arushiv

2015–2025

Publications

Pancreatic islets, skeletal muscle, and what sits underneath a GWAS signal once you look at one nucleus at a time.

Thesis

  1. 2019

    Understanding the Genetics of Gene Regulation Using Multi-Omics Profiling

    PhD Thesis, University of Michigan

Preprints under review

  1. 2025

    Combining functional annotation and multi-trait fine-mapping methods improves fine-mapping resolution at glycaemic trait loci

    Soenksen J, Chen J, Varshney A, et al. · BioRxiv

  2. 2023

    Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

    Varshney A, Manickam N, Orchard P, Tovar A, et al. · BioRxiv · First author

  3. 2023

    Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes

    Tovar A, Kyono Y, Nishino K, Bose M, et al. · BioRxiv

  4. 2023

    Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk

    Albanus RDO, Tang X, Taylor HJ, et al. · BioRxiv

  5. 2023

    An integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D associated genes and regulatory signals

    Zhao Z, Albanus RDO, Taylor H, et al. · Research Square

Peer-reviewed journal

  1. 2025

    Extensive differential gene expression and regulation by sex in human skeletal muscle

    Hanks SC, Mauger AS, Varshney A, et al. · Cell Genomics

  2. 2025

    Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

    Currin KW, Perrin HJ, Pandey GK, et al. · Genome Research

  3. 2024

    SMIM1 absence is associated with reduced energy expenditure and excess weight

    Stefanucci L, Moslemi C, Tomé AR, et al. · Med

  4. 2023

    Genetic risk converges on regulatory networks mediating early type 2 diabetes

    Walker J, Saunders D, Rai V, et al. · Nature

  5. 2023

    Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis

    Tenney AP, Di Gioia SA, Webb BD, et al. · Nature Genetics

  6. 2023

    Loci for insulin processing and secretion provide insight into type 2 diabetes risk

    Broadaway KA, Yin X, Williamson A, et al. · American Journal of Human Genetics

  7. 2023

    Genome-wide association analysis identifies ancestry-specific genetic variation associated with acute response to metformin and glipizide in SUGAR-MGH

    Li JH, Brenner LN, Kaur V, et al. · Diabetologia

  8. 2022

    Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program

    DiCorpo D, Gaynor SM, Russell EM, et al. · Communications Biology

  9. 2021

    Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

    Orchard P, Manickam N, Ventresca C, Varshney A, et al. · Genome Research

  10. 2021

    A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

    Varshney A, Kyono Y, Venkateswaran E, et al. · Diabetes · First author

  11. 2021

    The Trans-Ancestral Genomic Architecture of Glycaemic Traits

    Chen J, Spracklen CN, Marenne G, Varshney A, et al. · Nature Genetics · Co-first author

  12. 2021

    Chromatin information content landscapes inform transcription factor and DNA interactions

    Albanus RDO, Kyono Y, Hensley J, Varshney A, et al. · Nature Communications

  13. 2020

    Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

    Viñuela A, Varshney A, van de Bunt M, et al. · Nature Communications · Co-first author

  14. 2019

    Cell specificity of human regulatory annotations and their genetic effects on gene expression

    Varshney A, VanRenterghem H, Orchard P, et al. · Genetics · First author

  15. 2019

    Multiomic profiling identifies cis-regulatory networks underlying human pancreatic beta cell identity and function

    Lawlor N, Marquez E, Orchard P, et al. · Cell Reports

  16. 2018

    BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues

    Zou LS, Erdos MR, Taylor DL, et al. · BMC Genomics

  17. 2018

    Interactions between genetic variation and cellular environment in skeletal muscle gene expression

    Taylor DL, Knowles DA, Scott LJ, et al. · PLoS One

  18. 2017

    Strategies to develop endogenous stem cell-recruiting bioactive materials for tissue repair and regeneration

    Pacelli S, Basu S, Whitlow J, et al. · Advanced Drug Delivery Reviews

  19. 2017

    A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the ADCY5 Locus

    Roman TS, Cannon ME, Vadlamudi S, et al. · Diabetes

  20. 2017

    Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

    Varshney A, Scott LJ, Welch RP, Erdos MR, et al. · PNAS · Co-first author

  21. 2015

    Super Enhancers in Cancers, Complex Disease, and Developmental Disorders

    Niederriter AR, Varshney A, Parker SCJ, Martin DM · Genes

Selected talks

  1. 2021

    Context-specific genetic regulation of skeletal muscle biology

    The Biology of Genomes, American Diabetes Association and American Society of Human Genetics meetings

  2. 2020

    Single nuclei resolution chromatin and gene expression profiling in skeletal muscle across 287 genotyped individuals reveals cell-specific genetic regulatory architectures

    American Society for Human Genetics (ASHG) Meeting

  3. 2016

    Epigenetic profiling at high resolution reveals genetic regulatory signatures underlying islet gene expression and type 2 diabetes

    American Society for Human Genetics (ASHG) Meeting