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Publications

A comprehensive list of publications collected from each menu category
Scientific articles
Preprints (biorxiv, arxiv)
Selected posters
Protocols.io articles

Scientific articles

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Integrated intracellular organization and its variations in human iPS cells
Viana MP, Chen J, Knijnenburg TA, Vasan R, Yan C, Arakaki JE, Bailey M, Berry B, Borensztejn A, Brown EM, 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, Ferrante AJ, 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, Oluoch SA, 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, Labitigan RLD, Sanborn AL, Johnson GT, Gunawardane RN, Gaudreault N, Theriot JA, Rafelski SM. Nature, January 4, 2023.
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The dawn of interoperating spatial models in cell biology​
Iwasa JH, Lyons B, Johnson GT. Elsevier, December 2022.
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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.
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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.
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Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging
Goller CC, Johnson GT, Casimo K. CourseSource, 2022.
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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.
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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.
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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
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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
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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)
Horwitz R, Jones A, Daniel T. Science, November 16, 2018. ​
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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. ​
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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. ​
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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. ​
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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. ​
mol._biol._cell-2017-roberts-2854-74.pdf
File Size: 3262 kb
File Type: pdf
Download File

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Whole cell maps chart a course for 21st-century cell biology
Horwitz R, Johnson GT. Science, May 26, 2017. ​
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Cell Biology of the Stem Cell 
Hyman T, Horwitz R. ASCB Newsletter, December 2016. ​
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A Interdisciplinary Team Science in Cell Biology
Horwitz R. Trends in Cell Biology, November 2016. ​
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A Cellular Biophysics
Horwitz R. Biophysical Journal, March 2016. ​
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A Integrated, multi-scale, spatial–temporal cell biology – A next step in the post genomic era
Horwitz R. Methods, March 2016. ​

Preprinted versions

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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
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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.
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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.
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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
Picture
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
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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 .
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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. 
Picture
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. 
Picture
Building a 3D Integrated Cell
Johnson GR, Donovan-Maiye RM, Maleckar MM. BioRxiv, December 2017. 
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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. 
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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
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
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Preprint: Generative Modeling with Conditional Autoencoders: Building an Integrated Cell
Johnson GR, Donavan-Maiye RM, Maleckar MM. arXiv, April 2017. 

Protocols.io

Picture
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. ​
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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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  • About
      Institute
      1. News feed
      2. What we do
      3. Publications
      4. Allen Institute | allenInstitute.org
      5. Careers
      Site
      1. Home page
      2. Site updates
      3. Archived content
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data (images, genomics, features)
  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
  • 🔍
      SEARCHBAR