Scientific Publications

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The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models

Nature Methods, 2022-4-4

Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging

CourseSource, 2022-1-0

The new era of quantitative cell imaging-challenges and opportunities

Molecular Cell, 2022-1-20

A deep generative model of 3D single-cell organization

PLoS Computational Biology, 2022-1-18

It's time to incorporate diversity into our basic science and disease models

Nature Cell Biology, 2021-12-0

Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

Nature Methods, 2021-12-18

A mechanism for sarcomere breathing: volume change and advective flow within the myofilament lattice

Biophysical Journal, 2021-9-21

A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes

Scientific Reports, 2021-8-4

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Journal of Microscopy, 2021-7-2

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Cell Systems, 2021-5-21

In vivo X-ray diffraction and simultaneous EMG reveal the time course of myofilament lattice dilation and filament stretch

Journal of Experimental Biology, 2020-9-3

A Bayesian framework for the detection of diffusive heterogeneity

PLoS One, 2020-5-7

DLITE Uses Cell-Cell Interface Movement to Better Infer Cell-Cell Tensions

Biophysical Journal, 2019-11-5

Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs

Stem Cell Reports, 2019-4-4

The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images

bioRxiv, 2018-12-8

Paul G. Allen (1953–2018)

Science, 2018-11-16

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy.

Nature Methods, 2018-9-17

Endogenous Protein Tagging in Human Induced Pluripotent Stem Cells Using CRISPR/Cas9

Jove, 2018-8-25

CellProfiler 3.0: Next-generation image processing for biology

PLOS | Biology, 2018-7-3

Scarless gene tagging of transcriptionally silent genes in hiPSCs to visualize cardiomyocyte sarcomeres in live cells

bioRxiv, 2018-6-9

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