Bioinformatics

Conservation assessment of human splice site annotation based on a 470-genome alignment
Ilia Minkin, Steven L. Salzberg

bioRxiv 2023.12.01.569581; doi: https://doi.org/10.1101/2023.12.01.569581 New Results

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Unveiling Tissue Structure and Tumor Microenvironment from Spatial Omics by Hypergraph Learning
Yi Liao, Chong Zhang, Zhikang Wang, Fei Qi, Weitian Huang, Shangyan Cai, Junyu Li, Jiazhou Chen, Robin B. Gasser, Zhiyuan Yuan, Jiangning Song, Hongmin Cai

bioRxiv 2024.05.15.594168; doi: https://doi.org/10.1101/2024.05.15.594168 New Results

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Predictions from Deep Learning Propose Substantial Protein-Carbohydrate Interplay
Samuel W. Canner, Ronald L. Schnaar, Jeffrey J. Gray

bioRxiv 2025.03.07.641884; doi: https://doi.org/10.1101/2025.03.07.641884 New Results

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niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction
Jakob Troidl, Yiqing Liang, Johanna Beyer, Mojtaba Tavakoli, Johann Danzl, Markus Hadwiger, Hanspeter Pfister, James Tompkin

bioRxiv 2024.09.07.611785; doi: https://doi.org/10.1101/2024.09.07.611785 New Results

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Bioinformatic analysis of the variability of Tax1 and Tax2 proteins of the human T-cell lymphotropic virus (HTLV)
Roberto Reinosa-Fernández, Francisco Javier Hernández-Walias

bioRxiv 2025.03.13.642961; doi: https://doi.org/10.1101/2025.03.13.642961 New Results

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SMART: an approach for accurate formula assignment in spatially-resolved metabolomics
Yinghao Cao, Shengxi Li, Zhaoyi Liu, Zixian Jia, Weidong Zhuang, Xu Pan, Jinyu Zhou, Lifeng Yang, Lin Wang

bioRxiv 2025.03.12.642824; doi: https://doi.org/10.1101/2025.03.12.642824 New Results

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Re-annotating the EPICv2 manifest with genes, intragenic features, and regulatory elements
Bethan Mallabar-Rimmer, Philippa Wells, Alice Franklin, Jonathan Mill, Amy P Webster

bioRxiv 2025.03.12.642895; doi: https://doi.org/10.1101/2025.03.12.642895 New Results

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Multilingual model improves zero-shot prediction of disease effects on proteins
Ruyi Chen, Nathan Palpant, Gabriel Foley, Mikael Bodén

bioRxiv 2025.03.12.642937; doi: https://doi.org/10.1101/2025.03.12.642937 New Results

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seqLens: optimizing language models for genomic predictions
Mahdi Baghbanzadeh, Brendan Mann, Keith A. Crandall, Ali Rahnavard

bioRxiv 2025.03.12.642848; doi: https://doi.org/10.1101/2025.03.12.642848 New Results

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Predicting Kinase-Substrate Phosphorylation Site Using Autoregressive Transformer
Mahdi Pourmirzaei, Farzaneh Esmaili, Mohammadreza Pourmirzaei, Mohsen Rezaei, Dong Xu

bioRxiv 2025.03.12.642740; doi: https://doi.org/10.1101/2025.03.12.642740 New Results

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Bioinformatics

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