Publications
A comprehensive list of publications collected from each menu category
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models
Lyons B, Isaac E, Choi NH, Do TP, Domingus J, Iwasa J, Leonard A, Riel-Mehan M, Rodgers E, Schaefbauer L, Toloudis D, Waltner O, Wilhelm L, Johnson GT. Nature Methods, April 04, 2022. |
A deep generative model of 3D single-cell organization
Donovan-Maiye RM, Brown JM, Chan CK, Ding L, Yan C, Gaudreault N, Theriot JA, Maleckar MM, Knijnenburg TA, Johnson GR. PLOS Computational Biology, January 18, 2022. |
It’s time to incorporate diversity into our basic science and disease models
Horwitz R, Riley EA, Millan MT, Gunawardane RN. Nature Cell Biology, November 29, 2021. |
A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes
Grancharova T, Gerbin KA, Rosenberg AB, Roco CM, Arakaki JE, DeLizo CM, Dinh SQ, Donovan-Maiye RM, Hirano M, Nelson AM, Tang J, Theriot JA, Yan C, Menon V, Palecek SP, Seelig G, Gunawardane RN. Scientific Reports, August 04, 2021. |
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
Gerbin KA, Grancharova T, Donovan-Maiye RM, Hendershott MC, Anderson HG, Brown JM, Chen J, Dinh SQ, Gehring JL, Johnson GR, , Lee H, Nath A, Nelson AM, Sluzewski MF, Viana MP, Yan C, Zaunbrecher RJ, Cordes Metzler KR, Gaudreault N, Knijnenburg T, Rafelski SM, Theriot JA, Gunawardane RN. Cell Systems, June 16, 2021. |
A Bayesian framework for the detection of diffusive heterogeneity
Cass JA, Williams CD, Theriot J. PLoS One, May 7, 2020. |
"Not just a cog": a Q&A on team science in cell biology
Tompa R, Rafelski S, Johnson GT.ASCB Science News, May 7, 2020. |
DLITE Uses Cell-Cell Interface Movement to Better Infer Cell-Cell Tensions
Vasan R, Maleckar MM, Williams CD, Rangamani P. Biophysical Journal, November 5, 2019. |
A virtual laboratory on cell division using a publicly-available image database
Shelden EA, Offerdahl EG, Johnson GT. CourseSource: Evidence-based teaching resources for undergraduate biology education, May 2019. |
Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs
Roberts B, Hendershott MC, Arakaki J, Gerbin KA, Malik H, Nelson A, Gehring J, Hookway C, Ludmann SA, Yang R, Haupt A, Grancharova T, Valencia V, Fuqua MA, Tucker A, Rafelski SM, Gunawardane RN. Stem Cell Reports, May 2019. |
Seeing beyond sight: new computational approaches to understanding cells
Johnson GT, Rafelski S. ASCB Science News, December 20, 2018. |
Paul G. Allen (1953–2018)
Science, November 16, 2018. Horwitz R, Jones A, Daniel T. |
Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy
Nature Methods, September 7, 2018. Ounkomol C, Seshamani S, Maleckar MM, Collman F, Johnson GR. |
Endogenous Protein Tagging in Human Induced Pluripotent Stem Cells Using CRISPR/Cas9
Jove, August 25, 2018 Haupt A, Grancharova T, Arakaki J, Fuqua MA, Roberts B, Gunawardane RN. |
CellProfiler 3.0: Next-generation image processing for biology
PLOS | Biology, July 3, 2018 McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE. |
Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization
Molecular Biology of the Cell (MBoC), August 16, 2017. Roberts B, Haupt A, Tucker A, Grancharova T, Arakaki J, Fuqua MA, Nelson A, Hookway C, Ludmann SA, Mueller IA, Yang R, Horwitz AR, Rafelski SM, Gunawardane RN. ![]()
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Whole cell maps chart a course for 21st-century cell biology
Science, May 26, 2017. Horwitz R, Johnson GT. |
A Integrated, multi-scale, spatial–temporal cell biology – A next step in the post genomic era
Methods, March 2016. Horwitz R. |
A perspective on Microscopy Metadata: data provenance and quality control
Huisman M, Hammer M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Grunwald D, Strambio-De-Castillia C. arXiv, April 26, 2021 |
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Farzam F, Smith C, Grunwald D, Strambio-De-Castillia C. bioRXiv, April 26, 2021. |
Automated hiPSC culture and sample preparation for 3D live cell microscopy
Coston ME, Gregor BW, Arakaki J, Borensztejn A, Do TP, Fuqua MA, Haupt A, Hendershott MC, Leung W, Mueller IA, Nelson AM, Rafelski SM, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Wiegraebe W, Yan C, Gunawardane RN, Gaudreault N. bioRXiv, December 19, 2020. |
Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable
Viana MP, Chen J, Knijnenburg TA, Vasan R, Yan C, Arakaki JE, Bailey M, Berry B, Borensztejn A, Brown JM, Carlson S, Cass JA, Chaudhuri B, Metzler KRC, Coston ME, Crabtree ZJ, Davidson S, DeLizo CM, Dhaka S, Dinh SQ, Do TP, Domingus J, Donovan-Maiye RM, Foster TJ, Frick CL, Fujioka G, Fuqua MA, Gehring JL, Gerbin KA, Grancharova T, Gregor BW, Harrylock L, Haupt A, Hendershott MC, Hookway C, Horwitz AR, Hughes C, Isaac EJ, Johnson GR, Kim B, Leonard AN, Leung W, Lucas JJ, Ludmann SA, Lyons BM, Malik H, McGregor R, Medrash GE, Meharry SL, Mitcham K, Mueller IA, Murphy-Stevens TL, Nath A, Nelson AM, Paleologu L, Popiel TA, Riel-Mehan MM, Roberts B, Schaefbauer LM, Schwarzl M, Sherman J, Slaton S, Sluzewski MF, Smith JE, Sul Y, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Toloudis DT, Tucker AP, Valencia V, Wiegraebe W, Wijeratna T, Yang R, Zaunbrecher RJ, Science AI for C, Johnson GT, Gunawardane RN, Gaudreault N, Theriot JA, Rafelski SM. bioRXiv, December 10, 2020. |
Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
Gerbin KA, Grancharova T, Donovan-Maiye R, Hendershott MC, Brown J, Dinh SQ, Gehring JL, Hirano M, Johnson GR, Nath A, Nelson A, Roco CM, Rosenberg AB, Sluzewski MF, Viana MP, Yan C, Zaunbrecher RJ, Cordes Metzler KR, Menon V, Palecek SP, Seelig G, Gaudreault N, Knijnenburg T, Rafelski SM, Theriot JA, Gunawardane RN. bioRXiv, May 27, 2020. |
The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
bioRxiv, December 8, 2018 Chen J, Ding L, Viana MP, Hendershott MC, Yang R, Mueller IA, Rafelski S |
Scarless gene tagging of transcriptionally silent genes in hiPSCs to visualize cardiomyocyte sarcomeres in live cells
BioRxiv pre-print, June 2018. Roberts B, Arakaki J, Gerbin KA, Malik H, Nelson A, Hendershott MC, Hookway C, Ludmann SA, Mueller IA, Yang R, Rafelski SM, Gunawardane RN |
Building a 3D Integrated Cell
BioRxiv pre-print, December 2017. Johnson GR, Donovan-Maiye RM, Maleckar MM |
Three dimensional cross-modal image inference: label-free methods for subcellular structure prediction
BioRxiv pre-print, November 2017. Ounkomol C, Fernandes DA, Seshamani S, Maleckar MM, Collman F, Johnson GR. |
Final article published in Molecular Biology of the Cell (MBoC) available here.
Preprint: Systematic Gene Tagging using CRISPR/Cas9 in Human Stem Cells to Illuminate Cell Organization BioRxiv pre-print, April 2017. Roberts B, Haupt A, Tucker A, Grancharova T, Arakaki J, Fuqua MA, Nelson A, Hookway C, Ludmann SA, Mueller IA, Yang R, Horwitz AR, Rafelski SM, Gunawardane RN. |
Preprint: Generative Modeling with Conditional Autoencoders: Building an Integrated Cell
arXiv pre-print, April 2017. Johnson GR, Donavan-Maiye RM, Maleckar MM. |
Illumination Power and illumination stability
Protocols.io, February 2022. Nathalie G, Steve B, Rodrigo RB, Fabio B, Laszlo B, Veronika B, Ulrike B, Manel B, Craig B, Mariana TC, Pina C, Richard C, Nasser DM, Sam D, Frank E, Orestis F, Andreas F, Manfred G, David G, Marcel K, Birgit H, Gabriel K, Alex JL, Jeffrey MLD, Pascal L, Miso M, Michael SN, Britta SD, Stanley S, Sathya S, Roland T, Tse-Luen W, Kees VDO, Chloë VOT, Roland N, Laurent G. |
Maintenance of Undifferentiated hiPSC Cultures and Differentiation to Cardiomyocytes on Glass Surfaces
Protocols.io, March 2021. Angelique N, Stephanie QD, Kaytlyn G, Melissa H, Caroline H, Ruwanthi NG. |
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poster-isscr_creating-a-cardiomyocyte-pipeline-for_gene-edited-human_1.pdf | |
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