cff-version: 1.2.0
message: >
  If you use pynetphorest in your research, please cite this software
  alongside the foundational NetPhorest / KinomeXplorer, PTMcode v2,
  and NetworKIN phosphorylation network discovery papers.
title: "pynetphorest: modern NetPhorest-style scoring and phosphorylation crosstalk modeling in Python"
version: "0.1.2"
type: software

authors:
  - family-names: Mishra
    given-names: Abhinav
    email: mishraabhinav36@gmail.com
    orcid: "https://orcid.org//0009-0005-3179-7408"

repository-code: "https://github.com/bibymaths/pynetphorest"
license: "BSD-3-Clause"

keywords:
  - NetPhorest
  - kinase
  - phosphorylation
  - crosstalk
  - proteomics
  - phosphoproteomics
  - signal transduction
  - network biology

abstract: >
  pynetphorest is a modern Python toolkit that re-implements and extends
  the NetPhorest family of methods, enabling scalable kinase–substrate
  motif scoring, causal Writer→Reader inference, and machine-learning-based
  phosphorylation crosstalk prediction. The package includes a unified CLI,
  Snakemake workflows, threshold-sweep evaluation, and reproducible pipelines
  for proteome-wide analysis using NetPhorest atlases and PTMcode2 phosphorylation
  networks.


preferred-citation:
  type: software
  title: "pynetphorest"
  authors:
    - family-names: Mishra
      given-names: Abhinav
  year: 2025
  version: "0.1.0"
  repository-code: "https://github.com/<YOUR_GH_USERNAME>/pynetphorest"

references:

  - type: article
    title: "PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins"
    authors:
      - family-names: Minguez
        given-names: Pablo
      - family-names: Letunic
        given-names: Ivica
      - family-names: Parca
        given-names: Luca
      - family-names: Garcia-Alonso
        given-names: Luz
      - family-names: Dopazo
        given-names: Joaquin
      - family-names: Huerta-Cepas
        given-names: Jaime
      - family-names: Bork
        given-names: Peer
    journal: "Nucleic Acids Research"
    year: 2015
    volume: "43"
    issue: "Database issue"
    pages: "D494–D502"
    doi: "10.1093/nar/gku1081"

  - type: article
    title: "KinomeXplorer: an integrated platform for kinome biology studies"
    authors:
      - family-names: Horn
        given-names: Heiko
      - family-names: Schoof
        given-names: Erwin M.
      - family-names: Kim
        given-names: Jinwoo
    journal: "Nature Methods"
    year: 2014
    volume: "11"
    pages: "603–604"
    doi: "10.1038/nmeth.2968"

  - type: article
    title: "Systematic discovery of in vivo phosphorylation networks"
    authors:
      - family-names: Linding
        given-names: Rune
      - family-names: Jensen
        given-names: Lars Juhl
      - family-names: Ostheimer
        given-names: Gernot J.
      - family-names: van Vugt
        given-names: Marcel A.
      - family-names: Jørgensen
        given-names: Claus
      - family-names: Miron
        given-names: I. Michael
    journal: "Cell"
    year: 2007
    volume: "129"
    issue: "7"
    pages: "1415–1426"
    doi: "10.1016/j.cell.2007.05.052"