Allen Cell Explorer
  • About
    • What We Do
    • FAQs
    • Videos & Tutorials
    • Site Updates
    • < Forum >
    • < AllenInstitute.org >
  • Animated Cell
    • Educational Resources
    • Visual Guide to Human Cells
    • Visual Guide Tutorial
    • Research Projects >
      • Pathtrace rendering
  • Cells & Biology
    • Cell Catalog
    • About our Cells >
      • hiPS Cell Biology Overview
      • Cell Structure Observations
      • Cell Catalog QuickView
    • Genomics
    • Methods & SOPs >
      • Methods for Cells in the Lab
      • Cell Methods: Videos from the Lab
      • Methods for Microscopy
    • Research Projects >
      • hiPS Cells During Mitosis
      • Drug Perturbation Pilot
      • Differentiation Into Cardiomyocytes
      • Why Endogenous Tagging?
  • Data & Tools
    • Cell Catalog
    • 3D Cell Viewer
    • Cell Feature Explorer
    • Deep Cell Zoom
    • Segmenter
    • Data Downloading
    • Software & Code
    • Research Projects >
      • Extracting Information
  • Modeling & Analysis
    • Integrated Mitotic Stem Cell
    • Allen Integrated Cell
    • Label-free Determination
    • Data Notebook Exploration >
      • Cell Shape Analysis
      • Programmatic Data Access
    • Research Projects >
      • 3D Probabilistic Modeling
  • News & Publications
    • News Feed
    • Publications
    • Archived Content

Publications

A comprehensive list of publications collected from each menu category
Scientific articles
Preprinted versions
Other media
Posters

Scientific articles

Picture
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.
Picture
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.
Picture
Seeing beyond sight: new computational approaches to understanding cells
ASCB Newsletter, December 20, 2018. Johnson GT, Rafelski S.
Picture
Paul G. Allen (1953–2018)
Science, November 16, 2018. Horwitz R, Jones A, Daniel T.
Picture
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.
Picture
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.
Picture
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.
Picture
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.
mol._biol._cell-2017-roberts-2854-74.pdf
File Size: 3262 kb
File Type: pdf
Download File

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

Preprinted versions

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

Picture
poster-isscr_tagged-ipsc-open-source-collection_1.pdf
File Size: 2377 kb
File Type: pdf
Download File

Picture
poster-isscr_creating-a-cardiomyocyte-pipeline-for_gene-edited-human_1.pdf
File Size: 1985 kb
File Type: pdf
Download File

Home

Terms of Use

Citation Policy

Privacy Policy

FAQs

Help

Send us a message

Copyright © 2019 Allen Institute. All Rights Reserved.
cellscience.alleninstitute.org
  • About
    • What We Do
    • FAQs
    • Videos & Tutorials
    • Site Updates
    • < Forum >
    • < AllenInstitute.org >
  • Animated Cell
    • Educational Resources
    • Visual Guide to Human Cells
    • Visual Guide Tutorial
    • Research Projects >
      • Pathtrace rendering
  • Cells & Biology
    • Cell Catalog
    • About our Cells >
      • hiPS Cell Biology Overview
      • Cell Structure Observations
      • Cell Catalog QuickView
    • Genomics
    • Methods & SOPs >
      • Methods for Cells in the Lab
      • Cell Methods: Videos from the Lab
      • Methods for Microscopy
    • Research Projects >
      • hiPS Cells During Mitosis
      • Drug Perturbation Pilot
      • Differentiation Into Cardiomyocytes
      • Why Endogenous Tagging?
  • Data & Tools
    • Cell Catalog
    • 3D Cell Viewer
    • Cell Feature Explorer
    • Deep Cell Zoom
    • Segmenter
    • Data Downloading
    • Software & Code
    • Research Projects >
      • Extracting Information
  • Modeling & Analysis
    • Integrated Mitotic Stem Cell
    • Allen Integrated Cell
    • Label-free Determination
    • Data Notebook Exploration >
      • Cell Shape Analysis
      • Programmatic Data Access
    • Research Projects >
      • 3D Probabilistic Modeling
  • News & Publications
    • News Feed
    • Publications
    • Archived Content