Explanipedia

Powerful and accurate case-control analysis of spatial molecular data Open

Yakir Reshef, Lakshay Sood, Michelle Curtis, Laurie Rumker, Daniel Stein , et al. · 2025

As spatial molecular data grow in scope and resolution, there is a pressing need to identify key spatial structures associated with disease. Current approaches typically make restrictive assumptions such as representing tissue regions by l…

Granzyme K activates the entire complement cascade Open

C. Donado, Erin Theisen, Fan Zhang, Aparna Nathan, Madison L. Fairfield , et al. · 2025

Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis Open

Heather J. Faust, Tan-Yun Cheng, Ilya Korsunsky, Gerald F. Watts, Shani T. Gal-Oz , et al. · 2024

Fibroblasts play critical roles in tissue homeostasis, but in pathologic states they can drive fibrosis, inflammation, and tissue destruction. Little is known about what regulates the homeostatic functions of fibroblasts. Here, we perform …

Identifying genetic variants that influence the abundance of cell states in single-cell data Open

Laurie Rumker, Saori Sakaue, Yakir Reshef, Joyce B. Kang, Seyhan Yazar , et al. · 2024

Publisher Correction: Interferon subverts an AHR–JUN axis to promote CXCL13+ T cells in lupus Open

Calvin Law, Vanessa Sue Wacleche, Ye Cao, Arundhati Pillai, John M. Sowerby , et al. · 2024

Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium Open

Garrett S. Dunlap, Aaron B. Wagner, Nida Meednu, Ruoqiao Huiyi Wang, Fan Zhang , et al. · 2024

Rheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA and repertoire sequencing on paired synovial tissue and blood samples from 12 seropositive RA patients. We identi…

The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis Open

Kathryn Weinand, Saori Sakaue, Aparna Nathan, A. Helena Jonsson, Fan Zhang , et al. · 2024

Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles Open

Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K. Dey, Karthik A. Jagadeesh , et al. · 2024

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution Open

Joyce B. Kang, Amber Shen, Saisriram Gurajala, Aparna Nathan, Laurie Rumker , et al. · 2023

Identifying genetic variants that influence the abundance of cell states in single-cell data Open

Laurie Rumker, Saori Sakaue, Yakir Reshef, Joyce B. Kang, Seyhan Yazar , et al. · 2023

Introductory Paragraph To understand genetic mechanisms driving disease, it is essential but difficult to map how risk alleles affect the composition of cells present in the body. Single-cell profiling quantifies granular information about…

Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis Open

Fan Zhang, A. Helena Jonsson, Aparna Nathan, Kevin Wei, Nghia Millard , et al. · 2022

Summary Rheumatoid arthritis (RA) is a prototypical autoimmune disease that causes destructive tissue inflammation in joints and elsewhere. Clinical challenges in RA include the empirical selection of drugs to treat patients, inadequate re…

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

Yakir Reshef, Laurie Rumker, Joyce B. Kang, Aparna Nathan, Ilya Korsunsky , et al. · 2021

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

Yakir Reshef, Laurie Rumker, Joyce B. Kang, Aparna Nathan, Ilya Korsunsky , et al. · 2021

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples and associate with sample attributes like clinical phenotypes. Current statistical approaches typically map cells to…

Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators Open

Qiuming Yao, Paolo Ferragina, Yakir Reshef, Guillaume Lettre, Daniel E. Bauer , et al. · 2021

Motivation Genome-wide association studies (GWASs) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging. These genetic variants can overlap the binding sites of tran…

Functionally informed fine-mapping and polygenic localization of complex trait heritability Open

Omer Weissbrod, Farhad Hormozdiari, Christian Benner, Ran Cui, Jacob C. Ulirsch , et al. · 2020

Negative short-range genomic autocorrelation of causal effects on human complex traits Open

Armin Schoech, Omer Weissbrod, Luke J. O’Connor, Nick Patterson, Huwenbo Shi , et al. · 2020

Most models of complex trait genetic architecture assume that signed causal effect sizes of each SNP (defined with respect to the minor allele) are uncorrelated with those of nearby SNPs, but it is currently unknown whether this is the cas…

Equitability, Interval Estimation, and Statistical Power Open

Yakir Reshef, David N. Reshef, Pardis C. Sabeti, Michael Mitzenmacher · 2020

For analysis of a high-dimensional dataset, a common approach is to test a null hypothesis of statistical independence on all variable pairs using a non-parametric measure of dependence. However, because this approach attempts to identify …

Functionally-informed fine-mapping and polygenic localization of complex trait heritability Open

Omer Weissbrod, Farhad Hormozdiari, Christian Benner, Ran Cui, Jacob C. Ulirsch , et al. · 2019

Fine-mapping aims to identify causal variants impacting complex traits. Several recent methods improve fine-mapping accuracy by prioritizing variants in enriched functional annotations. However, these methods can only use information at ge…

Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability Open

Bryce van de Geijn, Hilary K. Finucane, Steven Gazal, Farhad Hormozdiari, Tiffany Amariuta , et al. · 2019

Regulatory variation plays a major role in complex disease and that cell type-specific binding of transcription factors (TF) is critical to gene regulation. However, assessing the contribution of genetic variation in TF-binding sites to di…

Interaction Patterns of Men Who Have Sex With Men on a Geosocial Networking Mobile App in Seven United States Metropolitan Areas: Observational Study Open

Nadia N. Abuelezam, Yakir Reshef, David S. Novak, Yonatan H. Grad, George R. Seage , et al. · 2019

Background The structure of the sexual networks and partnership characteristics of young black men who have sex with men (MSM) may be contributing to their high risk of contracting HIV in the United States. Assortative mixing, which refers…

Interaction Patterns of Men Who Have Sex With Men on a Geosocial Networking Mobile App in Seven United States Metropolitan Areas: Observational Study (Preprint) Open

Nadia N. Abuelezam, Yakir Reshef, David S. Novak, Yonatan H. Grad, George R. Seage , et al. · 2019

BACKGROUND The structure of the sexual networks and partnership characteristics of young black men who have sex with men (MSM) may be contributing to their high risk of contracting HIV in the United States. Assortative mixing, which refer…

Annotations capturing cell-type-specific TF binding explain a large fraction of disease heritability Open

Bryce van de Geijn, Hilary K. Finucane, Steven Gazal, Farhad Hormozdiari, Tiffany Amariuta , et al. · 2018

It is widely known that regulatory variation plays a major role in complex disease and that cell-type-specific binding of transcription factors (TF) is critical to gene regulation, but genomic annotations from directly measured TF binding …

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk Open

Yakir Reshef, Hilary K. Finucane, David R. Kelley, Alexander Gusev, Dylan Kotliar , et al. · 2018

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations Open

Po‐Ru Loh, Giulio Genovese, Robert E. Handsaker, Hilary K. Finucane, Yakir Reshef , et al. · 2018

Detecting Meaningful Relationships in Large Data Sets Open

Yakir Reshef · 2018

As data sets grow and algorithms scale, two questions have become central to data-rich science. The first is the exploration question: how can we avoid only testing hypotheses consistent with current models and instead find new, unanticipa…

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights Open

Alexander Gusev, Nicholas Mancuso, Hyejung Won, Maria Kousi, Hilary K. Finucane , et al. · 2018

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types Open

Hilary K. Finucane, Yakir Reshef, Verneri Anttila, Kamil Slowikowski, Alexander Gusev , et al. · 2018

Sequential regulatory activity prediction across chromosomes with convolutional neural networks Open

David R. Kelley, Yakir Reshef, Maxwell L. Bileschi, David Belanger, Cory Y. McLean , et al. · 2018

Models for predicting phenotypic outcomes from genotypes have important applications to understanding genomic function and improving human health. Here, we develop a machine-learning system to predict cell-type–specific epigenetic and tran…

An empirical study of the maximal and total information coefficients and leading measures of dependence Open

David N. Reshef, Yakir Reshef, Pardis C. Sabeti, Michael Mitzenmacher · 2018

In exploratory data analysis, we are often interested in identifying promising pairwise associations for further analysis while filtering out weaker ones. This can be accomplished by computing a measure of dependence on all variable pairs …

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk Open

Yakir Reshef, Hilary K. Finucane, David R. Kelley, Alexander Gusev, Dylan Kotliar , et al. · 2017

Biological interpretation of GWAS data frequently involves analyzing unsigned genomic annotations comprising SNPs involved in a biological process and assessing enrichment for disease signal. However, it is often possible to generate signe…

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