Author

Karl Mader

University of California, San Francisco

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:deep learning· 2 Research Focus:drug response / drug discovery· 2 Research Focus:gene regulatory network inference· 2 Assay:scATAC-seq· 2 Research Focus:cell type annotation· 1 Approach:contrastive learning· 1 Assay:CRISPR screen· 1

Frequent Co-Authors

Laralynne PrzybylaiD· 3 shared Shawn Shafer· 3 shared Kaivalya ShevadeiD· 2 shared Scot FedermaniD· 2 shared Volkan Sevi̇miD· 2 shared Adam Litterman· 1 shared Adam YalaiD· 1 shared Alexander R. GuptaiD· 1 shared

Activity by Year

2024-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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3 shared papersBioinformatics

Laralynne PrzybylaORCID

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Author profile →

3 papers

Recent·Most cited

Network-aware self-supervised learning enables high-content phenotypic screening for genetic modifiers of neuronal activity dynamics

Parker Grosjean, Kaivalya Shevade, Cuong Nguyen, Sarah Ancheta, Karl Mader, Ivan Franco, Seok-Jin Heo, Greyson R. Lewis, Dehua Zhao, Bhairavi Tolani, Steven Boggess, Angelique Di Domenico, Erik M. Ullian, Shawn Shafer, Adam Litterman, , Martin Kampmann

The paper introduces Plexus, a self-supervised model for capturing neuronal activity dynamics, and demonstrates its effectiveness in identifying genetic modifiers of neuronal activity in frontotemporal dementia.

Nature Machine Intelligence · Dec 17, 2025Peer-reviewedBioinformatics

Simultaneous single-cell CRISPR, RNA, and ATAC-seq enables multiomic CRISPR screens to identify gene regulatory relationships

Kaivalya Shevade, Yeqing Angela Yang, Kevin Feng, Karl Mader, Volkan Sevi̇m, Jacob Parsons, Gunisha Arora, Hasnaa A. Elfawy, Rachel Mace, Scot Federman, Rustam Esanov, Shawn Shafer, Eric D. Chow, Laralynne Przybyla

The paper introduces CAT-ATAC, a method combining CRISPR, RNA, and ATAC-seq in single cells to identify gene regulatory relationships and validate them with loss-of-function experiments.

bioRxiv · Feb 11, 2025 · PreprintGenomics

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

Gabriel B. Loeb, Pooja Kathail, Richard W. Shuai, Ryan Chung, Reinier J. Grona, Sailaja Peddada, Volkan Sevi̇m, Scot Federman, Karl Mader, Audrey Y. Chu, Jonathan Davitte, Juan Du, Alexander R. Gupta, Chun Ye, Shawn Shafer, , Jeremy F. Reiter

This paper identifies genetic variants in tubule epithelial regulatory elements that explain most heritable differences in human kidney function using GWAS, scATAC-seq, and functional assays.

Nature Genetics · Sep 10, 2024Peer-reviewedGenetics