Table of Contents

• Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike SequencesSarwan Ali, Pin-Yu Chen, Murray Patterson. 1-15 [doi]
• Efficient Sequence Embedding for SARS-CoV-2 Variants ClassificationSarwan Ali, Usama Sardar, Imdadullah Khan, Murray Patterson. 16-30 [doi]
• On Computing the Jaro Similarity Between Two StringsJoyanta Basak, Ahmed Soliman, Nachiket Deo, Kenneth Haase, Anup Mathur, Krista Park, Rebecca C. Steorts, Daniel Weinberg, Sartaj Sahni, Sanguthevar Rajasekaran. 31-44 [doi]
• Identifying miRNA-Disease Associations Based on Simple Graph Convolution with DropMessage and Jumping KnowledgeXuehua Bi, Chunyang Jiang, Cheng Yan, Kai Zhao, Linlin Zhang, Jianxin Wang. 45-57 [doi]
• Reconciling Inconsistent Molecular Structures from Biochemical DatabasesCasper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle. 58-71 [doi]
• Deep Learning Architectures for the Prediction of YY1-Mediated Chromatin LoopsAhtisham Fazeel Abbasi, Muhammad Nabeel Asim, Johan Trygg, Andreas Dengel 0001, Sheraz Ahmed. 72-84 [doi]
• MPFNet: ECG Arrhythmias Classification Based on Multi-perspective Feature FusionYuxia Guan, Ying An, Fengyi Guo, Jianxin Wang 0001. 85-96 [doi]
• PCPI: Prediction of circRNA and Protein Interaction Using Machine Learning MethodMd. Tofazzal Hossain, Md. Selim Reza, Xuelei Li, Yin Peng, Shengzhong Feng, Yanjie Wei. 97-106 [doi]
• Radiology Report Generation via Visual Recalibration and Context Gating-AwareXiaodi Hou, Guoming Sang, Zhi Liu, Xiaobo Li, Yijia Zhang. 107-119 [doi]
• Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics - Extended AbstractGuy Katriel, Udi Mahanaymi, Christoph Koutschan, Doron Zeilberger, Mike Steel, Sagi Snir. 120-135 [doi]
• TCSA: A Text-Guided Cross-View Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation LearningHongyang Lei, Huazhen Huang, Bokai Yang, Guosheng Cui, Ruxin Wang, Dan Wu, Ye Li 0002. 136-149 [doi]
• Multi-class Cancer Classification of Whole Slide Images Through Transformer and Multiple Instance LearningHaijing Luan, Taiyuan Hu, Jifang Hu, Ruilin Li, Detao Ji, Jiayin He, Xiaohong Duan, Chunyan Yang, Yajun Gao, Fan Chen, Beifang Niu. 150-164 [doi]
• ricME: Long-Read Based Mobile Element Variant Detection Using Sequence Realignment and Identity CalculationHuidong Ma, Cheng Zhong, Hui Sun, Danyang Chen, Haixiang Lin. 165-177 [doi]
• scGASI: A Graph Autoencoder-Based Single-Cell Integration Clustering MethodTian-Jing Qiao, Feng Li, Shasha Yuan, Ling-Yun Dai, Juan Wang 0003. 178-189 [doi]
• ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction DetectionQianqian Ren, Yahan Li, Feng Li, Jin-Xing Liu, Junliang Shang. 190-201 [doi]
• USTAR: Improved Compression of k-mer Sets with Counters Using de Bruijn GraphsEnrico Rossignolo, Matteo Comin. 202-213 [doi]
• Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody RepertoireHossein Saghaian, Pavel Skums, Yurij Ionov, Alex Zelikovsky. 214-226 [doi]
• Sequence-Based Nanobody-Antigen Binding PredictionUsama Sardar, Sarwan Ali, Muhammad Sohaib Ayub, Muhammad Shoaib, Khurram Bashir, Imdadullah Khan, Murray Patterson. 227-240 [doi]
• Approximating Rearrangement Distances with Replicas and Flexible Intergenic RegionsGabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Zanoni Dias. 241-254 [doi]
• The Ordered Covering Problem in Distance GeometryMichael Souza 0001, Nilton Maia, Carlile Lavor. 255-266 [doi]
• Phylogenetic Information as Soft Constraints in RNA Secondary Structure PredictionSarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler. 267-279 [doi]
• NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass SpectrometryShaokai Wang, Ming Zhu, Bin Ma. 280-291 [doi]
• On Sorting by Flanked TranspositionsHuixiu Xu, Xin Tong, Haitao Jiang, Lusheng Wang 0001, Binhai Zhu, Daming Zhu. 292-311 [doi]
• Integrative Analysis of Gene Expression and Alternative Polyadenylation from Single-Cell RNA-seq DataShuo Xu, Liping Kang, Xingyu Bi, Xiaohui Wu. 312-324 [doi]
• SaID: Simulation-Aware Image Denoising Pre-trained Model for Cryo-EM MicrographsZhidong Yang, Hongjia Li, Dawei Zang, Renmin Han, Fa Zhang 0001. 325-336 [doi]
• Reducing the Impact of Domain Rearrangement on Sequence Alignment and Phylogeny ReconstructionSumaira Zaman, Mukul S. Bansal. 337-350 [doi]
• Identification and Functional Annotation of circRNAs in Neuroblastoma Based on BioinformaticsJingjing Zhang, Md. Tofazzal Hossain, Zhen Ju, Wenhui Xi, Yanjie Wei. 351-363 [doi]
• SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive DisorderYan Zhang, Xin Liu, Panrui Tang, Zuping Zhang. 364-375 [doi]
• PDB2Vec: Using 3D Structural Information for Improved Protein AnalysisSarwan Ali, Prakash Chourasia, Murray Patterson. 376-386 [doi]
• Hist2Vec: Kernel-Based Embeddings for Biological Sequence ClassificationSarwan Ali, Haris Mansoor, Prakash Chourasia, Murray Patterson. 387-397 [doi]
• DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly DetectionYing An, Anxuan Xiong, Lin Guo. 398-408 [doi]
• On the Realisability of Chemical PathwaysJakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler. 409-419 [doi]
• A Brief Study of Gene Co-expression Thresholding AlgorithmsCarissa Bleker, Stephen K. Grady, Michael A. Langston. 420-430 [doi]
• Inferring Boolean Networks from Single-Cell Human Embryo DatasetsMathieu Bolteau, Jérémie Bourdon, Laurent David, Carito Guziolowski. 431-441 [doi]
• Enhancing t-SNE Performance for Biological Sequencing Data Through Kernel SelectionPrakash Chourasia, Taslim Murad, Sarwan Ali, Murray Patterson. 442-452 [doi]
• Genetic Algorithm with Evolutionary JumpsHafsa Farooq, Daniel Novikov, Akshay Juyal, Alexander Zelikovsky. 453-463 [doi]
• HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous DataYulong Li, Hongming Zhu, Xiaowen Wang, Qin Liu. 464-475 [doi]
• Clique-Based Topological Characterization of Chromatin Interaction HubsGatis Melkus, Sandra Silina, Andrejs Sizovs, Peteris Rucevskis, Lelde Lace, Edgars Celms, Juris Viksna. 476-486 [doi]
• Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection AlgorithmsBikram Sahoo, Temitope Adeyeha, Zandra Pinnix, Alex Zelikovsky. 487-497 [doi]
• Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast CancerBikram Sahoo, Zandra Pinnix, Alex Zelikovsky. 498-508 [doi]
• CSA-MEM: Enhancing Circular DNA Multiple Alignment Through Text Indexing AlgorithmsAndré Salgado, Francisco Fernandes, Ana Teresa Freitas. 509-517 [doi]
• A Convolutional Denoising Autoencoder for Protein Scaffold FillingJordan Sturtz, Richard Annan, Binhai Zhu, Xiaowen Liu, Letu Qingge. 518-529 [doi]
• Simulating Tumor Evolution from scDNA-Seq as an Accumulation of both SNVs and CNAsZahra Tayebi, Akshay Juyal, Alexander Zelikovsky, Murray Patterson. 530-540 [doi]
• CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-Cell Type IdentificationTai-Ge Wang, Xiang-Zhen Kong, Shengjun Li, Juan Wang 0003. 541-551 [doi]