Publications Collected

Scientific articles

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
ASCB Newsletter, December 20, 2018. Johnson GT, Rafelski S.

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.

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

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

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

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

Preprinted versions

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.

Other media about the Allen Institute for Cell Science

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