Boby Mathew
Associate Research ScientistCards
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Research
Publications
2022
RhoC in association with TET2/WDR5 regulates cancer stem cells by epigenetically modifying the expression of pluripotency genes
Thomas P, Srivastava S, Udayashankara A, Damodaran S, Yadav L, Mathew B, Suresh S, Mandal A, Srikantia N. RhoC in association with TET2/WDR5 regulates cancer stem cells by epigenetically modifying the expression of pluripotency genes. Cellular And Molecular Life Sciences 2022, 80: 1. PMID: 36469134, PMCID: PMC11073244, DOI: 10.1007/s00018-022-04645-z.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorCell MovementCell ProliferationDioxygenasesDNA-Binding ProteinsEpigenesis, GeneticEpithelial-Mesenchymal TransitionFemaleGene Expression Regulation, NeoplasticHumansIntracellular Signaling Peptides and ProteinsNeoplastic Stem CellsrhoC GTP-Binding ProteinUterine Cervical NeoplasmsConceptsEpithelial to mesenchymal transitionEpigenetic regulationExpression of pluripotency genesCancer stem cellsInhibition of RhoCRNA-seq analysisPluripotency genesRegulation of NANOGInfinium MethylationEPIC arrayOver-expressing cellsAssociated signaling pathwaysRegulation of cancer stem cellsChIP-seqRNA-seqDemethylated genomeAnoikis resistanceRhoCMethylationEPIC arrayCervical cancer progressionCells to radiationSignaling pathwayOver-expressionCombinatorial inhibitionUp-regulatedGenomeDeciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling
Mathew B, Bathla S, Williams KR, Nairn AC. Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling. Molecular & Cellular Proteomics 2022, 21: 100422. PMID: 36198386, PMCID: PMC9650050, DOI: 10.1016/j.mcpro.2022.100422.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProximity labelingBiological functionsComplex protein-protein interactionsProximity labeling methodProtein-DNA interactionsCell-cell communicationMost biological functionsDistinct cell typesProtein-RNANerve cell functionCell typesBiomolecular complexesCellular levelPhysical interactionProteomeCell functionSpecific subsetProteinSynaptic plasticityComplete catalogLabeling methodRecent advancesPowerful toolAxonal projectionsTranscriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity
Schneider M, Vedder L, Oyiga B, Mathew B, Schoof H, Léon J, Naz A. Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity. PLOS ONE 2022, 17: e0265981. PMID: 36095002, PMCID: PMC9467324, DOI: 10.1371/journal.pone.0265981.Peer-Reviewed Original ResearchNeuralLasso: Neural Networks Meet Lasso in Genomic Prediction
Mathew B, Hauptmann A, Léon J, Sillanpää M. NeuralLasso: Neural Networks Meet Lasso in Genomic Prediction. Frontiers In Plant Science 2022, 13: 800161. PMID: 35574107, PMCID: PMC9100816, DOI: 10.3389/fpls.2022.800161.Peer-Reviewed Original ResearchPrediction of complex traitsComplex traitsGenomic predictionGenome-wide marker informationMachine learningLocal epistasisPrediction accuracyElastic netGenomic BLUPMarker informationHeterogeneous stock miceEpistasis effectsPlant breeding programsNeural networkBreeding programsEpistasisGenetic factorsPlant breedingField data setData setsTraitsPlantsStock micePrediction methodBayesBPlasma Apolipoprotein-AIV Downregulated in Patients with Major Depressive Disorder having Suicidal Ideation Compared to those without Suicidal Ideation
Mathew B, Srinivasan K, Pradeep J, Thomas T, Mandal A. Plasma Apolipoprotein-AIV Downregulated in Patients with Major Depressive Disorder having Suicidal Ideation Compared to those without Suicidal Ideation. Current Proteomics 2022, 19: 226-231. DOI: 10.2174/1570164618666211104151005.Peer-Reviewed Original Research
2021
Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS
Díaz P, Sarmiento F, Mathew B, Ballvora A, Vásquez T. Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS. PLOS ONE 2021, 16: e0259690. PMID: 34748612, PMCID: PMC8575265, DOI: 10.1371/journal.pone.0259690.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesDrought stress indexTuber initiation stageMarker-assisted selectionWater deficitWater deficit responsesDiploid potatoesGenetic architectureGenotypes to water deficitResponse to water deficitTolerant potato cultivarsWater deficit conditionsWater deficit treatmentsWell-watered conditionsGene annotation analysisPotato cultivarsTolerance breedingPotato accessionsFresh weighDeficit treatmentsDeficit conditionsPhenotypic varianceWell-wateredAgricultural sustainabilityGenomic regionsImportance of correcting genomic relationships in single-locus QTL mapping model with an advanced backcross population
Mathew B, Léon J, Dadshani S, Pillen K, Sillanpää M, Naz A. Importance of correcting genomic relationships in single-locus QTL mapping model with an advanced backcross population. G3: Genes, Genomes, Genetics 2021, 11: jkab105. PMID: 33822941, PMCID: PMC8495747, DOI: 10.1093/g3journal/jkab105.Peer-Reviewed Original ResearchDetection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
Dadshani S, Mathew B, Ballvora A, Mason A, Léon J. Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach. Scientific Reports 2021, 11: 5527. PMID: 33750919, PMCID: PMC7970893, DOI: 10.1038/s41598-021-85226-1.Peer-Reviewed Original ResearchLinkage disequilibriumDiverse panelPhysical position of markersAllele frequency changesYears of breeding historyMarker-assisted breedingBiotic stress factorsOutlier lociGenome assemblySelective sweepsTranslocation regionReference assemblyAdjacent markersChromosome 2ASGenetic diversityPhysical positionK arrayLow LDAssisted breedingBreeding historyBreeding signaturesBread wheatGenetic studiesAegilops ventricosaAgronomic traitsExosomes as Emerging Biomarker Tools in Neurodegenerative and Neuropsychiatric Disorders—A Proteomics Perspective
Mathew B, Mansuri MS, Williams KR, Nairn AC. Exosomes as Emerging Biomarker Tools in Neurodegenerative and Neuropsychiatric Disorders—A Proteomics Perspective. Brain Sciences 2021, 11: 258. PMID: 33669482, PMCID: PMC7922222, DOI: 10.3390/brainsci11020258.Peer-Reviewed Original ResearchProtein dynamic rangeDifferent cell typesProteomic perspectiveRNA speciesExosome proteomicsDisease biomarker discoveryIsolation of exosomesProteomics researchCell typesPhysiological statusExosomesCell of originNovel reservoirVariable tissueBiomarker discoveryProteinProtein detectionProtein biomarkersCurrent progressProteomicsBiomarker toolSpeciesLow amountsRapid rateNeuropsychiatric disorders
2020
Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes
Duarte-Delgado D, Dadshani S, Schoof H, Oyiga B, Schneider M, Mathew B, Léon J, Ballvora A. Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes. BMC Plant Biology 2020, 20: 428. PMID: 32938380, PMCID: PMC7493341, DOI: 10.1186/s12870-020-02616-9.Peer-Reviewed Original ResearchConceptsSalt stress toleranceSalt stress responseBread wheatStress toleranceTolerant genotypesSalt stress-related traitsBread wheat genotypesSalt-responsive genesAbiotic stress factorsGenes related to protein synthesisSalt stress adaptationStress responseStress-related traitsStress-responsive genesWheat genotypesSodium exclusionQTL dissectionSalt stressSusceptible genotypesQTL regionsSalt toleranceMapping populationQTL intervalsBackgroundBread wheatWheat
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