Author

Ivan E. Ivanov

Chan Zuckerberg Biohub San FranciscoORCID 0000-0001-6389-0213Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Cell Biology· 2 Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Assay:imaging· 3 Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Approach:deep learning· 2 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Chad LiuiD· 4 shared Manuel D. LeonettiiD· 4 shared Shalin B. MehtaiD· 4 shared Carolina AriasiD· 3 shared Eduardo Hirata-MiyasakiiD· 3 shared Soorya PradeepiD· 3 shared Talon ChandleriD· 3 shared Ziwen LiuiD· 3 shared

Activity by Year

2024-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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Curved chords = mutual co-authorship

4 shared papersCell Biology

Chad LiuORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Systems BiologybioRxivPreprintAug 25, 2026

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

Chad Liu, Alexander V. Hillsley, Madhurya Sekhar…·Manuel D. Leonetti

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

2 citations

humanspatial transcriptomics

𝕏 PostBluesky

Cell BiologyCellPeer-reviewedDec 31, 2024

Global organelle profiling reveals subcellular localization and remodeling at proteome scale

Marco Y. Hein, Duo Peng, Verina Todorova…·Manuel D. Leonetti

The paper maps subcellular localization of human proteins and shows proteome remodeling during viral infection by combining organelle immuno-capture with mass spectrometry.

130 citationstop 1%

humanproteomics

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Cell BiologyPNAS NexusPeer-reviewedAug 9, 2024

Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells

Ivan E. Ivanov, Eduardo Hirata-Miyasaki, Talon Chandler…·Shalin B. Mehta

The paper introduces Mantis, a high-throughput 4D microscope, and shrimPy, software for analyzing 4D data, to study cellular dynamics and responses to perturbations like viral infection.

22 citations

imagingmicroscopy & imaging analysis

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BioinformaticsbioRxivPreprintMay 31, 2024

Robust virtual staining of landmark organelles

Ziwen Liu, Eduardo Hirata-Miyasaki, Soorya Pradeep…·Shalin B. Mehta

The paper develops robust virtual staining methods for cellular landmarks using deep learning, showing improved performance across cell types and imaging conditions.

6 citations

humanzebrafish

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