Stefano Davide Vianello, PhD
ORCID iD: 
0000-0002-4152-8990
0000-0002-4152-8990 Postdoctoral researcher, Marine EcoEvoDevo Unit
Current work address: 中央研究院所臨海研究站 (Linhai Marine Research Station, Academia Sinica) Taiwan
I am a postdoctoral researcher working in the Marine Eco-Evo-Devo Unit of Prof. Vincent Laudet at the LinHai Marine Research Station, Academia Sinica, Taiwan. My research focuses on the study of gastrointestinal changes during anemonefish metamorphosis, and on the role of thyroid hormones in this process; with a focus on the evolutionary conservation of gastrointestinal metamorphosis mechanisms across deuterostomes.
I completed my PhD in the Laboratory of Stem Cell Engineering of Prof. Matthias Lütolf at EPFL, Switzerland; in which I described the self-organisation properties of endoderm cells as they develop within stem-cell-based models of early embryonic development (gastruloids). I studied Natural Sciences in Cambridge (Girton College), specialising in Genetics. I then worked in the laboratory of Prof. Alfonso Martinez-Arias, Department of Genetics, to investigate the interactions between chemical signalling pathways involved in early embryonic development (Wnt and Notch signalling integration). I am an advocate for intersectional open science, preprinting, and knowledge equity, and a strong critic of the current politics of publishing in academia. Aside from my lab work, I am interested in data communication and visual storytelling in developmental biology.
Current work address: 中央研究院所臨海研究站 (Linhai Marine Research Station, Academia Sinica) Taiwan
I am a postdoctoral researcher working in the Marine Eco-Evo-Devo Unit of Prof. Vincent Laudet at the LinHai Marine Research Station, Academia Sinica, Taiwan. My research focuses on the study of gastrointestinal changes during anemonefish metamorphosis, and on the role of thyroid hormones in this process; with a focus on the evolutionary conservation of gastrointestinal metamorphosis mechanisms across deuterostomes.
I completed my PhD in the Laboratory of Stem Cell Engineering of Prof. Matthias Lütolf at EPFL, Switzerland; in which I described the self-organisation properties of endoderm cells as they develop within stem-cell-based models of early embryonic development (gastruloids). I studied Natural Sciences in Cambridge (Girton College), specialising in Genetics. I then worked in the laboratory of Prof. Alfonso Martinez-Arias, Department of Genetics, to investigate the interactions between chemical signalling pathways involved in early embryonic development (Wnt and Notch signalling integration). I am an advocate for intersectional open science, preprinting, and knowledge equity, and a strong critic of the current politics of publishing in academia. Aside from my lab work, I am interested in data communication and visual storytelling in developmental biology.
EcoEvoDevo endoderm metamorphosis gut development
Education and Professional Experience
- 2022-present | Marine Research Station, Academia Sinica
Postdoctoral researcher
"Towards an integrated understanding of metamorphosis in bilaterians"
Academia Sinica Grand Challenge Program - 2017-2021 | École polytechnique fédérale de Lausanne (EPFL)
PhD in Biotechnology and Bioengineering, with Teaching Assistantship
Laboratory of Stem Cell Bioengineering, with Prof M. Lütolf
"Endoderm development and morphogenesis in self-organising stem cell-based models of mouse embryogenesis"
“Characterising the mechanical and geometrical inputs of early mammalian development through bioengineered models of patterning and morphogenesis”
Swiss National Science Foundation Synergia Grant - 2016-2017 | Girton College, University of Cambridge
MPhil in Biological Science (Genetics)
“Wnt and Notch (Wntch) interactions in in vitro models of preimplantation embryonic development”, with Prof A. Martinez-Arias - 2013-2016 | Girton College, University of Cambridge
BA Hons Natural Sciences
Publications
- Herrera*, Vianello*, Mitchell, Chamot, Lorin-Nebel, Roux, Besseau, Gibert, Laudet; "From Genes to Pathways: A Curated Gene Approach to Accurate Pathway Reconstruction in Teleost Fish Transcriptomics", 2024 [doi:10.1101/2024.09.23.614382]
- Reynaud*, Vianello*, Lee, Salis, Wu, Frederich, Lecchini, Besseau, Roux, Laudet; "The multi-level effect of chlorpyrifos during clownfish metamorphosis", 2024 [PPR:PPR890713]
- Zwahlen, Gairin, Vianello, Mercader, Roux, Laudet; "The ecological function of thyroid hormones", 2024 [PMID:38310932]
- Roux, Vianello, Laudet; "Physiology of metamorphosis", 2023 [doi:doi.org/10.1016/B978-0-323-90801-6.00134-8]
- Suppinger, Zinner, Aizarani, Lukonin, Ortiz, Azzi, Stadler, Vianello, Palla, Kohler, Mayran, Lutolf, Liberali; "Multimodal characterization of murine gastruloid development", 2023 [PMID:37209681]
- Tischler, Swank, Hsiung, Vianello, Lutolf, Maerkl; "An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates", 2022 [PMID:35880022]
- Vianello, Lutolf; “In vitro endoderm emergence and self-organisation in the absence of extraembryonic tissues and embryonic architecture”, 2021 [PPR:PPR173378]
- Vianello; “Exploring and illustrating the mouse embryo: virtual objects to think and create with”,2020 [PPR:PPR243698]
- Vianello, Lutolf; “Understanding the Mechanobiology of Early Mammalian Development through Bioengineered Models”, 2019 [PMID:30913407]
Publications
Protocols, data, scripts
- Vianello; “Protocol to process Gastruloids for FACS”. 2021 [doi:dx.doi.org/10.17504/protocols.io.bvgrn3v6]
- Vianello, Girgin, Rossi, Lutolf; “Protocol to generate Gastruloids (LSCB, EPFL)”. 2020 [doi:dx.doi.org/10.17504/protocols.io.9j5h4q6]
- Vianello, Girgin, Rossi, Lutolf; “Protocol to immunostain Gastruloids (LSCB, EPFL)”. 2020 [doi:dx.doi.org/10.17504/protocols.io.7tzhnp6]
- Vianello, Girgin, Rossi, Lutolf; “Protocol to culture mESCs (LSCB, UPLUT)”. 2020 [doi:dx.doi.org/10.17504/protocols.io.7xbhpin]
- Vianello; “RNotebook FACS pipeline”. 2021
- Vianello, Sanchez, Bercowsky-Rama, Lutolf; “Gastruloid Intensity Profiler”. 2020
- Vianello; “3D models of mouse embryonic development”. 2020
Publications
Other
PreLights posts
- Vianello; ““English only please!” Real world effects of English-centred literature searches.”. preLights, 2021
- Vianello; “Bitter bites for a chocolate lover. Searching for RNAi targets to fight cocoa crop pests”. preLights, 2021
- Vianello, Sanchez; “Say “Aaaah!”. Foregut development and toothed tongues in the black Katy chiton”. preLights, 2021
- Vianello, Sanchez; “Navigating change: sentinels of the sea tell about ocean health and disease.”. preLights, 2021
- Vianello, Sanchez; “Gastruloids, pescoids, caveoids, surfoids. . . .In vitro embryonic models to study evo-eco-devo. New experimental approaches to cavefish development.”. preLights, 2020
- Vianello, Sanchez; “On the (h)edge: the germline precursors of a basal metazoa are induced at the interface between Hedgehog signalling domains”.preLights, 2020
- Vianello, Sanchez; “(Transiently) Comfortable in its own “skin”: formation of epithelium-like multicellular structures in a unicellular organism through conserved actomyosin-dependent mechanisms”. preLights, 2019
- Vianello, Sanchez; ; “Mind the gap: epiblast geometry at its extraembryonic boundary constrains BMP localization and ensures robust gradient formation”. preLights, 2019
- "No Diamonds for DevBio", August 2023
- “The “pre” in (my) “preprint” is for pre-figurative”. September 2021
- “Preprint highlighting in a haunted house [Part 1]”. August 2021
Posters
- Vianello, Lee, Wu, Roux, Laudet; Institute of Cellular and Organismic Biology (ICOB) departmental poster presentation , "Thyroid hormones trigger the appearance and differentiation of the stomach during the metamorphosis ofthe common clownfish (Amphiprion ocellaris)" | 11.2023 | [doi:doi.org/10.6084/m9.figshare.24457543.v1]
- Jovanic, Godovich, Vianello, Hadjantonakis; International Society for Stem Cell Research (ISSCR) annual meeting , "2D and 3D gastruloid models for investigating mammalian endoderm development" | 06.2023
- Vianello, Lutolf; BIRS-CMO Workshop: "Modelling and engineering the mouse embryo" Oaxaca, MX | Cancelled due pandemic 04.2020
- Vianello, Lutolf; European Summer School on Stem Cells and Regenerative Medicine Hydra, EL , "Studying the mechanobiology of early mammalian development using self-organising embryonic organoids" |09.2019
- Vianello, Lutolf; EMBO Symposium: Mechanical Forces in Development Heidelberg, DE , "Altering geometry and mechanics to coax the development of self-organising embryonic organoids" | 07.2019
- Vianello, Lutolf; EMBO Symposium: Synthetic Morphogenesis Heidelberg, DE , "Altering geometry and mechanics to coax the development of self-organising embryonic organoids" 03.2019
- Vianello; EMBO Workshop: Visualizing Biological Data | 03.2019
Talks
- ITALIAN SOCIETY OF EVOLUTIONARY BIOLOGY (SIBE) Speaker: "Thyroid hormones trigger stomach differentiation during metamorphosis of the common clownfish (Amphiprion ocellaris)", 09.2024
- EuroEvoDevo 2024: Meeting of the European Evolutionary Developmental Biology Society; Accepted speaker for the Fish Satellite Meeting: "Thyroid hormones trigger stomach differentiation during metamorphosis of the common clownfish (Amphiprion ocellaris)", 06.2023 *(could not attend)*
- EcoEvoDevo INTERGROUP SEMINARS (INTERNAL) Speaker: "Gut metamorphosis in the common clownfish Amphiprion ocellaris", 02.2023
- INTERNATIONAL SCIENCE COUNCIL: OPEN SCIENCE SOUTH ASIAN NETWORK CONFERENCE 2022. Invited speaker: "Preprints- A Pathway to Open Access", 09.2022
- eLife Early Career Researcher Wednesday Webinar Series Invited speaker: "Do-it-Yourself strategies to prefigurative publishing", 05.2022
- OASPA Open Access Scholarly Publishing Association Webinar; Invited speaker: "So can publishing respond to a crisis? An evidence-informed approach" 12.2021
- PREPRINTS IN MOTION PODCAST; Invited speaker: "Be the change you want to see: Prefigurative politics in academia" 11.2021
- ASAPbio FELLOWS TRAINING PROGRAMME virtual Invited speaker: "Preprint highlighting in a haunted house: Matthew effect, bias, preprint curation. 2021
- PHYSICS OF LIVING SYSTEMS (INTERNAL) Lausanne, CH "Squeezing, pressing, and bounding Gastruloids: mechanics and symmetry-breaking in vitro. 2019
- EUROTECH SUMMER SCHOOL: OPEN SCIENCE IN PRACTICE Lausanne, CH Invited speaker: "PreLights: a community-driven effort to highlighting preprints". 2019
- EMBO WORKSHOP: IMAGING MOUSE DEVELOPMENT Heidelberg, DE "Elucidating the role of mechanical cues during peri-implantation mouse development". 2019
Community involvement and responsibilities
- 2021: Preprint Curator, Sciety
- 2020-2021: Preprint Curator, The company of biologists
- 2019-2021: PreLights Contributor, The company of biologists
Teaching Training/Experience
- 2021: EPFL ENG-629: LECTURING AND PRESENTING IN ENGINEERING
- 2020: EPFL ENG-624: SCIENCE & ENGINEERING TEACHING AND LEARNING
- 2021: TEACHING ASSISTANT EPFL BIO-378 PHYSIOLOGY LAB 1
- 2018-2021: TEACHING ASSISTANT EPFL BIOENG-110 GENERAL BIOLOGY
- 24,25/10/2019: COURSE INSTRUCTOR CAMBIOSCIENCE PRACTICAL COURSE: DISCOVERING GASTRULOIDS
- 10/2016; 02/2017: DEMONSTRATOR UNIVERSITY OF CAMBRIDGE
Misc
- Languages: Italian (native) French (fluent) English (fluent)
- Affiliations: PSDB (Philippine Society for Developmental Biology) member TSDB (Taiwanese Society of Developmental Biology) member DORA (signatory)
- Hobbies:
- IT skills:
- Programming: R (e.g. Seurat; full scRNAseq and bulkRNAseq analysis, FACS processing) Python/Jupyter notebooks
- Software: MS Office LibreOffice GIMP/Photoshop Inkscape/Adobe Illustrator
- Web Development: PHP HTML SQL CSS
- Virtual Reality: Unity Blender Google cardboard
- familiarity with Unix environment