List of works - Simon Rogers

A Bayesian regression approach to the inference of regulatory networks from gene expression data

scientific article published on 6 May 2005

A community resource for paired genomic and metabolomic data mining

scientific article published in 2021

Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

scientific article published on 18 June 2021

An Optimal Frequency in Ca2+ Oscillations for Stomatal Closure Is an Emergent Property of Ion Transport in Guard Cells.

scientific article

Bayesian Approaches for Mass Spectrometry-Based Metabolomics

Bayesian model-based inference of transcription factor activity

scientific article

Comparative Metabologenomics Analysis of Polar Actinomycetes

scientific article published in 2021

Data mining and visualisation: general discussion

scientific article published on 01 August 2019

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra

scientific article published on 9 December 2018

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra

scientific article published on 01 August 2019

Disclosure control of machine learning models from trusted research environments (TRE): New challenges and opportunities

scientific article published in April 2023

EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture

scientific article published on 12 June 2018

Feature-based molecular networking in the GNPS analysis environment

scientific article published on 24 August 2020

Future challenges and new approaches: general discussion

scientific article published on 01 August 2019

Gestational age-dependent development of the neonatal metabolome

scientific article published on 17 September 2020

Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics.

scientific article

Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques.

scientific article

In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics

scientific article published on 09 October 2019

Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets

scientific article published on 2 February 2015

Infinite factorization of multiple non-parametric views

Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships

scientific article published on 11 September 2019

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

scientific article

Machine learning models in trusted research environments -- understanding operational risks

scientific article published on 14 December 2023

MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.

scientific article

Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts

scientific article published on 26 July 2018

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

scientific article published on 16 July 2019

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools

scientific article published on 31 May 2019

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

scientific article published on 14 September 2017

PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data

scientific article published on 14 August 2017

Predicting host taxonomic information from viral genomes: A comparison of feature representations

scientific article published on 26 May 2020

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

scientific article

Protein interaction detection in sentences via Gaussian processes: a preliminary evaluation

scientific article published in January 2011

Ranking Metabolite Sets by Their Activity Levels

scientific article

Rapid Development of Improved Data-Dependent Acquisition Strategies

scientific article published in 2021

ShinyKGode: an interactive application for ODE parameter inference using gradient matching.

scientific article published in July 2018

Simulated-to-real Benchmarking of Acquisition Methods in Metabolomics

scientific article published on 15 January 2023

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Statistical inference in mechanistic models: time warping for improved gradient matching.

scientific article published on 9 August 2017

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations

scientific article published on September 2014

Stronger findings from mass spectral data through multi-peak modeling

scientific article

The latent process decomposition of cDNA microarray data sets

scientific article

TopNEXt: Automatic DDA Exclusion Framework for Multi-Sample Mass Spectrometry Experiments

TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments

scientific article published on 26 June 2023

Topic modeling for untargeted substructure exploration in metabolomics

scientific article

Towards development of a statistical framework to evaluate myotonic dystrophy type 1 mRNA biomarkers in the context of a clinical trial

scientific article published on 14 April 2020

Tyrosine Kinase Inhibitor Independent Gene Expression Signature in CML Offers New Targets for LSPC Eradication Therapy

scientific article published on 26 October 2022

Tyrosine kinase inhibitor independent gene expression signature in CML offers new targets for LSPC eradication therapy

Unexpected Connections between Humidity and Ion Transport Discovered Using a Model to Bridge Guard Cell-to-Leaf Scales.

scientific article published in November 2017

Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics

scientific article

Using topic modeling to detect cellular crosstalk in scRNA-seq

scientific article published on 08 April 2022

ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics

scientific article published on 30 March 2022

matchms - processing and similarity evaluation of mass spectrometry data.

scientific article published on 31 August 2020

List of works by Simon Rogers

A Bayesian regression approach to the inference of regulatory networks from gene expression data

A community resource for paired genomic and metabolomic data mining

Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

An Optimal Frequency in Ca2+ Oscillations for Stomatal Closure Is an Emergent Property of Ion Transport in Guard Cells.

Bayesian Approaches for Mass Spectrometry-Based Metabolomics

Bayesian model-based inference of transcription factor activity

Comparative Metabologenomics Analysis of Polar Actinomycetes

Data mining and visualisation: general discussion

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra

Disclosure control of machine learning models from trusted research environments (TRE): New challenges and opportunities

EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture

Feature-based molecular networking in the GNPS analysis environment

Future challenges and new approaches: general discussion

Gestational age-dependent development of the neonatal metabolome

Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics.

Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques.

In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics

Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets

Infinite factorization of multiple non-parametric views

Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

Machine learning models in trusted research environments -- understanding operational risks

MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.

Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data

Predicting host taxonomic information from viral genomes: A comparison of feature representations

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

Protein interaction detection in sentences via Gaussian processes: a preliminary evaluation

Ranking Metabolite Sets by Their Activity Levels

Rapid Development of Improved Data-Dependent Acquisition Strategies

ShinyKGode: an interactive application for ODE parameter inference using gradient matching.

Simulated-to-real Benchmarking of Acquisition Methods in Metabolomics

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Statistical inference in mechanistic models: time warping for improved gradient matching.

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations

Stronger findings from mass spectral data through multi-peak modeling

The latent process decomposition of cDNA microarray data sets

TopNEXt: Automatic DDA Exclusion Framework for Multi-Sample Mass Spectrometry Experiments

TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments

Topic modeling for untargeted substructure exploration in metabolomics

Towards development of a statistical framework to evaluate myotonic dystrophy type 1 mRNA biomarkers in the context of a clinical trial

Tyrosine Kinase Inhibitor Independent Gene Expression Signature in CML Offers New Targets for LSPC Eradication Therapy

Tyrosine kinase inhibitor independent gene expression signature in CML offers new targets for LSPC eradication therapy

Unexpected Connections between Humidity and Ion Transport Discovered Using a Model to Bridge Guard Cell-to-Leaf Scales.

Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics

Using topic modeling to detect cellular crosstalk in scRNA-seq

ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics

matchms - processing and similarity evaluation of mass spectrometry data.