Literature

Journal Publications

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. Scientific Reports. 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. Nature Genetics. 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. Nature Medicine. 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. J Vis Exp. Jan; (): 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).

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, 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.

 

Piloco L, Alworth SV, Cho H, Lee JSJ.

Automatic receptor trafficking assay analysis using machine learning.

 

Alworth SV, Cho H, Lee JSJ.

Automatic Transfluor assay analysis using machine learning.

 

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

Learnable analysis module for subcellular, time lapse microscopy assays.

 

Alworth SA, Oh S, Phan T, Koh D, Thomas W E., Lee JSJ.

Robust tracking of multiple moving objects in subcellular time-lapse microscopy assays.

 

Alworth SV, Oh S, Phan T, Koh D, Thomas W E., Lee JSJ.

Adaptive spatial-temporal detection of multiple moving objects in subcellular time-lapse assays.

 

Oh S, Alworth SV, Kandere-Grzybowska K, Borisy GG, Grzybowski, BA, Lee JSJ.

Automated Kinetic Analysis in Individual Cell Motility Assays.

 

Cho H, Alworth SV, Oh S, Cheng Y, Kelley BG, Sullivan JM, Lee JSJ.

Spatial-temporal regulation improves the sensitivity and accuracy of synaptic vesicle recycling assays.

 

Cho H, Alworth SV, Oh S, Cheng Y, Kelley BG, Martin G, Sullivan JM, Lee JSJ.

Discovery framework for live cell synaptic vesicle recycling assays.

 

Alworth SV, Cho H, Oh S, Cheng Y, Kelley BG, Martin G.

Robust modeling for the automated analysis of synaptic vesicle recycling assays.

 

Kosak ST, Alworth SV, Scalzo D, Li F, Palmer S, Lee JSJ, Groudine M.

Homologous chromosomes associate during hematopoiesis.

 

Alworth S, Kelley BG, Oh S, Birnbaum C, Martin G, Sullivan JM, Lee JSJ.

Robust analysis of subcellular, time-lapse microscopy assays.