Computational and Systems Biology

Latest articles

1. 1. Biochemistry and Chemical Biology
   2. Computational and Systems Biology

   SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations

   Annamarie E Bustion, Renuka R Nayak ... Katherine S Pollard

   Computational reaction representations and profile hidden Markov model searches of metagenomics databases can be harnessed to accurately predict bacterial species and enzyme sequences responsible for biotransformations in the human gut microbiome.
2. 1. Computational and Systems Biology

   Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells

   Silvia Liu, Yan-Ping Yu ... Jian-Hua Luo
3. 1. Computational and Systems Biology
   2. Ecology

   Spatial structure favors microbial coexistence except when slower mediator diffusion weakens interactions

   Alexander Lobanov, Samantha Dyckman ... Babak Momeni
4. 1. Cell Biology
   2. Computational and Systems Biology

   An in silico FSHD muscle fiber for modeling DUX4 dynamics and predicting the impact of therapy

   Matthew V Cowley, Johanna Pruller ... Christopher RS Banerji

   Mathematical and experimental characterization of DUX4 expression dynamics in facioscapulohumeral muscular dystrophy muscle fibers, provides insights into pathology and open-source tools for in silico investigation of anti-DUX4 therapy.
5. 1. Cancer Biology
   2. Computational and Systems Biology

   Is tumor mutational burden predictive of response to immunotherapy?

   Carino Gurjao, Dina Tsukrov ... Leonid A. Mirny
6. 1. Computational and Systems Biology

   Predicting mechanisms of action at genetic loci associated with discordant effects on type 2 diabetes and abdominal fat accumulation

   Yonathan Tamrat Aberra, Lijiang Ma ... Mete Civelek

   Predicted effector genes at loci associated with abdominal obesity but protection from type 2 diabetes likely effect intermediate anthropometric and diabetic phenotypes.
7. 1. Computational and Systems Biology

   Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains

   Valentina Baldazzi, Delphine Ropers ... Hidde de Jong

   A coarse-grained model of microbial growth coupling fluxes of carbon and energy shows that resource allocation is a major explanatory factor of the observed variability of growth rates and growth yields across different bacterial strains.
8. 1. Computational and Systems Biology
   2. Physics of Living Systems

   How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

   Nicholas M. Boffi, Yipei Guo ... Ariel Amir
9. 1. Computational and Systems Biology
   2. Structural Biology and Molecular Biophysics

   Rapid protein stability prediction using deep learning representations

   Lasse M Blaabjerg, Maher M Kassem ... Kresten Lindorff-Larsen

   RaSP is a method for making rapid and accurate predictions of changes in protein stability that enabled us to calculate ~300 million stability changes for nearly all possible single amino acid changes in the human proteome.
10. 1. Computational and Systems Biology
    2. Ecology

    100 years of anthropogenic impact causes changes in freshwater functional biodiversity

    Niamh Eastwood, Jiarui Zhou ... Luisa Orsini