Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
Rogers, S. Girolami, M. Kolch, W. Waters, K.M. Liu, T. Thrall, B. Wiley, S.H.
Walter Kolch
Kolch Walter
ORCID: 0000-0001-5777-5016
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Lapatinib potentiates cytotoxicity of  YM155 in neuroblastoma via inhibition of the ABCB1 efflux transporter 10.1038/s41598-017-03129-6
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Katrina Waters
Waters Katrina
ORCID: 0000-0003-4696-5396
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A comprehensive collection of systems biology data characterizing the host response to viral infection 10.1038/sdata.2014.33
Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus 10.1128/JVI.05792-11
Expanding on successful concepts, models, and organization 10.1021/acs.est.6b03027
Estrogen regulation of human osteoblast function is determined by the stage of differentiation and the estrogen receptor isoform 10.1002/jcb.1242
Implications of Bioremediation of Polycyclic Aromatic Hydrocarbon- Contaminated Soils for Human Health and Cancer Risk 10.1021/acs.est.7b02956
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Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation 10.1002/hep.25649
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Cytochrome P450 1b1 in polycyclic aromatic hydrocarbon (PAH)-induced skin carcinogenesis: Tumorigenicity of individual PAHs and coal-tar extract, DNA adduction and expression of select genes in the Cyp1b1 knockout mouse 10.1016/j.taap.2015.05.019
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How adverse outcome pathways can aid the development and use of computational prediction models for regulatory toxicology 10.1093/toxsci/kfw207
Quantitative proteomic analysis of mitochondrial proteins reveals prosurvival mechanisms in the perpetuation of radiation-induced genomic instability 10.1016/j.freeradbiomed.2012.03.025
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Global gene expression analysis reveals pathway differences between teratogenic and non-teratogenic exposure concentrations of bisphenol A and 17β-estradiol in embryonic zebrafish 10.1016/j.reprotox.2013.03.009
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Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework 10.1021/acs.est.5b05311
Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data 10.1021/pr1005247
Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism 10.1016/j.chom.2016.01.002
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The effects of low-dose irradiation on inflammatory response proteins in a 3D reconstituted human skin tissue model 10.1667/RR2976.1
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models 10.1093/bioinformatics/btn553
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Diet-induced obesity reprograms the inflammatory response of the murine lung to inhaled endotoxin 10.1016/j.taap.2012.12.020
Hepatic leukemia factor promotes resistance to cell death: Implications for therapeutics and chronotherapy 10.1016/j.taap.2013.01.031
Comparative iron oxide nanoparticle cellular dosimetry and response in mice by the inhalation and liquid cell culture exposure routes 10.1186/s12989-014-0046-4
A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses 10.1371/journal.pone.0069374
Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus 10.1016/j.virol.2015.03.045
Macrophage responses to silica nanoparticles are highly conserved across particle sizes 10.1093/toxsci/kfn250
Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos, and ultrafine carbon black in mice 10.1093/toxsci/kfq363
Early life stage trimethyltin exposure induces ADP-ribosylation factor expression and perturbs the vascular system in zebrafish 10.1016/j.tox.2012.09.004
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Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems 10.1186/1752-0509-5-190
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MERS-CoV accessory orfs play key role for infection and pathogenesis 10.1128/mBio.00665-17
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Cellular dichotomy between anchorage-independent growth responses to bFGF and TPA reflects molecular switch in commitment to carcinogenesis 10.1002/mc.20558
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Comparative developmental toxicity of environmentally relevant oxygenated PAHs 10.1016/j.taap.2013.05.006
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Phenotypically anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish 10.1016/j.taap.2016.08.013
Time-dependent behavioral data from zebrafish reveals novel signatures of chemical toxicity using point of departure analysis 10.1016/j.comtox.2018.11.001
pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data 10.1021/acs.jproteome.8b00760
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Unified feature association networks through integration of transcriptomic and proteomic data 10.1371/journal.pcbi.1007241
Indoor versus Outdoor Air Quality during Wildfires 10.1021/acs.estlett.9b00599
Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network 10.1021/acs.analchem.9b03522
A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases 10.1038/s41597-021-00894-y
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
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
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Markov chain monte carlo inference for markov jump processes via the linear noise approximation 10.1098/rsta.2011.0541
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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
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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
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Detecting worm variants using machine learning 10.1145/1364654.1364657
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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
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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
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Probabilistic prediction of neurological disorders with a statistical assessment of neuroimaging data modalities 10.1214/12-AOAS562
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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
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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
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Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers 10.1186/1471-2105-11-594
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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
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The Latent Variable Data Model for Exploratory Data Analysis and Visualisation: A Generalisation of the Nonlinear Infomax Algorithm 10.1023/A:1009613012282
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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
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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
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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
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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
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ITFoM - The IT future of medicine 10.1016/j.procs.2011.12.012
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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
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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
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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
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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/
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
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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
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Proteomic Tissue-Based Classifier for Early Prediction of Prostate Cancer Progression 10.3390/cancers12051268
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Proteomic Analysis of Exosomes for Discovery of Protein Biomarkers for Prostate and Bladder Cancer 10.3390/cancers12092335
Steven Wiley
Wiley Steven / H. Steven Wiley
ORCID: 0000-0003-0232-6867
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