Computational and Systems Biology

Latest articles

1. 1. Computational and Systems Biology
   2. Evolutionary Biology

   An interpretable neural network unveils higher-order epistasis in large protein sequence-function relationships

   Palash Sethi, Juannan Zhou
2. 1. Computational and Systems Biology

   Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage

   Zhiwei Huang, Songhao Luo ... Jiajun Zhang

   DNA damage reshapes genome-wide transcriptional bursting, with distinct burst size and frequency programs associated with differentiation, apoptosis, and survival decisions.
3. 1. Biochemistry and Chemical Biology
   2. Computational and Systems Biology

   Investigating the native functions of [NiFe]-CODH through genomic context analysis

   Maximilian Böhm, Henrik Land
4. 1. Computational and Systems Biology

   Raw signal segmentation for estimating RNA modification from Nanopore direct RNA sequencing data

   Guangzhao Cheng, Aki Vehtari, Lu Cheng

   SegPore refines raw signal segmentation and alignment in nanopore direct RNA sequencing and thereby boosts the performance of RNA modification detection from in vitro data at single-read resolution.
5. 1. Computational and Systems Biology
   2. Genetics and Genomics

   JAX Animal Behavior System (JABS), a genetics-informed, end-to-end advanced behavioral phenotyping platform for the laboratory mouse

   Anshul Choudhary, Brian Q Geuther ... Vivek Kumar

   The JAX Animal Behavior System integrates standardized hardware, machine learning methods, and annotated datasets to enable reproducible behavioral phenotyping and genetic analysis across diverse mouse strains.
6. 1. Computational and Systems Biology
   2. Ecology

   Agent-based modeling reveals how bats navigate dense group emergences

   Omer Mazar, Yossi Yovel

   Acoustic jamming during bat emergence is weaker than expected because signal redundancy, echo integration, and simple movement rules enable robust navigation, as demonstrated by an agent‑based sensory-motor model.
7. 1. Medicine
   2. Computational and Systems Biology

   Global molecular landscape of early MASLD progression in obesity

   Qing Zhao, William De Nardo ... Philipp Kaldis
8. 1. Neuroscience
   2. Computational and Systems Biology

   Opposite and complementary roles of the two calcium thresholds for inducing LTP and LTD in models of striatal projection neurons

   Daniel Trpevski
9. 1. Computational and Systems Biology
   2. Neuroscience

   Motor biases reflect a misalignment between visual and proprioceptive reference frames

   Tianhe Wang, J Ryan Morehead ... Jonathan S Tsay

   The pattern of reaching biases is stable across contexts and can be attributed to a misalignment between eye-centric and body-centric representations of position.
10. 1. Computational and Systems Biology

    Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates

    Irene Lamberti, Jeffrey A Chao ... Felix Naef