Jeremy Gunawardena

Decoupling between activation time and steady-state level in input-output responses

The paper investigates mechanisms for output decoupling in molecular systems where steady-state levels change with input concentration while activation times remain constant.

Emergence of activation or repression in transcriptional control under a fixed molecular context

This study uses biophysical models to show that transcription factors can act as activators, repressors, or both, with their effects influenced by binding affinity and regulatory context.

A mathematical model clarifies the ABC Score formula used in enhancer-gene prediction

The paper derives a mathematical model explaining the ABC Score formula for enhancer-gene prediction and shows its limitations in capturing non-additive effects.

Learning in single cells: biochemically-plausible models of habituation

This paper shows that simple molecular networks can exhibit all single-stimulus habituation hallmarks through biochemically-plausible models.

MSModDetector: A Tool for Detecting Mass Shifts and Post-Translational Modifications in Individual Ion Mass Spectrometry Data

MSModDetector identifies PTM patterns in individual ion mass spectrometry data by detecting mass shifts and using linear programming to infer modifications.

The Hill function is the universal Hopfield barrier for sharpness of input-output responses

The paper shows that Hill functions are the universal limit for sharpness of input-output responses in thermodynamic equilibrium models.

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology

The paper integrates modeling and synthetic biology to show that transcriptional synergy depends on both kinetic regulation of the transcription cycle and TF binding.

Robustness and parameter geography in post-translational modification systems

The paper analyzes parameter geography in PTM systems to assess robustness, finding that bistability is rare under realistic enzyme mechanisms.

Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

The paper investigates the HbP2 enhancer in Drosophila, showing that cooperative binding of Bcd is insufficient to explain its sharp expression pattern, and identifies other factors like pioneer factors and histone modifiers as key contributors.

Analysing protein post-translational modform regions by linear programming

The paper uses linear programming to estimate modform distributions of proteins with multiple post-translational modifications, showing that combining bottom-up and top-down MS data reduces average modform range.

A multi-modal proteomics strategy for characterizing posttranslational modifications of tumor suppressor p53 reveals many sites but few modified forms

The paper uses a multi-modal proteomics approach to analyze PTMs of p53, revealing many modification sites but few distinct modified forms.