2024
BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks
Pelletier S, Leclercq M, Roux-Dalvai F, de Geus M, Leslie S, Wang W, Lam T, Nairn A, Arnold S, Carlyle B, Precioso F, Droit A. BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks. Nature Communications 2024, 15: 3777. PMID: 38710683, PMCID: PMC11074280, DOI: 10.1038/s41467-024-48177-5.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, LiquidHumansMass SpectrometryNeural Networks, ComputerReproducibility of ResultsConceptsLC-MS experimentsLC-MSLiquid chromatography mass spectrometry dataComplex biological samplesMass spectrometry dataLiquid chromatography mass spectrometryChromatography mass spectrometryMass spectrometrySpectrometry dataEffective removalBiological samplesExperimental conditionsBatch effect removalSample processing protocolBatch effectsSpectrometryBatch effect correction methodsCorrecting batch effectsRemoval of batch effects
2023
Mass spectrometry in cerebrospinal fluid uncovers association of glycolysis biomarkers with Alzheimer’s disease in a large clinical sample
de Geus M, Leslie S, Lam T, Wang W, Roux-Dalvai F, Droit A, Kivisakk P, Nairn A, Arnold S, Carlyle B. Mass spectrometry in cerebrospinal fluid uncovers association of glycolysis biomarkers with Alzheimer’s disease in a large clinical sample. Scientific Reports 2023, 13: 22406. PMID: 38104170, PMCID: PMC10725469, DOI: 10.1038/s41598-023-49440-3.Peer-Reviewed Original Research
2014
Decoding neuroproteomics: integrating the genome, translatome and functional anatomy
Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC. Decoding neuroproteomics: integrating the genome, translatome and functional anatomy. Nature Neuroscience 2014, 17: 1491-1499. PMID: 25349915, PMCID: PMC4737617, DOI: 10.1038/nn.3829.Peer-Reviewed Original Research
2013
Recent advances in quantitative neuroproteomics
Craft GE, Chen A, Nairn AC. Recent advances in quantitative neuroproteomics. Methods 2013, 61: 186-218. PMID: 23623823, PMCID: PMC3891841, DOI: 10.1016/j.ymeth.2013.04.008.Peer-Reviewed Original Research
1999
The design, synthesis, and biological evaluation of analogues of the serine-threonine protein phosphatase 1 and 2A selective inhibitor microcystin LA: rational modifications imparting PP1 selectivity
Aggen J, Humphrey J, Gauss C, Huang H, Nairn A, Chamberlin A. The design, synthesis, and biological evaluation of analogues of the serine-threonine protein phosphatase 1 and 2A selective inhibitor microcystin LA: rational modifications imparting PP1 selectivity. Bioorganic & Medicinal Chemistry 1999, 7: 543-564. PMID: 10220039, DOI: 10.1016/s0968-0896(98)00254-5.Peer-Reviewed Original ResearchConceptsPP1 selectivityProtein phosphatase 1Serine-threonine proteinMicrocystin-LAFirst-generation analogsSmall molecule inhibitorsPhosphatase 1Observed selectivityBiological evaluationMolecular modeling analysisMolecule inhibitorsRational modificationSelectivityStructural modificationsSynthesisAnaloguesInhibition assaysPP1MicrocystinsProteinLaModificationAssaysInhibitors