Yingxin Lin, PhD
Postdoctoral AssociateAbout
Research
Publications
2024
Antecedent Cardiac Arrest Status of Donation After Circulatory Determination of Death (DCDD) Kidney Donors and the Risk of Delayed Graft Function After Kidney Transplantation: A Cohort Study
Philipoff A, Lin Y, Teixeira-Pinto A, Gately R, Craig J, Opdam H, Chapman J, Pleass H, Rogers N, Davies C, McDonald S, Yang J, Lopez P, Wong G, Lim W. Antecedent Cardiac Arrest Status of Donation After Circulatory Determination of Death (DCDD) Kidney Donors and the Risk of Delayed Graft Function After Kidney Transplantation: A Cohort Study. Transplantation 2024, 108: 2117-2126. PMID: 38685196, DOI: 10.1097/tp.0000000000005022.Peer-Reviewed Original ResearchRisk of delayed graft functionCardiac arrestAllograft lossGraft functionDuration of cardiac arrestAssociated with DGFDelayed graft functionKidney transplant recipientsRisk of DGFGlomerular filtration rateRecipients of kidneysNew Zealand DialysisCirculatory determination of deathDetermination of deathArrest statusAllograft outcomesTransplant recipientsCardiorespiratory supportKidney transplantationFiltration rateCohort studyPosttransplant eGFRCox regressionOdds ratioAllograftSingle-cell RNA sequencing reveals melanoma cell state-dependent heterogeneity of response to MAPK inhibitors
Lim S, Lin Y, Lee J, Pedersen B, Stewart A, Scolyer R, Long G, Yang J, Rizos H. Single-cell RNA sequencing reveals melanoma cell state-dependent heterogeneity of response to MAPK inhibitors. EBioMedicine 2024, 107: 105308. PMID: 39216232, PMCID: PMC11402938, DOI: 10.1016/j.ebiom.2024.105308.Peer-Reviewed Original ResearchMelanoma cellsTranscriptional cell statesTreatment responseSingle-cell RNA sequencingResponse to MAPK inhibitorsPlasticity of melanoma cellsBRAF/MEK inhibitor treatmentImmunotherapy-resistant tumorsMelanoma Institute AustraliaNational Health and Medical Research Council of AustraliaImpact treatment responseMelanoma cell statesPro-inflammatory signalingNational Health and Medical Research CouncilCell statesPro-inflammatory IL6Melanoma tumorsHeterogeneous cancerInhibitor resistanceInhibitor treatmentMelanomaBRAF/MEKRNA sequencingMAPK inhibitorStudy treatment responsesSANTO: a coarse-to-fine alignment and stitching method for spatial omics
Li H, Lin Y, He W, Han W, Xu X, Xu C, Gao E, Zhao H, Gao X. SANTO: a coarse-to-fine alignment and stitching method for spatial omics. Nature Communications 2024, 15: 6048. PMID: 39025895, PMCID: PMC11258319, DOI: 10.1038/s41467-024-50308-x.Peer-Reviewed Original ResearchBIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data
Fu X, Lin Y, Lin D, Mechtersheimer D, Wang C, Ameen F, Ghazanfar S, Patrick E, Kim J, Yang J. BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Nature Communications 2024, 15: 509. PMID: 38218939, PMCID: PMC10787788, DOI: 10.1038/s41467-023-44560-w.Peer-Reviewed Original ResearchConceptsGene expressionSingle-cell transcriptomic dataSpatial expression analysisMap of gene expressionSpatial mapping of gene expressionTranscriptome dataBiological discoveryExpression analysisTranscriptomic platformsOversized cellsPublic repositoriesCell morphologyState-of-the-art methodsSelf-supervised learningDeep learning-based frameworkState-of-the-artTissue typesLearning-based frameworkHigh-resolution spatial mappingCellsExpressionSignificant analytical challengeSegmentation performanceLoss functionRecent advances
2023
Thinking process templates for constructing data stories with SCDNEY
Cao Y, Tran A, Kim H, Robertson N, Lin Y, Torkel M, Yang P, Patrick E, Ghazanfar S, Yang J. Thinking process templates for constructing data stories with SCDNEY. F1000Research 2023, 12: 261. DOI: 10.12688/f1000research.130623.2.Peer-Reviewed Original ResearchData integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
Lin Y, Wu T, Chen X, Wan S, Chao B, Xin J, Yang J, Wong W, Wang Y. Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE. Genome Research 2023, 34: gr.277960.123. PMID: 38190633, PMCID: PMC10903952, DOI: 10.1101/gr.277960.123.Peer-Reviewed Original ResearchPcdh19 mediates olfactory sensory neuron coalescence during postnatal stages and regeneration
Martinez A, Chung A, Huang S, Bisogni A, Lin Y, Cao Y, Williams E, Kim J, Yang J, Lin D. Pcdh19 mediates olfactory sensory neuron coalescence during postnatal stages and regeneration. IScience 2023, 26: 108220. PMID: 37965156, PMCID: PMC10641745, DOI: 10.1016/j.isci.2023.108220.Peer-Reviewed Original ResearchOlfactory sensory neuronsLateral glomeruliProjection of olfactory sensory neuronsMouse olfactory systemComplement of genesCell adhesion moleculesOlfactory bulbSensory neuronsCadherin superfamilySevere phenotypeSingle cell analysisPostnatal stagesAdhesion moleculesOlfactory systemGlomeruliOlfactory mapGenesOdorant receptorsProtocadherinMaleDifferential effectsCell analysisMOR28FemalesSuperfamilySingle cell profiling of tumour biopsies and heterogeneity in response of dedifferentiated melanoma.
Lim E, Lin Y, Pedersen B, Stewart A, Scolyer R, Long G, Yang J, Rizos H. Single cell profiling of tumour biopsies and heterogeneity in response of dedifferentiated melanoma. JCO Global Oncology 2023, 9: 64-64. DOI: 10.1200/go.2023.9.supplement_1.64.Peer-Reviewed Original ResearchResistance to MAPK inhibitionPro-inflammatory IL-6BRAF/MEK inhibitorsIL-6MAPK inhibitionTumor biopsiesAdvanced BRAF V600-mutant melanomaResponse to second-line treatmentTreated with immune checkpoint inhibitorsDT treatmentBRAF-mutant melanoma patientsResponse to MAPK inhibitionMelanoma cellsBRAF V600-mutant melanomaV600-mutant melanomaImmune checkpoint inhibitorsSecond-line treatmentTNFA signalingEx vivo treatmentElevated IL-6Increased IL-6Treated ex vivoDifferentiation stateImmune cell proportionsProportion of melanoma cellsAtlas-scale single-cell multi-sample multi-condition data integration using scMerge2
Lin Y, Cao Y, Willie E, Patrick E, Yang J. Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Nature Communications 2023, 14: 4272. PMID: 37460600, PMCID: PMC10352351, DOI: 10.1038/s41467-023-39923-2.Peer-Reviewed Original ResearchThinking process templates for constructing data stories with SCDNEY
Cao Y, Tran A, Kim H, Robertson N, Lin Y, Torkel M, Yang P, Patrick E, Ghazanfar S, Yang J. Thinking process templates for constructing data stories with SCDNEY. F1000Research 2023, 12: 261. DOI: 10.12688/f1000research.130623.1.Peer-Reviewed Original Research