Scientific Publications

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

Nature Methods, 2022-4-4

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

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

CourseSource, 2022-1-0

Goller CC, Johnson GT, Casimo K

The new era of quantitative cell imaging-challenges and opportunities

Molecular Cell, 2022-1-20

Bagheri N, Carpenter AE, Lundberg E, Plant AL, Horwitz R

A deep generative model of 3D single-cell organization

PLoS Computational Biology, 2022-1-18

Donovan-Maiye RM, Brown JM, Chan CK, Ding L, Yan C, Gaudreault N, Theriot JA, Maleckar MM, Knijnenburg TA, Johnson GR

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

Nature Cell Biology, 2021-12-0

Horwitz R, Riley EAU, Millan MT, Gunawardane RN

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

Nature Methods, 2021-12-18

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 CS, Grunwald D, Strambio-De-Castillia C

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

Biophysical Journal, 2021-9-21

Cass JA, Williams CD, Irving TC, Lauga E, Malingen S, Daniel TL, Sponberg SN

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

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.

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

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 FP, 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.

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

Cell Systems, 2021-5-21

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 TA, Rafelski SM, Theriot JA, Gunawardane RN.

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

Malingen SA, Asencio AM, Cass JA, Ma W, Irving TC, Daniel TL

A Bayesian framework for the detection of diffusive heterogeneity

PLoS One, 2020-5-7

Cass JA, Williams CD, Theriot J

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

Biophysical Journal, 2019-11-5

Vasan R, Maleckar MM, Williams CD, Rangamani P

Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs

Stem Cell Reports, 2019-4-4

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

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

bioRxiv, 2018-12-8

Chen J, Ding L, Viana MP, Hendershott MC, Yang R, Mueller IA, Rafelski S

Paul G. Allen (1953–2018)

Science, 2018-11-16

Horwitz R, Jones A, Daniel T

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

Nature Methods, 2018-9-17

Ounkomol C, Seshamani S, Maleckar MM, Collman F, Johnson GR

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

Jove, 2018-8-25

Haupt A, Grancharova T, Arakaki J, Fuqua MA, Roberts B, Gunawardane RN

CellProfiler 3.0: Next-generation image processing for biology

PLOS | Biology, 2018-7-3

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

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

bioRxiv, 2018-6-9

Roberts B, Arakaki J, Gerbin KA, Malik H, Nelson A, Hendershott MC, Hookway C, Ludmann SA, Mueller IA, Yang R, Rafelski SM, Gunawardane RN

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