Bioinformatics

STmiR: A Novel XGBoost-Based Framework for Spatially Resolved miRNA Activity Prediction in Cancer Transcriptomics
Jiaqi Yuan, Peng Xu, Zheng Ye, Wenbin Liu

bioRxiv 2025.03.18.644021; doi: https://doi.org/10.1101/2025.03.18.644021 Confirmatory Results

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A Simple Generative Model for the Prediction of T-Cell Receptor - Peptide Binding in T-Cell Therapy for Cancer
Athanasios Papanikolaou, Vladimir Sivtsov, Enrica Zereik, Eliana Ruggiero, Chiara Bonini, Fabio Bonsignorio

bioRxiv 2025.03.18.643937; doi: https://doi.org/10.1101/2025.03.18.643937 New Results

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Clumps: A Sequential Clustering Approach to Partitioning Sets of Phylogenies with Non-Identical Leaf Sets
Ana Serra Silva, Mark Wilkinson

bioRxiv 2025.03.18.641816; doi: https://doi.org/10.1101/2025.03.18.641816 New Results

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NOX transmembrane electron transfer is governed by a subtly balanced, self-adjusting charge distribution
Baptiste Etcheverry, Marc Baaden, Aurélien de la Lande, Fabien Cailliez

bioRxiv 2025.03.18.643896; doi: https://doi.org/10.1101/2025.03.18.643896 New Results

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Predicting allergy and postpartum depression from incomplete compositional microbiome
Andrey Shternshis, Bangzhuo Tong, Alkistis Skalkidou, Carolina Wahlby, Dave Zachariah, Luisa W Hugerth, Prashant Singh

bioRxiv 2025.02.28.640766; doi: https://doi.org/10.1101/2025.02.28.640766 New Results

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AACDB: Antigen-Antibody Complex Database — a Comprehensive Database Unlocking Insights into Interaction Interface
Yuwei Zhou, Wenwen Liu, Ziru Huang, Yushu Gou, Siqi Liu, Lixu Jiang, Yue Yang, Jian Huang

bioRxiv 2024.11.12.623267; doi: https://doi.org/10.1101/2024.11.12.623267 New Results

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3D Structure-based Generative Small Molecule Drug Design: Are We There Yet?
Bo Yang, Chijian Xiang, Tongtong Li, Yunong Xu, Jianing Li

bioRxiv 2024.12.27.629537; doi: https://doi.org/10.1101/2024.12.27.629537 New Results

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Penalized likelihood optimization for censored missing value imputation in proteomics
Lucas Etourneau, Laura Fancello, Samuel Wieczorek, Nelle Varoquaux, Thomas Burger

bioRxiv 2023.11.09.566355; doi: https://doi.org/10.1101/2023.11.09.566355 New Results

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MSI-VISUAL: New visualization methods for mass spectrometry imaging and tools for interactive mapping and exploration of m/z values
Jacob Gildenblat, Jens Pahnke

bioRxiv 2025.03.18.643852; doi: https://doi.org/10.1101/2025.03.18.643852 New Results

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Domain-specific embeddings uncover latent genetics knowledge
Steve S Ho, Ryan E Mills

bioRxiv 2025.03.17.643817; doi: https://doi.org/10.1101/2025.03.17.643817 New Results

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Bioinformatics

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