Bayesian model-based inference of transcription factor activity
Rogers, S.
Khanin, R.
Girolami, M.
BMC Bioinformatics, 2007
Simon Rogers
Rogers Simon
ORCID: 0000-0003-3578-4477
An Optimal Frequency in Ca2+ Oscillations for Stomatal Closure Is an Emergent Property of Ion Transport in Guard Cells
10.1104/pp.15.01607
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.
10.1093/bioinformatics/btv072
MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.
10.1093/bioinformatics/btu370
Probabilistic assignment of formulas to mass peaks in metabolomics experiments.
10.1093/bioinformatics/btn642
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models.
10.1093/bioinformatics/btn553
Bayesian model-based inference of transcription factor activity.
10.1186/1471-2105-8-S2-S2
Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques.
10.1098/rsif.2005.0093
A Bayesian regression approach to the inference of regulatory networks from gene expression data.
10.1093/bioinformatics/bti487
The latent process decomposition of cDNA microarray data sets.
10.1109/TCBB.2005.29
HDP-Align: Hierarchical Dirichlet Process Clustering for Multiple Peak Alignment of Liquid Chromatography Mass Spectrometry Data
10.1101/074831
Topic modeling for untargeted substructure exploration in metabolomics
10.1073/pnas.1608041113
Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics
10.1104/pp.17.00170
Unexpected Connections between Humidity and Ion Transport Discovered Using a Model to Bridge Guard Cell-to-Leaf Scales
10.1105/tpc.17.00694
Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts
10.1038/s41598-018-28810-2
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1101/491506
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1039/C8FD00235E
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture
10.1104/pp.18.00217
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.1101/744227
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.3390/metabo9100219
Gestational-age-dependent development of the neonatal metabolome
10.1101/2020.03.27.20045534
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Predicting host taxonomic information from viral genomes: A comparison of feature representations
10.1371/journal.pcbi.1007894
Decomposing metabolite set activity levels with PALS
10.1101/2020.06.07.138974
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1101/2020.06.12.148205
matchms - processing and similarity evaluation of mass spectrometry data
10.1101/2020.08.06.239244
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1101/2020.08.11.245928
Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification
10.1101/2020.08.19.255653
matchms - processing and similarity evaluation of mass spectrometry data.
10.21105/joss.02411
Rapid Development of Improved Data-dependent Acquisition Strategies
10.1101/2020.09.11.293092
User guide to the red blood cell model (RCM), a multiplatform JAVA-based model of human red blood cell homeostasis
10.1101/2020.03.07.981779
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification
10.1093/bioinformatics/btaa998
Comparative Metabologenomics Analysis of Polar Actinomycetes
10.3390/md19020103
Ranking Metabolite Sets by Their Activity Levels
10.3390/metabo11020103
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1371/journal.pcbi.1008724
Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits
10.1371/journal.pcbi.1008706
PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells
10.1371/journal.pcbi.1008496
Rapid Development of Improved Data-Dependent Acquisition Strategies
10.1021/acs.analchem.0c03895
Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches
10.1039/D1NP00023C
Using topic modeling to detect cellular crosstalk in scRNA-seq
10.1101/2021.07.26.453767
Mark Girolami
Girolami Mark
ORCID: 0000-0003-3008-253X
A Methodology for Prognostics Under the Conditions of Limited Failure Data Availability
10.1109/ACCESS.2019.2960310
Bayesian inference for model selection: An application to aberrant signalling pathways in chronic myeloid leukaemia
10.1017/CBO9781139012751.009
Manifold MCMC for mixtures
10.1002/9781119995678.ch12
Preface
10.1002/9781119970606
Definition of valid proteomic biomarkers: A bayesian solution
10.1007/978-3-642-04031-3_13
Biologically valid linear factor models of gene expressions
10.1093/bioinformatics/bth354
Propagative broad learning for nonparametric modeling of ambient effects on structural health indicators
10.1177/1475921720916923
Inferring meta-covariates in classification
10.1007/978-3-642-04031-3_14
In vivo multiplex molecular imaging of vascular inflammation using surface-enhanced Raman spectroscopy
10.7150/thno.28665
Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques
10.1098/rsif.2005.0093
Discussion of the paper: "sampling schemes for generalized linear dirichlet process random effects models" by M. Kyung, J. Gill, and G. Casella
10.1007/s10260-011-0170-3
Markov chain monte carlo inference for markov jump processes via the linear noise approximation
10.1098/rsta.2011.0541
A general framework for a principled hierarchical visualization of multivariate data
10.1007/3-540-45675-9_78
Topic based language models for ad hoc Information Retrieval
10.1109/IJCNN.2004.1381205
Statistical analysis of differential equations: introducing probability measures on numerical solutions
10.1007/s11222-016-9671-0
The organisation and visualisation of document corpora: A probabilistic approach
10.1109/DEXA.2000.875081
A Bayesian approach to multiscale inverse problems with on-the-fly scale determination
10.1016/j.jcp.2016.08.031
Probabilistic numerics and uncertainty in computations
10.1098/rspa.2015.0142
Blind source separation of more sources than mixtures using overcomplete representations
10.1109/97.752062
Hyperpriors for matérn fields with applications in bayesian inversion
10.3934/ipi.2019001
Rejoinder: Geodesic Monte Carlo on embedded manifolds
10.1111/sjos.12058
Accelerated whole-core analysis optimization with wellsite tomography instrumentation and Bayesian inversion
10.30632/PJV60N3-2019a2
Statistical and probabilistic fundamentals of ICA
10.1049/ic:20040613
Population MCMC methods for history matching and uncertainty quantification
10.3997/2214-4609.20144977
Probabilistic model checking of DTMC Models of user activity patterns
10.1007/978-3-319-10696-0_11
Population MCMC methods for history matching and uncertainty quantification
10.1007/s10596-011-9232-8
ParCrys: A Parzen window density estimation approach to protein crystallization propensity prediction
10.1093/bioinformatics/btn055
Protein interaction sentence detection using multiple semantic kernels
10.1186/2041-1480-2-1
Detecting worm variants using machine learning
10.1145/1364654.1364657
Generalised independent component analysis through unsupervised learning with emergent bussgang properties
10.1109/ICNN.1997.614168
Bayesian Probabilistic Numerical Methods in Time-Dependent State Estimation for Industrial Hydrocyclone Equipment
10.1080/01621459.2019.1574583
A determinant-free method to simulate the parameters of large Gaussian fields
10.1002/sta4.153
Noise reduction and speech enhancement via temporal anti-Hebbian learning
10.1109/ICASSP.1998.675494
BioBayes: A software package for Bayesian inference in systems biology
10.1093/bioinformatics/btn338
Clinical proteomics: A need to define the field and to begin to set adequate standards
10.1002/prca.200600771
Investigating the Relationship between Language Model Perplexity and IR Precision-Recall Measures
10.1145/860500.860505
Novelty detection employing an L2 optimal non-parametric density estimator
10.1016/j.patrec.2004.05.004
Latent variable models for the topographic organisation of discrete and strictly positive data
10.1016/S0925-2312(01)00659-2
Automated, High Accuracy Classification of Parkinsonian Disorders: A Pattern Recognition Approach
10.1371/journal.pone.0069237
Extraction of independent signal sources using a deflationary exploratory projection pursuit network with lateral inhibition
10.1049/ip-vis:19971418
Estimating Bayes factors via thermodynamic integration and population MCMC
10.1016/j.csda.2009.07.025
Probabilistic prediction of neurological disorders with a statistical assessment of neuroimaging data modalities
10.1214/12-AOAS562
An Alternative Perspective on Adaptive Independent Component Analysis Algorithms
10.1162/089976698300016981
A probabilistic framework for the hierarchic organisation and classification of document collections
10.1023/A:1013677411002
A common neural-network model for unsupervised exploratory data analysis and independent component analysis
10.1109/72.728398
Combining feature spaces for classification
10.1016/j.patcog.2009.04.002
Burglary in London: insights from statistical heterogeneous spatial point processes
10.1111/rssc.12431
Fast extraction of semantic features from a latent semantic indexed text corpus
10.1023/A:1013801028884
A digital twin of bridges for structural health monitoring
10.12783/shm2019/32287
Class Prediction from Disparate Biological Data Sources Using an Iterative Multi-Kernel Algorithm
10.1007/978-3-642-04031-3_37
Sequential activity profiling: Latent dirichlet allocation of Markov chains
10.1007/s10618-005-0362-2
Analysing User Behaviour Through Dynamic Population Models
10.1145/2468356.2468405
Embedded ridge approximations
10.1016/j.cma.2020.113383
A unifying information-theoretic framework for independent component analysis
10.1016/S0898-1221(00)00101-2
Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species
10.1126/scisignal.2000517
Markov chain monte carlo methods for state-space models with point process observations
10.1162/NECO_a_00281
An empirical analysis of the probabilistic K-nearest neighbour classifier
10.1016/j.patrec.2007.05.018
A probabilistic hierarchical clustering method for organising collections of text documents
10.1109/ICPR.2000.906043
On the geometric ergodicity of Hamiltonian Monte Carlo
10.3150/18-BEJ1083
EWS-FLI1 employs an E2F switch to drive target gene expression
10.1093/nar/gkv123
Comment on article by Schmidl et al.
10.1214/13-BA801B
Riemann manifold Langevin and Hamiltonian Monte Carlo methods
10.1111/j.1467-9868.2010.00765.x
Erratum: Bayesian ranking of biochemical system models (Bioinformatics (2008) vol. 24(6) (833-839))
10.1093/bioinformatics/btn475
Probabilistic multi-class multi-kernel learning: On protein fold recognition and remote homology detection
10.1093/bioinformatics/btn112
Solving large-scale PDE-constrained Bayesian inverse problems with Riemann manifold Hamiltonian Monte Carlo
10.1088/0266-5611/30/11/114014
Geometry and Dynamics for Markov Chain Monte Carlo
10.1146/annurev-statistics-031017-100141
Decoding post-stroke motor function from structural brain imaging
10.1016/j.nicl.2016.07.014
A temporal model of linear anti-Hebbian learning
10.1007/BF00426022
MCMC_CLIB-an advanced MCMC sampling package for ODE models
10.1093/bioinformatics/btu429
Systems biology: Opening new avenues in clinical research
10.1093/ndt/gfq033
Clustering via kernel decomposition
10.1109/TNN.2005.860840
Bayesian probabilistic numerical methods
10.1137/17M1139357
Statistical analysis of nonlinear dynamical systems using differential geometric sampling methods
10.1098/rsfs.2011.0051
Semi-supervised prediction of protein interaction sentences exploiting semantically encoded metrics
10.1007/978-3-642-04031-3_24
A comparative evaluation of stochastic-based inference methods for Gaussian process models
10.1007/s10994-013-5388-x
Classification of protein interaction sentences via gaussian Processes
10.1007/978-3-642-04031-3_25
Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species (Science Signaling (2010) 3, (er8))
10.1126/scisignal.3134er8
Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers
10.1186/1471-2105-11-594
Hierarchic bayesian models for kernel learning
10.1145/1102351.1102382
Convergence rates for a class of estimators based on Stein’s method
10.3150/17-BEJ1016
Probabilistic integration: A role in statistical computation?
10.1214/18-STS660
A variational method for learning sparse and overcomplete representations
10.1162/089976601753196003
Analysis of free text in electronic health records for identification of cancer patient trajectories
10.1038/srep46226
Uncovering smartphone usage patterns with multi-view mixed membership models
10.1002/sta4.103
Protein interaction detection in sentences via gaussian processes: A preliminary evaluation
10.1504/IJDMB.2011.038577
The topographic organization and visualization of binary data using multivariate-Bernoulli latent variable models
10.1109/72.963773
Bat detective—Deep learning tools for bat acoustic signal detection
10.1371/journal.pcbi.1005995
The Latent Variable Data Model for Exploratory Data Analysis and Visualisation: A Generalisation of the Nonlinear Infomax Algorithm
10.1023/A:1009613012282
Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease
10.1074/mcp.M110.001917
An extended exploratory projection pursuit network with linear and nonlinear anti-hebbian lateral connections applied to the cocktail party problem
10.1016/S0893-6080(97)00090-7
The Controlled Thermodynamic Integral for Bayesian Model Evidence Evaluation
10.1080/01621459.2015.1021006
Orthogonal series density estimation and the kernel eigenvalue problem
10.1162/089976602317250942
vbmp: Variational Bayesian Multinomial Probit Regression for multi-class classification in R
10.1093/bioinformatics/btm535
Symmetric adaptive maximum likelihood estimation for noise cancellation and signal separation
10.1049/el:19970977
The geometric foundations of Hamiltonian Monte Carlo
10.3150/16-BEJ810
Accurate prediction of BRCA1 and BRCA2 heterozygous genotype using expression profiling after induced DNA damage
10.1158/1078-0432.CCR-05-2805
A Bayesian regression approach to the inference of regulatory networks from gene expression data
10.1093/bioinformatics/bti487
Statistical methods to enable practical on-site tomographic imaging of whole-core samples
10.1190/geo2018-0436.1
Bayesian ranking of biochemical system models
10.1093/bioinformatics/btm607
Efficiency and robustness in Monte Carlo sampling for 3-D geophysical inversions with Obsidian v0.1.2: Setting up for success
10.5194/gmd-12-2941-2019
Bayesian inference for differential equations
10.1016/j.tcs.2008.07.005
Regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis
10.1038/ncomms12111
Pattern recognition with a Bayesian kernel combination machine
10.1016/j.patrec.2008.08.016
Kernel PCA for feature extraction and de-noising in nonlinear regression
10.1007/s521-001-8051-z
A combined latent class and trait model for the analysis and visualization of discrete data
10.1109/34.946989
The silicon trypanosome
10.1017/S0031182010000466
Using higher-order dynamic bayesian networks to model periodic data from the circadian clock of arabidopsis thaliana
10.1007/978-3-642-04031-3_7
The latent process decomposition of cDNA microarray data sets
10.1109/TCBB.2005.29
Editorial: special edition on probabilistic numerics
10.1007/s11222-019-09892-y
The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology.
10.1016/B978-0-12-800143-1.00003-8
Probabilistic hyperspace analogue to language
10.1145/1076034.1076135
Posterior inference for sparse hierarchical non-stationary models
10.1016/j.csda.2020.106954
Disease classification from capillary electrophoresis: Mass spectrometry
10.1007/11551188_20
Geometric MCMC for infinite-dimensional inverse problems
10.1016/j.jcp.2016.12.041
Rejoinder: Probabilistic integration: A role in statistical computation?
10.1214/18-STS683
ITFoM - The IT future of medicine
10.1016/j.procs.2011.12.012
Multiclass relevance vector machines: Sparsity and accuracy
10.1109/TNN.2010.2064787
Adaptive support vector regression filter: A signal detection application
10.1049/cp:19991176
An assessment of feature relevance in predicting protein function from sequence
10.1007/978-3-540-28651-6_8
On an Equivalence between PLSI and LDA
10.1145/860435.860537
Bayesian uncertainty quantification for transmissibility of influenza, norovirus and Ebola using information geometry
10.1098/rsif.2016.0279
Systems biology to battle vascular disease
10.1093/ndt/gfq025
Bayesian approaches for mechanistic ion channel modeling
10.1007/978-1-62703-450-0-13
Special Issue: Big data and predictive computational modeling
10.1016/j.jcp.2016.03.028
Markov Chain Monte Carlo from Lagrangian Dynamics
10.1080/10618600.2014.902764
Putting the Scientist in the Loop - Accelerating Scientific Progress with Interactive Machine Learning
10.1109/ICPR.2014.12
Probabilistic assignment of formulas to mass peaks in metabolomics experiments
10.1093/bioinformatics/btn642
Online learning with (multiple) kernels: A review
10.1162/NECO_a_00406
Zero variance differential geometric markov chain monte carlo algorithms
10.1214/13-BA848
Advances in urinary proteome analysis and biomarker discovery
10.1681/ASN.2006090956
A nonlinear model of the binaural cocktail party effect
10.1016/S0925-2312(98)00058-7
On the use of diagonal and class-dependent weighted distances for the probabilistic k-nearest neighbor
10.1007/978-3-642-21257-4_33
Information-Geometric Markov chain Monte Carlo methods using diffusions
10.3390/e16063074
Topic identification in dynamical text by complexity pursuit
10.1023/A:1022990829563
Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells
10.1371/journal.pone.0099458
BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression
10.1371/journal.pgen.1000080
Preferential Attachment of Specific Fluorescent Dyes and Dye Labeled DNA Sequences in a Surface Enhanced Raman Scattering Multiplex
10.1021/acs.analchem.5b02776
Emulation of higher-order tensors in manifold Monte Carlo methods for Bayesian Inverse Problems
10.1016/j.jcp.2015.12.032
Probability density estimation from optimally condensed data samples
10.1109/TPAMI.2003.1233899
Probabilistic numerical methods for PDE-constrained Bayesian inverse problems
10.1063/1.4985359
Uncertainty quantification of density and stratification estimates with implications for predicting ocean dynamics
10.1175/JTECH-D-18-0200.1
On Russian Roulette estimates for Bayesian inference with doubly-intractable likelihoods
10.1214/15-STS523
Multi-fidelity approach to Bayesian parameter estimation in subsurface heat and fluid transport models
10.1016/j.scitotenv.2020.140846
Langevin diffusions and the Metropolis-adjusted Langevin algorithm
10.1016/j.spl.2014.04.002
Geodesic Monte Carlo on embedded manifolds
10.1111/sjos.12036
Classifying EEG for brain computer interfaces using Gaussian processes
10.1016/j.patrec.2007.10.009
Employing Latent Dirichlet Allocation for fraud detection in telecommunications
10.1016/j.patrec.2007.04.015
Employing optimized combinations of one-class classifiers for automated currency validation
10.1016/j.patcog.2004.02.002
Predictive response-relevant clustering of expression data provides insights into disease processes
10.1093/nar/gkq550
Recommendations for biomarker identification and qualification in clinical proteomics
10.1126/scitranslmed.3001249
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
10.1093/bioinformatics/btn553
Independent component analysis using an extended infomax algorithm for mixed subgaussian and supergaussian sources
10.1162/089976699300016719
The role of statistics in data-centric engineering
10.1016/j.spl.2018.02.035
Stochastic modelling of urban Structure
10.1098/rspa.2017.0700
Inferring sparse kernel combinations and relevance vectors: An application to subcellular localization of proteins
10.1109/ICMLA.2008.124
Variational Bayesian multinomial probit regression with gaussian process priors
10.1162/neco.2006.18.8.1790
A dynamic probabilistic model to visualise topic evolution in text streams
10.1023/A:1013673310093
Mercer kernel-based clustering in feature space
10.1109/TNN.2002.1000150
The synthesis of data from instrumented structures and physics-based models via Gaussian processes
10.1016/j.jcp.2019.04.065
Control functionals for Monte Carlo integration
10.1111/rssb.12185
Contribution by M. A. Girolami
10.1214/13-STS459
Pseudo-marginal Bayesian inference for Gaussian processes
10.1109/TPAMI.2014.2316530
Bat echolocation call identification for biodiversity monitoring: a probabilistic approach
10.1111/rssc.12217
Bayesian solution uncertainty quantification for differential equations
10.1214/16-BA1017
Semi-parametric analysis of multi-rater data
10.1007/s11222-009-9125-z
Bayesian Statistical Inference in Ion-Channel Models with Exact Missed Event Correction
10.1016/j.bpj.2016.04.053
Non-parametric Bayes to infer playing strategies adopted in a population of mobile gamers
10.1002/sta4.75
Infinite factorization of multiple non-parametric views
10.1007/s10994-009-5155-1
Bayesian model-based inference of transcription factor activity
10.1186/1471-2105-8-S2-S2
Bayesian methods to detect dye-labelled DNA oligonucleotides in multiplexed Raman spectra
10.1111/j.1467-9876.2010.00744.x
Analysis of complex, multidimensional datasets
10.1016/j.ddtec.2006.03.010
Unique Reporter-Based Sensor Platforms to Monitor Signalling in Cells
10.1371/journal.pone.0050521
An expectation-maximization approach to nonlinear component analysis
10.1162/089976601300014439
Construction with digital twin information systems
10.1017/dce.2020.16
Statistical finite elements for misspecified models
10.1073/pnas.2015006118
Digital twin of an urban-integrated hydroponic farm
10.1017/dce.2020.21
Anomaly detection in a fleet of industrial assets with hierarchical statistical modeling
10.1017/dce.2020.19
Scaling digital twins from the artisanal to the industrial
10.1038/s43588-021-00072-5
Integration in reproducing kernel Hilbert spaces of Gaussian kernels
10.1090/mcom/3659
PeriPy - A high performance OpenCL peridynamics package
10.1016/j.cma.2021.114085
