2020
Convergent network effects along the axis of gene expression during prostate cancer progression
Charmpi K, Guo T, Zhong Q, Wagner U, Sun R, Toussaint N, Fritz C, Yuan C, Chen H, Rupp N, Christiansen A, Rutishauser D, Rüschoff J, Fankhauser C, Saba K, Poyet C, Hermanns T, Oehl K, Moore A, Beisel C, Calzone L, Martignetti L, Zhang Q, Zhu Y, Martínez M, Manica M, Haffner M, Aebersold R, Wild P, Beyer A. Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biology 2020, 21: 302. PMID: 33317623, PMCID: PMC7737297, DOI: 10.1186/s13059-020-02188-9.Peer-Reviewed Original ResearchConceptsHigh-throughput genomic measurementsProstate cancer progressionGene expressionMolecular networksCopy number alterationsCancer progressionComplex genomic alterationsTumor phenotypePrediction of recurrence-free survivalGenomic measurementsRecurrence-free survivalProstate cancer patientsProteomic alterationsGenomic aberrationsAggressive tumor phenotypeGenomic alterationsDownstream proteinsGenomic effectsNetwork-based approachProstate samplesTumor siteBiochemical stateMalignant tumorsProtein levelsTumor tissues
2010
Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop
Martínez M, Soriano J, Tlusty T, Pilpel Y, Furman I. Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop. Physical Review E 2010, 81: 031924. PMID: 20365787, DOI: 10.1103/physreve.81.031924.Peer-Reviewed Original ResearchConceptsSingle-cell levelRegulatory RNAsGene expression variabilityIndividual cellsPost-transcriptional regulationNoncoding regulatory RNAsCell population levelNegative feedback loopSingle-cell experimentsRegulatory networksRNA transcriptsRepress translationRegulatory transcriptsPost-transcriptionallyExpression variabilityRNAStochastic eventsMessenger RNATranscriptionProtein expressionMessengerCell populationsPopulation levelCellsFeedback loop
2008
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
Shalem O, Dahan O, Levo M, Martinez M, Furman I, Segal E, Pilpel Y. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Molecular Systems Biology 2008, 4: msb200859. PMID: 18854817, PMCID: PMC2583085, DOI: 10.1038/msb.2008.59.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression Regulation, FungalGenome, FungalKineticsRNA, MessengerStress, PhysiologicalTranscription, GeneticYeastsConceptsInduced genesRepressed genesMRNA productionTranscriptional responses to stressGenome-wide interplayResponse to stressResponse to environmental changesMRNA decay ratesCondition-specific changesSteady-state levelsTranscriptional arrestGenesTranscriptomeEnvironmental changesMRNARegulatory armYeastMicroarrayDegradationProduction