List of works - Paul Kirk

A Bayesian Mixture Modelling Approach For Spatial Proteomics

A Bayesian mixture modelling approach for spatial proteomics

scientific article published on 27 November 2018

A Bayesian semi-parametric model for thermal proteome profiling

scientific article published on 29 June 2021

A Bioconductor workflow for the Bayesian analysis of spatial proteomics

scientific article published on 11 April 2019

A Comprehensive Evaluation of Nasal and Bronchial Cytokines and Chemokines Following Experimental Rhinovirus Infection in Allergic Asthma: Increased Interferons (IFN-γ and IFN-λ) and Type 2 Inflammation (IL-5 and IL-13)

scientific article

A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits

scientific article published in 2021

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

scientific article

A general moment expansion method for stochastic kinetic models.

scientific article published in May 2013

A graph theoretical approach to data fusion

scientific article

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

scientific article published on 09 November 2020

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

scientific article published on 5 May 2020

ABC-SysBio--approximate Bayesian computation in Python with GPU support

scientific article

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm

scientific article

Balancing the robustness and predictive performance of biomarkers.

scientific article published on 2 August 2013

Bayesian correlated clustering to integrate multiple datasets

scientific article published on 9 October 2012

Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements.

scientific article

Cellular population dynamics control the robustness of the stem cell niche.

scientific article published on 9 October 2015

Derivative processes for modelling metabolic fluxes.

scientific article published on 26 February 2014

Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes

scientific article published on 04 October 2011

Detection of quantitative trait loci from RNA-seq data with or without genotypes using BaseQTL

scientific article published on 24 June 2021

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.

scientific article

Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics

scientific article published on 12 December 2019

GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution

scientific article published on 01 March 2020

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data

scientific article

Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases

scientific article published on 25 November 2020

Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE

scientific article published on 5 January 2021

Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation

scientific article

MDI-GPU: accelerating integrative modelling for genomic-scale data using GP-GPU computing.

scientific article

MEANS: python package for Moment Expansion Approximation, iNference and Simulation.

scientific article

MR-Clust: Clustering of genetic variants in Mendelian randomization with similar causal estimates

scientific article published on 11 September 2020

Model selection in systems and synthetic biology

scientific article published on 08 April 2013

Model selection in systems biology depends on experimental design

scientific article

Multiple kernel learning for integrative consensus clustering of 'omic datasets

scientific article published on 27 June 2020

Multivariate moment closure techniques for stochastic kinetic models.

scientific article published in September 2015

Noise-augmented directional clustering of genetic association data identifies distinct mechanisms underlying obesity

scientific article published on 27 January 2022

P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish.

scientific article

Parameter inference for biochemical systems that undergo a Hopf bifurcation

scientific article

Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB.

scientific article published in May 2015

Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis.

scientific article

Retroviruses integrate into a shared, non-palindromic DNA motif.

scientific article published on 14 November 2016

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling.

scientific article published on June 2016

SYSBIONS: nested sampling for systems biology

scientific article

SYSTEMS BIOLOGY. Systems biology (un)certainties.

scientific article

The RNA landscape of the human placenta in health and disease

scientific article published on 11 May 2021

Topological sensitivity analysis for systems biology

scientific article

Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes

scientific article published on 12 March 2022

List of works by Paul Kirk

A Bayesian Mixture Modelling Approach For Spatial Proteomics

A Bayesian mixture modelling approach for spatial proteomics

A Bayesian semi-parametric model for thermal proteome profiling

A Bioconductor workflow for the Bayesian analysis of spatial proteomics

A Comprehensive Evaluation of Nasal and Bronchial Cytokines and Chemokines Following Experimental Rhinovirus Infection in Allergic Asthma: Increased Interferons (IFN-γ and IFN-λ) and Type 2 Inflammation (IL-5 and IL-13)

A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

A general moment expansion method for stochastic kinetic models.

A graph theoretical approach to data fusion

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

ABC-SysBio--approximate Bayesian computation in Python with GPU support

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm

Balancing the robustness and predictive performance of biomarkers.

Bayesian correlated clustering to integrate multiple datasets

Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements.

Cellular population dynamics control the robustness of the stem cell niche.

Derivative processes for modelling metabolic fluxes.

Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes

Detection of quantitative trait loci from RNA-seq data with or without genotypes using BaseQTL

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.

Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics

GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data

Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases

Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE

Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation

MDI-GPU: accelerating integrative modelling for genomic-scale data using GP-GPU computing.

MEANS: python package for Moment Expansion Approximation, iNference and Simulation.

MR-Clust: Clustering of genetic variants in Mendelian randomization with similar causal estimates

Model selection in systems and synthetic biology

Model selection in systems biology depends on experimental design

Multiple kernel learning for integrative consensus clustering of 'omic datasets

Multivariate moment closure techniques for stochastic kinetic models.

Noise-augmented directional clustering of genetic association data identifies distinct mechanisms underlying obesity

P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish.

Parameter inference for biochemical systems that undergo a Hopf bifurcation

Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB.

Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis.

Retroviruses integrate into a shared, non-palindromic DNA motif.

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling.

SYSBIONS: nested sampling for systems biology

SYSTEMS BIOLOGY. Systems biology (un)certainties.

The RNA landscape of the human placenta in health and disease

Topological sensitivity analysis for systems biology

Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes