Publications
A comprehensive list of publications collected from each menu category
Scientific articles
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A Bayesian framework for the detection of diffusive heterogeneity
Cass JA, Williams CD, Theriot J. PLoS One, May 7, 2020. |
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"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. |
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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. |
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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. |
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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. |
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Seeing beyond sight: new computational approaches to understanding cells
Johnson GT, Rafelski S. ASCB Science News, December 20, 2018. |
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Paul G. Allen (1953–2018)
Science, November 16, 2018. Horwitz R, Jones A, Daniel T. |
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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. |
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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. |
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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. |
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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. |
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A Integrated, multi-scale, spatial–temporal cell biology – A next step in the post genomic era
Methods, March 2016. Horwitz R. |
Preprinted versions
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Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable
bioRxiv, December 10, 2020 Viana M, et al |
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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. |
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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 |
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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 |
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Building a 3D Integrated Cell
BioRxiv pre-print, December 2017. Johnson GR, Donovan-Maiye RM, Maleckar MM |
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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. |
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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. |
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Preprint: Generative Modeling with Conditional Autoencoders: Building an Integrated Cell
arXiv pre-print, April 2017. Johnson GR, Donavan-Maiye RM, Maleckar MM. |
Other media about the Allen Institute for Cell Science
To explore a variety of articles, interviews, and videos about the Allen Institute for Cell Science, please visit our general News page at the Allen Institute home site.
Posters
| poster-isscr_tagged-ipsc-open-source-collection_1.pdf |
| poster-isscr_creating-a-cardiomyocyte-pipeline-for_gene-edited-human_1.pdf |