Publications Collected

Scientific articles

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.

Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging
Goller CC, Johnson GT, Casimo K. CourseSource, 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.

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
Nelson G, Boehm U, Bagley S, Bajcsy P, Bischof J, Brown CM, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Alexopoulos I, Aumayr K, Avilov S, Bakker GJ, Bammann RR, Bassi A, Beckert H, Beer S, Belyaev Y, Bierwagen J, Birngruber KA, Bosch M, Breitlow J, Cameron LA, Chalfoun J, Chambers JJ, Chen CL, Conde-Sousa E, Corbett AD, Cordelieres FB, Nery ED, Dietzel R, Eismann F, Fazeli E, Felscher A, Fried H, Gaudreault N, Goh WI, Guilbert T, Hadleigh R, Hemmerich P, Holst GA, Itano MS, Jaffe CB, Jambor HK, Jarvis SC, Keppler A, Kirchenbuechler D, Kirchner M, Kobayashi N, Krens G, Kunis S, Lacoste J, Marcello M, Martins GG, Metcalf DJ, Mitchell CA, Moore J, Mueller T, Nelson MS, Ogg S, Onami S, Palmer AL, Paul-Gilloteaux P, Pimentel JA, Plantard L, Podder S, Rexhepaj E, Royon A, Saari MA, Schapman D, Schoonderwoert V, Schroth-Diez B, Schwartz S, Shaw M, Spitaler M, Stoeckl MT, Sudar D, Teillon J, Terjung S, Thuenauer R, Wilms CD, Wright GD, Nitschke R. Journal of Microscopy, Volume 284, Issue 1, July 02, 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.

scRNA-seq dataset

Analysis code on GitHub

GitHub notebook for figures

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.

Imaging dataset

View images on Cell Feature Explorer

Analysis code on GitHub

GitHub notebook for figures

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)
Horwitz R, Jones A, Daniel T. Science, November 16, 2018.

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy
Ounkomol C, Seshamani S, Maleckar MM, Collman F, Johnson GR. Nature Methods, September 7, 2018.

Endogenous Protein Tagging in Human Induced Pluripotent Stem Cells Using CRISPR/Cas9
Haupt A, Grancharova T, Arakaki J, Fuqua MA, Roberts B, Gunawardane RN. Jove, August 25, 2018.

CellProfiler 3.0: Next-generation image processing for biology
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. PLOS | Biology, July 3, 2018.

Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization
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. Molecular Biology of the Cell (MBoC), August 16, 2017.

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Whole cell maps chart a course for 21st-century cell biology
Horwitz R, Johnson GT. Science, May 26, 2017.

Cell Biology of the Stem Cell
Hyman T, Horwitz R. ASCB Newsletter, December 2016.

A Interdisciplinary Team Science in Cell Biology
Horwitz R. Trends in Cell Biology, November 2016.

A Cellular Biophysics
Horwitz R. Biophysical Journal, March 2016.

A Integrated, multi-scale, spatial–temporal cell biology – A next step in the post genomic era
Horwitz R. Methods, March 2016.

Preprinted versions

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.

Full dataset

12X colony overview dataset

Supplementary MYH10 repeat dataset

Demo & tutorials for accessing data

GitHub notebook for figures

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.

Dataset for all analyses

Cell line used in the study: ACTN2-GFP

Analysis code on GitHub

GitHub notebook for figures

The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
Chen J, Ding L, Viana MP, Hendershott MC, Yang R, Mueller IA, Rafelski S. BioRxiv, December 8, 2018 .

Scarless gene tagging of transcriptionally silent genes in hiPSCs to visualize cardiomyocyte sarcomeres in live cells
Roberts B, Arakaki J, Gerbin KA, Malik H, Nelson A, Hendershott MC, Hookway C, Ludmann SA, Mueller IA, Yang R, Rafelski SM, Gunawardane RN. BioRxiv, June 2018.

Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy
Ounkomol C, Seshamani S, Maleckar MM, Collman F, Johnson GR. BioRxiv, May 2018.

Building a 3D Integrated Cell
Johnson GR, Donovan-Maiye RM, Maleckar MM. BioRxiv, December 2017.

Three dimensional cross-modal image inference: label-free methods for subcellular structure prediction
Ounkomol C, Fernandes DA, Seshamani S, Maleckar MM, Collman F, Johnson GR. BioRxiv, November 2017.

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
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. BioRxiv, April 2017

Preprint: Generative Modeling with Conditional Autoencoders: Building an Integrated Cell
Johnson GR, Donavan-Maiye RM, Maleckar MM. arXiv, April 2017.

Protocols.io

Illumination Power and illumination stability
Gaudreault N, Bagley S, Bammann RR, Barachati F, Barna L, Boczonadi V, Boehm U, Bosch M, Brideau C, Carvalho MT, Colarusso P, Cole R, Darwish-Miranda N, Duwé S, Eismann F, Faklaris O, Felscher A, Gonnert M, Grunwald D, Kirchner M, Hoffmann B, Krens G, Laude AJ, LeDue JM, Lorentz P, Mitkovski M, Nelson MS, Schroth-Diez B, Schwartz S, Srinivasan S, Thuenauer R, Wee TL, Oord KVD, Oostende-Triplet CV, Nitschke R, Gelman L. Protocols.io, February 2022.

Maintenance of Undifferentiated hiPSC Cultures and Differentiation to Cardiomyocytes on Glass Surfaces
Nelson A, Dinh SQ, Gerbin K, Hendershott M, Hookway C, Gunawardane RN. Protocols.io, March 2021.

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