Reporter cell lines Genome-edited and lentiviral reporter systems make cell cycle, lineage state, and functional activity visible during experiments instead of only at endpoint. Research
Research area · Stem cells and reporters
Instrumented cells
Instrumented cells build the inside-out measurement layer for SPL: engineered hiPSCs, genetic reporters, lineage and cell-cycle sensors, and live-cell assays that make morphogenesis, cell state, and function measurable over time.
Our
Unique vision
This theme contains the work we previously described as stem cells and genome editing: human stem-cell systems, engineered reporter lines, fluorescent sensors, and live assays such as CALIPERS. The point is to make the cell itself an instrumented biological object, so state and function can be read while experiments unfold.
Platforms and capabilities
Cells built to report state
Reporter cell lines Genome-edited and lentiviral reporter systems make cell cycle, lineage state, and functional activity visible during experiments instead of only at endpoint. 
Cardiac and developmental models Human cardiac and early-developmental systems let the lab watch structure, function, and cell state emerge together under controlled conditions. 
Live phenotyping workflows Longitudinal imaging connects perturbations to cell behavior over time, allowing the lab to ask how engineered cells build, repair, or reorganize tissue-like systems. Related publications
Articles and preprints in this area
Including collaborations; listed newest to oldest.
Peer-reviewed article MicroSplit: semantic unmixing of fluorescent microscopy data Ashesh Ashesh, Federico Carrara, Igor Zubarev, Vera Galinova, Melisande Croft, Melissa Pezzotti, Daozheng Gong, Francesca Casagrande, Elisa Colombo, Stefania Giussani, Elena Restelli, Eugenia Cammarota, Juan Manuel Battagliotti, Nikolai Klena, Moises Di Sante, Raghabendra Adhikari, Daniel Feliciano, Gaia Pigino, Elena Taverna, Oliver Harschnitz, Nicola Maghelli, Norbert Scherer, Damian Edward Dalle Nogare, Joran Deschamps, Francesco Pasqualini, Florian Jug Nature Methods · 2026 · DOI 10.1038/s41592-026-03082-1 Pre-print article CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies Moises Di Sante, Melissa Pezzotti, Julius Zimmermann, Alessandro Enrico, Joran Deschamps, Elisa Balmas, Silvia Becca, Alessandro Reali, Alessandro Bertero, Florian Jug, Francesco S. Pasqualini bioRxiv · 2024 · DOI 10.1101/2024.12.19.629259 Peer-reviewed article muSplit: image decomposition for fluorescence microscopy Ashesh, Alexander Krull, Moises Di Sante, Francesco Silvio Pasqualini, Florian Jug IEEE/CVF International Conference on Computer Vision · 2023 · DOI 10.1109/iccv51070.2023.01940 Peer-reviewed article A tissue-engineered scale model of the heart ventricle Luke A MacQueen, Sean P Sheehy, Christophe O Chantre, John F Zimmerman, Francesco S Pasqualini, Xujie Liu, Josue A Goss, Patrick H Campbell, Grant M Gonzalez, Sung-Jin Park, Andrew K Capulli, John P Ferrier, T Fettah Kosar, L Mahadevan, William T Pu, Kevin Kit Parker Nature Biomedical Engineering · 2018 · DOI 10.1038/s41551-018-0271-5 Peer-reviewed article Laminar ventricular myocardium on a microelectrode array-based chip Kujala VJ, Pasqualini FS, Goss JA, Nawroth JC, Parker KK Journal of Materials Chemistry B · 2016 · DOI 10.1039/c6tb00324a Peer-reviewed article Angiotensin II Induced Cardiac Dysfunction on a Chip Horton RE, Yadid M, McCain ML, Sheehy SP, Pasqualini FS, Park SJ, Cho A, Campbell P, Parker KK PLOS ONE · 2016 · DOI 10.1371/journal.pone.0146415 Peer-reviewed article Matrix elasticity regulates the optimal cardiac myocyte shape for contractility McCain ML, Yuan H, Pasqualini FS, Campbell PH, Parker KK American Journal of Physiology-Heart and Circulatory Physiology · 2014 · DOI 10.1152/ajpheart.00799.2013 Review Translational cardiac stem cell therapy: advancing from first-generation to next-generation cell types Cambria E, Pasqualini FS, Wolint P, Gunter J, Steiger J, Bopp A, Hoerstrup SP, Emmert MY npj Regenerative Medicine · 2017 · DOI 10.1038/s41536-017-0024-1 Peer-reviewed article Coupling primary and stem cell-derived cardiomyocytes in an in vitro model of cardiac cell therapy Aratyn-Schaus Y, Pasqualini FS, Yuan H, McCain ML, Ye GJ, Sheehy SP, Campbell PH, Parker KK Journal of Cell Biology · 2016 · DOI 10.1083/jcb.201508026 Peer-reviewed article Structural phenotyping of stem cell-derived cardiomyocytes Francesco Silvio Pasqualini, Sean Paul Sheehy, Ashutosh Agarwal, Yvonne Aratyn-Schaus, Kevin Kit Parker Stem Cell Reports · 2015 · DOI 10.1016/j.stemcr.2015.01.020 Peer-reviewed article Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang DZ, Li K, Wang J, Wanders RJ, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK, Pu WT Nature Medicine · 2014 · DOI 10.1038/nm.3545 Peer-reviewed article Quality metrics for stem cell-derived cardiac myocytes Sheehy SP, Pasqualini F, Grosberg A, Park SJ, Aratyn-Schaus Y, Parker KK Stem Cell Reports · 2014 · DOI 10.1016/j.stemcr.2014.01.015
Tools and resources
Useful links
Addgene pLV-EF1A-FUCCIplex Direct plasmid page for the EF1A FUCCIplex lentiviral construct. Addgene pLV-CMV-FUCCIplex Direct plasmid page for the CMV FUCCIplex lentiviral construct. Addgene pLV-cTnT-FUCCIplex Direct plasmid page for cardiac-lineage FUCCIplex expression. Addgene R26-CAG-BST-FUCCIplex Direct plasmid page for the Rosa26/CAG FUCCIplex knock-in construct.