Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network

Tractable molecular adaptation patterns in a designed complex peptide system

(2022) Ankit Jain et al.   Chem

Analysis of sloppiness in model simulations: Unveiling parameter uncertainty when mathematical models are fitted to data

(2022) Gloria M. Monsalve-Bravo et al.   Science Advances

Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments

(2022) Hayley Boigenzahn et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Prebiotically Plausible Autocatalytic Peptide Amyloids

(2021) Saroj K. Rout et al.   CHEMISTRY-A EUROPEAN JOURNAL

Prebiotic Peptides: Molecular Hubs in the Origin of Life

(2020) Moran Frenkel-Pinter et al.   CHEMICAL REVIEWS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

The kinetics and mechanisms of reactions in the flow systems glycine–sodium trimetaphosphate–imidazoles: the crucial role of imidazoles in prebiotic peptide syntheses

(2020) Nikita Yu. Serov et al.   AMINO ACIDS

Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization

(2020) Sourav Maity et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions

(2019) Andrew J. Surman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconciling modern machine-learning practice and the classical bias–variance trade-off

(2019) Mikhail Belkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Point of Inflection and Reflection on Systems Chemical Biology

(2019) Eachan O. Johnson et al.   ACS Chemical Biology

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH

(2018) Izabela Sibilska et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Practical High-Throughput Experimentation for Chemists

(2017) Michael Shevlin   ACS Medicinal Chemistry Letters

Kinetics of prebiotic depsipeptide formation from the ester–amide exchange reaction

(2016) Sheng-Sheng Yu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems

(2016) Andrew White et al.   PLoS Computational Biology

Driving the Model to Its Limit: Profile Likelihood Based Model Reduction

(2016) Tim Maiwald et al.   PLoS One

Perspective: Sloppiness and emergent theories in physics, biology, and beyond

(2015) Mark K. Transtrum et al.   JOURNAL OF CHEMICAL PHYSICS

Prebiotic network evolution: six key parameters

(2015) Philippe Nghe et al.   Molecular BioSystems

Prebiotic synthesis and selection of macromolecules: Thermal cycling as a condition for synthesis and combinatorial selection

(2014) S. D. Varfolomeev et al.   GEOCHEMISTRY INTERNATIONAL

Ester Formation and Hydrolysis during Wet–Dry Cycles: Generation of Far-from-Equilibrium Polymers in a Model Prebiotic Reaction

(2014) Irena Mamajanov et al.   MACROMOLECULES

Prebiotic Systems Chemistry: New Perspectives for the Origins of Life

(2013) Kepa Ruiz-Mirazo et al.   CHEMICAL REVIEWS

Parameter uncertainty in biochemical models described by ordinary differential equations

(2013) J. Vanlier et al.   MATHEMATICAL BIOSCIENCES

Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

(2013) Andreas Raue et al.   PLoS One

Optimal experiment selection for parameter estimation in biological differential equation models

(2012) Mark K Transtrum et al.   BMC BIOINFORMATICS

Theory, modelling and simulation in origins of life studies

(2012) Peter V. Coveney et al.   CHEMICAL SOCIETY REVIEWS

Complexity reduction preserving dynamical behavior of biochemical networks

(2012) Mochamad Apri et al.   JOURNAL OF THEORETICAL BIOLOGY

LUCApedia: a database for the study of ancient life

(2012) Aaron David Goldman et al.   NUCLEIC ACIDS RESEARCH

Principal component analysis based methods in bioinformatics studies

(2011) S. Ma et al.   BRIEFINGS IN BIOINFORMATICS

Analyzing the Functional Properties of the Creatine Kinase System with Multiscale ‘Sloppy’ Modeling

(2011) Hannes Hettling et al.   PLoS Computational Biology

Effects of pH and temperature on dimerization rate of glycine: Evaluation of favorable environmental conditions for chemical evolution of life

(2010) Kasumi Sakata et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Sloppy models, parameter uncertainty, and the role of experimental design

(2010) Joshua F. Apgar et al.   Molecular BioSystems

Sloppiness, robustness, and evolvability in systems biology

(2008) Bryan C Daniels et al.   CURRENT OPINION IN BIOTECHNOLOGY

Systems chemistry

(2007) R. Frederick Ludlow et al.   CHEMICAL SOCIETY REVIEWS