2022
Deep generative modeling and clustering of single cell Hi-C data
Liu Q, Zeng W, Zhang W, Wang S, Chen H, Jiang R, Zhou M, Zhang S. Deep generative modeling and clustering of single cell Hi-C data. Briefings In Bioinformatics 2022, 24: bbac494. PMID: 36458445, DOI: 10.1093/bib/bbac494.Peer-Reviewed Original ResearchConceptsCell-to-cell variabilityHi-C dataFormation of chromatin contactsHi-C analysisHi-C technologyArchitecture of DNAChromatin contactsGenome conformationChromatin architectureChromatin organizationGene regulationCellular functionsIndividual cellsCell typesComputational approachDeep generative neural networksComplex mechanismsGenerative neural networkDeep generative modelsCellsChromatinGenesDNAData clusteringNeural network
2019
hicGAN infers super resolution Hi-C data with generative adversarial networks
Liu Q, Lv H, Jiang R. hicGAN infers super resolution Hi-C data with generative adversarial networks. Bioinformatics 2019, 35: i99-i107. PMID: 31510693, PMCID: PMC6612845, DOI: 10.1093/bioinformatics/btz317.Peer-Reviewed Original ResearchConceptsResolution Hi-C dataLow-resolution Hi-C dataHi-C dataTopologically associating domainsEnhancing Hi-C data resolutionFormation of chromatin contactsPairs of genomic regionsAccuracy of downstream analysesHigh-resolution Hi-C matricesHigher sequencing costsGenome-wide technologiesDistal regulatory elementsMeasure physical contactsCell typesChromatin contactsSequencing costsGenome conformationChromatin loopsGenomic regionsChromatin conformationGenomic analysisSupplementary dataRegulatory elementsDownstream analysisTarget genesA chromosome-scale assembly of the major African malaria vector Anopheles funestus
Ghurye J, Koren S, Small S, Redmond S, Howell P, Phillippy A, Besansky N. A chromosome-scale assembly of the major African malaria vector Anopheles funestus. GigaScience 2019, 8: giz063. PMID: 31157884, PMCID: PMC6545970, DOI: 10.1093/gigascience/giz063.Peer-Reviewed Original ResearchConceptsReference genomeHigh-quality reference genomeCurrent reference assemblyHaploid genome sizeMajor African malaria vector Anopheles funestusN50 scaffold sizeChromosome-scale assemblyReference genome assemblyN50 contig sizeChromosome-scale scaffoldsMalaria vector Anopheles funestusAfrican malaria vector Anopheles funestusMbp of sequenceSingle-molecule sequencingPrimary assemblyAnopheles funestusHi-C dataImportant disease vectorChromosome scaffoldingGenome sizeGenome assemblyContig sizeReference assemblyGenomic variationAssociation of phenotypic
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