Computational and Systems Biology

Latest articles

1. 1. Computational and Systems Biology
   2. Physics of Living Systems

   An engineered multi-step differentiation program in Escherichia coli for self-organized spatial patterning

   Emanuele Boni, Hélène Siboulet ... Yolanda Schaerli
2. 1. Computational and Systems Biology

   TopoMetry systematically learns and evaluates the latent geometry of single-cell data

   David S Oliveira, Ana I Domingos, Licio A Velloso
3. 1. Computational and Systems Biology
   2. Developmental Biology

   A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales

   Alice Gros, Jules Vanaret ... Sham Tlili

   The Tapenade pipeline enables single-cell, whole-mount 3D quantification in dense multilayer organoids, linking spatial gene co-expression and nuclear deformation to emerging tissue-scale organization.
4. 1. Computational and Systems Biology
   2. Evolutionary Biology

   Quantifying microbial fitness in high-throughput experiments

   Justus Wilhelm Fink, Michael Manhart
5. 1. Biochemistry and Chemical Biology
   2. Computational and Systems Biology

   Experimental verification of the error minimization theory using non-standard genetic codes constructed in vitro

   Ryota Miyachi, Norikazu Ichihashi
6. 1. Biochemistry and Chemical Biology
   2. Computational and Systems Biology

   Identification and classification of ion channels across the tree of life provide functional insights into understudied CALHM channels

   Rahil Taujale, Sung Jin Park ... Natarajan Kannan

   An evolution-guided framework is proposed to accelerate the discovery and therapeutic targeting of understudied dark channels by integrating sequence, structure, and functional data from diverse organisms.
7. 1. Developmental Biology
   2. Computational and Systems Biology

   Dorsal/NF-κB exhibits a dorsal-to-ventral mobility gradient in the Drosophila embryo

   Hadel Al Asafen, Natalie M Clark ... Gregory T Reeves
8. 1. Biochemistry and Chemical Biology
   2. Computational and Systems Biology

   Selective suppression and biasing of chemokine receptors CCR9 and ACKR4 through targeting CCL25 with de novo miniproteins

   Bas de Boer, Thomas D Lamme ... Christopher T Schafer
9. 1. Computational and Systems Biology

   Fully computational design of PAM-relaxed Staphylococcus aureus Cas9 with expanded targeting capability using UniDesign

   Youcai Xiong, Li-Kuang Tsai ... Xiaoqiang Huang

   A fully computationally designed SaCas9 variant expands PAM recognition to NNNRRT, achieving up to 116-fold higher editing at noncanonical sites while matching the performance of experimentally evolved variants.
10. 1. Computational and Systems Biology

    Dynamic architecture of mycobacterial outer membranes revealed by all-atom simulations

    Turner P Brown, Matthieu Chavent, Wonpil Im

    The first all-atom models of the mycobacterial outer membrane reveal how lipid organization and asymmetry generate a structurally heterogeneous barrier that underlies its unique permeability properties.