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Bioinformatics & computational biology

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2,115 studies

  1. Accurate and scalable decontamination of imaging-based spatial transcriptomics via optimal transport
    Y. Chen, Y. Liu, Z. Chao +9
    bioRxivPreprintCC BY-NC-NDFull textBioinformatics & computational biologybioRxiv
  2. Interpretable Machine Learning Reveals Complementary Age-Related Signatures in the Oral and Gut Microbiome
    C. A. Ruthbah, T. H. Sadi, N. E. S. Jahan +1
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  3. Accounting for pseudo-replication of Linkage Disequilibrium for contemporary Ne estimation
    L. Zhou, T.-Y. J. Hui, A. Burt
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  4. Benchmarking CUT&RUN analysis using motif enrichment
    L. Tan, C. Viner, X. H. Li +6
    bioRxivPreprintAll rights reservedFull textBioinformatics & computational biologybioRxiv
  5. Towards reconstruction of the human interactome from positive and negative experimental evidence
    J. As, K. Pelz, J. Bernett +4
    bioRxivPreprintCC BYFull text1 citedBioinformatics & computational biologybioRxiv
  6. RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics
    O. M. Kozlov, A. Togkousidis, C. Stelz +3
    bioRxivPreprintCC BY-NCFull textBioinformatics & computational biologybioRxiv
  7. Self-Architecting Protein Transformers: An Empirical Study
    G. Cirrincione, E. Ficarra, M. Lovino
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  8. Seamless Whole Slide Label-Free Virtual Staining
    Dou Hoon Kwark, Kianoush Falahkheirkhah, Ji-hun Oh +3
    arXivPreprintarXiv licenceFull textBioinformatics & computational biologyarXiv
  9. Discovering Subtypes of Neurodegenerative Progression with a Scalable Connectome-Constrained Dynamic Model
    Daniel Semchin, Emile d'Angremont, Hao Ding +6
    arXivPreprintarXiv licenceFull textBioinformatics & computational biologyNeurosciencearXiv
  10. scDEFT: A deep learning framework for drug-effect prediction and counterfactual reasoning
    Murthy Devarakonda
    arXivPreprintCC BY-NC-ND 4.0Full textBioinformatics & computational biologyarXiv
  11. ProMeta: Few-shot PROTAC-targeted degradation prediction across E3 ligases
    Yuansheng Liu, Yufei Ye, Tao Tang +3
    arXivPreprintarXiv licenceFull textBioinformatics & computational biologyarXiv
  12. Multi-Task Bacterial Colony Detection and Classification Using YOLOv8 with Edge Optimization for Resource-Constrained Deployment
    Belaguppa Manjunath Ashwin Desai, Rohan Rajesh, Shreyas Murthy +2
    arXivPreprintCC BY-NC-SA 4.0Full textBioinformatics & computational biologyarXiv
  13. UPLC-MS metabolite profiling and antioxidant efficacy of Neopestalotiopsisclavispora isolated from Oroxylum indicum (L.) Kurz Stem Bark
    Sushma Swaroopa, Amshumala Bhoothakallu Lolajaksha, Tamizh Selvan Gnanasekaran +3
    PLOS OnePeer-reviewedCC BY 4.0Full textBioinformatics & computational biologyPLOS
  14. Scenario-dependent functional connectivity in a crowded seascape: habitat suitability, shipping pressure and marine infrastructure in the North Sea
    Catia Matos
    EcoEvoRxivPreprintCC BY 4.0Full textBioinformatics & computational biologyEcologyEvolutionary biologyEcoEvoRxiv
  15. A Scalable Distributed-Memory MPI Implementation of Smith-Waterman with Token-Passing Traceback
    M. Fatima, W. Ali
    bioRxivPreprintCC BY-NCFull textBioinformatics & computational biologybioRxiv
  16. Population Intelligence: Smallest-Model Numerical Experiment
    T. Xu, P. Wan, M. Xiong
    bioRxivPreprintCC BY-NCFull textBioinformatics & computational biologybioRxiv
  17. An interpretable peptide-HLA model emergently learns binding energetics and structure
    S. F. Chen, R. J. Steele, E. K. Oermann
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  18. How effective are contrastive learning-based approaches for activity-cliff prediction?
    A. Surendran, R. A. Miranda Quintana
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  19. Profiling proteome-level amino acid substitutions in Alzheimer's disease brain tissue
    P. Zhao
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  20. Dynamics of bleomycin-induced lung injury at single-nucleus resolution
    C. Lopez-Martinez, Y.-H. Chow, W. A. Altemeier +2
    bioRxivPreprintAll rights reservedFull textBioinformatics & computational biologybioRxiv
  21. Resolving context-specific protein-protein interactomes forbiological discovery and therapeutic target prioritisation
    A. Thomas, L. Fournier, V. Jung +4
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  22. LucaCell: a sequence-centric foundation model for cross-species single-cell analysis
    Y. Sun, Y. He, M. Ren +8
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  23. PHACTn enables training-free, context-independent inference of nucleotide variant tolerance across the genome
    C. Yildirim, N. Kuru, O. Adebali
    bioRxivPreprintCC BY-NC-NDFull textBioinformatics & computational biologybioRxiv
  24. LIGER2: Scalable Single-Cell Integration with On-Disk Datasets
    Y. Wang, A. Robbins, G. Gadhvi +1
    bioRxivPreprintCC BY-NC-NDFull textBioinformatics & computational biologybioRxiv
  25. Heterogeneous graph neural networks with biological prior knowledge for interpretable drug repurposing in triple-negative breast cancer
    C. Fernandez-Lozano, D. Ferreiro, P. V.-del-Rio
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv