This paper expands the RatGTEx resource with transcriptome-wide associations across 3,160 RNA-seq samples, identifying 7,473 gene-trait links and 144,876 QTLs for 22,599 genes.

bioRxiv · Nov 6, 2026 · PreprintGenetics

Replication of Host St6galnac1-Microbiome Association Across Distinct Experimental Conditions in Heterogeneous Stock Rats

Mohammad Sadegi, Benjamin B. Johnson, Thiago Missfeldt Sanches, Gavrila Ang, Jennifer Cao, Madison Ambre, Molly Brennan, Olivier George, Rob D. Knight, Amelie Baud, Abraham A. Palmer, Oksana Polesskaya

The paper replicates the association between St6galnac1 and Paraprevotella abundance in stool samples from non-fasted HS rats, confirming the association across different experimental conditions.

bioRxiv · Oct 16, 2026 · PreprintGenomics

Genomic SEM reveals shared genetic architecture and expands locus discovery for locomotor activity in heterogeneous stock rats

Apurva S. Chitre, Thiago Missfeldt Sanches, Gavrila Ang, Nana K. Amissah, Rodolfo Avila, Hannah V. Bimschleger, Paola Campo, Nazzareno Cannella, Denghui Chen, Riyan Cheng, Katarina A Cohen, Ayteria D. Crow, Eric Dereschewitz, Michelle R. Doyle, Maya Eid, , Abraham A. Palmer

The paper uses Genomic SEM to identify loci underlying locomotor activity in rats, finding 31 loci compared to fewer from other methods.

bioRxiv · Oct 6, 2026 · PreprintGenetics

Genome-wide association study in Heterogeneous Stock rats identifies genetic loci associated with aversion-based learning and cocaine aversion

Zachary Tatom, Maya Eid, Thiago Missfeldt Sanches, Apurva S. Chitre, Gavrila Ang, Kendra S Ziegler, Beverly F Peng, Elaine Keung, Khai‐Minh Nguyen, Katarina A Cohen, Yizhi Wang, Riyan Cheng, Denghui Chen, Benjamin B. Johnson, Oksana Polesskaya, , Abraham A. Palmer

bioRxiv · Aug 8, 2026 · PreprintGenetics

Genome-wide association study of cocaine self-administration behavior in Heterogeneous Stock rats

Montana Kay Lara, Lieselot L. G. Carrette, Thiago Missfeldt Sanches, Oksana Polesskaya, Alicia Avelar, Angela Beeson, Hassiba Beldjoud, Brent Boomhower, Molly Brennan, Denghui Chen, Riyan Cheng, Lindsey China, Apurva S. Chitre, Dana Conlisk, McKenzie J. Fannon, , Olivier George

This study performs a GWAS on cocaine self-administration in rats, identifying six genome-wide significant loci, including one linked to carboxylesterase genes involved in cocaine metabolism.

Nature Communications · Jun 11, 2026Peer-reviewedGenetics

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats

Hélène Tonnelé, Denghui Chen, Felipe Morillo, Jorge Garcia-Calleja, Apurva S. Chitre, Benjamin B. Johnson, Thiago Missfeldt Sanches, Riyan Cheng, Marc Jan Bonder, Antonio González, Tomasz Kościółek, Anthony M. George, Wenyan Han, Katie Holl, Aidan P. Horvath, , Amelie Baud

The paper identifies host genetic effects on microbiome composition in rats and finds evidence of indirect genetic effects contributing to missing heritability.

Nature Communications · Dec 18, 2025Peer-reviewedGenetics

Ivermectin Reduces Withdrawal-Induced Alcohol Intake via CeA GABAergic Enhancement

Paola Campo, Ran Qiao, Michelle R. Doyle, Daniel B. Munro, Benjamin B. Johnson, Abraham A. Palmer, Marsida Kallupi, Giordano de Guglielmo

This study shows ivermectin reduces alcohol intake during withdrawal by enhancing GABAergic inhibition in the CeA, specifically in rats with high P2rx4 expression.

bioRxiv · Oct 14, 2025 · PreprintPharmacology & Toxicology

Genome-wide association study reveals multiple loci for nociception and opioid consumption behaviors associated with heroin vulnerability in outbred rats

Brittany N. Kuhn, Nazzareno Cannella, Apurva S. Chitre, Khai‐Minh Nguyen, Katarina A Cohen, Denghui Chen, Beverly F Peng, Kendra S Ziegler, Bonnie Lin, Benjamin B. Johnson, Thiago Missfeldt Sanches, Ayteria D. Crow, Veronica Lunerti, Arkobrato Gupta, Eric Dereschewitz, , Abraham A. Palmer

This study identifies genetic loci associated with opioid use disorder-related behaviors in rats using a genome-wide association approach and network-based clustering.

Molecular Psychiatry · Feb 25, 2025Peer-reviewedGenetics

Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population

Faith Okamoto, Apurva S. Chitre, Thiago Missfeldt Sanches, Denghui Chen, Daniel B. Munro, Allegra T. Aron, Angela Beeson, Hannah V. Bimschleger, Maya Eid, Angel Garcia Martinez, Wenyan Han, Katie Holl, Tyler Jackson, Benjamin B. Johnson, Christopher P. King, , Abraham A. Palmer

The paper genotypes Y and mitochondrial chromosomes in heterogeneous stock rats and finds no significant associations with complex traits, except for gene expression on these chromosomes.

G3 Genes Genomes Genetics · Sep 5, 2024Peer-reviewedBioinformatics

Genome-wide association study of delay discounting in Heterogenous Stock rats

Montana Kay Lara, Apurva S. Chitre, Denghui Chen, Benjamin B. Johnson, Khai‐Minh Nguyen, Katarina A Cohen, Sakina A. Muckadam, Bonnie Lin, Kendra S Ziegler, Angela Beeson, Thiago Missfeldt Sanches, Leah C. Solberg Woods, Oksana Polesskaya, Abraham A. Palmer, Suzanne H. Mitchell

This study identifies genetic loci associated with delay discounting in Heterogenous Stock rats using GWAS, implicating Slc35f1 and Adgrl3 as potential genes involved in this behavior.

bioRxiv · Dec 12, 2023 · PreprintGenomics

RATTACA: Genetic predictions in Heterogeneous Stock rats offer a new tool for genetic correlation and experimental design

Benjamin B. Johnson, Thiago Missfeldt Sanches, Mika Okamoto, Khai‐Minh Nguyen, Clara A. Ortez, Oksana Polesskaya, Abraham A. Palmer

RATTACA uses genotype data from Heterogeneous Stock rats to predict trait values, enabling genetic correlation analysis and experimental design without extensive phenotyping.

bioRxiv · Sep 18, 2023 · PreprintGenomics