2024
Detecting Boolean Asymmetric Relationships with a Loop Counting Technique and its Implications for Analyzing Heterogeneity within Gene Expression Datasets
Zhou H, Lin W, Labra S, Lipton S, Elman J, Schork N, Rangan A. Detecting Boolean Asymmetric Relationships with a Loop Counting Technique and its Implications for Analyzing Heterogeneity within Gene Expression Datasets. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2024, PP: 1-12. PMID: 39471117, DOI: 10.1109/tcbb.2024.3487434.Peer-Reviewed Original ResearchSubsets of genesGene-gene relationshipsGene expression dataGene-gene interactionsGene expression datasetsRNA-sequencing data setsDetected biclustersExpression datasetsGene pathwaysSubsets of cellsGenesRegulatory effectsBiclusteringCorrelated expressionAsymmetric interactionsSymmetric interactionsInteractionExpressionCells
2011
Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012
Galluzzi L, Vitale I, Abrams J, Alnemri E, Baehrecke E, Blagosklonny M, Dawson T, Dawson V, El-Deiry W, Fulda S, Gottlieb E, Green D, Hengartner M, Kepp O, Knight R, Kumar S, Lipton S, Lu X, Madeo F, Malorni W, Mehlen P, Nuñez G, Peter M, Piacentini M, Rubinsztein D, Shi Y, Simon H, Vandenabeele P, White E, Yuan J, Zhivotovsky B, Melino G, Kroemer G. Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death & Differentiation 2011, 19: 107-120. PMID: 21760595, PMCID: PMC3252826, DOI: 10.1038/cdd.2011.96.Peer-Reviewed Original ResearchConceptsCell death subroutinesCell death modalitiesCell deathDeath modalitiesMitotic catastropheMolecular definitionCell death morphologyAutophagic cell deathUtility of expressionNomenclature CommitteeExtrinsic apoptosisDeath morphologyRegulated necrosisIntrinsic apoptosisGenetic explorationFunctional classificationApoptosisBiochemical featuresVivo settingsSubstantial progressExpressionDeath
2000
How Are Neuronal Genes Expressed in Neurons? Regulation of NMDA Receptor Subunit Type 1 Gene as a Model
Okamoto S, Sherman K, Lipton S. How Are Neuronal Genes Expressed in Neurons? Regulation of NMDA Receptor Subunit Type 1 Gene as a Model. 2000, 355-360. DOI: 10.1007/978-4-431-66973-9_47.Peer-Reviewed Original ResearchType 1 geneRegulation of expressionGene regulationNeuronal genesEssential subunitDifferentiation proceedsTranscriptional levelFunctional NMDA receptorsNeuronal differentiationGenesVariety of moleculesNR1 geneNeuronal functionRegulationCentral nervous systemNR1ExpressionSynaptic responsesNMDA receptorsNeuronal activityNervous systemSubunitsNeuronsDifferentiationBest model
1999
Absence of binding activity of neuron-restrictive silencer factor is necessary, but not sufficient for transcription of NMDA receptor subunit type 1 in neuronal cells
Okamoto S, Sherman K, Lipton S. Absence of binding activity of neuron-restrictive silencer factor is necessary, but not sufficient for transcription of NMDA receptor subunit type 1 in neuronal cells. Brain Research 1999, 74: 44-54. PMID: 10640675, DOI: 10.1016/s0169-328x(99)00250-8.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell DifferentiationDown-RegulationGene Expression RegulationHeLa CellsHumansLuciferasesMutationNeuronsPromoter Regions, GeneticProtein BindingReceptors, N-Methyl-D-AspartateRecombinant Fusion ProteinsRepressor ProteinsResponse ElementsRNA, MessengerSequence Homology, Nucleic AcidTranscription FactorsTranscription, GeneticTumor Cells, CulturedConceptsNRSF/RESTNeuron-restrictive silencer factorPromoter activityNR1 geneSilencer factorCell linesNRSE/RE1Set of genesNeuronal cellsType I geneNonneuronal cell linesREST proteinNeuronal cell lineI geneP19 cellsConsensus sequenceNeuronal differentiationGenesHeLa cellsTranscriptionNonneuronal cellsIndependent mannerNeuronal specificityMRNA levelsExpression
1993
Expression of endogenous NMDAR1 transcripts without receptor protein suggests post-transcriptional control in PC12 cells.
Sucher N, Brose N, Deitcher D, Awobuluyi M, Gasic G, Bading H, Cepko C, Greenberg M, Jahn R, Heinemann S, Lipton S. Expression of endogenous NMDAR1 transcripts without receptor protein suggests post-transcriptional control in PC12 cells. Journal Of Biological Chemistry 1993, 268: 22299-22304. PMID: 8226739, DOI: 10.1016/s0021-9258(18)41528-1.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAnimalsAstrocytesBase SequenceCell DifferentiationCell LineCells, CulturedDimethylphenylpiperazinium IodideDNA PrimersGene ExpressionGene Expression Regulation, NeoplasticGenetic VariationHippocampusHumansKidneyMacromolecular SubstancesMembrane PotentialsMolecular Sequence DataMolecular WeightNerve Growth FactorsN-MethylaspartatePC12 CellsPolymerase Chain ReactionReceptors, N-Methyl-D-AspartateRNA, MessengerSynaptic MembranesTranscription, GeneticTransfectionConceptsNMDAR1 proteinPC12 cellsPost-transcriptional controlPost-transcriptional mechanismsNative PC12 cellsParticular cell typeUndifferentiated rat pheochromocytoma (PC12) cellsExpression of RNAPC12 cell lineTranslational regulationIsoform CRat pheochromocytoma cellsNorthern hybridizationExpression vectorReceptor proteinCell typesIon channelsProteinFunctional NMDACell linesPheochromocytoma cellsCytomegalovirus promoterModel systemRNAExpressionhMEF2C gene encodes skeletal muscle- and brain-specific transcription factors.
McDermott J, Cardoso M, Yu Y, Andres V, Leifer D, Krainc D, Lipton S, Nadal-Ginard B. hMEF2C gene encodes skeletal muscle- and brain-specific transcription factors. Molecular And Cellular Biology 1993, 13: 2564-2577. PMID: 8455629, PMCID: PMC359588, DOI: 10.1128/mcb.13.4.2564.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAmino Acid SequenceAnimalsBase SequenceBrainCells, CulturedCloning, MolecularConsensus SequenceDNA-Binding ProteinsGene ExpressionGenesHumansImmunologic TechniquesIn Vitro TechniquesMEF2 Transcription FactorsMiceMolecular Sequence DataMusclesMyogenic Regulatory FactorsNeuronsOligodeoxyribonucleotidesPolymerase Chain ReactionRNA, MessengerSequence AlignmentTissue DistributionTranscription FactorsTranscription, GeneticConceptsSkeletal muscleSubset of neuronsCortical neuronsBrain-specific transcription factorTranscription factorsMRNA levelsPotential targetTrans-activating activityMuscleMEF2 transcription factorsNeuronsBrainBrain transcriptsMEF2 factorsMuscle-specific enhancerExpressionMyogenic differentiationTissue-specific isoformsUbiquitous expressionFactorsTissue-specific patternsGenesNeurogenesishMEF2C Gene Encodes Skeletal Muscle- and Brain-Specific Transcription Factors
McDermott J, Cardoso M, Yu Y, Andres V, Leifer D, Krainc D, Lipton S, Nadal-Ginard B. hMEF2C Gene Encodes Skeletal Muscle- and Brain-Specific Transcription Factors. Molecular And Cellular Biology 1993, 13: 2564-2577. DOI: 10.1128/mcb.13.4.2564-2577.1993.Peer-Reviewed Original ResearchSkeletal muscleSubset of neuronsCortical neuronsBrain-specific transcription factorTranscription factorsMRNA levelsPotential targetTrans-activating activityMuscleMEF2 transcription factorsNeuronsBrainBrain transcriptsMEF2 factorsMuscle-specific enhancerExpressionMyogenic differentiationTissue-specific isoformsUbiquitous expressionFactorsTissue-specific patternsGenesNeurogenesis