All Stories

  1. Metabolic homeostasis and growth in abiotic cells

    Article • Proceedings of the National Academy of Sciences, May 2023, Proceedings of the National Academy of Sciences

    Saugat Poudel

  2. Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks

    Article • Proceedings of the National Academy of Sciences, April 2023, Proceedings of the National Academy of Sciences

    Saugat Poudel

  3. Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism

    Article • PLoS Computational Biology, August 2022, PLOS

    Saugat Poudel

  4. RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

    Article • PLoS Genetics, September 2021, PLOS

    Saugat Poudel

  5. Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

    Article • PLoS Computational Biology, June 2021, PLOS

    Saugat Poudel

  6. Independent component analysis recovers consistent regulatory signals from disparate datasets

    Article • PLoS Computational Biology, February 2021, PLOS

    Saugat Poudel

  7. MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

    Article • PLoS Computational Biology, January 2021, PLOS

    Saugat Poudel

  8. Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

    Article • PLoS Computational Biology, January 2021, PLOS

    Saugat Poudel

  9. Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

    Article • Proceedings of the National Academy of Sciences, September 2020, Proceedings of the National Academy of Sciences

    Saugat Poudel

  10. Decoding the regulatory network underlying Staphylococcus aureus gene expression.

    Article • Proceedings of the National Academy of Sciences, July 2020, Proceedings of the National Academy of Sciences

    Saugat Poudel

  11. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

    Article • PLoS Computational Biology, March 2020, PLOS

    Saugat Poudel

  12. Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

    Article • PLoS Computational Biology, December 2019, PLOS

    Saugat Poudel

  13. Estimating Cellular Goals from High-Dimensional Biological Data

    Article • July 2019, ACM (Association for Computing Machinery)

    Saugat Poudel

  14. Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

    Article • Applied and Environmental Microbiology, July 2018, ASM Journals

    Saugat Poudel

  15. Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism

    Article • Vox Sanguinis, March 2017, Wiley

    ottarr Rolfsson, Giuseppe Paglia, Saugat Poudel