The paper develops a platform for storing, visualizing, and analyzing large-scale 3D images in HPC environments using a scalable storage format and web-based annotation tools.

bioRxiv · Oct 4, 2024 · PreprintBioinformatics

Multi-ancestry GWAS deciphers genetic architecture of abdominal aortic aneurysm and highlights PCSK9 as a therapeutic target

Tanmoy Roychowdhury, Derek M. Klarin, Michael G. Levin, Joshua Michael Spin, Yae Hyun Rhee, Alicia C. Deng, Colwyn Ansel Headley, Ida L. Surakka, Noah L. Tsao, Corry Gellatly, Verena Zuber, Fred Y. Shen, Whitney Hornsby, Ina Holst Laursen, Shefali S. Verma, , Scott M. Damrauer

This study identifies 144 genetic loci associated with abdominal aortic aneurysm and highlights PCSK9 as a therapeutic target through Mendelian Randomization and pre-clinical validation.

medRxiv · May 27, 2022 · PreprintGenetic & Genomic Medicine

A Spinal Circuit That Transmits Innocuous Cool Sensations

Lorraine Horwitz, Han Kyu Lee, Chia Chun Hor, Fred Y. Shen, Wei Cai, Chen Li, Emily Ling-Lin Pai, Tin Long Rex Fung, Ilma Rovcanin, Kevin Patrick Pipe, X.Z. Shawn Xu, Dawen Cai, Bo Duan

The paper identifies a spinal circuit that transmits innocuous cool sensations by characterizing a specific population of interneurons.

bioRxiv · Mar 23, 2022 · PreprintNeuroscience

Multi-ancestry meta-analysis identifies 2 novel loci associated with ischemic stroke and reveals heterogeneity of effects between sexes and ancestries

Ida L. Surakka, Kuan-Han Wu, Whitney Hornsby, Brooke N. Wolford, Fred Y. Shen, Wei Zhou, Jennifer E. Huffman, Anita Pandit, Yao Hu, Ben Michael Brumpton, Anne Heidi Skogholt, Maiken Elvestad Gabrielsen, Robin G. Walters, The TOPMed Stroke Working Group, Million Veteran Program (MVP), Kristian Hveem, , Cristen J. Willer

This paper identifies two novel genetic loci associated with ischemic stroke and finds sex and ancestry differences in their effects.

medRxiv · Feb 28, 2022 · PreprintGenetic & Genomic Medicine

Unsupervised Neural Tracing in Densely Labeled Multispectral Brainbow Images

Bin Duan, Logan A. Walker, Douglas H. Roossien, Fred Y. Shen, Dawen Cai, Yan Yan

This paper introduces an unsupervised method for tracing neurons in multispectral Brainbow images, achieving more accurate results than existing methods by reducing segmentation and continuity errors.

IEEE International Symposium on Biomedical Imaging (ISBI) · Apr 13, 2021Peer-reviewedNeuroscience

The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and a multi-informatic analysis paradigm

Sylvia N. Michki, Ye Li, Kayvon Sanjasaz, Yimeng Zhao, Fred Y. Shen, Logan A. Walker, Wenjia Cao, Cheng‐Yu Lee, Dawen Cai

The paper uses targeted scRNA-seq and multi-informatic analysis to characterize neural differentiation in Drosophila brain neuroblast lineages and provides a visualization tool for gene function curation.

Cell Reports · Apr 1, 2021Peer-reviewedNeuroscience

Light microscopy based approach for mapping connectivity with molecular specificity

Fred Y. Shen, Margaret M. Harrington, Logan A. Walker, Hon Pong Jimmy Cheng, Edward S. Boyden, Dawen Cai

The paper introduces a light microscopy method called spectral connectomics to map neural connectivity with molecular specificity by combining genetic labeling and immunostaining.

Nature Communications · Sep 15, 2020Peer-reviewedNeuroscience

Neuronal morphology and projection analysis by multispectral tracing in densely labeled mouse brain

Douglas H. Roossien, Benjamin V. Sadis, Yan Yan, John M. Webb, Lia Y. Min, Aslan S. Dizaji, Luke J. Bogart, Cristina N. Mazuski, Robert S. Huth, Johanna S. Stecher, Sriakhila Akula, Fred Y. Shen, Ye Li, Tingxin Xiao, Madeleine Vandenbrink, , Dawen Cai

The paper develops nTracer, an ImageJ plugin for reconstructing neuronal morphology in densely labeled mouse brains using multispectral tracing.

Bioinformatics · Feb 2, 2019Peer-reviewedNeuroscience