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.
Bioinformatics, 2008-12
https://doi.org/10.1093/bioinformatics/btn553
Walter Kolch
Kolch Walter
ORCID: 0000-0001-5777-5016
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Katrina Waters
Waters Katrina
ORCID: 0000-0003-4696-5396
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Transplacental carcinogenesis with dibenzo[def,p]chrysene (DBC): Timing of maternal exposures determines target tissue response in offspring 10.1016/j.canlet.2011.11.010
A comprehensive collection of systems biology data characterizing the host response to viral infection 10.1038/sdata.2014.33
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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
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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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How adverse outcome pathways can aid the development and use of computational prediction models for regulatory toxicology 10.1093/toxsci/kfw207
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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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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
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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
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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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Probabilistic numerics and uncertainty in computations 10.1098/rspa.2015.0142
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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
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Detecting worm variants using machine learning 10.1145/1364654.1364657
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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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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
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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
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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
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Kernel PCA for feature extraction and de-noising in nonlinear regression 10.1007/s521-001-8051-z
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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 the use of diagonal and class-dependent weighted distances for the probabilistic k-nearest neighbor 10.1007/978-3-642-21257-4_33
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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
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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
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Stochastic modelling of urban Structure 10.1098/rspa.2017.0700
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Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome 10.1371/journal.pone.0017287
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Blood Peptidome-Degradome Profile of Breast Cancer 10.1371/journal.pone.0013133
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Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy 10.1074/mcp.M800008-MCP200
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models 10.1093/bioinformatics/btn553
Spatial mapping of the neurite and soma proteomes reveals a functional Cdc42/Rac regulatory network 10.1073/pnas.0706545105
Accurate mass measurements in proteomics 10.1021/cr068288j
Head-to-head comparison of serum fractionation techniques 10.1021/pr0604920
Quantitative analysis of human immunodeficiency virus type 1-infected CD4(+) cell proteome: Dysregulated cell cycle progression and nuclear transport coincide with robust virus production 10.1128/JVI.00288-07
The use of a quantitative cysteinyl-peptide enrichment technology for high-throughput quantitative proteomics 10.1007/978-1-59745-255-7_7
Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications 10.1074/mcp.M600162-MCP200
Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment 10.1021/pr0503681
Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry 10.1074/mcp.T600039-MCP200
High dynamic range characterization of the trauma patient plasma proteome 10.1074/mcp.M600068-MCP200|10.1074/mcp.M600068/MCP200
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry 10.1021/pr0502065
Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome 10.1002/pmic.200401055
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High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology 10.1021/ac049485q
Capillary electrophoresis-electrospray mass spectrometry for the characterization of high-mannose-type N-glycosylation and differential oxidation in glycoproteins by charge reversal and protease/glycosidase digestion 10.1021/ac0106748
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Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues 10.1021/acs.analchem.7b01878
Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway 10.1021/acs.analchem.8b00071
Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells 10.1038/s42003-018-0107-6
Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility–Mass Spectrometry 10.1021/acs.analchem.8b02397
Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards 10.1021/acs.jproteome.8b00688
Phosphoproteome Analysis Reveals Estrogen-ER Pathway as a Modulator of mTOR Activity Via DEPTOR 10.1074/mcp.RA119.001506
An Integrative Analysis of Tumor Proteomic and Phosphoproteomic Profiles to Examine the Relationships Between Kinase Activity and Phosphorylation 10.1074/mcp.RA119.001540
Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides 10.1021/acs.analchem.9b01814
High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform 10.1021/acs.analchem.9b03349
Proteomic Tissue-Based Classifier for Early Prediction of Prostate Cancer Progression 10.3390/cancers12051268
Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography–Mass Spectrometry for High-Throughput Single-Cell Proteomics 10.1021/acs.analchem.0c01551
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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Computational modeling of the EGF-receptor system: A paradigm for systems biology 10.1016/S0962-8924(02)00009-0
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Chapter 9 Receptors as Models for the Mechanisms of Membrane Protein Turnover and Dynamics 10.1016/S0070-2161(08)60331-7
An enzymatic method for radiolabeling vertebrate vitellogenin 10.1016/0003-2697(84)90180-5
A steady state model for analyzing the cellular binding, internalization and degradation of polypeptide ligands 10.1016/0092-8674(81)90061-1
Goldfish (Carassius auratus) vitellogenin: Induction, isolation, properties and relationship to yolk proteins 10.1016/0305-0491(80)90422-8
New methods for the purification of vertebrate vitellogenin 10.1016/0003-2697(79)90338-5
Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway 10.1126/scisignal.aaf0891
How low can you go? 10.7554/eLife.33604
Inferring Reaction Networks using Perturbation Data 10.1101/351767
Generating Synthetic Signaling Networks for in Silico Modeling Studies 10.1101/2020.05.08.084848
Summary of the Sussex-Huawei locomotion-transportation recognition challenge
Observation of a manifold in the chaotic phase space of an asymmetric optical microcavity
Localized temporal variation of Earth's inner-core boundary from high-quality waveform doublets
Off-axis multi-wavelength dispersion controlling metalens for multi-color imaging
Impact of United States political sanctions on international collaborations and research in Iran