GEMS associates GWAS variants with cell types using sequence-to-function predictions, revealing cell-type-specific mechanisms for disease risk variants.

bioRxiv · Oct 16, 2026 · PreprintGenetics

Decoding sequence determinants of gene expression in diverse cellular and disease states

Avantika Lal, Alexander Karollus, Laura M. Gunsalus, David Garfield, Surag Nair, Alex M. Tseng, M. Grace Gordon, John Blischak, Bryce Van De Geijn, Tushar Bhangale, Jenna L. Collier, Nathaniel Diamant, Tommaso Biancalani, Héctor Corrada Bravo, Gabriele Scalia, Gökçen Eraslan

The paper introduces Decima, a model that predicts cell type- and condition-specific gene expression from DNA sequence using single-cell RNA sequencing data.

Nature Methods · May 25, 2026Peer-reviewedGenomics

Large-scale Rare Variant Burden Testing in Parkinson's Disease Identifies Novel Associations with Genes Involved in Neuro-inflammation

Mary B. Makarious, Julie Lake, Vanessa Pitz, Allen Ye Fu, Joseph L. Guidubaldi, Caroline Warly Solsberg, Sara Bandrés‐Ciga, Hampton L. Leonard, Jonggeol Jeffrey Kim, Kimberley J. Billingsley, Francis P. Grenn, Pilar Álvarez Jerez, Chelsea X. Alvarado, Hirotaka Iwaki, Michael Ta, , Cornelis Blauwendraat

medRxiv · Nov 8, 2022 · PreprintGenetic & Genomic Medicine

Genome-wide association study and functional validation implicates JADE1 in tauopathy

Kurt W. Farrell, SoongHo Kim, Natalia Han, Megan A. Iida, Elias M. Gonzalez, Marcos Otero‐García, Jamie M. Walker, Timothy E. Richardson, Alan Edward Renton, Shea J. Andrews, Brian Fulton‐Howard, Jack Humphrey, Ricardo A. Vialle, Kathryn R. Bowles, Kátia de Paiva Lopes, , John F. Crary

This study identifies JADE1 as a novel genetic factor in tauopathy through genome-wide association and functional validation in human and Drosophila models.

Acta Neuropathologica · Oct 31, 2021Peer-reviewedNeuroscience

South Asian patient population genetics reveal strong founder effects and high rates of homozygosity - new resources for precision medicine

Jeffrey D. Wall, J. Fah Sathirapongsasuti, Ravi Kr Gupta, Anamitra Barik, Rajesh Kumar, Asif Rasheed, Venkatesan Radha, Saurabh Belsare, Ramesh Menon, Sameer Phalke, Anuradha Mittal, John Z. Fang, Deepak Tanneeru, Manjari Deshmukh, Akshi Bassi, , Andrew S. Peterson

The paper characterizes the genetic structure of South Asian populations, identifies founder effects and high homozygosity, and develops a custom SNP array for genetic studies in the region.

bioRxiv · Oct 2, 2020 · PreprintGenomics

Polygenic Risk for Skin Autoimmunity Impacts Immune Checkpoint Blockade in Bladder Cancer

Zia Khan, Flavia Di Nucci, Antonia Kwan, Christian Hammer, Sanjeev Mariathasan, Vincent Rouilly, Jonathan Carroll, Magnus Fontes, Sergio Ley Acosta, Ellie Guardino, Haiyin Chen‐Harris, Tushar Bhangale, Ira Mellman, Jonathan E. Rosenberg, Thomas B. Powles, , Matthew L. Albert

The paper shows that polygenic risk scores for skin autoimmunity affect the response to immune checkpoint blockade in bladder cancer, with higher vitiligo and psoriasis scores linked to better outcomes.

Proceedings of the National Academy of Sciences · May 19, 2020Peer-reviewedGenetics

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

Chun Ye, Jenny Chen, Alexandra–Chloé Villani, Rachel E. Gate, Meena Subramaniam, Tushar Bhangale, Mark N. Lee, Towfique Raj, Raktima Raychowdhury, Weibo Li, Noga Rogel, Sean Simmons, Selina H. Imboywa, Portia I. Chipendo, Cristin Aubin, , Nir Hacohen

The paper identifies genetic variants influencing isoform usage in the anti-viral response, revealing ERAP2's role in balancing selection and influenza-specific regulation.

Genome Research · Dec 1, 2018Peer-reviewedGenomics

Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer’s disease

Nisha Rathore, Sree Ranjani Ramani, Homer Pantua, Jian Payandeh, Tushar Bhangale, Arthur Wüster, Manav Kapoor, Yonglian Sun, Sharookh B. Kapadia, Lino C. Gonzalez, Ali A. Zarrin, Alison Goate, David Hansen, Timothy W. Behrens, Robert Graham

The paper identifies a PILRA variant that reduces ligand binding and HSV-1 infection, potentially protecting against Alzheimer’s disease.

PLoS Genetics · Nov 2, 2018Peer-reviewedGenetics