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, 22: 27-38. 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 interactionsInteractionExpressionCellsEnzymatic and non-enzymatic transnitrosylation: “SCAN”ning the SNO-proteome
Nakamura T, Lipton S. Enzymatic and non-enzymatic transnitrosylation: “SCAN”ning the SNO-proteome. Molecular Cell 2024, 84: 191-193. PMID: 38242098, DOI: 10.1016/j.molcel.2023.12.018.Peer-Reviewed Original Research
2014
Essential versus accessory aspects of cell death: recommendations of the NCCD 2015
Galluzzi L, Bravo-San Pedro JM, Vitale I, Aaronson SA, Abrams JM, Adam D, Alnemri ES, Altucci L, Andrews D, Annicchiarico-Petruzzelli M, Baehrecke EH, Bazan NG, Bertrand MJ, Bianchi K, Blagosklonny MV, Blomgren K, Borner C, Bredesen DE, Brenner C, Campanella M, Candi E, Cecconi F, Chan FK, Chandel NS, Cheng EH, Chipuk JE, Cidlowski JA, Ciechanover A, Dawson TM, Dawson VL, De Laurenzi V, De Maria R, Debatin KM, Di Daniele N, Dixit VM, Dynlacht BD, El-Deiry WS, Fimia GM, Flavell RA, Fulda S, Garrido C, Gougeon ML, Green DR, Gronemeyer H, Hajnoczky G, Hardwick JM, Hengartner MO, Ichijo H, Joseph B, Jost PJ, Kaufmann T, Kepp O, Klionsky DJ, Knight RA, Kumar S, Lemasters JJ, Levine B, Linkermann A, Lipton SA, Lockshin RA, LĂłpez-OtĂn C, Lugli E, Madeo F, Malorni W, Marine JC, Martin SJ, Martinou JC, Medema JP, Meier P, Melino S, Mizushima N, Moll U, Muñoz-Pinedo C, Nuñez G, Oberst A, Panaretakis T, Penninger JM, Peter ME, Piacentini M, Pinton P, Prehn JH, Puthalakath H, Rabinovich GA, Ravichandran KS, Rizzuto R, Rodrigues CM, Rubinsztein DC, Rudel T, Shi Y, Simon HU, Stockwell BR, Szabadkai G, Tait SW, Tang HL, Tavernarakis N, Tsujimoto Y, Vanden Berghe T, Vandenabeele P, Villunger A, Wagner EF, Walczak H, White E, Wood WG, Yuan J, Zakeri Z, Zhivotovsky B, Melino G, Kroemer G. Essential versus accessory aspects of cell death: recommendations of the NCCD 2015. Cell Death & Differentiation 2014, 22: 58-73. PMID: 25236395, PMCID: PMC4262782, DOI: 10.1038/cdd.2014.137.Peer-Reviewed Original ResearchConceptsRegulated cell deathAccidental cell deathCell deathCellular demiseCourse of apoptosisAdaptive responseExecutioner caspasesMammalian systemsLethal signalPhysiologic programGenetic interventionsNomenclature CommitteeBiochemical phenomenaCytoprotective effectsMechanical stimuliCaspasesTransductionBiochemical correlatesApoptosisCytoprotectionDeathCellsActivationResponseVariants
2009
Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes
Galluzzi L, Aaronson SA, Abrams J, Alnemri ES, Andrews DW, Baehrecke EH, Bazan NG, Blagosklonny MV, Blomgren K, Borner C, Bredesen DE, Brenner C, Castedo M, Cidlowski JA, Ciechanover A, Cohen GM, De Laurenzi V, De Maria R, Deshmukh M, Dynlacht BD, El-Deiry WS, Flavell RA, Fulda S, Garrido C, Golstein P, Gougeon ML, Green DR, Gronemeyer H, Hajnóczky G, Hardwick JM, Hengartner MO, Ichijo H, Jäättelä M, Kepp O, Kimchi A, Klionsky DJ, Knight RA, Kornbluth S, Kumar S, Levine B, Lipton SA, Lugli E, Madeo F, Malorni W, Marine J, Martin SJ, Medema JP, Mehlen P, Melino G, Moll UM, Morselli E, Nagata S, Nicholson DW, Nicotera P, Nuñez G, Oren M, Penninger J, Pervaiz S, Peter ME, Piacentini M, Prehn JH, Puthalakath H, Rabinovich GA, Rizzuto R, Rodrigues CM, Rubinsztein DC, Rudel T, Scorrano L, Simon HU, Steller H, Tschopp J, Tsujimoto Y, Vandenabeele P, Vitale I, Vousden KH, Youle RJ, Yuan J, Zhivotovsky B, Kroemer G. Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes. Cell Death & Differentiation 2009, 16: 1093-1107. PMID: 19373242, DOI: 10.1038/cdd.2009.44.Peer-Reviewed Original ResearchConceptsCell deathNumerous human diseasesDead cellsHigher eukaryotesModel organismsCellular demisePhysiological processesHuman diseasesInterpretation of assaysNovel therapeutic strategiesPathological scenariosCell culturesBiomedical researchCellsEukaryotesAssaysTherapeutic strategiesTremendous implicationsOrganismsDeregulationCascadeDozens of methodsDeathDepth investigation
1996
BCL-2 delay apoptosis and PARP cleavage induced by NO donors in GT1-7 cells
Bonfoco E, Zhivotovsky B, Rossi A, Aguilar-Santelises M, Orrenius S, Lipton S, Nicotera P. BCL-2 delay apoptosis and PARP cleavage induced by NO donors in GT1-7 cells. Neuroreport 1996, 8: 273-276. PMID: 9051794, DOI: 10.1097/00001756-199612200-00054.Peer-Reviewed Original Research
1995
An astrocytic binding site for neuronal Thy-1 and its effect on neurite outgrowth.
Dreyer E, Leifer D, Heng J, McConnell J, Gorla M, Levin L, Barnstable C, Lipton S. An astrocytic binding site for neuronal Thy-1 and its effect on neurite outgrowth. Proceedings Of The National Academy Of Sciences Of The United States Of America 1995, 92: 11195-11199. PMID: 7479964, PMCID: PMC40598, DOI: 10.1073/pnas.92.24.11195.Peer-Reviewed Original ResearchConceptsNeurite outgrowthThy-1 functionsNeuronal Thy-1Thy-1Abundant glycoproteinMammalian neuronsNervous systemAnti-idiotype monoclonal antibodyCentral nervous system neuronsMonoclonal antibodiesBinding sitesCentral nervous systemAnti-idiotype antibodiesCertain monoclonal antibodiesBinding assaysCompetitive binding assaysProteinOutgrowthSystem neuronsDendritic developmentAntibodiesNeuronsSitesGlycoproteinCellsTranscriptional or translational inhibition blocks low dose NMDA-mediated cell death
Dreyer E, Zhang D, Lipton S. Transcriptional or translational inhibition blocks low dose NMDA-mediated cell death. Neuroreport 1995, 6: 942-944. PMID: 7612888, DOI: 10.1097/00001756-199504190-00029.Peer-Reviewed Original Research
1994
Greater sensitivity of larger retinal ganglion cells to NMDA-mediated cell death
Dreyer E, Pan Z, Storm S, Lipton S. Greater sensitivity of larger retinal ganglion cells to NMDA-mediated cell death. Neuroreport 1994, 5: 629-631. PMID: 7912962, DOI: 10.1097/00001756-199401000-00024.Peer-Reviewed Original ResearchConceptsLarge retinal ganglion cellsRetinal ganglion cellsGanglion cellsGlutamate-mediated cell deathN-methyl-D-aspartate (NMDA) subtypeIntact rat eyesCell deathNeuronal lossGlutamate toxicityGlutamate receptorsRat eyesPattern of lossNMDAGlaucomaToxic effectsDeathCellsGlutamateTissue cultureGreater sensitivitySubtypesNeuronsSimilar fashionReceptors
1992
l-Homocysteic acid selectively activates N-methyl-d-aspartate receptors of rat retinal ganglion cells
Zhang D, Lipton S. l-Homocysteic acid selectively activates N-methyl-d-aspartate receptors of rat retinal ganglion cells. Neuroscience Letters 1992, 139: 173-177. PMID: 1351663, DOI: 10.1016/0304-3940(92)90545-i.Peer-Reviewed Original ResearchConceptsRat retinal ganglion cellsRetinal ganglion cellsGanglion cellsRat RGCsN-methyl-D-aspartate receptorsNMDA receptor-channel complexConcentrations of NMDAL-homocysteic acidWhole-cell recordingsReceptor-channel complexRetinal transmittersMaximal responseHomocysteic acidNMDAPatch electrodePossible roleMillimolar concentrationsHCACellsReceptorsResponseA slowly inactivating K+ current in retinal ganglion cells from postnatal rat
Sucher N, Lipton S. A slowly inactivating K+ current in retinal ganglion cells from postnatal rat. Visual Neuroscience 1992, 8: 171-176. PMID: 1558829, DOI: 10.1017/s0952523800009330.Peer-Reviewed Original ResearchConceptsRetinal ganglion cellsGanglion cellsPostnatal ratsTiger salamander retinaPatch-clamp techniqueWhole-cell configurationRat neuronsSalamander retinaPharmacological propertiesRatsRelated cellsRetinaVoltage-independent timeCellsExtracellular CO2External applicationChannel typesLower vertebratesLast findingNeuronsTea
1991
Immunofluorescent characterization of retinal ganglion cell neurites cultured on substrates coated with antibodies against Thy-1
Leifer D, Dreyer E, Lipton S. Immunofluorescent characterization of retinal ganglion cell neurites cultured on substrates coated with antibodies against Thy-1. Experimental Neurology 1991, 113: 386-390. PMID: 1680742, DOI: 10.1016/0014-4886(91)90030-g.Peer-Reviewed Original ResearchConceptsRetinal ganglion cellsGanglion cellsThy-1Rat retinal ganglion cellsMicrotubule-associated protein 2Display immunoreactivityImmunofluorescent characterizationAntibodiesAxonal compartmentProtein 2Neurite outgrowthDays of cultureDendritic featuresCellsCytoskeletal proteinsImmunoreactivityCell membrane
1990
Neural nicotinic acetylcholine responses in sensory neurons from postnatal rat
Sucher N, Cheng T, Lipton S. Neural nicotinic acetylcholine responses in sensory neurons from postnatal rat. Brain Research 1990, 533: 248-254. PMID: 2289141, DOI: 10.1016/0006-8993(90)91346-i.Peer-Reviewed Original ResearchConceptsDRG cellsPostnatal ratsInward currentsFunctional nicotinic acetylcholine receptorsDorsal root ganglion cellsNicotinic acetylcholine responsesAgonist-induced currentsNicotinic acetylcholine receptorsPatch-clamp techniqueWhole-cell configurationAcetylcholine responseNicotinic responsesGanglion cellsNeuronal bungarotoxinNeuronal typesSensory neuronsNicotinic acetylcholineAcetylcholine receptorsNewborn animalsAcetylcholineIrreversible blockPresence of toxinsRatsCellsDMPPBlockade of nicotinic responses in rat retinal ganglion cells by neuronal bungarotoxin
Aizenman E, Loring R, Lipton S. Blockade of nicotinic responses in rat retinal ganglion cells by neuronal bungarotoxin. Brain Research 1990, 517: 209-214. PMID: 2375991, DOI: 10.1016/0006-8993(90)91028-f.Peer-Reviewed Original ResearchConceptsRat retinal ganglion cellsRetinal ganglion cellsNeuronal bungarotoxinGanglion cellsTotal blockadeFunctional nicotinic receptorsAcetylcholine-induced currentsNicotinic acetylcholine responsesNicotinic currentsAcetylcholine responseNicotinic responsesComplete blockadeNicotinic receptorsSuperfusion methodPressure ejectionToxin applicationBlockadePatch electrodeBungarotoxinCellsHigh affinityResponseReceptors
1989
Two pharmacological classes of quisqualate-induced electrical responses in rat retinal ganglion cells in vitro
Aizenman E, Karschin A, Lipton S. Two pharmacological classes of quisqualate-induced electrical responses in rat retinal ganglion cells in vitro. European Journal Of Pharmacology 1989, 174: 9-22. PMID: 2575535, DOI: 10.1016/0014-2999(89)90868-6.Peer-Reviewed Original ResearchConceptsRetinal ganglion cellsRat retinal ganglion cellsGanglion cellsType I cellsPharmacological classesExcitatory amino acid agonistsAmino acid agonistsI cellsType II cellsType III cellsQuisqualate responseCell typesAMPA responsesFurther pharmacological manipulationPharmacological manipulationPharmacological propertiesPatch electrodeII cellsIII cellsAgonistsAntagonistElicited responsesAMPAType IICells
1988
Characterization of GABA- and glycine-induced currents of solitary rodent retinal ganglion cells in culture
Tauck D, Frosch M, Lipton S. Characterization of GABA- and glycine-induced currents of solitary rodent retinal ganglion cells in culture. Neuroscience 1988, 27: 193-203. PMID: 3200439, DOI: 10.1016/0306-4522(88)90230-8.Peer-Reviewed Original ResearchConceptsGanglion cellsBicuculline methiodideRodent retinal ganglion cellsReversal potentialRetinal ganglion cellsWhole-cell recordingsAgonist-induced currentsRodent retinaD-tubocurarineMicroM GABAMicroM glycineReceptor desensitizationGABAPatch electrodeDesensitizationStrychnineMembrane conductancePicrotoxininMethiodideTaurineCellsSolitary cellsSpace clampTissue cultureResponse
1987
Bursting of calcium-activated cation-selective channels is associated with neurite regeneration in a mammalian central neuron
Lipton S. Bursting of calcium-activated cation-selective channels is associated with neurite regeneration in a mammalian central neuron. Neuroscience Letters 1987, 82: 21-28. PMID: 2447529, DOI: 10.1016/0304-3940(87)90165-0.Peer-Reviewed Original ResearchConceptsPostnatal rat retinal ganglion cellsNeurite regenerationRat retinal ganglion cellsMammalian central nervous systemRetinal ganglion cellsMammalian central neuronsCentral nervous systemPatch-clamp techniqueCell-attached patchesGanglion cellsCentral neuronsNervous systemIntracellular Ca2Internal calciumCation-selective channelsSingle-channel currentsNeuronsProlonged periodCells
1984
Monoclonal Antibody to Thy-1 Enhances Regeneration of Processes by Rat Retinal Ganglion Cells In Culture
Leifer D, Lipton S, Barnstable C, Masland R. Monoclonal Antibody to Thy-1 Enhances Regeneration of Processes by Rat Retinal Ganglion Cells In Culture. Science 1984, 224: 303-306. PMID: 6143400, DOI: 10.1126/science.6143400.Peer-Reviewed Original Research
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