Literature

Journal Publications

Brent AE, Rajan A (2020).

Insulin and Leptin/Upd2 Exert Opposing Influences on Synapse Number in Fat-Sensing Neurons. Cell Metabolism. Sept; Epub ahead of print.

Read the BioRxiv version here.

Higaki T, Mizuno H (2020).

Four-dimensional imaging with virtual reality to quantitatively explore jigsaw puzzle-like morphogenesis of Arabidopsis cotyledon pavement cells. Plant Biotechnology. Sept; 20-0605

Hernández IC, Yang W, Mohan S, Jowett N (2020).

Label-free histomorphometry of peripheral nerve by stimulated Raman spectroscopy. Muscle Nerve. Jul; 62(1): 137-142

Menendez L, Trecek T, Gopalakrishnan S, Tao L, Markowitz AL, Yu HV, Wang X, Llams J, Hunag C, Lee J, Kalluri R, Ichida J, Segil N (2020).

Generation of inner ear hair cells by direct lineage conversion of primary somatic cells. eLife. Jun; 9: e55249.

Chou VT, Yesilyurt HG, Lai H, Long JB, Arnes M, Obbad K, Jones M, Sasaki H, Lucas LAG, Alworth S, Lee JS, Van Vactor D (2020).

3D particle tracing for noninvasive in vivo analysis of synaptic microtubule dynamics in denrites and neuromuscular junctions of drosophila. JoVE-J Vis Exp. May; 159: e61159.

Rahman M, Chang IY, Harned A, Maheshwari R, Amoateng K, Narayan K, Cohen-Fix O (2019).

C. elegans pronuclei fuse after fertilization through a novel membrane structure. J Cell Biol. Dec; 219(2): e201909137

Berenson DF, Zatulovskiy E, Skotheim JM (2019).

Constitutive expression of a fluorescent protein reports the size of live human cells. Mol Biol Cell. Nov. 30(24): 2943-3012

Glaser AK, Reder NP, Chen Y, Yin C, Wei L, Kang S, Barner LA, Xie W, McCarty EF, Mao C, Halpern AR, Stoltzfus CR, Daniels JS, Gerner MY, Nicovich PR, Vaughan JC, True LD, Liu JTC. (2019).

Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues. Nat Commun. Jul; 10: 2781.

Chester D, Kathard R, Nortey J, Nellenbach K, Brown AC (2018).

Viscoelastic properties of microgel thin films control fibroblast modes of migration and pro-fibrotic responses. Biomaterials. Dec; 185: 371-382

McKenzie AJ, Hicks SR, Svec KV, Naughton H, Edmunds ZL, Howe AK (2018).

The mechanical microenvironment regulates ovarian cancer cell morphology, migration, and spheroid disaggregation. Sci Rep. May; 8: 7228

Kramer NJ, Haney MS, Morgens DW, Jovicic A, Couthouis J, Li A, Ousey J, Ma R, Bierri G, Tsui K, Shi Y, Hertz NT, Tessier-Lavigne M, Ichida JK, Bassik MC, Gitler AD (2018).

CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat protein toxicity. Nat Genet. Apr; 50(4): 603-612

Shi Y, Lin S, Staats KA, Li Y, Chang W, Hung S, Hendricks E, Linares GR, Wang Y, Son EY, Wen X, Kisler K, Wilkinson B, Menendez L, Sugawara T, Woolwine P, Huang M, Cowan MJ, Ge B, Koutsodendris N, Sandor KP, Komberg J, Vangoor VR, Senthilkumar K, Hennes V, Seah C, Nelson AR, Cheng T, Lee SJ, August PR, Chen JA, Wisniewski N, Hanson-Smith V, Belgard TG, Zhang A, Coba M, Grunseich C, Ward ME, van den Berg LH, Pasterkamp RJ, Trotti D, Zlokovic BV, Ichida JK (2018).

Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons. Nat Med. Feb; 24:313.

Guess T, Lai H, Smith SE, Sircy L, Cunningham K, Nelson DE, McClelland E (2018).

Size matters: measurement of capsule diameter in cryptococcus neoformans. joVE-J Vis Exp. Jan; 132: e57171.

Alworth SV, Watanabe H, Lee JSJ (2010).

Teachable, high content analytics for live cell, phase contrast movies. J Biomol Screen. Sep;15(8):968-77.

Kosak ST, Scalzo D, Li F, Palmer S, Enver T, Alworth SV, Lee JSJ, Groudine M. (2007).

Coordinated gene regulation during hematopoiesis is regulated to genomice organization. PLoS Biol. Nov;5(11):e309.

Scientific Posters

Jones M, Birnbaum C, Graff B, McElroy S, Lai H, Chou VT, Long JB, Arnes M, Obbad K, Alworth SV, Huang CC, Lucas LAG, Van Vactor D, Lee JSJ (2017).

Efficient microscopy image visualization and cell tracking analysis of multi-gigabyte datasets. Poster presented at the American Society for Cell Biology and European Molecular Biology Organization meeting. Philadelphia, PA.

Vivian T. Chou, Jennifer B. Long, Hoyin Lai, Mercedes Arnes, Kamal Obbad, Luciano A.G. Lucas, Sam Alworth, D. Van Vactor (2017).

Developing a 3D particle tracking tool for in vivo analysis of pre-synaptic microtubule dynamics at the Drosophila neuromuscular junction. Poster presented at the American Society for Cell Biology and European Molecular Biology Organization meeting. Philadelphia, PA.

Jones M, Sasaki H, Huang CC, Lee JSJ (2017).

Automated novel neuronal type discoveries by machine learning. Poster presented at the American Society for Cell Biology and European Molecular Biology Organization meeting. Philadelphia, PA.

Jones M, Huang CC, Sasaki H, Cheng TY, Sugawara T, Shi Y, Ichida J, Lee JSJ (2017).

A machine learning framework for kinetic phenotypic prediction of neurological disease states in patient-derived cell models. Poster presented at the American Society for Cell Biology and European Molecular Biology Organization meeting. Philadelphia, PA.

Cheng TY, Linares GR, Sasaki H, Lai H, Donaldson WH, Huang CC, Ichida J, Lee JSJ (2016).

Machine learning-enabled analytical tool for kinetic drug screening of induced motor neuron survival in ALS patient panels. Poster presented at the American Society for Cell Biology annual meeting. San Francisco CA.

Sasaki H, Cheng TY, Jones M, Li Y, Lai H, Huang CC, Ichida J, Lee JSJ (2016).

Inference of survival states in induced motor neurons of neurological diseases. Poster presented at the American Society for Cell Biology annual meeting. San Francisco CA.

Lai H, Kenyon ZA, Collins NJ, Alworth SV, Piloco L, Daheron L, Lee JSJ (2016).

Computer-assisted scoring method for human induced pluripotent stem cell colony characterization and selection. Poster presented at the International Society for Stem Cell Research 14th annual meeting. San Francisco CA.

Alworth SV, Collins NJ, Kenyon ZA, Piloco L, Daheron L, Rubin LL, Cowan CA, Lee JSJ (2015).

SVCell software, powered by machine learning, enables the automated and standardized generation of patient-specific, clonal cell lines with reduced variability. Poster presented at the World Stem Cell Summit. Atlanta GA.

Alworth SV, Collins NJ, Kenyon ZA, Piloco L, Daheron L, Rubin LL, Cowan CA, Lee JSJ (2015).

Reference metrics for human induced pluripotent stem cell colony selection. Poster presented at the New York Stem Cell Foundation conference. New York NY.

Jones MW, Huang CC, Alworth SV, Lee JSJ (2015).

Validation of a 3D particle tracking tool for next-generation neuroscience microscopy. Poster presented at the Society for Neuroscience annual conference, Chicago IL.

Alworth SV, Kenyon ZA, Collins NJ, Hendriks WT, Nakada C, Kiyota Y, Daheron L, Rubin LL, Cowan CA, Lee JSJ (2014).

Validation of label-free, real-time selection of fully reprogrammed iPSC colonies using kinetic image pattern recognition. Poster presented at International Society for Stem Cell Research 12th annual meeting. Vancouver BC.

Kenyon Z, Lai H, Watanabe H, Tsuboi T, Lee JSJ (2013).

Exocytotic event kinetic measurements for molecular target functional characterization. Poster presented at the American Society for Cell Biology annual conference, New Orleans LA.

Alworth SV, Hendriks WT, Kenyon ZA, Entwisle S, Bricker T, Nakada C, Kiyota Y, Daheron L, Rubin LL, Cowan CA, Lee JSJ (2013).

Automatic, label-free and real-time selection of iPSC colonies at the time of colony emergence during reprogramming. Poster presented at the International Society for Stem Cell Research 11th annual meeting, Boston MA.

Alworth SV, Hendriks WT, Kenyon ZA, Entwisle S, Bricker T, Nakada C, Kiyota Y, Daheron L, Rubin LL, Cowan CA, Lee JSJ (2013).

Alworth SV, Blumenstein A, Arvanites AC, Ichida J, Nakada C, Kiyota Y, Eggan K, Rubin LL, Lee JSJ (2013).

Machine learning based image analysis for the automated counting of motor neurons in a live cell screening system without the use of specialized fluorescent probes. Poster presented at the International Society for Stem Cell Research 11th annual meeting, Boston MA.

Alworth SV, Entwisle S, Hendriks WT, Kenyon ZA, Brickler T, Daheron L, Rubin LL, Cowan CA, Lee JSJ (2013).

A software tool for the automatic, label-free selection of induced pluripotent stem cell colonies at early time points during reprogramming. Poster presented at the GTC Stem Cell Summit conference, Boston MA.

Lee JSJ, Kenyon Z, Wadadekar T, Watanabe H, Numano R, Tsuboi T (2012).

Configurable Tool for Automated Exocytotic Events Quantification. Poster presented at the American Society for Cell Biology annual conference, San Francisco, CA.

Lai H, Hendriks WT, Wadadekar TV, Alworth SV, Daheron L, Nakada C, Kiyota Y, Cowan CA, Rubin LL, Lee JSJ (2011).

Teachable tool for standardization of human induced pluripotent stem cell colony selection from live cell microscopy image sequences. Poster presented at the American Society for Cell Biology annual conference, Denver CO.

Lee JSJ, Huang C, Alworth SV, Watanabe H, Saito K, Arai Y, Nagai T (2011).

Validation of automated subcellular tracking tool for kinetic image analysis. Poster presented at the American Society for Cell Biology annual conference, Denver CO.

Huang CC, Oh S, Watanabe, H, Tsuboi T, Lee JSJ (2011).

Automated Exocytotic Events Detection and Quantitative Characterization. Poster presented at the Society for Neuroscience annual conference, Washington DC.

Lee JSJ, Huang CC, Alworth SV, Watanabe H, Tsuboi T (2011).

Validation of Automated Vesicle Tracking for Total Internal Reflection Microscopy. Poster presented at the Society for Neuroscience annual conference, Washington DC.

Oh S, Huang CC, Watanabe H, Tsuboi T, Lee JSJ (2010).

Automated Model Guided Quantification of Exocytotic Vesicle Dynamics. Poster presented at the American Society for Cell Biology annual conference, Philadelphia, PA.

Lee JSJ, Alworth SV, Huang CC, Oh S, Watanabe H, Horikawa K, Nagai T (2008).

Automatic Quantitative Characterization of Rapid Protein Dynamics in Live Cell Microscopy Assays. Poster presented at the American Society for Cell Biology annual conference, San Francisco, CA.

Hendriks WT, Alworth SV, Kenyon ZA, Lai H, Nakada C, Daheron L, Kiyota Y, Lee JSJ, Rubin LL, Cowan CA.

Assessment of an imaging protocol for real-time selection of human iPSC colonies using live cell microscopy and image recognition software.

Lee JSJ, Kenyon Z, Wadadekar T, Watanabe H, Numano R, Tsuboi T.

Configurable tool for Automated Exocytotic Events Quantification.

Lee JSJ, Huang C, Kenyon Z, Watanabe H, Tsuboi T.

Automated Kinetic Characterization of Exocytotic Events in Total Internal reflection microscopy.

Lee JSJ, Alworth SV, Huang C, Oh S, Watanabe H, Saito K, Horikawa K.

Automated Kinetic Characterization of Intracellular Single-molecule Tracking.

Lee JSJ, Alworth SV, Huang C, Oh S, Watanabe H, Horikawa K, Saito K, Nagai T.

Automatic quantitative characterization of kinetic events during exocytosis.

Oh S, Cheng Y, Alworth SV, Lee JSJ.

Characterization of complex biological phenomena in time-lapse microscopy.