Publications

Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics.

Author(s): Reshef YA, Rumker L, Kang JB, Nathan A, Korsunsky I, Asgari S, Murray MB, Moody DB, Raychaudhuri S|Journal: Nat Biotechnol|PMID: 34675423| October 2021

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples…

Modeling memory T cell states at single-cell resolution identifies in vivo state-dependence of eQTLs influencing disease

Author(s): Nathan A, Asgari S, Ishigaki K, Amariuta T, Luo Y, Beynor JI, Baglaenko Y, Suliman S, Price A, Lecca L, Murray MB, Moody DB, Raychaudhuri S|Journal: bioRxiv| July 2021

Many non-coding genetic variants cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated…

Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease.

Author(s): Nathan A, Beynor JI, Baglaenko Y, Suliman S, Ishigaki K, Asgari S, Huang CC, Luo Y, Zhang Z, Lopez K, Lindestam Arlehamn CS, Ernst JD, Jimenez J, Calderón RI, Lecca L, Van Rhijn I, Moody DB, Murray MB, Raychaudhuri S|Journal: Nat Immunol|PMID: 34031617| May 2021

Multimodal T cell profiling can enable more precise characterization of elusive cell states underlying disease. Here, we integrated single-cell RNA…

A sex-specific evolutionary interaction between ADCY9 and CETP

Author(s): Gamache I, Legault MA, Grenier JC, Sanchez R, Rhéaume E, Asgari S, Barhdadi A, Zada YF, Trochet H, Luo Y, Lecca L, Murray M, Raychaudhuri S, Tardif JC, Dubé MP, Hussin JG|Journal: bioRxiv| May 2021

Pharmacogenomic studies have revealed associations between rs1967309 in the adenylyl cyclase type 9 (ADCY9) gene and clinical responses to the…

Axes of inter-sample variability among transcriptional neighborhoods reveal disease associated cell states in single-cell data

Author(s): Reshef YA, Rumker L, Kang JB, Nathan A, Murray MB, Moody DB, Raychaudhuri S|Journal: bioRxiv| April 2021

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples…

A positively selected FBN1 missense variant reduces height in Peruvian individuals.

Author(s): Asgari S, Luo Y, Akbari A, Belbin GM, Li X, Harris DN, Selig M, Bartell E, Calderon R, Slowikowski K, Contreras C, Yataco R, Galea JT, Jimenez J, Coit JM, Farroñay C, Nazarian RM, O'Connor TD, Dietz HC, Hirschhorn JN, Guio H, Lecca L, Kenny EE, Freeman EE, Murray MB, Raychaudhuri S|Journal: Nature|PMID: 32499652| May 2020

On average, Peruvian individuals are among the shortest in the world. Here we show that Native American ancestry is associated…