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Publications

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces.

Ding J, Regev A. Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces. Nat Commun. 2021;12(1):2554. doi:10.1038/s41467-021-22851-4

Genome-wide enhancer maps link risk variants to disease genes.

Nasser J, Bergman DT, Fulco CP, et al. Genome-wide enhancer maps link risk variants to disease genes. Nature. 2021;593(7858):238-243. doi:10.1038/s41586-021-03446-x

Avadomide induces degradation of ZMYM2 fusion oncoproteins in hematologic malignancies.

Renneville A, Gasser JA, Grinshpun DE, et al. Avadomide induces degradation of ZMYM2 fusion oncoproteins in hematologic malignancies. Blood Cancer Discov. 2021;2(3):250-265. doi:10.1158/2643-3230.bcd-20-0105

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease.

de Goede O. Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease. Cell. 2021;184(10):2633-2648.e19. doi:10.1016/j.cell.2021.03.050

Association of Prediagnostic Blood Metabolomics with Prostate Cancer Defined by ERG or PTEN Molecular Subtypes.

Feng X, Zhou CK, Clish CB, et al. Association of Prediagnostic Blood Metabolomics with Prostate Cancer Defined by ERG or PTEN Molecular Subtypes. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2021;30(5):1000-1008. doi:10.1158/1055-9965.EPI-20-1363

Improving host-directed therapy for tuberculous meningitis by linking clinical and multi-omics data.

van Crevel R, consortium U. Improving host-directed therapy for tuberculous meningitis by linking clinical and multi-omics data. Tuberculosis (Edinburgh, Scotland). 2021;128:102085. doi:10.1016/j.tube.2021.102085

Glycolysis Metabolites and Risk of Atrial Fibrillation and Heart Failure in the PREDIMED Trial.

Becerra-Tomás N, Ruiz-Canela M, Hernández-Alonso P, et al. Glycolysis Metabolites and Risk of Atrial Fibrillation and Heart Failure in the PREDIMED Trial. Metabolites. 2021;11(5). doi:10.3390/metabo11050306

Circulating amino acids and amino acid-related metabolites and risk of breast cancer among predominantly premenopausal women.

Zeleznik OA, Balasubramanian R, Zhao Y, et al. Circulating amino acids and amino acid-related metabolites and risk of breast cancer among predominantly premenopausal women. NPJ breast cancer. 2021;7(1):54. doi:10.1038/s41523-021-00262-4

Critical assessment of protein intrinsic disorder prediction.

Necci M, Piovesan D, CAID Predictors, DisProt Curators, Tosatto SCE. Critical assessment of protein intrinsic disorder prediction. Nat Methods. 2021;18(5):472-481. doi:10.1038/s41592-021-01117-3

ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.

Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Curr Protoc. 2021;1(5):e89. doi:10.1002/cpz1.89