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e-south/README.md

👋 Hi, I'm @e-south

  • PhD Candidate in the Dunlop Lab, part of the Biological Design Center at Boston University.
  • Previously at Imperial College London and James Madison University.
  • I’m interested in systems, synthetic, and computational biology. My research focuses on developing genetic circuits, high-throughput functional assays, and DNA sequence-to-expression models to engineer cell physiology for synthetic biology applications.

📂 Highlights

densearrays

A computational method for designing nucleotide sequences with densely packed DNA-protein binding sites.

deg2tfbs

A pipeline for processing RNA-seq and proteomic datasets from E. coli. This tool identifies differentially expressed genes (DEGs) between conditions, maps them to associated transcription factors using RegulonDB, and retrieves their corresponding transcription factor binding sites (TFBSs).

  • Related Repo: Utilizes sourced datasets (e.g., from RegulonDB, EcoCyc, and primary literature) from dnadesign-data.

dnadesign

A collection of Python modules and data analysis pipelines for studying and designing regulatory DNA elements, with an initial focus on bacterial stress promoters.

  • Related Repo: Utilizes sourced datasets from dnadesign-data.
  • Features: Integrates tools from densearrays and deg2tfbs to drive promoter analysis and design.

📬 Get in Touch

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  1. dense-arrays dense-arrays Public

    We introduce a computational technique that efficiently assembles sets of DNA-protein binding sites into dense, contiguous stretches of double-stranded DNA.

    Python

  2. deg2tfbs deg2tfbs Public

    Pipeline for differential expression analysis (DEGs), transcription factor mapping, and TFBS identification.

    Python

  3. dnadesign-data dnadesign-data Public

    This repository contains datasets, such as RegulonDB, EcoCyc, primary literature data.

    Python

  4. dnadesign dnadesign Public

    A collection of Python modules and data analysis pipelines, all related to DNA sequence design.

    Python

  5. CIDARLAB/ibis CIDARLAB/ibis Public

    Graph-based Datastructure Library for Genetic and Boolean Circuits.

    Python 1 2