Browse our latest Computational and Systems Biology articles

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    1. Computational and Systems Biology
    2. Genetics and Genomics

    Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

    Jie Lin, Yujian Wen ... Hao Zhu
    Compared with human-specific transcriptional factors, human-specific lncRNAs identified upon human lncRNAs’ orthologs in mammals have greatly evolved DNA-binding sites in archaic and modern humans in genes determining human traits.
    1. Computational and Systems Biology

    Thymic selection of the T cell receptor repertoire is biased toward autoimmunity in females

    Hélène Vantomme, Valentin Quiniou ... David Klatzmann
    Revised
    Reviewed Preprint v2
    Updated
    • Valuable
    • Incomplete
    1. Computational and Systems Biology
    2. Physics of Living Systems

    A Coma Pattern-Based Autofocusing Method Resolves Bacterial Cold Shock Response at Single-Cell Level

    Sihong Li, Zhixin Ma ... Shuqiang Huang
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

    Luke J Dillard, Gina Calabrese ... Charles Farber
    Single-cell transcriptomics data from mouse bone-relevant cells was used to inform human bone mineral density genome-wide association studies and prioritize genetic targets with potential causal roles in the development of osteoporosis.
    1. Neuroscience
    2. Computational and Systems Biology

    Miniscope Processing Suite (MPS): An Intuitive, No-Code, Scalable Pipeline for Long-Duration Calcium Imaging

    Ari Peden-Asarch, Meredith Weinstock ... John F Neumaier
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

    Zachary L Reitz, Bita Pourmohsenin ... Marnix H Medema
    Automated detection of metallophore biosynthesis reveals that metal-chelating non-ribosomal peptides are widespread, chemically diverse, and deeply rooted in bacterial evolution.
    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.
    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.