Table of Contents

• Integrative Analysis of Ovarian Serious Adenocarcinoma to Understand Disease Network BiologySahar Qazi, Khalid Raza. 3-17 [doi]
• GAGAM: A Genomic Annotation-Based Enrichment of scATAC-seq Data for Gene Activity MatrixLorenzo Martini, Roberta Bardini, Alessandro Savino, Stefano Di Carlo. 18-32 [doi]
• Finding Significantly Enriched Cells in Single-Cell RNA Sequencing by Single-Sample ApproachesAnna Mrukwa, Michal Marczyk, Joanna Zyla. 33-44 [doi]
• Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model BacteriumKarel Sedlár, Ralf Zimmer. 45-56 [doi]
• Comparative Study of Synthetic Bulk RNA-Seq GeneratorsFelitsiya Shakola, Dean Palejev, Ivan Ivanov. 57-70 [doi]
• Investigating Sources of Zeros in 10× Single-Cell RNAseq DataHanna Slowik, Joanna Zyla, Michal Marczyk. 71-80 [doi]
• Exhaled Breath Condensate Study for Biomarkers DiscoveryS. Patsiris, Themis P. Exarchos, Panayiotis M. Vlamos. 83-89 [doi]
• Statistical Learning Analysis of Thyroid Cancer Microarray DataIván Petrini, Rocío L. Cecchini, Marilina Mascaró, Ignacio Ponzoni, Jessica Andrea Carballido. 90-102 [doi]
• Migrating CUDA to oneAPI: A Smith-Waterman Case StudyManuel Costanzo, Enzo Rucci, Carlos García Sánchez, Marcelo R. Naiouf, Manuel Prieto-Matías. 103-116 [doi]
• Fuzzy-Inference System for Isotopic Envelope Identification in Mass Spectrometry Imaging DataAnna Glodek. 119-132 [doi]
• Receptor Tyrosine Kinase KIT: A New Look for an Old ReceptorJulie Ledoux, Luba Tchertanov. 133-137 [doi]
• Human Vitamin K Epoxide Reductase as a Target of Its Redox ProteinJulie Ledoux, Maxim Stolyarchuk, Luba Tchertanov. 138-141 [doi]
• A Distance Geometry Procedure Using the Levenberg-Marquardt Algorithm and with Applications in Biology but Not onlyDouglas Soares Gonçalves, Antonio Mucherino. 142-152 [doi]
• A Semi-supervised Graph Deep Neural Network for Automatic Protein Function AnnotationAkrem Sellami, Bishnu Sarker, Salvatore Tabbone, Marie-Dominique Devignes, Sabeur Aridhi. 153-166 [doi]
• Strong Prevalence of the Function over Taxonomy in Human tRNA GenesYana Nedorez, Michael G. Sadovsky. 169-178 [doi]
• A Methodology for Co-simulation-Based Optimization of Biofabrication ProtocolsLeonardo Giannantoni, Roberta Bardini, Stefano Di Carlo. 179-192 [doi]
• A 3D Multicellular Simulation Layer for the Synthetic Biology CAD Infobiotics Workbench SuiteRichard Oliver Matzko, Laurentiu Mierla, Savas Konur. 193-207 [doi]
• Integrating in-vivo Data in CFD Simulations and in in-vitro Experiments of the Hemodynamic in Healthy and Pathologic Thoracic AortaAlessandro Mariotti, Emanuele Gasparotti, Emanuele Vignali, Pietro Marchese, Simona Celi, Maria-Vittoria Salvetti. 208-219 [doi]
• Sensitivity Analysis of Adhesion in Computational Model of Elastic DoubletAlzbeta Bohiniková, Iveta Jancigová, Ivan Cimrák, James J. Feng. 220-233 [doi]
• Increasing the Accuracy of Optipharm's Virtual Screening Predictions by Implementing Molecular FlexibilitySavíns Puertas-Martín, Juana López Redondo, Ester M. Garzón, Horacio Pérez Sánchez, Pilar M. Ortigosa. 234-245 [doi]
• Comparisons of Knowledge Graphs and Entity Extraction in Breast Cancer Subtyping Biomedical Text AnalysisJean Davidson, Grif Hawblitzel, McClain Kressman, Andrew Doud, Harsha Lakshmankumar, Ella Thomas, Paul Kim, Ava Jakusovszky, Paul Anderson. 249-259 [doi]
• Towards XAI: Interpretable Shallow Neural Network Used to Model HCP's fMRI Motor Paradigm DataJosé Diogo Marques dos Santos, José Paulo Marques dos Santos. 260-274 [doi]
• A Deep Learning-Based Method for Uncovering GPCR Ligand-Induced Conformational States Using Interpretability TechniquesMario A. Gutierrez-Mondragon, Caroline König, Alfredo Vellido. 275-287 [doi]
• Data Transformation for Clustering Utilization for Feature Detection in Mass SpectrometryVojtech Barton, Helena Skutkova. 288-299 [doi]
• Spolmap: An Enriched Visualization of CRISPR DiversityChristophe Guyeux, Guislaine Refregier, Christophe Sola. 300-308 [doi]
• How to Compare Various Clustering Outcomes? Metrices to Investigate Breast Cancer Patient Subpopulations Based on Proteomic ProfilesJoanna Tobiasz, Joanna Polanska. 309-318 [doi]
• Sperm-cell Detection Using YOLOv5 ArchitectureMichal Dobrovolny, Jakub Benes, Ondrej Krejcar, Ali Selamat. 319-330 [doi]
• Comparative Analysis of Supervised Cell Type Detection in Single-Cell RNA-seq DataAkram Vasighizaker, Sheena Hora, Yash Trivedi, Luis Rueda. 333-345 [doi]
• PathWeigh - Quantifying the Behavior of Biochemical Pathway CascadesDani Livne, Sol Efroni. 346-352 [doi]
• Translational Challenges of Biomedical Machine Learning Solutions in Clinical and Laboratory SettingsCarlos Vega, Miroslav Kratochvíl, Venkata P. Satagopam, Reinhard Schneider 0002. 353-358 [doi]
• Human Multi-omics Data Pre-processing for Predictive Purposes Using Machine Learning: A Case Study in Childhood ObesityÁlvaro Torres-Martos, Augusto Anguita-Ruiz, Mireia Bustos-Aibar, Sofia Cámara-Sánchez, Rafael Alcalá, Concepción Maria Aguilera, Jesús Alcalá-Fdez. 359-374 [doi]
• Feature Density as an Uncertainty Estimator Method in the Binary Classification Mammography Images Task for a Supervised Deep Learning ModelRicardo Javier Fuentes-Fino, Saúl Calderón Ramírez, Enrique Domínguez, Ezequiel López-Rubio, Marco A. Hernandez-Vasquez, Miguel A. Molina-Cabello. 375-388 [doi]
• Iterative Clustering for Differential Gene Expression AnalysisOlga Georgieva. 389-398 [doi]
• Comparison of Batch Effect Removal Methods for High Dimensional Mass Cytometry DataAleksandra Suwalska, Nelita du Plessis-Burger, Gian van der Spuy, Joanna Polanska. 399-410 [doi]
• Evaluating Performance of Regression and Classification Models Using Known Lung Carcinomas Prognostic MarkersShrikant D. Pawar, Karuna Mittal, Chandrajit Lahiri. 413-418 [doi]
• Approximate Pattern Matching Using Search Schemes and In-Text VerificationLuca Renders, Lore Depuydt, Jan Fostier. 419-435 [doi]
• KFinger: Capturing Overlaps Between Long Reads by Using Lyndon FingerprintsPaola Bonizzoni, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza. 436-449 [doi]
• Can We Detect T Cell Receptors from Long-Read RNA-Seq Data?Justyna Mika, Serge M. Candéias, Christophe Badie, Joanna Polanska. 450-463 [doi]