Computational and Systems Biology

Latest articles

1. 1. Computational and Systems Biology
   2. Immunology and Inflammation

   The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling

   Anastasia O Smirnova, Anna M Miroshnichenkova ... Alexander Komkov

   A hallmark property of non-functional clonotypes was used to develop a universal and fully computational method for detection and correction of multiplex PCR-specific quantitative bias in adaptive immune receptor repertoire.
2. 1. Computational and Systems Biology
   2. Evolutionary Biology

   Evolved bacterial resistance to the chemotherapy gemcitabine modulates its efficacy in co-cultured cells

   Serkan Sayin, Brittany Rosener ... Amir Mitchell
3. 1. Computational and Systems Biology
   2. Neuroscience

   Cellular and circuit organization of the locus coeruleus of adult mice

   Andrew McKinney, Ming Hu ... Xiaolong Jiang
4. 1. Computational and Systems Biology

   Generative power of a protein language model trained on multiple sequence alignments

   Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol
5. 1. Computational and Systems Biology
   2. Structural Biology and Molecular Biophysics

   Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains

   Artur Meller, Jeffrey M. Lotthammer ... Gregory R Bowman
6. 1. Computational and Systems Biology
   2. Neuroscience

   A hardware system for real time decoding of in vivo calcium imaging data

   Zhe Chen, Garrett J Blair ... Hugh T Blair
7. 1. Computational and Systems Biology
   2. Immunology and Inflammation

   Structure-based prediction of T cell receptor:peptide-MHC interactions

   Philip Bradley

   The AlphaFold protein structure prediction network can be specialized for T cell receptor docking, leading to improved models of ternary complexes and some ability to discriminate correct from incorrect peptide epitopes.
8. 1. Computational and Systems Biology
   2. Neuroscience

   Temporal derivative computation in the dorsal raphe network revealed by an experimentally-driven augmented integrate-and-fire modeling framework

   Emerson F Harkin, Michael B Lynn ... Jean-Claude Beique
9. 1. Computational and Systems Biology

   Transformer-based deep learning for predicting protein properties in the life sciences

   Abel Chandra, Laura Tünnermann ... Regina Gratz

   The recent developments in large-scale machine learning, especially with the recent Transformer models, display much potential for solving computational problems within protein biology and outcompete traditional computational methods in many recent studies and benchmarks.
10. 1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

    Hjörleifur Einarsson, Marco Salvatore ... Robin Andersson

    A flexible transcription initiation architecture and a uniform regulatory grammar buffer expression variability and the effects of genetic variants on essential genes while a rigid transcription initiation architecture and a diverse regulatory grammar ensure condition-specific responsiveness of other genes.