List of works - Wouter Boomsma

3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data ⬇️

scholarly article by Maurice Weiler et al published 2018 in Advances in Neural Information Processing Systems 31

A Continuous Relaxation for Discrete Bayesian Optimization ⬇️

scientific article published on 26 April 2024

A Monte Carlo Study of the Early Steps of Functional Amyloid Formation

scientific article published on 8 January 2016

A generative, probabilistic model of local protein structure

scientific article

A sticky cage can slow down folding

scientific article published on March 2013

A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences ⬇️

scientific article published on 7 June 2024

A systematic analysis of regression models for protein engineering

scientific article published on 3 May 2024

An efficient null model for conformational fluctuations in proteins

scientific article published on 10 May 2012

Ancient biomolecules from deep ice cores reveal a forested southern Greenland

scientific article

Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories

Barnaba: software for analysis of nucleic acid structures and trajectories

scientific article published on 12 November 2018

Bayesian inference of protein ensembles from SAXS data

scientific article

Beyond rotamers: a generative, probabilistic model of side chains in proteins

scientific article

Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

scientific article published on 25 February 2016

Combining experiments and simulations using the maximum entropy principle

scientific article

Comparing molecular dynamics force fields in the essential subspace.

scientific article

Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I.

scientific article

Deep learning assisted single particle tracking for automated correlation between diffusion and function

Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients

scientific article

Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo.

scientific article published on 20 December 2017

ENCORE: Software for Quantitative Ensemble Comparison.

scientific article published on 27 October 2015

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

scientific article

Fast large-scale clustering of protein structures using Gauss integrals

scientific article published on 22 December 2011

Fast phylogenetic DNA barcoding

scientific article (publication date: 27 December 2008)

Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method.

scientific article

Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space

scientific article

Generative probabilistic models extend the scope of inferential structure determination

scientific article

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors

scientific article published on 11 November 2019

Implicit Variational Inference for High-Dimensional Posteriors ⬇️

scientific article published on 10 October 2023

Inference of structure ensembles of flexible biomolecules from sparse, averaged data

scientific article

Kermut: Composite kernel regression for protein variant effects ⬇️

scientific article published on 9 April 2024

Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components

scientific article published in 2023

Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

scientific article published on 06 September 2018

Orchestration of signaling by structural disorder in class 1 cytokine receptors

scientific article published on 24 August 2020

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure

scientific article

Potentials of mean force for protein structure prediction vindicated, formalized and generalized

scientific article

Probabilistic Determination of Native State Ensembles of Proteins

scientific article published on 30 June 2014

Probabilistic Models of Local Biomolecular Structure and Their Applications

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

scientific article (publication date: 2013)

Proteins, physics and probability kinematics: a Bayesian formulation of the protein folding problem

Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

scientific article published on 09 October 2019

Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides

scientific article published on 8 March 2016

Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling

scientific article published on 28 January 2014

Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion

scientific article published on 3 August 2021

Spherical convolutions and their application in molecular modelling ⬇️

scholarly article by Wouter Boomsma & Jes Frellsen published 2017 in Advances in Neural Information Processing Systems 30

Statistical assignment of DNA sequences using Bayesian phylogenetics

scientific article published in October 2008

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

article

Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation

scientific article

Subtle Monte Carlo Updates in Dense Molecular Systems

scientific article published on 18 January 2012

The PCNA interaction motifs revisited: thinking outside the PIP-box

scientific article published on 27 May 2019

List of works by Wouter Boomsma

3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data ⬇️

A Continuous Relaxation for Discrete Bayesian Optimization ⬇️

A Monte Carlo Study of the Early Steps of Functional Amyloid Formation

A generative, probabilistic model of local protein structure

A sticky cage can slow down folding

A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences ⬇️

A systematic analysis of regression models for protein engineering

An efficient null model for conformational fluctuations in proteins

Ancient biomolecules from deep ice cores reveal a forested southern Greenland

Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories

Barnaba: software for analysis of nucleic acid structures and trajectories

Bayesian inference of protein ensembles from SAXS data

Beyond rotamers: a generative, probabilistic model of side chains in proteins

Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

Combining experiments and simulations using the maximum entropy principle

Comparing molecular dynamics force fields in the essential subspace.

Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I.

Deep learning assisted single particle tracking for automated correlation between diffusion and function

Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients

Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo.

ENCORE: Software for Quantitative Ensemble Comparison.

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

Fast large-scale clustering of protein structures using Gauss integrals

Fast phylogenetic DNA barcoding

Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method.

Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space

Generative probabilistic models extend the scope of inferential structure determination

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors

Implicit Variational Inference for High-Dimensional Posteriors ⬇️

Inference of structure ensembles of flexible biomolecules from sparse, averaged data

Kermut: Composite kernel regression for protein variant effects ⬇️

Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components

Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

Orchestration of signaling by structural disorder in class 1 cytokine receptors

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure

Potentials of mean force for protein structure prediction vindicated, formalized and generalized

Probabilistic Determination of Native State Ensembles of Proteins

Probabilistic Models of Local Biomolecular Structure and Their Applications

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

Proteins, physics and probability kinematics: a Bayesian formulation of the protein folding problem

Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides

Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling

Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion

Spherical convolutions and their application in molecular modelling ⬇️

Statistical assignment of DNA sequences using Bayesian phylogenetics

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation

Subtle Monte Carlo Updates in Dense Molecular Systems

The PCNA interaction motifs revisited: thinking outside the PIP-box