Computational and Systems Biology

Latest articles

1. 1. Computational and Systems Biology

   Predicting dynamic expression patterns in budding yeast with a fungal DNA language model

   Kuan-Hao Chao, Majed Mohamed Magzoub ... David R Kelley
2. 1. Computational and Systems Biology

   Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription, and splicing from single-cell RNA sequencing data with TSvelo

   Jiachen Li, Zhe Wang ... Ye Yuan

   TSvelo provides a comprehensive RNA velocity mathematics framework that can model the cascade of gene regulation, transcription, and splicing.
3. 1. Microbiology and Infectious Disease
   2. Computational and Systems Biology

   A new diagnostic modality for bovine tuberculosis: accurate and robust classification of infected cattle using transcriptomics and machine learning

   John F O’Grady, Adriana Ivich ... David E MacHugh
4. 1. Immunology and Inflammation
   2. Computational and Systems Biology

   A predictive systems vaccinology framework enables rational optimization of MVA-based vaccines

   Vincent Deman, Philippe Castera ... Anne-Sophie Beignon
5. 1. Computational and Systems Biology
   2. Immunology and Inflammation

   +Clonal stochasticity in early NK cell response to mouse cytomegalovirus is generated by mature subsets of varying proliferative ability

   Darren Wethington, Saeed Ahmad ... Jayajit Das

   Stochastic fluctuations play an important role in the MCMV-induced NK cell clonal expansion that ultimately gives rise to memory NK cells.
6. 1. Computational and Systems Biology

   A real-time, multi-animal model for automatic face detection and identification of freely moving common marmosets based on YOLOv8 algorithms

   Jiayue Yang, James Wang, Justine Cléry
7. 1. Microbiology and Infectious Disease
   2. Computational and Systems Biology

   REPOP: bacterial population quantification from plate counts

   Pedro Pessoa, Carol Yunxiao Lu ... Steve Pressé
8. 1. Biochemistry and Chemical Biology
   2. Computational and Systems Biology

   Squidly harnesses enzyme functional hierarchy and contrastive learning to efficiently predict catalytic residues from sequence

   William JF Rieger, Mikael Bodén ... Ariane Mora

   Squidly enables efficient identification of enzyme catalytic residues by integrating functional hierarchies into a contrastive learning framework, requiring only protein sequences to produce scalable predictions across the known enzyme landscape.
9. 1. Neuroscience
   2. Computational and Systems Biology

   Opening the black box: a modular approach to spike sorting

   Samuel Garcia, Chris Halcrow ... Pierre Yger
10. 1. Computational and Systems Biology
    2. Neuroscience

    Individual differences drive social hierarchies in male mouse societies

    Jonathan Reinwald, Sarah Ghanayem ... Wolfgang Kelsch

    Automated, long-term tracking reveals that social rank in male mice is a stable individual trait that persists across group changes, with chasing serving to negotiate rank among dominant individuals.