Author

Masaru Shimasawa

Stanford UniversityORCID 0000-0003-4656-7638Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1

Frequent Co-Authors

Betty B. LiuiD· 1 shared Cecelia J. AndrewsiD· 1 shared Doron LipsoniD· 1 shared Eli J. CostaiD· 1 shared Geovanni L Janer CarattiniiD· 1 shared Lacramioara BintuiD· 1 shared Nicole V. DelRossoiD· 1 shared Nika IremadzeiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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1 shared paperGenomics

Betty B. LiuORCID

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2 papers

Recent·Most cited

Bifunctional transcriptional effector domains control gene expression pulses in an occupancy-dependent manner

Cecelia J. Andrews, Eli J. Costa, Geovanni L Janer Carattini, Nicole V. DelRosso, Taihei Fujimori, Masaru Shimasawa, Lacramioara Bintu

This paper identifies bifunctional transcriptional effector domains that generate gene expression pulses by switching from activation to repression based on DNA occupancy, and develops a kinetic model to program cell states.

bioRxiv · Dec 12, 2025 · PreprintSystems Biology

An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin

Betty B. Liu, Masaru Shimasawa, Sidney Y. Vermeulen, Samuel H. Kim, Nika Iremadze, Doron Lipson, Zohar Shipony, William James Greenleaf

The paper develops RoboATAC, an automated ATAC-seq method, to study how TF dosage affects chromatin accessibility and gene expression, finding that DNA sequence predicts dosage sensitivity and nucleosome positioning patterns vary by TF.

bioRxiv · Jul 24, 2025 · PreprintGenomics