# Bibliography — Felix Y. Zhou

> Sources: Google Scholar (`iRTxWEMAAAAJ`) · OpenAlex (`A5030230235`). Last updated: 2026-08-21.
> Affiliation: Vanderbilt University.
> h-index: 20 · Citations: ~1,827 · Total publications: 46.

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## 2026

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 1 | Modulation of Oncogenic KRAS Signaling by Branched Actin-driven Cell Membrane Protrusions | Gihana GM, Bhatt K, Chang B-J, Murali VS, **Zhou FY**, Noh J, Ravishankar R et al. | *bioRxiv* 2026 [preprint] | — | — |
| 2 | Quantitative multi-scale morphodynamic analysis reveals ratchet-like collective DVE migration and epiblast retrograde cell flow during anterior patterning in the mouse embryo | Stower MJ†, **Zhou FY**†, Valani R, Rozman J, Hathrell H, Godwin J, Lu X et al. | *eLife* [Reviewed Preprint], 2026 | https://doi.org/10.7554/eLife.111884 | — |
| 3 | Unraveling Subcellular Ultrastructure with Cyclically Multiplexed Expansion Microscopy | Gałecki S, Chang B-J, **Zhou FY**, Shen Q, Stoddard D, Chen B, Nicastro D et al. | *bioRxiv* 2026.01.01.697161 [preprint] | — | — |
| 4 | Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue | Wong AYH, Lu YD, Zhao Z, **Zhou F**, Park H, Maliga Z, Anang Y et al. | *bioRxiv* 2026.05.17.725158 [preprint] | — | — |
| 5 | Advanced Tissue Clearing and Axially Swept Light-Sheet Microscopy for High-Resolution Imaging of Neural Systems | Borges HM, Haug J, Lin J, Calvache S, **Zhou FY**, Luo X, Pop IV, Zhong Z et al. | *Light Sheet Microscopy* pp. 23–47, 2026 [book chapter] | — | — |
| 9 | Development of a universal imaging 'phenome' using shape, appearance and motion (SAM) features and the SAM Phenotype Observation Tool (SPOT) | **Zhou FY**, Norton-Steele A, Marsh L, Byrne H, Harrington HA, Lu X | *Nature Communications* 17:8409, 2026 | https://doi.org/10.1038/s41467-026-75505-8 | 1 |
| 10 | Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT) | **Zhou FY**, Jacobs BA, Norton-Steele A, Han X, Zhou L, Carroll TM, Ruiz Puig C, Chadwick J, Qin X, Lisle R, Marsh L, Byrne HM, Harrington HA, Lu X | *Nature Communications* 17:8410, 2026 | https://doi.org/10.1038/s41467-026-75506-7 | 1 |
| 45 | Deciphering the Multiscale Morphology of Somatic Oncogenic Alterations in Hepatocellular Carcinoma | Shen Q, Ngo T, Mazloom-Farsibaf H, Wong K, Li L, Bhatt K, **Zhou FY**, Chang B-J, Wang X, Shang Z, Haug J, Borges HM, Fiolka R, Zhu H, Dean KM | *bioRxiv* 2026 [preprint] | — | — |
| 46 | Learning the Geometry of Data: A Mathematical Review of Shape Space Analysis | Choi GPT†, Dao Duc K†, Faigenbaum-Golovin S†, Habermann K†, Hartman E†, von Tycowicz C†, Zhang C†, Zhao W†, **Zhou F**† | *arXiv* 2606.17022, 2026 [preprint] | https://arxiv.org/abs/2606.17022 | — |

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## 2025

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 6 | Highly multiplexed 3D profiling of cell states and immune niches in human tumors | Yapp C, Nirmal AJ, **Zhou F**, Wong AYH, Tefft JB, Lu YD, Shang Z et al. | *Nature Methods* 22(10):2180–2193, 2025 | — | 54 |
| 7 | Universal consensus 3D segmentation of cells from 2D segmented stacks (u-segment3D) | **Zhou FY**, Marin Z, Yapp C, Zou Q, Nanes BA, Daetwyler S, Jamieson AR et al. | *Nature Methods* 2025 | — | 33 |
| 8 | Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy | Daetwyler S, Mazloom-Farsibaf H, **Zhou FY**, Segal D, Sapoznik E, Chen B et al. | *Nature Methods* 2025 | — | 27 |
| 11 | Calcium signaling is required for anterior patterning in the mouse embryo | Stower MJ, Tyser RCV, Thowfeequ S, **Zhou F**, Portela M, Miti K et al. | *PLOS Biology* 23(10):e3003430, 2025 | — | 1 |
| 12 | Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy | Chen B, Millett-Sikking A, Gałecki S, Daetwyler S, Jiou J, Monistrol J, **Zhou FY** et al. | *bioRxiv* 2025.10.04.680473 [preprint] | — | 1 |
| 13 | Mapping Cell Morphology to a Standard Coordinate System for Analyzing Dynamic Cell Signaling | Yu S, Danuser G, **Zhou FY** | *NeurIPS 2025 Workshop for Imageomics* | — | — |
| 14 | Caveolin-1 regulates context-dependent signaling and survival in Ewing sarcoma | Segal D, Wang X, Mazloom-Farsibaf H, Rajendran D, Butler E, Chen B, **Zhou FY** et al. | *bioRxiv* 2024.09.23.614468 [preprint; under peer review at Review Commons] | — | — |

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## 2024

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 15 | Proteolysis-free amoeboid migration of melanoma cells through crowded environments via bleb-driven worrying | Driscoll MK, Welf ES, Weems A, Sapoznik E, **Zhou F**, Murali VS et al. | *Developmental Cell* 59(18):2414–2428, 2024 | — | 39 |
| 16 | Detecting temporal shape changes with the Euler characteristic transform | Marsh L, **Zhou FY**, Qin X, Lu X, Byrne HM, Harrington HA | *Transactions of Mathematics and Its Applications* 8(2):tnae002, 2024 | — | 23 |
| 17 | An integrated approach identifies the molecular underpinnings of murine anterior visceral endoderm migration | Thowfeequ S, Fiorentino J, Hu D, Solovey M, Ruane S, Whitehead M, **Zhou F** et al. | *Developmental Cell* 59(17):2347–2363, 2024 | — | 18 |
| 18 | Projective light-sheet microscopy with flexible parameter selection | Chen B, Chang B-J, Daetwyler S, **Zhou F**, Sharma S, Lee DM, Nayak A et al. | *Nature Communications* 15(1):2755, 2024 | — | 12 |
| 19 | RhoU forms homo-oligomers to regulate cellular responses | Clayton NS, Hodge RG, Infante E, Alibhai D, **Zhou F**, Ridley AJ | *Journal of Cell Science* 137(2):jcs261645, 2024 | — | 7 |
| 20 | Methods and systems for characterizing morphodynamic profiles of objects | **Zhou FY**, Lu X | *WO Patent* WO2024100225A1, 2024 [patent, pending] | — | — |
| 21 | Anchorage-independent cell proliferation promoted by fascin's F-actin bundling | Isogai T, Murali VS, **Zhou F**, Wang X, Rajendran D, Perez-Castro L et al. | *bioRxiv* 2024.05.04.592404 [preprint] | — | 1 |

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## 2023

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 22 | Blebs promote cell survival by assembling oncogenic signalling hubs | Weems AD, Welf ES, Driscoll MK, **Zhou FY**, Mazloom-Farsibaf H, Chang B-J, Murali VS, Gihana GM et al. | *Nature* 615(7952):517–525, 2023 | 10.1038/s41586-023-05758-6 | 154 |
| 23 | Mesoscopic oblique plane microscopy via light-sheet mirroring | Daetwyler S, Chang B-J, Chen B, Voigt FF, Rajendran D, **Zhou F**, Fiolka R | *Optica* 10(11):1571–1581, 2023 | — | 24 |
| 24 | Surface-guided computing to quantify dynamic interactions between cell morphology and molecular signals in 3D | **Zhou FY**, Wimalasena VK, Zou Q, Weems A, Gihana GM, Jenkins E et al. | *bioRxiv* 2023.04.12.536640 [preprint] | — | 16 |
| 25 | Single-cell phenomics reveals behavioural and mechanical heterogeneities underpinning collective migration during mouse anterior patterning | Stower M†, **Zhou F**†, Hathrell H, Yeung J, Thowfeequ S, Godwin J et al. | *bioRxiv* 2023.03.31.534937 [preprint] | — | 10 |
| 26 | Methods and systems for analyzing time ordered image data | **Zhou F**, Lu X, Ruiz-Puig C, Rittscher J | *US Patent* 11,748,885, 2023 [patent] | — | 9 |
| 27 | Quality assessment in video endoscopy | Rittscher J, Ali S, Bailey A, East JE, Braden B, **Zhou F**, Lu X | *US Patent* 12,249,065, 2025 [patent] (assignee: Oxford University Innovation Ltd) | [Google Patents](https://patents.google.com/patent/US12249065B2/en) | — |

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## 2022

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 28 | Resolution doubling in light-sheet microscopy via oblique plane structured illumination | Chen B, Chang B-J, Roudot P, **Zhou F**, Sapoznik E, Marlar-Pavey M et al. | *Nature Methods* 2022 | — | 87 |
| 29 | Human ZBP1 induces cell death-independent inflammatory signaling via RIPK3 and RIPK1 | Peng R, Wang C-K, Wang-Kan X, Idorn M, Kjær M, **Zhou FY**, Fiil BK et al. | *EMBO Reports* 23(12):e55839, 2022 | — | 91 |
| 30 | Centrioles generate a local pulse of Polo/PLK1 activity to initiate mitotic centrosome assembly | Wong SS, Wilmott ZM, Saurya S, Alvarez-Rodrigo I, **Zhou FY**, Chau KY et al. | *EMBO Journal* 41(11):e110891, 2022 | — | 35 |
| 31 | ASPP2 maintains the integrity of mechanically stressed pseudostratified epithelia during morphogenesis | Royer C, Sandham E, Slee E, Schneider F, Lagerholm CB, Godwin J, **Zhou F** et al. | *Nature Communications* 13(1):941, 2022 | — | 23 |
| 32 | Increasing the field-of-view in oblique plane microscopy via optical tiling | Chen B, Chang B-J, **Zhou FY**, Daetwyler S, Sapoznik E, Nanes BA et al. | *Biomedical Optics Express* 13(11):5616–5627, 2022 | — | 26 |
| 33 | Centriole distal-end proteins CP110 and Cep97 influence centriole cartwheel growth at the proximal end | Aydogan MG, Hankins LE, Steinacker TL, Mofatteh M, Saurya S, **Zhou FY** et al. | *Journal of Cell Science* 135(14):jcs260015, 2022 | — | 17 |
| 34 | Enhanced cholesterol biosynthesis promotes breast cancer metastasis via modulating CCDC25 expression and neutrophil extracellular traps | Tang Q, Liang B, Zhang L, Li X, Li H, Jing W, Jiang Y, **Zhou F** et al. | *Scientific Reports* 12(1):17350, 2022 | — | 38 |
| 35 | Multiscale Pixel Spatiotemporal Information Flows (u-infotrace) | **Zhou FY**, Ravishankar R | *NeurIPS 2022 Workshop on Causality for Dynamical Systems* | — | — |

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## 2021

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 36 | A deep learning framework for quality assessment and restoration in video endoscopy | Ali S, **Zhou F**, Bailey A, Braden B, East JE, Lu X, Rittscher J | *Medical Image Analysis* 68:101900, 2021 | 10.1016/j.media.2020.101900 | 187 |

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## 2020

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 37 | An objective comparison of detection and segmentation algorithms for artefacts in clinical endoscopy | Ali S†, **Zhou F**†, Braden B, Bailey A, Yang S et al. | *Scientific Reports* 10(1):2748, 2020 | — | 152 |
| 38 | Visualization of T cell migration in the spleen reveals a network of perivascular pathways that guide entry into T zones | Chauveau A, Pirgova G, Cheng HW, De Martin A, **Zhou FY**, Wideman S et al. | *Immunity* 52(5):794–807, 2020 | — | 82 |
| 39 | An autonomous oscillation times and executes centriole biogenesis | Aydogan MG, Steinacker TL, Mofatteh M, Wilmott ZM, **Zhou FY** et al. | *Cell* 181(7):1566–1581, 2020 | — | 56 |

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## 2019

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 40 | Diverse and robust molecular algorithms using reprogrammable DNA self-assembly | Woods D, Doty D, Myhrvold C, Hui J, **Zhou F**, Yin P, Winfree E | *Nature* 567(7748):366, 2019 | 10.1038/s41586-019-1014-9 | 365 |
| 41 | Motion sensing superpixels (MOSES) — a systematic computational framework to quantify and discover cellular motion phenotypes | **Zhou FY**, Ruiz-Puig C, Owen RP, White MJ, Rittscher J, Lu X | *eLife* 8:e40162, 2019 | — | 24 |
| 42 | Endoscopy artifact detection (EAD 2019) challenge dataset | Ali S, **Zhou F**, Daul C, Braden B, Bailey A, Realdon S, East J et al. | *arXiv*:1905.03209, 2019 [preprint] | — | 112 |
| 43 | Characterization of Biological Motion Using Motion Sensing Superpixels | **Zhou FY**, Ruiz-Puig C, Owen RP, White MJ, Rittscher J, Lu X | *Bio-protocol* 9(18):e3365, 2019 | — | 4 |

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## 2018

| # | Title | Authors | Venue | DOI / URL | Citations |
|---|-------|---------|-------|-----------|-----------|
| 44 | Cell autonomous role of iASPP deficiency in causing cardiocutaneous disorders | Dedeić Z, Sutendra G, Hu Y, Chung K, Slee EA, White MJ, **Zhou FY** et al. | *Cell Death & Differentiation* 25(7):1289, 2018 | — | 21 |

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*Bold = Felix Y. Zhou. [preprint] = not yet peer reviewed. [patent] = patent filing. [patent, pending] = application filed, not yet granted.*

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## Excluded

The following entries were reviewed and removed. Do not re-add.

| Reason | Title | Venue |
|--------|-------|-------|
| Conference abstract only | Abstract A030: Branched Actin-driven Cell Membrane Protrusions Regulate Oncogenic KRAS Molecular Signaling | *Cancer Research* 86(5_Suppl):A030, 2026 |
| Book chapter; primary content covered by Yapp et al. Nature Methods 2025 (entry #6) | 3D Tissue Cyclic Immunofluorescence (3D CyCIF) | Book chapter, 2025 |