Publications by authors named "Can Ergen"

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Deep generative modeling of sample-level heterogeneity in single-cell genomics.
Pierre Boyeau, Justin Hong, Adam Gayoso, Martin Kim, José L McFaline-Figueroa, Can Ergen

Nat Methods· November 2025

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High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.
Luke W Koblan, Kathryn E Yost, Pu Zheng, William N Colgan, Matthew G Jones, Can Ergen

Science· October 2025

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Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age.
Steven B Wells, Daniel B Rainbow, Michal Mark, Peter A Szabo, Can Ergen

Nat Immunol· September 2025

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Scvi-hub: an actionable repository for model-driven single-cell analysis.
Can Ergen, Valeh Valiollah Pour Amiri, Martin Kim, Ori Kronfeld, Aaron Streets

Nat Methods· September 2025

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AMICI: Attention Mechanism Interpretation of Cell-cell Interactions.
Justin Hong, Khushi Desai, Tu Duyen Nguyen, Achille Nazaret, Nathan Levy, Can Ergen

bioRxiv· September 2025

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ZEB2 is a master switch controlling the tumor-associated macrophage program.
Fadi Sheban, Truong San Phan, Ken Xie, Florian Ingelfinger, Chamutal Gur, Can Ergen

Cancer Cell· July 2025

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High-resolution spatial mapping of cell state and lineage dynamics with PEtracer.
Luke W Koblan, Kathryn E Yost, Pu Zheng, William N Colgan, Matthew G Jones, Can Ergen

bioRxiv· June 2025

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Consensus prediction of cell type labels in single-cell data with popV.
Can Ergen, Galen Xing, Chenling Xu, Martin Kim, Michael Jayasuriya

Nat Genet· December 2024

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VI-VS: calibrated identification of feature dependencies in single-cell multiomics.
Pierre Boyeau, Stephen Bates, Can Ergen, Michael I Jordan, Nir Yosef

Genome Biol· November 2024

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Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span.
Joshua I Gray, Daniel P Caron, Steven B Wells, Rebecca Guyer, Peter Szabo, Can Ergen

Sci Immunol· June 2024

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Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age.
Steven B Wells, Daniel B Rainbow, Michal Mark, Peter A Szabo, Can Ergen

bioRxiv· January 2024

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Tr1 Cells Emerge and Suppress Effector Th17 Cells in Glomerulonephritis.
Shiwa Soukou-Wargalla, Christoph Kilian, Lis N Velasquez, Andres Machicote, Philine Letz, Can Ergen

J Immunol· December 2023

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Single-cell multiomic analysis of thymocyte development reveals drivers of CD4 T cell and CD8 T cell lineage commitment.
Zoë Steier, Dominik A Aylard, Laura L McIntyre, Isabel Baldwin, Esther Jeong Yoon Kim, Can Ergen

Nat Immunol· September 2023

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DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection.
Fabian Hausmann, Can Ergen, Robin Khatri, Matteo Marouf, Sonja Hänzelmann

Genome Biol· September 2023

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DestVI identifies continuums of cell types in spatial transcriptomics data.
Romain Lopez, Baoguo Li, Hadas Keren-Shaul, Pierre Boyeau, Merav Kedmi, Can Ergen

Nat Biotechnol· September 2022

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Liver fibrosis affects the targeting properties of drug delivery systems to macrophage subsets in vivo.
Can Ergen, Patricia Maria Niemietz, Felix Heymann, Maike Baues, Felix Gremse

Biomaterials· June 2019

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The CCR2 Macrophage Subset Promotes Pathogenic Angiogenesis for Tumor Vascularization in Fibrotic Livers.
Matthias Bartneck, Peter L Schrammen, Diana Möckel, Olivier Govaere, Anke Liepelt, Can Ergen

Cell Mol Gastroenterol Hepatol· May 2019

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Transjugular Intrahepatic Portosystemic Shunt: A Possible Risk Factor for Direct-Acting Antiviral Treatment Failure in Patients With Hepatitis C?
Felix Piecha, Jan-Michael Gänßler, Sabine Jordan, Can Ergen, Harald Ittrich

Hepatol Commun· May 2019

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Molecular and functional heterogeneity of IL-10-producing CD4 T cells.
Leonie Brockmann, Shiwa Soukou, Babett Steglich, Paulo Czarnewski, Lilan Zhao, Can Ergen

Nat Commun· December 2018

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Targeting and Modulation of Liver Myeloid Immune Cells by Hard-Shell Microbubbles.
Klaudia T Warzecha, Matthias Bartneck, Diana Möckel, Lia Appold, Can Ergen

Adv Biosyst· May 2018

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Targeting distinct myeloid cell populations in vivo using polymers, liposomes and microbubbles.
Can Ergen, Felix Heymann, Wa'el Al Rawashdeh, Felix Gremse, Matthias Bartneck

Biomaterials· January 2017

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Chemokine (C-C motif) receptor 2-positive monocytes aggravate the early phase of acetaminophen-induced acute liver injury.
Jana C Mossanen, Oliver Krenkel, Can Ergen, Olivier Govaere, Anke Liepelt

Hepatology· November 2016

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M-CSF and GM-CSF Receptor Signaling Differentially Regulate Monocyte Maturation and Macrophage Polarization in the Tumor Microenvironment.
Eva Van Overmeire, Benoît Stijlemans, Felix Heymann, Jiri Keirsse, Yannick Morias, Can Ergen

Cancer Res· January 2016

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Liver inflammation abrogates immunological tolerance induced by Kupffer cells.
Felix Heymann, Julia Peusquens, Isis Ludwig-Portugall, Marlene Kohlhepp, Can Ergen

Hepatology· July 2015

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Long term intravital multiphoton microscopy imaging of immune cells in healthy and diseased liver using CXCR6.Gfp reporter mice.
Felix Heymann, Patricia M Niemietz, Julia Peusquens, Can Ergen, Marlene Kohlhepp

J Vis Exp· March 2015

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