2023
Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil
de Oliveira L, de Rezende I, Navarini V, Marchioro S, Torres A, Croda J, Croda M, Gonçalves C, Xavier J, de Castro E, Lima M, Iani F, Adelino T, Aburjaile F, Demarchi L, Taira D, Zardin M, Fonseca V, Giovanetti M, Andrews J, Alcantara L, Simionatto S. Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil. Frontiers In Public Health 2023, 11: 1195779. PMID: 37965526, PMCID: PMC10641392, DOI: 10.3389/fpubh.2023.1195779.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 lineagesIntroduction eventsCharacterization of SARS-CoV-2Nanopore sequencing platformSARS-CoV-2 positive samplesMultiple SARS-CoV-2 variantsMultiple introduction eventsPhylogenetic reconstructionPhylogenetic dataGenome sequenceSequencing platformsGenomic characterizationSARS-CoV-2Genomic surveillanceSARS-CoV-2 variantsLineagesMato GrossoMortality rateViral dynamicsIndigenous populationCo-circulationPrevalence of malesMidwestern BrazilPositive samplesIndigenous mobilizationChapter 3 Single-cell transcriptomics
Marczyk M, Kujawa T, Papiez A, Polanska J. Chapter 3 Single-cell transcriptomics. 2023, 67-84. DOI: 10.1016/b978-0-323-91810-7.00015-7.ChaptersSingle-cell transcriptomicsSingle-cell technologiesCell trajectory inferenceGene expression dataSimilar cell typesTranscriptional signalsCancer cell line dataRNAseq dataGene expressionCellular heterogeneitySequencing platformsBreast cancer cell line dataExpression dataCell line dataGroups of cellsTrajectory inferenceCell typesIndividual cellsMolecular characteristicsProper processingCellsTranscriptomicsGenesExpressionCertain steps
2022
DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations
Chen Z, King W, Hwang A, Gerstein M, Zhang J. DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations. Science Advances 2022, 8: eabq3745. PMID: 36449617, PMCID: PMC9710871, DOI: 10.1126/sciadv.abq3745.Peer-Reviewed Original ResearchOrdinary differential equationsDifferential equationsTranscriptome dynamicsSingle-cell gene expression measurementsNeural ordinary differential equationsSingle-cell sequencing technologiesVelocity fieldIndividual cellsGene expression changesGene expression profilesDynamical systemsGene expression measurementsTranscriptional dynamicsRNA velocityDifferent sequencing platformsChaotic propertiesSequencing technologiesCell statesPerturbation analysisRegulatory relationshipsData-Driven DiscoveryExpression changesExpression profilesSequencing platformsDriver genesInvestigating Sources of Zeros in 10× Single-Cell RNAseq Data
Slowik H, Zyla J, Marczyk M. Investigating Sources of Zeros in 10× Single-Cell RNAseq Data. Lecture Notes In Computer Science 2022, 13347: 71-80. DOI: 10.1007/978-3-031-07802-6_6.Peer-Reviewed Original ResearchSingle-cell levelSingle-cell RNA sequencingSingle-cell RNAseq dataNumber of transcriptsMulti-omics dataGene expression estimatesRibosomal genesRNA sequencingExpression profilingEnrichment analysisRNAseq dataBiological pathwaysSequencing platformsExpression dataGenesExpression estimatesIndividual cellsBreast cancer cell linesCancer cell linesCell linesSingle experimentLow mappabilityTranscriptsSequencingProfilingPrognostic mutational subtyping in de novo diffuse large B-cell lymphoma
Kim E, Jiang Y, Xu T, Bazeos A, Knapp A, Bolen C, Humphrey K, Nielsen T, Penuel E, Paulson J. Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma. BMC Cancer 2022, 22: 231. PMID: 35236331, PMCID: PMC8892802, DOI: 10.1186/s12885-022-09237-5.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntineoplastic Combined Chemotherapy ProtocolsBridged Bicyclo Compounds, HeterocyclicClinical Trials, Phase II as TopicClinical Trials, Phase III as TopicEnhancer of Zeste Homolog 2 ProteinExome SequencingFemaleHumansLymphoma, Large B-Cell, DiffuseMaleMiddle AgedMutationPrognosisProto-Oncogene Proteins c-bcl-2RNA-SeqSulfonamidesTreatment OutcomeConceptsSequence dataWhole-exome sequencing dataExome-sequencing dataTargeted sequencing platformsExome sequencing dataTargeted sequencing dataBackgroundDiffuse large B-cell lymphomaLarge B-cell lymphomaSequencing platformsRNA-seqDe novo DLBCLImproved overall survivalTarget sequenceB-cell lymphomaVenetoclax therapyMutation subtypesPrognostic subsetsMutationsOverall survivalMolecular subsetsSubset distributionMutation groupSurvival outcomesMutation profilesClinical associations
2021
Functional testing for variant prioritization in a family with long QT syndrome
Najari Beidokhti M, Bertalovitz AC, Ji W, McCormack J, Jeffries L, Sempou E, Khokha MK, McDonald TV, Lakhani SA. Functional testing for variant prioritization in a family with long QT syndrome. Molecular Genetics And Genomics 2021, 296: 823-836. PMID: 33876311, DOI: 10.1007/s00438-021-01780-3.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionAMP-Activated Protein KinasesDNA Mutational AnalysisElectrocardiographyERG1 Potassium ChannelExome SequencingFamilyFemaleGenetic TestingHeart Function TestsHEK293 CellsHumansKCNQ1 Potassium ChannelLong QT SyndromeMiddle AgedMutationPedigreePhenotypePolymerase Chain ReactionPolymorphism, Single NucleotideProtein Serine-Threonine KinasesConceptsWhole-exome sequencingFunctional characterizationSilico analysisPrecise genetic etiologyHeterologous expression systemNext-generation sequencing platformsNovel genetic variantsDeleterious phenotypesFunction phenotypesExpression systemSequencing platformsSecond individualHeritable diseaseVariant prioritizationGenetic variantsLong QT syndromeExome sequencingGenetic etiologyGenetic settingClinical genetics settingPhenotypeFamilyGene panelFamily membersVariantsGenome-wide detection and analysis of CRISPR-Cas off-targets
Rodríguez T, Dadafarin S, Pratt H, Liu P, Amrani N, Zhu L. Genome-wide detection and analysis of CRISPR-Cas off-targets. Progress In Nucleic Acid Research And Molecular Biology 2021, 181: 31-43. PMID: 34127199, DOI: 10.1016/bs.pmbts.2021.01.012.Peer-Reviewed Original ResearchConceptsProtospacer-adjacent motifOff-target identificationGUIDE-seqGenome-wide detectionHigh-throughput sequencingShort Palindromic Repeats (CRISPR) technologyOff-target sitesSequencing platformsThroughput sequencingTreat human diseasesOpen-source pipelineDocker imageHuman diseasesGene editingOff-targetsBiological studiesIncreased multiplexingProfiling approachSequenceIn vivoBioconductorSgRNAMotifRNAIdentification
2018
Widespread somatic loss of heterozygosity as a possible marker of disease aggressiveness in metastatic well differentiated pancreatic neuroendocrine tumors.
Akala O, Shah R, Untch B, Kelly V, Chou J, Ladanyi M, Berger M, Klimstra D, Reidy D, Raj N. Widespread somatic loss of heterozygosity as a possible marker of disease aggressiveness in metastatic well differentiated pancreatic neuroendocrine tumors. Journal Of Clinical Oncology 2018, 36: 275-275. DOI: 10.1200/jco.2018.36.4_suppl.275.Peer-Reviewed Original ResearchLoss of heterozygositySomatic loss of heterozygosityNext-generation sequencingPancreatic neuroendocrine tumorsAltered tumorsWild typeNeuroendocrine tumorsOverall survivalWT tumorsCancer-related genesMarkers of disease aggressivenessGenome-wideClinically heterogeneous tumorsHigh grade pathologySequencing platformsInferior overall survivalAggressive pathological featuresKi-67 indexNGS platformChromosome 1Allele-specificSomatic lossMEN1 alterationsGenetic alterationsGrade pathology
2017
Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nature Medicine 2017, 23: 703-713. PMID: 28481359, PMCID: PMC5461196, DOI: 10.1038/nm.4333.Peer-Reviewed Original ResearchConceptsMemorial Sloan-Kettering Cancer CenterCancer-related genesProspective clinical sequencingAdvanced solid cancersSequencing platformsStructural variantsGenomic landscapeGenomic mutationsDetailed clinical annotationMutational landscapeSequencing resultsNumber alterationsCancer CenterPatient enrollmentClinical trialsMSK-IMPACTMetastatic cancerSolid cancersNew insightsNormal tissuesClinical sequencingCancer therapyPatientsCancerClinical annotation
2016
Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways
Cappi C, Brentani H, Lima L, Sanders SJ, Zai G, Diniz BJ, Reis VN, Hounie AG, Conceição do Rosário M, Mariani D, Requena GL, Puga R, Souza-Duran FL, Shavitt RG, Pauls DL, Miguel EC, Fernandez TV. Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways. Translational Psychiatry 2016, 6: e764-e764. PMID: 27023170, PMCID: PMC4872454, DOI: 10.1038/tp.2016.30.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsPPI networkPathway analysisProtein-protein interaction networkGenome-wide association studiesNovo single nucleotide variantsParticular biological pathwaysRare genetic variationDisease gene prioritizationDirect molecular interactionWhole-exome sequencing studiesGene discoveryNetwork genesSpecific risk genesNetwork enrichmentGenetic variationInteraction networksGene prioritizationCandidate genesAssociation studiesBiological pathwaysSequencing platformsSequencing studiesWhole-exome sequencingGenes
2015
Characterization of DNA variants in the human kinome in breast cancer
Agarwal D, Qi Y, Jiang T, Liu X, Shi W, Wali VB, Turk B, Ross JS, Fraser Symmans W, Pusztai L, Hatzis C. Characterization of DNA variants in the human kinome in breast cancer. Scientific Reports 2015, 5: 14736. PMID: 26420498, PMCID: PMC4588561, DOI: 10.1038/srep14736.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorBreast NeoplasmsFemaleGene Expression Regulation, NeoplasticGenetic Predisposition to DiseaseGenetic VariationHigh-Throughput Nucleotide SequencingHumansMiddle AgedMutationNeoplasm GradingNeoplasm MetastasisNeoplasm StagingPhosphotransferasesPolymorphism, Single NucleotideReproducibility of ResultsTranscriptomeConceptsBreast cancerHuman kinomeKinase geneGreater mutational loadNucleic acid variationPrimary cancer samplesPrimary breast cancerHistologic grade 1Major functional impactSOLiD sequencing platformIndividual breast cancersNon-synonymous variantsFine-needle biopsyGrade 3 casesCancer-related genesNucleotide variationsDNA variantsSequencing platformsMetastatic lesionsMutational loadAcid variationsCancer biologyGenesNeedle biopsyAdditional cancers
2014
An Atypical Orphan Carbohydrate-NRPS Genomic Island Encodes a Novel Lytic Transglycosylase
Guo X, Crawford JM. An Atypical Orphan Carbohydrate-NRPS Genomic Island Encodes a Novel Lytic Transglycosylase. Cell Chemical Biology 2014, 21: 1271-1277. PMID: 25219963, PMCID: PMC4224617, DOI: 10.1016/j.chembiol.2014.07.025.Peer-Reviewed Original ResearchConceptsGenome synteny analysisSynteny analysisGenomic islandsLytic transglycosylaseNatural product gene clustersOrphan biosynthetic pathwaysGene deletion analysisGenome sequencing platformsRare structural featureBiochemical reconstructionHypothetical proteinsGene clusterAcetyl-glucosamine moietyHeterologous expressionDeletion analysisProtein homologyBiosynthetic pathwayIsland contentNew small moleculesSequencing platformsMetabolic chemistryTransglycosylasePathwaySmall moleculesNatural products
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