2025
A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization
Koroglu M, Bilguvar K. A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization. Methods In Molecular Biology 2025, 2889: 207-233. PMID: 39745615, DOI: 10.1007/978-1-0716-4322-8_15.Peer-Reviewed Original ResearchConceptsGenomic dataHigh-throughput sequencing technologyGenomic data analysisField of genomicsNext-generation sequencingVariant callingNGS technologiesSequencing technologiesBioinformatics approachComprehensive computational approachSequenceComputational approachCancer researchGenomeTranscriptomeBioinformaticsNGSProteomicsNext-generationDNARNAEfficient sequenceAnnotationVariantsFragments
2024
RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs
Li Y, Liu X, Cheng F, Pan X, Yang Y. RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs. 2024, 00: 48-53. DOI: 10.1109/bibm62325.2024.10821865.Peer-Reviewed Original ResearchMultiple RNA-binding proteinsRNA-binding proteinsRNA transcriptsRNA-protein binding sitesRBP binding sitesFull-length transcriptsBinding sitesPredicted binding siteSequence dataRNA informationRNA fragmentsGene expressionTranscriptionRNASequence lengthSequenceSitesGenesProteinMachine learning methodsImbalanced labelsImbalanced dataData imbalanceFragmentsExpressionSingle-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA
Cheng J, Swarup N, Morselli M, Huang W, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong D. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Research 2024, 52: e50-e50. PMID: 38797520, PMCID: PMC11194076, DOI: 10.1093/nar/gkae276.Peer-Reviewed Original ResearchTranscription start siteMethylation profilesCell-free DNAWhole-genome bisulfite sequencingCytosine methylation changesLevels of DNA methylationSingle-base resolutionUpstream transcription start siteBS-seqStart siteBisulfite sequencingCpG islandsDNA fragmentationBisulfite conversionMethylation changesDNA methylationBisulfite treatmentLarge DNAsMethylation analysisDNANon-cancer samplesBisulfiteFragmentsHemopoietic cellsMethylationDecoding protein binding landscape on circular RNAs with base-resolution transformer models
Wu H, Liu X, Fang Y, Yang Y, Huang Y, Pan X, Shen H. Decoding protein binding landscape on circular RNAs with base-resolution transformer models. Computers In Biology And Medicine 2024, 171: 108175. PMID: 38402841, DOI: 10.1016/j.compbiomed.2024.108175.Peer-Reviewed Original ResearchConceptsRNA-binding protein binding sitesRNA-binding proteinsCircRNA transcriptsBinding sitesBinding to RNA-binding proteinsSingle-nucleotide resolutionCovalent loop structureCircular RNAsBound nucleotideBinding motifBinding landscapeGene expressionTranscriptionRNANucleotideLoop structureCircRNAsProteinEndogenous RNAFragmentsSitesComputational methodsMotifGenesConvolutional neural network
2023
tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments
Li N, Yao S, Yu G, Lu L, Wang Z. tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments. Nucleic Acids Research 2023, 52: d345-d350. PMID: 37811890, PMCID: PMC10767876, DOI: 10.1093/nar/gkad815.Peer-Reviewed Original ResearchChemical interactions modulate λ6‐85 stability in cells
Knab E, Davis C. Chemical interactions modulate λ6‐85 stability in cells. Protein Science 2023, 32: e4698. PMID: 37313657, PMCID: PMC10288553, DOI: 10.1002/pro.4698.Peer-Reviewed Original ResearchThe C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion
Onuchic L, Padovano V, Schena G, Rajendran V, Dong K, Shi X, Pandya R, Rai V, Gresko N, Ahmed O, Lam T, Wang W, Shen H, Somlo S, Caplan M. The C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion. Nature Communications 2023, 14: 1790. PMID: 36997516, PMCID: PMC10063565, DOI: 10.1038/s41467-023-37449-1.Peer-Reviewed Original ResearchConceptsPolycystin-1Nicotinamide nucleotide transhydrogenaseTerminal tailCystic phenotypeAutosomal dominant polycystic kidney diseaseCyst cell proliferationC-terminal domainAmino acid residuesLethal monogenic disorderC-terminal cleavageNucleotide transhydrogenaseAcid residuesMitochondrial functionTransgenic expressionPKD1 geneRedox stateShort fragmentsCell proliferationMonogenic disordersDominant polycystic kidney diseasePolycystic kidney diseaseGene therapy strategiesProteinPhenotypeFragmentsGenome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer
Budhraja K, McDonald B, Stephens M, Contente-Cuomo T, Markus H, Farooq M, Favaro P, Connor S, Byron S, Egan J, Ernst B, McDaniel T, Sekulic A, Tran N, Prados M, Borad M, Berens M, Pockaj B, LoRusso P, Bryce A, Trent J, Murtaza M. Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer. Science Translational Medicine 2023, 15: eabm6863. PMID: 36630480, PMCID: PMC10080578, DOI: 10.1126/scitranslmed.abm6863.Peer-Reviewed Original ResearchConceptsGenome-wide analysisNucleotide frequenciesDNA fragmentsGenome-wide differencesFragment endsNovel cancer diagnosticsCopy number amplificationChromatin accessibilityGenomic regionsGenomic positionsGC contentDNA sequencesSequencing dataDifferent cancer typesNumber amplificationCell typesCellular originSomatic mutationsCancer cellsFragment lengthCell-free DNADNACancer typesFragmentsSequence
2019
C‐terminal phosphorylation of latrophilin‐1/ADGRL1 affects the interaction between its fragments
Rahman M, Manser C, Benlaouer O, Suckling J, Blackburn J, Silva J, Ushkaryov Y. C‐terminal phosphorylation of latrophilin‐1/ADGRL1 affects the interaction between its fragments. Annals Of The New York Academy Of Sciences 2019, 1456: 122-143. PMID: 31553068, DOI: 10.1111/nyas.14242.Peer-Reviewed Original ResearchConceptsN-terminal fragmentG protein-coupled receptorsC-terminal fragmentLatrophilin-1Protein-coupled receptorsAdhesion G protein-coupled receptorsProtein tyrosine phosphatase σG protein-mediated signalingProtein-mediated signalingPhosphorylated C-terminal fragmentsTerminal phosphorylationIndependent proteinsPlasma membraneSeparate proteinsΑ-latrotoxinAffinity columnProteinEndocrine cellsFragmentsHigh affinityLow affinityMultiple sitesCopurifiesDephosphorylationComplexesMolecular and taxonomic analyses in troglobiotic Alpioniscus (Illyrionethes) species from the Dinaric Karst (Isopoda: Trichoniscidae)
Bedek J, Taiti S, Bilandžija H, Ristori E, Baratti M. Molecular and taxonomic analyses in troglobiotic Alpioniscus (Illyrionethes) species from the Dinaric Karst (Isopoda: Trichoniscidae). Zoological Journal Of The Linnean Society 2019, 187: 539-584. DOI: 10.1093/zoolinnean/zlz056.Peer-Reviewed Original ResearchNominal speciesNuclear gene fragmentsFuture species identificationDinaric karstMost nominal speciesNew morphological charactersSpecies richnessDetailed morphological analysisWidespread taxaDistinct lineagesPhylogenetic methodsMorphological charactersTerrestrial isopodsGene fragmentsTaxonomic analysisDNA fragmentsSpecies identificationDifferent speciesBody part ratiosTaxaMolecular analysisSpeciesMorphological analysisTroglobiontsFragmentsGSAP modulates γ-secretase specificity by inducing conformational change in PS1
Wong E, Liao G, Chang J, Xu P, Li Y, Greengard P. GSAP modulates γ-secretase specificity by inducing conformational change in PS1. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 6385-6390. PMID: 30850537, PMCID: PMC6442608, DOI: 10.1073/pnas.1820160116.Peer-Reviewed Original Research
2018
Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes
Grochowski CM, Gu S, Yuan B, Julia T, Brennand KJ, Sebat J, Malhotra D, McCarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMB. Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Human Mutation 2018, 39: 939-946. PMID: 29696747, PMCID: PMC5995661, DOI: 10.1002/humu.23537.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingSmall supernumerary marker chromosomeChromosomal fragmentsMarker chromosomesGenomic structureComparative genomic hybridization analysisSupernumerary marker chromosomeGenomic hybridization analysisTemporal originHybridization analysisArray comparative genomic hybridization analysisChromosome 9Short armRepair mechanismsMarker genotypesChromosomesPrecise architectureProband's maternal grandmotherStructural variationsPsychiatric phenotypesFurther complexityFragmentsDuplicationSequencingPhenotype
2015
Aldehyde Capture Ligation for Synthesis of Native Peptide Bonds
Raj M, Wu H, Blosser S, Vittoria M, Arora P. Aldehyde Capture Ligation for Synthesis of Native Peptide Bonds. Journal Of The American Chemical Society 2015, 137: 6932-6940. PMID: 25966041, DOI: 10.1021/jacs.5b03538.Peer-Reviewed Original ResearchConceptsBond formationAmide bond formationNative peptide bondChemoselective reactivityChemoselective reactionAmine terminusIntramolecular reactionSynthetic proteinsPeptide bondReactionAmino acid residuesBioconjugatesFormationAcid residuesAldehydesCarboxylBondsAminesSynthesisReactivityFragmentsPeptidesResidues
2014
Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer
Schauder CM, Wu X, Saheki Y, Narayanaswamy P, Torta F, Wenk MR, De Camilli P, Reinisch KM. Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer. Nature 2014, 510: 552-555. PMID: 24847877, PMCID: PMC4135724, DOI: 10.1038/nature13269.Peer-Reviewed Original Research
2013
Polycystin-1 cleavage and the regulation of transcriptional pathways
Merrick D, Bertuccio CA, Chapin HC, Lal M, Chauvet V, Caplan MJ. Polycystin-1 cleavage and the regulation of transcriptional pathways. Pediatric Nephrology 2013, 29: 505-511. PMID: 23824180, PMCID: PMC3844055, DOI: 10.1007/s00467-013-2548-y.Peer-Reviewed Original ResearchConceptsAutosomal dominant polycystic kidney diseaseFluid-filled renal cystsPolycystin-2Transcriptional pathwaysPolycystin-1Primary ciliaProtein productsPhysiological functionsCommon genetic causeParent proteinProteolytic cleavageCleavage fragmentsGenetic causeGenesEnd-stage renal diseaseDominant polycystic kidney diseasePolycystic kidney diseaseBiological activityPathwayRenal diseaseKidney diseaseCleavageRenal parenchymaFragmentsRenal cysts
2010
Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes
Vasan N, Hutagalung A, Novick P, Reinisch KM. Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 14176-14181. PMID: 20660722, PMCID: PMC2922553, DOI: 10.1073/pnas.1009419107.Peer-Reviewed Original ResearchConceptsGolgi-associated retrograde proteinC-terminusC-terminal fragmentGolgi-associated retrograde protein (GARP) complexCommon evolutionary originAlpha-helical bundleTrans-Golgi networkEndosome-derived vesiclesMembrane trafficVesicle recognitionEvolutionary originProtein complexesOligomeric GolgiTerminusSubunitsProteinComplexesDsl1ExocystFragmentsEndosomesGolgiFamilyMutationsVesicles
2007
Substrate‐Based Fragment Identification and Optimization for Inhibitor Discovery
Ellman J. Substrate‐Based Fragment Identification and Optimization for Inhibitor Discovery. The FASEB Journal 2007, 21: a209-a209. DOI: 10.1096/fasebj.21.5.a209-c.Peer-Reviewed Original ResearchFragment-based approachSmall molecule ligandsFragment-based methodsMolecule ligandsFragment approachInhibitor discoveryLow molecular weight inhibitorsEfficient conversionSubstrate screeningLigandsHigh-throughput methodSelective ligandsFragment identificationWeight inhibitorsSelective low molecular weight inhibitorsCleavage efficiencyThroughput methodEfficient methodSelective drugsRelevant proteasesDesign principlesFragmentsDiscoveryLow affinityConversion
2005
Antibody Mediated Transduction of Therapeutic Proteins into Living Cells
Hansen JE, Weisbart RH, Nishimura RN. Antibody Mediated Transduction of Therapeutic Proteins into Living Cells. The Scientific World JOURNAL 2005, 5: 782-788. PMID: 16170440, PMCID: PMC5936519, DOI: 10.1100/tsw.2005.98.Commentaries, Editorials and LettersMeSH KeywordsAnimalsAutoantibodiesBiological Transport, ActiveCells, CulturedDrug Delivery SystemsEndocytosisGene Products, tatHIV-1HumansImmunoglobulin FragmentsLymphokinesMicePeptide FragmentsProtein TransportProteinsSialoglycoproteinsSignal Transductiontat Gene Products, Human Immunodeficiency VirusConceptsProtein transduction domainTransduction domainNovel protein transduction domainTherapeutic proteinsReceptor-mediated endocytosisSuch proteinsHIV-1 Tat proteinCell-penetrating peptidesMAb 3E10Active proteinLiving cellsCell membraneProteinTat proteinProtein therapyCellsSingle-chain fragmentTherapeutic peptidesRecent studiesFv fragmentDomainFragmentsDirect deliveryEndocytosisTransductionStructural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity
Stein AJ, Fuchs G, Fu C, Wolin SL, Reinisch KM. Structural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity. Cell 2005, 121: 529-539. PMID: 15907467, PMCID: PMC1769319, DOI: 10.1016/j.cell.2005.03.009.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsBinding SitesCells, CulturedCrystallography, X-RayInsectaModels, MolecularMolecular Sequence DataNucleic Acid ConformationProtein BindingProtein Structure, TertiaryRibonucleoproteinsRNARNA Processing, Post-TranscriptionalRNA-Binding ProteinsRNA, Small CytoplasmicRNA, Small NuclearXenopus laevis
2004
Separation Force Measurements Reveal Different Types of Modulation of E-cadherin-based Adhesion by Nectin-1 and -3*
Martinez-Rico C, Pincet F, Perez E, Thiery J, Shimizu K, Takai Y, Dufour S. Separation Force Measurements Reveal Different Types of Modulation of E-cadherin-based Adhesion by Nectin-1 and -3*. Journal Of Biological Chemistry 2004, 280: 4753-4760. PMID: 15550395, DOI: 10.1074/jbc.m412544200.Peer-Reviewed Original ResearchConceptsE-cadherin-based adhesionsNectin-3E-cadherin-dependent cell adhesionExtracellular fragmentE-cadherin-mediated adhesionE-cadherin-expressing cellsNectin-1Cell adhesionCell-cell adhesionIndependent cell adhesion moleculesAdherens junctionsCell adhesion moleculeCell doubletsSignificant agonistic effectKey moleculesE-cadherinL cellsCadherinNectinAdhesion moleculesCellsAdhesionFragmentsHomodimerHeterodimers
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply