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Articles by Chenchen Pan
Computer Science > Machine Learning
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A deep-learning framework reveals whole-body perturbations at cell level
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Abstract Many diseases, including obesity, have systemic effects that perturb multiple organ systems throughout the body1,2. However, tools for comprehensive, high-resolution analysis of disease-associated changes at the whole-body scale have been lacking. Here we developed MouseMapper, a suite of foundation-model-based deep-learning algorithms enabling multi-system analysis of disease across the entire mouse body.
By Doris Kaltenecker, Izabela Horvath, Rami Al-Maskari, Ying Chen, Zeynep Ilgin Kolabas, Luciano Hoeher, Mihail Ivilinov Todorov, Saketh Kapoor, Louis B Kuemmerle, Hanno Steinke, Mayar Ali, Florian Kofler, Pauline Morigny, Julia Geppert, Denise Jeridi, Bastian Wittmann, Jie Luo, Suprosanna Shit, Melissa Ertürk, Laurent Simons, Chenchen Pan, Marie Piraud, Daniel Rueckert, Maria Rohm, Farida Hellal, Markus Elsner, Harsharan Singh Bhatia, Ingo Bechmann, Bjoern Menze, Stephan Herzig, Johannes Christian Paetzold, Mauricio Berriel Diaz, Ali Erturk, David-Paul Minde, Sena Gül Turhan, Tim Wohlgemuth, Carolina Cigankova, Victor Miro Kolenic, Nilsu Gür, Eren Aydeniz, Alara Yücecan
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Nature
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Bilirubin-Albumin Nanoparticle-Encapsulated Hydrogels for the Treatment of Pelvic Organ Prolapse
Biological and Medical Applications of Materials and InterfacesJanuary 22, 2026 Qiyin Zhu The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China School of Pharmacy, Anhui Medical University, Hefei 230032, China Chenchen Pan School of Pharmacy, Anhui Medical University, Hefei 230032, China Yuerong Ma School of Pharmacy, Anhui Medical University, Hefei 230032, China Xueli Li School of Pharmacy, Anhui Medical University, Hefei 230032, China Huixian Li School of Pharmacy,...
Rapid coating of millimeter‐scale hydrogel capsules with interfacial polymerization
CONFLICT OF INTEREST STATEMENT The authors declare no conflicts of interest. REFERENCES 1, , , , , , , J. Colloid Interface Sci. 2011, 353, 61. 2, , , , Chem. Eng. Sci. 2013, 104, 55. 3, , , , Langmuir 2018, 34, 13534. 4, , , , , , , J. Colloid Interface Sci. 2019, 536, 414. 5, Top. Curr. Chem. 2003, 227, 145. 6, , , , , , J. Colloid Interface Sci. 2019, 541, 407. 7, , , , , , , , Int. J. Pharm. 2012, 427, 417. 8, , , , , , Food Hydrocolloids 2021, 117, 106706. 9, , , , , , , , Polymers 2020, 12, 688. 10, , , , J.
Rapid coating of millimeter‐scale hydrogel capsules with interfacial polymerization
CONFLICT OF INTEREST STATEMENT The authors declare no conflicts of interest. REFERENCES 1, , , , , , , J. Colloid Interface Sci. 2011, 353, 61. 2, , , , Chem. Eng. Sci. 2013, 104, 55. 3, , , , Langmuir 2018, 34, 13534. 4, , , , , , , J. Colloid Interface Sci. 2019, 536, 414. 5, Top. Curr. Chem. 2003, 227, 145. 6, , , , , , J. Colloid Interface Sci. 2019, 541, 407. 7, , , , , , , , Int. J. Pharm. 2012, 427, 417. 8, , , , , , Food Hydrocolloids 2021, 117, 106706. 9, , , , , , , , Polymers 2020, 12, 688. 10, , , , J.
Obesity-associated hyperleptinemia alters the gliovascular interface of the hypothalamus to promote hypertension
Highlights • The hypothalamic gliovascular interface is dynamically remodeled during obesity • Circulating leptin couples hypercaloric states with hypothalamic microangiopathy • Leptin-induced astroglial HIF1α-VEGF drives angiogenesis in the hypothalamus • VEGF in astrocytes promotes the development of arterial hypertension during obesity Summary Pathologies of the micro- and macrovascular systems are a hallmark of the metabolic syndrome, which can lead to chronically elevated blood pressure.
Shrinkage-mediated imaging of entire organs and organisms using uDISCO
Abstract Recent tissue-clearing approaches have become important alternatives to standard histology approaches. However, light scattering in thick tissues and the size restrictions on samples that can be imaged with standard light-sheet microscopy pose limitations for analyzing large samples such as an entire rodent body. We developed 'ultimate DISCO' (uDISCO) clearing to overcome these limitations in volumetric imaging.
Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body
Highlights • DeepMACT is a deep learning-based pipeline for comprehensive analysis of metastases • DeepMACT identifies micrometastases and single cancer cells in full-body 3D scans • DeepMACT reveals the efficacy of antibody-drug targeting in the entire body • DeepMACT indicates that the tumor microenvironment affects drug targeting efficacy Summary Reliable detection of disseminated tumor cells and of the biodistribution of tumor-targeting therapeutic antibodies within the entire body has...
Deep learning reveals cancer metastasis and therapeutic antibody targeting in whole body
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Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull-meninges connections
Abstract Analysis of entire transparent rodent bodies after clearing could provide holistic biological information in health and disease, but reliable imaging and quantification of fluorescent protein signals deep inside the tissues has remained a challenge. Here, we developed vDISCO, a pressure-driven, nanobody-based whole-body immunolabeling technology to enhance the signal of fluorescent proteins by up to two orders of magnitude.
Panoptic vDISCO imaging reveals neuronal connectivity, remote trauma effects and meningeal vessels in intact transparent mice
Panoptic vDISCO imaging reveals neuronal connectivity, remote trauma effects and meningeal vessels in intact transparent mice Ruiyao Cai, Chenchen Pan, Alireza Ghasemigharagoz, Mihail I. Todorov, Benjamin Foerstera, Shan Zhao, Harsharan S. Bhatia, Leander Mrowka, Delphine Theodorou, Markus Rempfler, Anna Xavier, Benjamin T. Kress, Corinne Benakis, Arthur Liesz, Bjoern Menze, Martin Kerschensteiner, Maiken Nedergaard, Ali Erturk bioRxiv 374785; doi: https://doi.org/10.1101/374785
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