2024
SANTO: 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 ResearchMeSH KeywordsAlgorithmsAnimalsBreast NeoplasmsEmbryo, MammalianEpigenomicsFemaleGenomicsHumansImaging, Three-DimensionalMiceTranscriptomeTumor Microenvironment
2023
HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol
Cheng Z, Li L, Zhang Y, Ren Y, Gu J, Wang X, Zhao H, Lu H. HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol. Briefings In Bioinformatics 2023, 24: bbac601. PMID: 36736372, DOI: 10.1093/bib/bbac601.Peer-Reviewed Original ResearchMeSH KeywordsAlpha-FetoproteinsCarcinoma, HepatocellularHepatitis BHepatitis B virusHumansLiver NeoplasmsTumor MicroenvironmentConceptsHepatocellular carcinomaClinical stageImmune microenvironmentTumor sizeHepatitis B virus infectionLow alpha-fetoprotein levelsMetabolism-related proteinsRelevant subgroupsB virus infectionSevere liver dysfunctionGood liver functionHigh AFP levelsAlpha-fetoprotein levelsPrimary liver malignancySmaller tumor sizeLarger tumor sizeLower clinical stageHigher clinical stageCancer-related deathProliferation activityPrevention of HBVNear-normal levelsLow proliferation activityLiver dysfunctionHigh proliferation activity
2019
NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution
Tang D, Park S, Zhao H. NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution. Bioinformatics 2019, 36: 1344-1350. PMID: 31593244, PMCID: PMC8215918, DOI: 10.1093/bioinformatics/btz748.Peer-Reviewed Original Research