| 1 | -- | 2 | Hsiao-Fang Sunny Sun, Yi-Ping Phoebe Chen. Editorial |
| 3 | -- | 13 | Hui Bi, Shumei Cao, Hanying Yan, Zhongyi Jiang, Jun Zhang, Ling Zou 0002. Resting State Functional Connectivity Analysis During General Anesthesia: A High-Density EEG Study |
| 14 | -- | 18 | Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed, Alexandre G. de Brevern. Shaking the β-Bulges |
| 19 | -- | 30 | Madhusudan Paul, Ashish Anand. A New Family of Similarity Measures for Scoring Confidence of Protein Interactions Using Gene Ontology |
| 31 | -- | 39 | Runhua Huang, Chengchuang Lin, Aihua Yin, Hanbiao Chen, Li Guo, Gansen Zhao, Xiaomao Fan, Shuangyin Li, Jinji Yang. A Clinical Dataset and Various Baselines for Chromosome Instance Segmentation |
| 40 | -- | 47 | Ying Qian, Xuelian Li, Qian Zhang 0003, Jiongmin Zhang. SPP-CPI: Predicting Compound-Protein Interactions Based On Neural Networks |
| 48 | -- | 56 | Jin Zhao 0005, Haodi Feng, Daming Zhu, Yu Lin 0001. MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly |
| 57 | -- | 67 | Anuradha Wickramarachchi, Yu Lin 0001. GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs |
| 68 | -- | 74 | Shuai Lu, Yuguang Li, Fei Wang, Xiaofei Nan, Shoutao Zhang. Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction |
| 75 | -- | 86 | Tzu-Hsien Yang. An Aggregation Method to Identify the RNA Meta-Stable Secondary Structure and its Functionally Interpretable Structure Ensemble |
| 87 | -- | 94 | Trinh-Trung-Duong Nguyen, The-Anh Tran, Nguyen-Quoc-Khanh Le, Dinh-Minh Pham, Yu-Yen Ou. An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches |
| 95 | -- | 96 | Barbara Di Camillo, Giuseppe Nicosia. Guest Editorial: Deep Learning For Genomics |
| 97 | -- | 106 | Jim Clauwaert, Willem Waegeman. Novel Transformer Networks for Improved Sequence Labeling in genomics |
| 107 | -- | 120 | Zhong Chen 0003, Wensheng Zhang, Hong-Wen Deng, Kun Zhang 0012. Effective Cancer Subtype and Stage Prediction via Dropfeature-DNNs |
| 121 | -- | 134 | Francisco Cristovao, Silvia Cascianelli, Arif Canakoglu, Mark J. Carman, Luca Nanni, Pietro Pinoli, Marco Masseroli. Investigating Deep Learning Based Breast Cancer Subtyping Using Pan-Cancer and Multi-Omic Data |
| 135 | -- | 145 | Gautier Viaud, Prasanna Mayilvahanan, Paul-Henry Cournède. Representation Learning for the Clustering of Multi-Omics Data |
| 146 | -- | 154 | Tuan Nguyen, Giang T. T. Nguyen, Thin Nguyen, Duc-Hau Le. Graph Convolutional Networks for Drug Response Prediction |
| 155 | -- | 165 | Satyajit Mahapatra, Vivek Raj Gupta, Sitanshu Sekhar Sahu, Ganapati Panda. Deep Neural Network and Extreme Gradient Boosting Based Hybrid Classifier for Improved Prediction of Protein-Protein Interaction |
| 166 | -- | 167 | Zhipeng Cai 0001, Min Li 0007, Pavel Skums. Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications |
| 168 | -- | 179 | Cheng Yan, Guihua Duan, Yayan Zhang, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang 0001. Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning |
| 180 | -- | 191 | Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yan Huang 0032, Yubao Wu. Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms |
| 192 | -- | 206 | Sudipta Acharya, Laizhong Cui, Yi Pan 0001. A Refined 3-in-1 Fused Protein Similarity Measure: Application in Threshold-Free Hub Detection |
| 207 | -- | 208 | Zhipeng Cai 0001, Giri Narasimhan, Pavel Skums. Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications |
| 209 | -- | 219 | Shan Gao, Renmin Han, Xiangrui Zeng, Zhiyong Liu 0002, Min Xu 0009, Fa Zhang 0001. Macromolecules Structural Classification With a 3D Dilated Dense Network in Cryo-Electron Tomography |
| 220 | -- | 229 | Davide Storato, Matteo Comin. K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification |
| 230 | -- | 242 | Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal. TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread |
| 243 | -- | 254 | Jun Wang 0035, Huiling Zhang, Wei Ren, Maozu Guo 0001, Guoxian Yu. EpiMC: Detecting Epistatic Interactions Using Multiple Clusterings |
| 255 | -- | 266 | P. V. Sunil Kumar, Adheeba Thahsin, Manju M, Gopakumar G. A Heterogeneous Information Network Model for Long Non-Coding RNA Function Prediction |
| 267 | -- | 274 | Hansheng Li, Jianping Li, Yuxin Kang, Chunbao Wang, Feihong Liu, Wenli Hui, Qirong Bo, Lei Cui 0004, Jun Feng 0003, Lin Yang 0002. A Novel Encoding and Decoding Calibration Guiding Pathway for Pathological Image Analysis |
| 275 | -- | 283 | Sadaf Gull, Fayyaz A. Minhas. 0: Species-Specific Prediction of Anti-microbial Peptides Using Zero and Few Shot Learning |
| 284 | -- | 294 | Mahdi Pursalim, Kwoh Chee Keong 0001. An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks |
| 295 | -- | 304 | Yuning Yang, Jiawen Yu, Zhe Liu, Xi Wang, Han Wang, Zhiqiang Ma, Dong Xu 0002. An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network |
| 305 | -- | 316 | Xiaoke Ma, Peng-Gang Sun, Maoguo Gong. An Integrative Framework of Heterogeneous Genomic Data for Cancer Dynamic Modules Based on Matrix Decomposition |
| 317 | -- | 327 | Fei Liu 0006, Ena Yamamoto, Katsunobu Shirahama, Tsubasa Saitoh, Shuhei Aoyama, Yumiko Harada, Ryutaro Murakami, Hiroshi Matsuno. Analysis of Pattern Formation by Colored Petri Nets With Quantitative Regulation of Gene Expression Level |
| 328 | -- | 342 | Sanzo Miyazawa. Boltzmann Machine Learning and Regularization Methods for Inferring Evolutionary Fields and Couplings From a Multiple Sequence Alignment |
| 343 | -- | 354 | Devleena Ghosh, Chittaranjan Mandal 0002. Clustering Based Parameter Estimation of Thyroid Hormone Pathway |
| 355 | -- | 368 | Rubén Langarita, Adrià Armejach, Javier Setoain, Pablo Ibáñez-Marín, Jesús Alastruey-Benedé, Miquel Moretó. Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps |
| 369 | -- | 382 | Md. Rezaul Karim 0001, Michael Cochez, Achille Zappa, Ratnesh Sahay, Dietrich Rebholz-Schuhmann, Oya Beyan, Stefan Decker. Convolutional Embedded Networks for Population Scale Clustering and Bio-Ancestry Inferencing |
| 383 | -- | 394 | Rizwan Qureshi, Avirup Ghosh, Hong Yan 0001. Correlated Motions and Dynamics in Different Domains of Epidermal Growth Factor Receptor With L858R and T790M Mutations |
| 395 | -- | 406 | Chunxiang Peng, Xiao-gen Zhou, Gui-jun Zhang. De novo Protein Structure Prediction by Coupling Contact With Distance Profile |
| 407 | -- | 417 | Mohammad A. Rezaei, Yanjun Li 0005, Dapeng Wu 0001, Xiaolin Li 0001, Chenglong Li. Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction |
| 418 | -- | 428 | Anju Sharma, Rajnish Kumar, Rahul Semwal, Imlimaong Aier, Pankaj Tyagi, Pritish Kumar Varadwaj. DeepOlf: Deep Neural Network Based Architecture for Predicting Odorants and Their Interacting Olfactory Receptors |
| 429 | -- | 442 | Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler. Generic Context-Aware Group Contributions |
| 443 | -- | 454 | Rituparna Sinha, Rajat Kumar Pal, Rajat K. De. GenSeg and MR-GenSeg: A Novel Segmentation Algorithm and its Parallel MapReduce Based Approach for Identifying Genomic Regions With Copy Number Variations |
| 455 | -- | 464 | Chang Sun, Ping Xuan, Tiangang Zhang, Yilin Ye. Graph Convolutional Autoencoder and Generative Adversarial Network-Based Method for Predicting Drug-Target Interactions |
| 465 | -- | 478 | Kiya Govek, Camden Sikes, Yangqiaoyu Zhou, Layla Oesper. GraPhyC: Using Consensus to Infer Tumor Evolution |
| 479 | -- | 490 | Peng Peng, Yipu Zhang, Yongfeng Ju, Kaiming Wang, Gang Li 0029, Vince D. Calhoun, Yu-Ping Wang 0002. Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis |
| 491 | -- | 500 | Ozlem Muslu, Charles Tapley Hoyt, Mauricio Lacerda, Martin Hofmann-Apitius, Holger Fröhlich. GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning |
| 501 | -- | 512 | Sai Zhang, Jin Li 0007, Wei Zhou 0011, Tong Li 0004, Yang Zhang, Jingru Wang. Higher-Order Proximity-Based MiRNA-Disease Associations Prediction |
| 513 | -- | 521 | Yu-Ting Tan, Le Ou-Yang, Xingpeng Jiang, Hong Yan 0001, Xiao-fei Zhang. Identifying Gene Network Rewiring Based on Partial Correlation |
| 522 | -- | 530 | Samet Tenekeci, Zerrin Isik. Integrative Biological Network Analysis to Identify Shared Genes in Metabolic Disorders |
| 531 | -- | 542 | Anup Kumar Halder, Soumyendu Sekhar Bandyopadhyay, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu. JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment |
| 543 | -- | 557 | Anna Bernasconi 0002, Arif Canakoglu, Marco Masseroli, Stefano Ceri. META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration |
| 558 | -- | 568 | Eunji Kim, Ivan Ivanov, Edward R. Dougherty. Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network - A Boolean Network Modeling Perspective |
| 569 | -- | 574 | Yajun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang. On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions |
| 575 | -- | 584 | Kuo Yang, Yi Zheng, Kezhi Lu, Kai Chang, Ning Wang, Zixin Shu, Jian Yu, Baoyan Liu, Zhuye Gao, Xuezhong Zhou. PDGNet: Predicting Disease Genes Using a Deep Neural Network With Multi-View Features |
| 585 | -- | 592 | Rahul Semwal, Imlimaong Aier, Utkarsh Raj, Pritish Kumar Varadwaj. Pr[m]: An Algorithm for Protein Motif Discovery |
| 593 | -- | 604 | Wei Zhong, Feng Gu. Predicting Local Protein 3D Structures Using Clustering Deep Recurrent Neural Network |
| 605 | -- | 613 | Dewu Ding, Xiao Sun 0006. Relating Translation Efficiency to Protein Networks Provides Evolutionary Insights in Shewanella and Its Implications for Extracellular Electron Transfer |
| 614 | -- | 623 | Neng Huang, Fan Nie, Peng Ni, Feng Luo, Jianxin Wang 0001. SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism |
| 624 | -- | 632 | Priyadarshini Rai, Debarka Sengupta, Angshul Majumdar. SelfE: Gene Selection via Self-Expression for Single-Cell Data |
| 633 | -- | 642 | Yan Liu, Hao Liang, Quan Zou 0001, Zengyou He. Significance-Based Essential Protein Discovery |
| 643 | -- | 652 | Qiao Ning, Zhiqiang Ma 0003, Xiaowei Zhao, Minghao Yin. SSKM_Succ: A Novel Succinylation Sites Prediction Method Incorporating K-Means Clustering With a New Semi-Supervised Learning Algorithm |