The paper identifies microglial states associated with Parkinson's disease genetic risk and Lewy body pathology using single-cell profiling and integrates data with AMP PD.

medRxiv · Oct 28, 2026 · PreprintGenetic & Genomic Medicine

Peripheral Immune Alterations and T Cell Clonal Dynamics Across the Parkinson's Disease Spectrum

Mikaela R. Rosen, J. Oriol Narcis Majos, Daniele Mattei, Elena Mejia, Carlos Perez Mandry, Beomjin Jang, Kailash BP, Tatsuhiko Naito, Amanda Allan, Tarek Khashan, Charlie Argyrou, Mengxi Yang, Deborah Raymond, Casey Young, Kelly Astudillo, , Towfique Raj

This study uses single-cell RNA sequencing and TCR profiling to analyze immune changes in Parkinson's disease across different stages and identifies sex-dependent immune alterations and TCR diversity.

medRxiv · Sep 29, 2026 · PreprintGenetic & Genomic Medicine

SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders

Beomjin Jang, Kailash BP, Alex Tokolyi, Winston H. Dredge, Ashvin Ravi, Sang‐Hyuk Jung, Tatsuhiko Naito, Beomsu Kim, Min Seo Kim, Minyoung Cho, Mi-So Park, Mikaela R. Rosen, Joel Blanchard, Jack Humphrey, David A. Knowles, , Towfique Raj

SingleBrain integrates snRNA-seq and genotype data to map cis-eQTLs across brain cell types, identifying novel disease-associated genes and causal variants.

Nature Genetics · Mar 19, 2026Peer-reviewedGenetic & Genomic Medicine

Meta-analysis of genetic regulation of RNA editing in the human brain identifies new genes underlying neurological disease

Winston H. Dredge, Kailash BP, Aline Réal, Benjamin Z. Muller, Beomjin Jang, Ting Fu, Hyomin Seo, Hong‐Hee Won, Michael S. Breen, Xinshu Grace Xiao, David A. Knowles, Jack Humphrey, Towfique Raj

The paper identifies 38,731 edQTLs in 3,554 genes through a meta-analysis of A-to-I RNA editing in the human brain and links 24 GWAS loci for neurological disorders to edQTLs.

medRxiv · Sep 30, 2025 · PreprintGenetic & Genomic Medicine

Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk

Aline Réal, Kailash BP, Winston H. Dredge, Benjamin Z. Muller, Beomjin Jang, Alex Tokolyi, Hong‐Hee Won, Jack Humphrey, Towfique Raj, David A. Knowles

The paper maps genetic effects on splicing in 10,725 brain samples, identifying 68,358 cis-sQTLs and 97 loci where splicing mediates neurological disease risk.

medRxiv · Sep 25, 2025 · PreprintGenetic & Genomic Medicine

Alzheimer's disease rewires gene coexpression networks coupling different brain regions

Sanga Mitra, Kailash BP, C R Srivatsan, Naga Venkata Saikumar, Philge Philip, Manikandan Narayanan

This study identifies gene coexpression rewiring between brain regions in Alzheimer's disease using differential correlation analysis of RNA-seq data from multiple brain regions.

npj Systems Biology and Applications · May 9, 2024Peer-reviewedSystems Biology

APOE genotype or presence of brain amyloid alters the plasma proteome in cognitively normal, elderly subjects

Sarah M. Philippi, Kailash BP, Towfique Raj, Joseph M. Castellano

The paper examines how APOE genotype and brain amyloid presence affect plasma proteome composition in cognitively normal elderly individuals, identifying associated molecular pathways.

bioRxiv · Dec 28, 2022 · PreprintNeuroscience

ChassiDex: A microbial database useful for synthetic biology applications

Kailash BP, D. Karthik, Mousami Shinde, Nikhita Damaraju, Anantha-Barathi Muthukrishnan, Shashi Bala Prasad, Guhan Jayaraman

ChassiDex provides a database of model organisms for synthetic biology, offering tools to generate codon tables and facilitating host organism switching for researchers.

bioRxiv · Jul 16, 2019 · PreprintSynthetic Biology