Projects and Publications
Throughout his career, Jason Otterstrom has contributed to numerous cutting-edge research projects and published extensively in leading scientific journals. Below is a curated selection of his most impactful work.
Highlighted Projects
| Year | |
|---|---|
| AI-based Image Analysis of Zebrafish Summary Clients using zebrafish models with automated microscopes required a reliable method for image analysis. Jason collaborated with clients and IDEA Bio-Medical’s R&D team to develop AI-based deep-learning models for this purpose. He was instrumental in quality assurance, proof-of-concept testing, and the successful product release. Outcome • Contributed to development of an AI-powered zebrafish software product (view). • Co-authored a publication with the client showcasing the software’s application (view). • Invited to write a review article on automated microscopy for zebrafish screening (view). | 2021 |
| CellViewer Summary As part of this EU-funded H2020-FET-OPEN project, Jason contributed to the development of an automated super-resolution microscope to visualize DNA, RNA, and proteins in live cells. He worked on multi-color imaging techniques, image analysis pipelines, and contributed to predictive models for stem cell differentiation. Jason also served as the key interface between his lab and IDEA Bio-Medical, providing critical input on microscopy methods. View project description here. Outcome • Co-Authored publication with PhD students Álvaro Castells-García (view) and Pablo Gómez-García (view), whom he mentored during the project. • Contributed to new IP at IDEA Bio-Medical, enabling automated immersion oil dispensing for inverted fluorescence microscopy. | 2016 |
| Marie Curie Fellowship Summary Jason earned a prestigious H2020-IF-Marie Curie postdoc fellowship, scoring 98/100 on his proposal, along with the ICFONest+ fellowship. His project aimed to create a 3D visualization of chromatin—DNA and histone proteins—at the nanoscale using localization-based super-resolution microscopy. View project description here. Outcome • Published a first-author paper cited over 100 times, demonstrating chromatin structure nanoscale imaging (view). • Developed a method combining two super-resolution microscopy techniques for multi-color imaging of histones and DNA. | 2015 |
| Neutralizing Antibodies for Influenza Virus – Academia-Industry Partnership Summary In collaboration with Crucell BV (Johnson & Johnson), Jason led efforts to visualize individual influenza virus particles during the membrane fusion stage of infection. His work demonstrated virus neutralization, revealing the mechanism of action for the special neutralizing antibodies provided by Crucell. Outcome • Co-authored publication cited over 200 times, mapping influenza vulnerabilities for neutralizing antibody design (view). • Published a first-author paper demonstrating the stoichiometry of virus neutralization by antibodies (view). | 2013 |
Scientific Publications
View publication list:
• Orcid ID: 0000-0002-0176-9976
• Google Schlolar Profile
| Topic | Citation | Year |
|---|---|---|
| Zebrafish | A high-throughput zebrafish screen identifies novel candidate treatments for Kaposiform Lymphangiomatosis (KLA) I Bassi, A Jabali, N Farag, S Egozi et al. bioRxiv, 2024.03. 21.586124 | 2024 |
| Zebrafish | Technologies bringing young Zebrafish from a niche field to the limelight J Otterstrom, A Lubin, EM Payne, Y Paran SLAS technology 27 (2), 109-120 | 2022 |
| Super-Resolution Microscopy | Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches A Castells-Garcia, I Ed-daoui, E González-Almela, C Vicario, et al. Nucleic Acids Research 50 (1), 175–190 | 2022 |
| Zebrafish | A versatile, automated and high-throughput drug screening platform for zebrafish embryos A Lubin, J Otterstrom, Y Hoade, I Bjedov et al. Biology Open 10 (9), bio058513 | 2021 |
| Super-Resolution Microscopy | Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo J Otterstrom, A Castells-Garcia, C Vicario, PA Gomez-Garcia, et al. Nucleic Acids Research 47 (16), 8470-8484 | 2019 |
| Fluorescence Microscopy | Using enhanced number and brightness to measure protein oligomerization dynamics in live cells F Cutrale, D Rodriguez, V Hortigüela, CL Chiu, et al. Nature Protocols 14 (2), 616-638 | 2019 |
| Super-Resolution Microscopy | Excitation-multiplexed multicolor superresolution imaging with fm-STORM and fm-DNA-PAINT PA Gómez-García, ET Garbacik, J Otterstrom, MF Garcia-Parajo, … Proceedings of the National Academy of Sciences 115 (51), 12991-12996 | 2018 |
| Fluorescence Microscopy | Eph-ephrin signaling modulated by polymerization and condensation of receptors S Ojosnegros, F Cutrale, D Daniel Rodríguez, J Otterstrom, et al. Proceedings of the National Academy of Sciences 114 (50), 13188-13193 | 2017 |
| Super-Resolution Microscopy | 3D motion of vesicles along microtubules helps them to circumvent obstacles in cells I Verdeny-Vilanova, F Wehnekamp, N Mohan, Á Sandoval-Álvarez, et al. Journal of Cell Science 130 (11), 1904-1916 | 2017 |
| Influenza Virus & Microscopy | Relating influenza virus membrane fusion kinetics to stoichiometry of neutralizing antibodies at the single-particle level J Otterstrom, B Brandenburg, MH Koldijk, J Juraszek, et al. Proceedings of the National Academy of Sciences 111 (48), E5143-E5148 | 2014 |
| Influenza Virus & Microscopy | Visualizing Influenza Virus Membrane Fusion: Inhibition and Kinetics J Otterstrom PhD Thesis | 2014 |
| Influenza Virus & Microscopy | Mechanisms of hemagglutinin targeted influenza virus neutralization B Brandenburg, W Koudstaal, J Goudsmit, V Klaren, et al. PloS one 8 (12), e80034 | 2013 |
| Influenza Virus & Microscopy | Visualization of membrane fusion, one particle at a time J Otterstrom, AM van Oijen Biochemistry 52 (10), 1654-1668 | 2013 |
| Chromatin & Microscopy | Nudging Through a Nucleosome J Otterstrom, AM va Oijen Science 325 (5940), 547-548 | 2009 |
| Comparative Physiology | The face that sank the Essex: potential function of the spermaceti organ in aggression DR Carrier, SM Deban, J Otterstrom Journal of Experimental Biology 205 (12), 1755-1763 | 2002 |
Scientific Expertise
Automated Microscopy
Jason is an expert in the market-space of cutting-edge, automated microscopes aimed at enhancing precision and efficiency in cellular analysis. These innovations streamline laboratory research by enabling real-time, high-resolution imaging, critical for studying intricate cellular processes..
Automated Cell Analysis
As a scientist, Jason has developed novel techniques for automated cell analysis, offering precise, detailed insights into cellular behavior, utilizing advanced image processing algorithms, including machine learning.
Biophotonics Research
Jason investigated light’s interaction with biological systems, unlocking new opportunities in biomedical research. His work has contributed to innovations in biophotonics, particularly through advanced fluorescence and optical imaging techniques that enable nanoscale visualization of biological processes..
Affiliations
ICFO – The Photonic Sciences Institute
As a Marie Curie postdoctoral researcher at ICFO, Jason made significant contributions to biophotonics and cellular analysis over four years. He designed and managed a 3D multi-color super-resolution fluorescence microscope, co-authored five scientific articles, and mentored two PhD students. Jason also led collaborations between his lab and a partner lab, identified critical knowledge gaps to develop novel data analysis algorithms, and successfully managed project milestones and deliverables throughout the research process.
Rijksuniversiteit Groningen
During his PhD, Jason spent three years as a visiting scholar at the Zernike Institute, collaborating with Prof. Antoine van Oijen in transitioning his lab from Harvard. He managed an academia-industry partnership with Crucell BV, applying innovative single-virus visualization techniques to uncover the mechanism of action for neutralizing antibodies. Jason co-authored four scientific papers during this period and mentored several students, contributing significantly to both research output and academic growth.
Harvard Medical School
Jason earned his PhD from the Biophysics program at Harvard Medical School, focusing on single-molecule biophysics under Prof. Antoine van Oijen. His research advanced a project enabling the in vitro visualization of individual influenza virus particles during membrane fusion, the first step of viral infection. Jason constructed and managed a fluorescence microscope for single-molecule detection, designed fully automated MATLAB-based data analysis programs, and trained users to optimize the system’s performance.
Contact for Collaborations
If you are interested in collaborating with Jason Otterstrom or would like to learn more about his projects and publications, feel free to reach out via the contact form on this website.