ELEMENT/CITATION.cff at main · jramirezgen/ELEMENT · GitHub

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cff-version: 1.2.0
message: "If you use ELEMENT, please cite it as below."
type: software
title: "ELEMENT: Enzymatic-Level Equation-based Mechanistic Elementary-route Network Toolkit"
version: 2.0.0
date-released: "2026-05-28"
url: "https://github.com/jramirezgen/ELEMENT"
repository-code: "https://github.com/jramirezgen/ELEMENT"
license: Apache-2.0
abstract: >
  ELEMENT is an organism-agnostic MATLAB platform for mechanistic metabolic route
  discovery, multi-omics ranking, and phenotype simulation from any genome-scale
  metabolic model (GEM). It integrates sparse MILP route discovery (S·v=0
  guaranteed), elementary enzymatic ODE kinetics (no QSSA, Ullah et al. 2006
  framework), population-level bridge fitting, and a composite multi-omics scoring
  system (C1-C10 + C_dyn). Validated on Shewanella xiamenensis LC6 for azo dye
  decolorization (score 0.7199, PASS).

authors:
  - family-names: "Ramirez Quispe"
    given-names: "Jefferson David"
    affiliation: "Universidad Nacional Mayor de San Marcos (UNMSM)"
    orcid: ""

  - family-names: "Ramirez Roca"
    given-names: "Pablo Sergio"
    affiliation: "Universidad Nacional Mayor de San Marcos (UNMSM)"

  - family-names: "Reyes"
    given-names: "Bryan Cesar"
    affiliation: "Universidad Nacional Mayor de San Marcos (UNMSM)"

  - family-names: "Susuki Pacheco"
    given-names: "Asami"
    affiliation: "Universidad Nacional Mayor de San Marcos (UNMSM)"

  - family-names: "Huamantalla Huamán"
    given-names: "Magerlyn"
    affiliation: "Universidad Nacional Mayor de San Marcos (UNMSM)"

  - family-names: "Herrera Quiñones"
    given-names: "Josemaria"
    affiliation: "Universidad Nacional Mayor de San Marcos (UNMSM)"

  - family-names: "Beraun Gasco"
    given-names: "Piero"
    affiliation: "Universidad Nacional Mayor de San Marcos (UNMSM)"

keywords:
  - genome-scale metabolic model
  - GEM
  - COBRA Toolbox
  - metabolic route discovery
  - MILP
  - elementary kinetics
  - multi-omics
  - azo dye decolorization
  - Shewanella
  - bioremediation
  - phenotype simulation
  - MATLAB
  - mechanistic modeling