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Showing 1–5 of 5 results
Advanced filters: Author: Avantika Lal Clear advanced filters

  • Bacterial DNA primarily exists in a negatively supercoiled or under-wound state. Here, by mapping the supercoiling state, the authors show that there is a gradient of supercoiling across the bacterial chromosome with the terminus being more negatively supercoiled than the origin.

    • Avantika Lal
    • Amlanjyoti Dhar
    • Sankar Adhya
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-8

  • ATAC-seq measures chromatin accessibility as a proxy for the activity of DNA regulatory regions across the genome. Here the authors present AtacWorks, a deep learning tool to denoise and identify accessible chromatin regions from low cell count, low-coverage, or low-quality ATAC-seq data.

    • Avantika Lal
    • Zachary D. Chiang
    • Jason D. Buenrostro
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-11

  • Identifying molecular subtypes of cancer can improve personalized treatment. Here the authors present CIMLR, an algorithm that integrates multi-omic data to reveal cancer subtypes; subtypes discovered by CIMLR differ in activity of cancer-associated pathways and are significantly predictive of patient outcomes.

    • Daniele Ramazzotti
    • Avantika Lal
    • Arend Sidow
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-14

  • Ferrarini & Lal et al. developed a novel bioinformatic pipeline to explore how SARS-CoV-2 interacts with human respiratory cells using public available host gene expression and viral genome sequence data. Several human genes and proteins were predicted to play a role in the viral life cycle and the host response to SARS-CoV-2 infection.

    • Mariana G. Ferrarini
    • Avantika Lal
    • Vanessa Aguiar-Pulido
    ResearchOpen Access
    Communications Biology
    Volume: 4, P: 1-15