Works matching AU Husmeier, Dirk

Results: 55

Detecting Recombination in 4-Taxa DNA Sequence Alignments with Bayesian Hidden Markov Models and Markov Chain Monte Carlo.

Published in:

Molecular Biology & Evolution, 2003, v. 20, n. 3, p. 315, doi. 10.1093/molbev/msg039

By:

Husmeier, Dirk;
McGuire, Gráinne

Publication type:

Article

Statistical modelling of cell movement.

Published in:

Statistica Neerlandica, 2018, v. 72, n. 3, p. 265, doi. 10.1111/stan.12140

By:

Giurghita, Diana;
Husmeier, Dirk

Publication type:

Article

MCMC methods for inference in a mathematical model of pulmonary circulation.

Published in:

Statistica Neerlandica, 2018, v. 72, n. 3, p. 306, doi. 10.1111/stan.12132

By:

Păun, L. Mihaela;
Qureshi, M. Umar;
Colebank, Mitchel;
Hill, Nicholas A.;
Olufsen, Mette S.;
Haider, Mansoor A.;
Husmeier, Dirk

Publication type:

Article

Segregation and Recombination of a Multipartite Mitochondrial DNA in Populations of the Potato Cyst Nematode Globodera pallida.

Published in:

Journal of Molecular Evolution, 2007, v. 64, n. 6, p. 689, doi. 10.1007/s00239-007-0023-8

By:

Armstrong, Miles;
Husmeier, Dirk;
Phillips, Mark;
Blok, Vivian

Publication type:

Article

Sensitivity analysis and inverse uncertainty quantification for the left ventricular passive mechanics.

Published in:

Biomechanics & Modeling in Mechanobiology, 2022, v. 21, n. 3, p. 953, doi. 10.1007/s10237-022-01571-8

By:

Lazarus, Alan;
Dalton, David;
Husmeier, Dirk;
Gao, Hao

Publication type:

Article

Hemodynamic assessment of pulmonary hypertension in mice: a model-based analysis of the disease mechanism.

Published in:

Biomechanics & Modeling in Mechanobiology, 2019, v. 18, n. 1, p. 219, doi. 10.1007/s10237-018-1078-8

By:

Qureshi, M. Umar;
Colebank, Mitchel J.;
Paun, L. Mihaela;
Ellwein Fix, Laura;
Chesler, Naomi;
Haider, Mansoor A.;
Hill, Nicholas A.;
Husmeier, Dirk;
Olufsen, Mette S.

Publication type:

Article

Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks.

Published in:

Bioinformatics, 2006, v. 22, n. 20, p. 2523, doi. 10.1093/bioinformatics/btl391

By:

Adriano V. Werhli;
Marco Grzegorczyk;
Dirk Husmeier

Publication type:

Article

A regularized discriminative model for the prediction of protein–peptide interactions.

Published in:

Bioinformatics, 2006, v. 22, n. 5, p. 532, doi. 10.1093/bioinformatics/bti804

By:

Wolfgang P. Lehrach;
Dirk Husmeier;
Christopher K. I. Williams

Publication type:

Article

Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models.

Published in:

Bioinformatics, 2005, v. 21, p. ii166, doi. 10.1093/bioinformatics/bti1127

By:

Husmeier, Dirk

Publication type:

Article

Detecting interspecific recombination with a pruned probabilistic divergence measure.

Published in:

Bioinformatics, 2005, v. 21, n. 9, p. 1797, doi. 10.1093/bioinformatics/bti151

By:

Dirk Husmeier;
Frank Wright;
Iain Milne

Publication type:

Article

TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.

Published in:

Bioinformatics, 2004, v. 20, n. 11, p. 1806, doi. 10.1093/bioinformatics/bth155

By:

Iain Milne;
Frank Wright;
Glenn Rowe;
David F. Marshall;
Dirk Husmeier;
Gràinne McGuire

Publication type:

Article

Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks.

Published in:

Bioinformatics, 2003, v. 19, n. 17, p. 2271, doi. 10.1093/bioinformatics/btg313

By:

Dirk Husmeier

Publication type:

Article

Detecting recombination with MCMC.

Published in:

Bioinformatics, 2002, v. 18, p. S345, doi. 10.1093/bioinformatics/18.suppl_1.S345

By:

Husmeier, Dirk;
McGuire, Gráinne

Publication type:

Article

A Bayesian approach to discriminate between alternative DNA sequence segmentations.

Published in:

Bioinformatics, 2002, v. 18, n. 2, p. 226, doi. 10.1093/bioinformatics/18.2.226

By:

Husmeier, Dirk;
Wright, Frank

Publication type:

Article

Probabilistic divergence measures for detecting interspecies recombination.

Published in:

Bioinformatics, 2001, v. 17, p. 123, doi. 10.1093/bioinformatics/17.suppl_1.s123

By:

Husmeier, Dirk;
Wright, Frank

Publication type:

Article

A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 3, p. 1, doi. 10.1371/journal.pcbi.1010885

By:

Harvey, William T.;
Davies, Vinny;
Daniels, Rodney S.;
Whittaker, Lynne;
Gregory, Victoria;
Hay, Alan J.;
Husmeier, Dirk;
McCauley, John W.;
Reeve, Richard

Publication type:

Article

System Relaxation and Thermodynamic Integration.

Published in:

Molecular Simulation, 1992, v. 8, n. 3-5, p. 285, doi. 10.1080/08927029208022483

By:

Schlitter, Jürgen;
Husmeier, Dirk

Publication type:

Article

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

Published in:

Bioinformatics, 2018, v. 34, n. 13, p. 2314, doi. 10.1093/bioinformatics/bty089

By:

Wandy, Joe;
Niu, Mu;
Giurghita, Diana;
Daly, Rónán;
Rogers, Simon;
Husmeier, Dirk

Publication type:

Article

Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes.

Published in:

Bioinformatics, 2011, v. 27, n. 5, p. 693, doi. 10.1093/bioinformatics/btq711

By:

Grzegorczyk, Marco;
Husmeier, Dirk

Publication type:

Article

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops.

Published in:

Bioinformatics, 2009, v. 25, n. 1, p. 126, doi. 10.1093/bioinformatics/btn575

By:

Milne, Lain;
Lindner, Dominik;
Bayer, Micha;
Husmeier, Dirk;
McGuire, Gráinne;
Marshall, David F.;
Wright, Frank

Publication type:

Article

Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler.

Published in:

Bioinformatics, 2008, v. 24, n. 18, p. 2071, doi. 10.1093/bioinformatics/btn367

By:

Marco Grzegorczyk;
Dirk Husmeier;
Kieron D. Edwards;
Peter Ghazal;
Andrew J. Millar

Publication type:

Article

Classification of myocardial blood flow based on dynamic contrast‐enhanced magnetic resonance imaging using hierarchical Bayesian models.

Published in:

Journal of the Royal Statistical Society: Series C (Applied Statistics), 2022, v. 71, n. 5, p. 1085, doi. 10.1111/rssc.12568

By:

Yang, Yalei;
Gao, Hao;
Berry, Colin;
Carrick, David;
Radjenovic, Aleksandra;
Husmeier, Dirk

Publication type:

Article

Improving cardio‐mechanic inference by combining in vivo strain data with ex vivo volume–pressure data.

Published in:

Journal of the Royal Statistical Society: Series C (Applied Statistics), 2022, v. 71, n. 4, p. 906, doi. 10.1111/rssc.12560

By:

Lazarus, Alan;
Gao, Hao;
Luo, Xiaoyu;
Husmeier, Dirk

Publication type:

Article

Fast parameter inference in a biomechanical model of the left ventricle by using statistical emulation.

Published in:

Journal of the Royal Statistical Society: Series C (Applied Statistics), 2019, v. 68, n. 5, p. 1555, doi. 10.1111/rssc.12374

By:

Davies, Vinny;
Noè, Umberto;
Lazarus, Alan;
Gao, Hao;
Macdonald, Benn;
Berry, Colin;
Luo, Xiaoyu;
Husmeier, Dirk

Publication type:

Article

Improving the identification of antigenic sites in the H1N1 influenza virus through accounting for the experimental structure in a sparse hierarchical Bayesian model.

Published in:

Journal of the Royal Statistical Society: Series C (Applied Statistics), 2019, v. 68, n. 4, p. 859, doi. 10.1111/rssc.12338

By:

Davies, Vinny;
Harvey, William T.;
Reeve, Richard;
Husmeier, Dirk

Publication type:

Article

Statistical inference of the mechanisms driving collective cell movement.

Published in:

Journal of the Royal Statistical Society: Series C (Applied Statistics), 2017, v. 66, n. 4, p. 869, doi. 10.1111/rssc.12203

By:

Ferguson, Elaine A.;
Matthiopoulos, Jason;
Insall, Robert H.;
Husmeier, Dirk

Publication type:

Article

A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana.

Published in:

BMC Bioinformatics, 2013, v. 14, n. Suppl 10, p. 1, doi. 10.1186/1471-2105-14-S10-S3

By:

Higham, Catherine F.;
Husmeier, Dirk

Publication type:

Article

Approximate parameter inference in systems biology using gradient matching: a comparative evaluation.

Published in:

2016

By:

Macdonald, Benn;
Niu, Mu;
Rogers, Simon;
Filippone, Maurizio;
Husmeier, Dirk

Publication type:

journal article

R package for statistical inference in dynamical systems using kernel based gradient matching: KGode.

Published in:

Computational Statistics, 2021, v. 36, n. 1, p. 715, doi. 10.1007/s00180-020-01014-x

By:

Niu, Mu;
Wandy, Joe;
Daly, Rónán;
Rogers, Simon;
Husmeier, Dirk

Publication type:

Article

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

Published in:

Computational Statistics, 2018, v. 33, n. 2, p. 1091, doi. 10.1007/s00180-017-0753-z

By:

Niu, Mu;
Macdonald, Benn;
Rogers, Simon;
Filippone, Maurizio;
Husmeier, Dirk

Publication type:

Article

A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution.

Published in:

Computational Statistics, 2017, v. 32, n. 3, p. 803, doi. 10.1007/s00180-017-0730-6

By:

Davies, Vinny;
Reeve, Richard;
Harvey, William;
Maree, Francois;
Husmeier, Dirk

Publication type:

Article

Targeting Bayes factors with direct-path non-equilibrium thermodynamic integration.

Published in:

Computational Statistics, 2017, v. 32, n. 2, p. 717, doi. 10.1007/s00180-017-0721-7

By:

Grzegorczyk, Marco;
Aderhold, Andrej;
Husmeier, Dirk

Publication type:

Article

Modelling non-stationary dynamic gene regulatory processes with the BGM model.

Published in:

Computational Statistics, 2011, v. 26, n. 2, p. 199, doi. 10.1007/s00180-010-0201-9

By:

Grzegorczyk, Marco;
Husmeier, Dirk;
Rahnenführer, Jörg

Publication type:

Article

GENE REGULATORY NETWORK RECONSTRUCTION BY BAYESIAN INTEGRATION OF PRIOR KNOWLEDGE AND/OR DIFFERENT EXPERIMENTAL CONDITIONS.

Published in:

Journal of Bioinformatics & Computational Biology, 2008, v. 6, n. 3, p. 543, doi. 10.1142/S0219720008003539

By:

WERHLI, ADRIANO V.;
HUSMEIER, DIRK

Publication type:

Article

Regularization of non-homogeneous dynamic Bayesian networks with global information-coupling based on hierarchical Bayesian models.

Published in:

Machine Learning, 2013, v. 91, n. 1, p. 105, doi. 10.1007/s10994-012-5326-3

By:

Grzegorczyk, Marco;
Husmeier, Dirk

Publication type:

Article

Non-homogeneous dynamic Bayesian networks with Bayesian regularization for inferring gene regulatory networks with gradually time-varying structure.

Published in:

Machine Learning, 2013, v. 90, n. 2, p. 191, doi. 10.1007/s10994-012-5311-x

By:

Dondelinger, Frank;
Lèbre, Sophie;
Husmeier, Dirk

Publication type:

Article

Non-homogeneous dynamic Bayesian networks for continuous data.

Published in:

Machine Learning, 2011, v. 83, n. 3, p. 355, doi. 10.1007/s10994-010-5230-7

By:

Grzegorczyk, Marco;
Husmeier, Dirk

Publication type:

Article

Improving the structure MCMC sampler for Bayesian networks by introducing a new edge reversal move.

Published in:

Machine Learning, 2008, v. 71, n. 2-3, p. 265, doi. 10.1007/s10994-008-5057-7

By:

Marco Grzegorczyk;
Dirk Husmeier

Publication type:

Article

A hierarchical machine learning framework for the analysis of large scale animal movement data.

Published in:

Movement Ecology, 2021, v. 9, n. 1, p. 1, doi. 10.1186/s40462-021-00242-0

By:

Torney, Colin J.;
Morales, Juan M.;
Husmeier, Dirk

Publication type:

Article

Analysis of Cardiac Amyloidosis Progression Using Model-Based Markers.

Published in:

Frontiers in Physiology, 2020, v. 11, p. 1, doi. 10.3389/fphys.2020.00324

By:

Li, Wenguang;
Lazarus, Alan;
Gao, Hao;
Martinez-Naharro, Ana;
Fontana, Marianna;
Hawkins, Philip;
Biswas, Swethajit;
Janiczek, Robert;
Cox, Jennifer;
Berry, Colin;
Husmeier, Dirk;
Luo, Xiaoyu

Publication type:

Article

Bayesian optimisation for efficient parameter inference in a cardiac mechanics model of the left ventricle.

Published in:

International Journal for Numerical Methods in Biomedical Engineering, 2022, v. 38, n. 5, p. 1, doi. 10.1002/cnm.3593

By:

Borowska, Agnieszka;
Gao, Hao;
Lazarus, Alan;
Husmeier, Dirk

Publication type:

Article

Markov chain Monte Carlo with Gaussian processes for fast parameter estimation and uncertainty quantification in a 1D fluid‐dynamics model of the pulmonary circulation.

Published in:

International Journal for Numerical Methods in Biomedical Engineering, 2021, v. 37, n. 2, p. 1, doi. 10.1002/cnm.3421

By:

Paun, L. Mihaela;
Husmeier, Dirk

Publication type:

Article

Predicting ecological regime shift under climate change: New modelling techniques and potential of molecular-based approaches.

Published in:

Current Zoology, 2013, v. 59, n. 3, p. 403, doi. 10.1093/czoolo/59.3.403

By:

STAFFORD, Richard;
SMITH, V. Anne;
HUSMEIER, Dirk;
GRIMA, Thomas;
GUINN, Barbara-ann

Publication type:

Article

Computational framework for the generation of one‐dimensional vascular models accounting for uncertainty in networks extracted from medical images.

Published in:

Journal of Physiology, 2024, v. 602, n. 16, p. 3929, doi. 10.1113/JP286193

By:

Bartolo, Michelle A.;
Taylor‐LaPole, Alyssa M.;
Gandhi, Darsh;
Johnson, Alexandria;
Li, Yaqi;
Slack, Emma;
Stevens, Isaiah;
Turner, Zachary G.;
Weigand, Justin D.;
Puelz, Charles;
Husmeier, Dirk;
Olufsen, Mette S.

Publication type:

Article

Segmenting bacterial and viral DNA sequence alignments with a trans-dimensional phylogenetic factorial hidden Markov model.

Published in:

Journal of the Royal Statistical Society: Series C (Applied Statistics), 2009, v. 58, n. 3, p. 307, doi. 10.1111/j.1467-9876.2008.00648.x

By:

Lehrach, Wolfgang P.;
Husmeier, Dirk

Publication type:

Article

Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2015, v. 14, n. 2, p. 143, doi. 10.1515/sagmb-2014-0041

By:

Grzegorczyk, Marco;
Aderhold, Andrej;
Husmeier, Dirk

Publication type:

Article

Statistical inference of regulatory networks for circadian regulation.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2014, v. 13, n. 3, p. 227, doi. 10.1515/sagmb-2013-0051

By:

Aderhold, Andrej;
Husmeier, Dirk;
Grzegorczyk, Marco

Publication type:

Article

A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2012, v. 11, n. 4, p. -1, doi. 10.1515/1544-6115.1761

By:

Grzegorczyk, Marco;
Husmeier, Dirk

Publication type:

Article

Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2008, v. 7, n. 1, p. 1, doi. 10.2202/1544-6115.1399

By:

Husmeier, Dirk;
Mantzaris, Alexander V.

Publication type:

Article

Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2007, v. 6, n. 1, p. 1, doi. 10.2202/1544-6115.1282

By:

Werhli, Adriano V.;
Husmeier, Dirk

Publication type:

Article