDA: A Deep Learning Framework for Predicting lncRNA-Disease Associations |
| 2364 | -- | 2374 | Nelson R. C. Monteiro, Bernardete Ribeiro, Joel P. Arrais. Drug-Target Interaction Prediction: End-to-End Deep Learning Approach |
| 2375 | -- | 2383 | Chuan-Yuan Wang, Na Yu, Ming-Juan Wu, Ying-Lian Gao, Jin-Xing Liu, Juan Wang 0003. Dual Hyper-Graph Regularized Supervised NMF for Selecting Differentially Expressed Genes and Tumor Classification |
| 2384 | -- | 2393 | Hanif Yaghoobi, Esmaeil Babaei, Bashdar Mahmud Hussen, Ali Emami. EBST: An Evolutionary Multi-Objective Optimization Based Tool for Discovering Potential Biomarkers in Ovarian Cancer |
| 2394 | -- | 2408 | Hongwei Huo, Xiaoyang Chen, Xu Guo, Jeffrey Scott Vitter. Efficient Compression and Indexing for Highly Repetitive DNA Sequence Collections |
| 2409 | -- | 2419 | Sanjay S. Bankapur, Nagamma Patil. Enhanced Protein Structural Class Prediction Using Effective Feature Modeling and Ensemble of Classifiers |
| 2420 | -- | 2430 | Zhiyuan Zhu, Zonglei Zhen, Xia Wu, Shuo Li 0001. Estimating Functional Connectivity by Integration of Inherent Brain Function Activity Pattern Priors |
| 2431 | -- | 2444 | Yunhe Wang 0002, Zhiqiang Ma, Ka Chun Wong, Xiangtao Li. Evolving Multiobjective Cancer Subtype Diagnosis From Cancer Gene Expression Data |
| 2445 | -- | 2458 | Xiangtao Li, Shixiong Zhang, Ka Chun Wong. Evolving Transcriptomic Profiles From Single-Cell RNA-Seq Data Using Nature-Inspired Multiobjective Optimization |
| 2459 | -- | 2470 | Yu-Hao Ke, Jen-Wei Huang, Wei-Chen Lin, Bijay Prasad Jaysawal. Finding Possible Promoter Binding Sites in DNA Sequences by Sequential Patterns Mining With Specific Numbers of Gaps |
| 2471 | -- | 2482 | Javier Pérez-Rodríguez, Aida de Haro-García, Nicolás García-Pedrajas. Floating Search Methodology for Combining Classification Models for Site Recognition in DNA Sequences |
| 2483 | -- | 2491 | Xingyi Li, Ju Xiang, Jianxin Wang 0001, Jinyan Li, Fang-Xiang Wu, Min Li 0007. FUNMarker: Fusion Network-Based Method to Identify Prognostic and Heterogeneous Breast Cancer Biomarkers |
| 2492 | -- | 2501 | Payal Gaggar, Manish Kumar, Kunal Mukhopadhyay. Genome-Scale Identification, in Silico Characterization and Interaction Study Between Wheat SNARE and NPSN Gene Families Involved in Vesicular Transport |
| 2502 | -- | 2513 | Hao Li, Yuqi Wang, Zhen Zhang, Yihong Tan, Zhiping Chen, Xiangyi Wang, Tingrui Pei, Lei Wang 0069. Identifying Microbe-Disease Association Based on a Novel Back-Propagation Neural Network Model |
| 2514 | -- | 2525 | Kai Shi 0004, Wei Lin 0003, Xing-Ming Zhao. Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics |
| 2526 | -- | 2534 | Hilal Tayara, Kil To Chong. Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning |
| 2535 | -- | 2545 | Jiawei Luo, Cong Shen, Zihan Lai, Jie Cai, Pingjian Ding. Incorporating Clinical, Chemical and Biological Information for Predicting Small Molecule-microRNA Associations Based on Non-Negative Matrix Factorization |
| 2546 | -- | 2554 | Hai-Cheng Yi, Zhu-Hong You, Zhen-Hao Guo, De-Shuang Huang, Keith C. C. Chan. Learning Representation of Molecules in Association Network for Predicting Intermolecular Associations |
| 2555 | -- | 2565 | Jie Xing, Zheren Li, Biyuan Wang, Yuji Qi, Bingbin Yu, Farhad Ghazvinian Zanjani, Aiwen Zheng, Remco Duits, Tao Tan. Lesion Segmentation in Ultrasound Using Semi-Pixel-Wise Cycle Generative Adversarial Nets |
| 2566 | -- | 2576 | Antara Pal, Pegi Haliti, Bhushan Dharmadhikari, Wu Qi, Prabir Patra. Manipulating Extracellular Matrix Organizations and Parameters to Control Local Cancer Invasion |
| 2577 | -- | 2585 | Xiaowei Zhao, Yiqin Yang, Minghao Yin. MHRWR: Prediction of lncRNA-Disease Associations Based on Multiple Heterogeneous Networks |
| 2586 | -- | 2597 | Beiji Zou, Yulan Dai, Qi He, Chengzhang Zhu, Geng Liu, Yu Su, Rui Tang. Multi-Label Classification Scheme Based on Local Regression for Retinal Vessel Segmentation |
| 2598 | -- | 2611 | Lijia Ma, Shiqiang Wang, Qiuzhen Lin, Jianqiang Li 0001, Zhuhong You, Jiaxiang Huang, Maoguo Gong. Multi-Neighborhood Learning for Global Alignment in Biological Networks |
| 2612 | -- | 2623 | Surama Biswas, Sriyankar Acharyya. Multi-objective Simulated Annealing Variants to Infer Gene Regulatory Network: A Comparative Study |
| 2624 | -- | 2634 | Jie Yang, Song He, Zhongnan Zhang, Xiaochen Bo. NegStacking: Drug-Target Interaction Prediction Based on Ensemble Learning and Logistic Regression |
| 2635 | -- | 2648 | Pascal Schlosser, Jochen Knaus, Maximilian Schmutz, Konstanze Döhner, Christoph Plass, Lars Bullinger, Rainer Claus, Harald Binder, Michael Lübbert, Martin Schumacher. Netboost: Boosting-Supported Network Analysis Improves High-Dimensional Omics Prediction in Acute Myeloid Leukemia and Huntington's Disease |
| 2649 | -- | 2658 | Nadia S. Taou, Michael A. Lones. Optimising Boolean Synthetic Regulatory Networks to Control Cell States |
| 2659 | -- | 2670 | Koyel Mandal, Rosy Sarmah, Dhruba Kumar Bhattacharyya. POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data |
| 2671 | -- | 2681 | Ping Xuan, Bingxu Chen, Tiangang Zhang, Yan Yang. Prediction of Drug-Target Interactions Based on Network Representation Learning and Ensemble Learning |
| 2682 | -- | 2691 | Ke Yan 0003, Jie Wen 0001, Yong Xu 0001, Bin Liu 0014. Protein Fold Recognition Based on Auto-Weighted Multi-View Graph Embedding Learning Model |
| 2692 | -- | 2701 | Xiguo Yuan, Chao Ma, Haiyong Zhao, Liying Yang 0001, Shuzhen Wang, Jianing Xi. STIC: Predicting Single Nucleotide Variants and Tumor Purity in Cancer Genome |
| 2702 | -- | 2713 | Sara Montagna, Michele Braccini, Andrea Roli. The Impact of Self-Loops on Boolean Networks Attractor Landscape and Implications for Cell Differentiation Modelling |
| 2714 | -- | 2723 | Yushan Qiu, Hao Jiang 0009, Wai-Ki Ching. Unsupervised Learning Framework With Multidimensional Scaling in Predicting Epithelial-Mesenchymal Transitions |
| 2724 | -- | 2732 | Jiunn-Liang Lin, Wei-Liang Kuo, Yi-Hao Huang 0001, Tai-Lang Jong, Ao-Lin Hsu, Wen-Hsing Hsu. Using Convolutional Neural Networks to Measure the Physiological Age of Caenorhabditis elegans |
| 2733 | -- | 2740 | Shiming Wang, Jie Li, Yadong Wang. WMMDCA: Prediction of Drug Responses by Weight-Based Modular Mapping in Cancer Cell Lines |
| 2741 | -- | 2746 | Getulio Pereira, Preetam Ghosh, Anderson Santos. A Bridging Centrality Plugin for GEPHI and a Case Study for Mycobacterium Tuberculosis H37Rv |
| 2747 | -- | 2752 | Victor Luncasu, Madalina Raschip. A Graph-Based Approach for the DNA Word Design Problem |
| 2753 | -- | 2758 | Hongmei Jiao, Qikun Shen, Yan Shi 0008, Peng Shi 0001. Adaptive Tracking Control for Uncertain Cancer-Tumor-Immune Systems |
| 2759 | -- | 2765 | Davide Chicco, Luca Oneto. An Enhanced Random Forests Approach to Predict Heart Failure From Small Imbalanced Gene Expression Data |
| 2766 | -- | 2767 | Maxim A. Sikolenko, Leonid N. Valentovich. Barapost: Binning of Nucleotide Sequences According to Taxonomic Annotation |
| 2768 | -- | 2774 | Yan Zheng, Hao Wang, Yijie Ding, Fei Guo. CEPZ: A Novel Predictor for Identification of DNase I Hypersensitive Sites |
| 2775 | -- | 2780 | Ying Song, Shuangjia Zheng, Liang Li, Xiang Zhang, Xiaodong Zhang, Ziwang Huang, Jianwen Chen, Ruixuan Wang, Huiying Zhao, Yutian Chong, Jun Shen, Yunfei Zha, Yuedong Yang. Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images |
| 2781 | -- | 2787 | Fan Lu, Yilong Lin, Chongbin Yuan, Xiao-fei Zhang, Le Ou-Yang. EnTSSR: A Weighted Ensemble Learning Method to Impute Single-Cell RNA Sequencing Data |
| 2788 | -- | 2794 | Yan Liu, Wenfang Chen, Zengyou He. Essential Protein Recognition via Community Significance |
| 2795 | -- | 2801 | Noorul Amin, Annette McGrath, Yi-Ping Phoebe Chen. FexRNA: Exploratory Data Analysis and Feature Selection of Non-Coding RNA |
| 2802 | -- | 2808 | Eric Chen, Justin Chu, Jessica Zhang, René L. Warren, Inanç Birol. GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies |
| 2809 | -- | 2815 | Yinuo Lyu, Zhen Zhang, Jiawei Li, Wenying He, Yijie Ding, Fei Guo. iEnhancer-KL: A Novel Two-Layer Predictor for Identifying Enhancers by Position Specific of Nucleotide Composition |
| 2816 | -- | 2822 | Gabriel Vilallonga, Daniel Riesco, Antônio-Carlos Guimarães de Almeida, Antônio Márcio Rodrigues, Sérgio V. A. Campos. In Silico Laboratory Experiments Using Statistical Model Checking: A New Model of the Palytoxin-Induced Pump Channel as Case Study |
| 2823 | -- | 2827 | Nathan Davidov, Amanda Hernandez, Justin Jian, Patrick McKenna, K. A. Medlin, Roadra Mojumder, Megan Owen, Andrew Quijano, Amanda Rodriguez, Katherine St. John, Katherine Thai, Meliza Uraga. Maximum Covering Subtrees for Phylogenetic Networks |
| 2828 | -- | 2834 | Philippe Pognonec, Axel Gustovic, Zied Djabari, Thierry Pourcher, Michel Barlaud. Mitotic Index Determination on Live Cells From Label-Free Acquired Quantitative Phase Images Using a Supervised Autoencoder |
| 2835 | -- | 2840 | Hovakim Grabski, Siranuysh Ginosyan, Susanna Tiratsuyan. Molecular Simulations and Markov State Modeling Reveal Inactive Form of Quorum Sensing Regulator SdiA of Escherichia Coli |
| 2841 | -- | 2847 | Thin Nguyen, Samuel C. Lee, Thomas P. Quinn, Buu Minh Thanh Truong, Xiaomei Li, Truyen Tran 0001, Svetha Venkatesh, Thuc Duy Le. PAN: Personalized Annotation-Based Networks for the Prediction of Breast Cancer Relapse |
| 2848 | -- | 2854 | Amelia Villegas-Morcillo, Angel M. Gomez, Juan Andres Morales-Cordovilla, Victoria E. Sánchez. Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks |
| 2855 | -- | 2861 | Marta Casanellas, Jesús Fernández-Sánchez, Marina Garrote-López. SAQ: Semi-Algebraic Quartet Reconstruction |
| 2862 | -- | 2869 | Chia-Yen Lee, Jun-Hua Zeng, Sheng-Yu Lee, Ru Band Lu, Po-Hsiu Kuo. SNP Data Science for Classification of Bipolar Disorder I and Bipolar Disorder II |
| 2870 | -- | 2876 | Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Klairton Lima Brito, Laurent Bulteau, Ulisses Dias, Zanoni Dias. Sorting Signed Permutations by Intergenic Reversals |
| 2877 | -- | 2883 | Sergi Maicas, Jaume Segura-Garcia. Spatial Distribution of Antibiotic-Producing Bacteria in Urban Areas. A Case Study in València (Spain) |
| 2884 | -- | 2890 | Jiaan Dai, Fengchao Yu, Chen Zhou, Weichuan Yu. Understanding the Limit of Open Search in the Identification of Peptides With Post-translational Modifications - A Simulation-Based Study |
| 2891 | -- | 2897 | Yesen Sun, Le Ou-Yang, Dao-Qing Dai. WMLRR: A Weighted Multi-View Low Rank Representation to Identify Cancer Subtypes From Multiple Types of Omics Data |