2022
Cancer Relevance of Human Genes
Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal Of The National Cancer Institute 2022, 114: 988-995. PMID: 35417011, PMCID: PMC9275765, DOI: 10.1093/jnci/djac068.Peer-Reviewed Original ResearchConceptsCore cancer genesHuman genesFunctional importanceSomatic mutation frequencySelection pressureGene/protein networksCancer genesHigher somatic mutation frequencyNegative selection pressureGene-gene interaction networksMutation frequencyProtein-truncating variantsGenomic contextCell viabilityGenes decreasesCancer Genome AtlasInteraction networksProtein networkCancer relevanceCancer cell viabilityCell survivalGenesCancer biologyGenome AtlasSearch tools
2019
GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner
Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. PLOS Genetics 2019, 15: e1007860. PMID: 31469829, PMCID: PMC6742416, DOI: 10.1371/journal.pgen.1007860.Peer-Reviewed Original ResearchConceptsNon-coding variantsTranscription factorsLarge linkage disequilibrium blocksCell type-specific mannerPhenotype of interestMolecular effectsFine-mapping causal variantsCell-specific mannerParticular cell typeLinkage disequilibrium blockEvolutionary conservationTF bindingChIP-seqRegulatory networksPerformance of GRAMCausal variantsReporter geneGene expressionExpression profilesGenomic variantsAssociated geneLuciferase assayCell typesK562 cell lineSpecific mannerGenomics and data science: an application within an umbrella
Navarro FCP, Mohsen H, Yan C, Li S, Gu M, Meyerson W, Gerstein M. Genomics and data science: an application within an umbrella. Genome Biology 2019, 20: 109. PMID: 31142351, PMCID: PMC6540394, DOI: 10.1186/s13059-019-1724-1.Peer-Reviewed Original ResearchData ScienceGenomics