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List of works by Jonathan R. Karr

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

scientific article

Accelerated discovery via a whole-cell model

scientific article

DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python

scientific article published on 16 November 2020

Guidelines for Reproducibly Building and Simulating Systems Biology Models

scientific article published on 18 July 2016

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

scientific article published on 10 July 2008

NetworkPainter: dynamic intracellular pathway animation in Cytobank

scientific article

Organizing genome engineering for the gigabase scale

scientific article published on 04 February 2020

Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

scientific article published in September 2021

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

scientific article published on 8 December 2020

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

scientific article published on 28 May 2015

The principles of whole-cell modeling

scientific article published on 23 June 2015

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

scientific article published in March 2024

Toward Community Standards and Software for Whole-Cell Modeling

scientific article

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

scientific article

WholeCellViz: data visualization for whole-cell models

scientific article

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