Publications

2020
Rushad Patell, Geeda Maddaleni, Laura Dodge, Mary Buss, and Jason Freed. 7/13/2020. “Communication Skills Training for Internal Medicine Residents Using a Brief Animated Video.” J Cancer Educ. Publisher's Version
PROGRAM AUTHOR: Rushad Patell , Geeda Maddaleni   
 
timorth, jane, tane, Lane F. Fargher, Mariza deAndrade, Mary Arimond, and Joel Atlas. 2020. “ddddd”.
2019
3/1/2019. “An RNA-binding Protein,”.Abstract
Lin28 is an evolutionarily conserved RNA-binding protein that inhibits processing of pre-let-7 microRNAs (miRNAs) and regulates translation of mRNAs that control developmental timing, pluripotency, metabolism, and tumorigenesis. The RNA features that mediate Lin28 binding to the terminal loops of let-7 pre-miRNAs and to Lin28-responsive elements (LREs) in mRNAs are not well defined. Here we show that Lin28 target datasets are enriched for RNA sequences predicted to contain stable planar structures of 4 guanines known as G-quartets (G4s). The imino NMR spectra of pre-let-7 loops and LREs contain resonances characteristic of G4 hydrogen bonds. These sequences bind to a G4-binding fluorescent dye, N-methyl-mesoporphyrin IX (NMM). Mutations and truncations in the RNA sequence that prevent G4 formation also prevent Lin28 binding. The addition of Lin28 to a pre-let-7 loop or an LRE reduces G4 resonance intensity and NMM binding, suggesting that Lin28 may function to remodel G4s. Further, we show that NMM inhibits Lin28 binding. Incubation of a human embryonal carcinoma cell line with NMM reduces its stem cell traits. In particular it increases mature let-7 levels, decreases OCT4, HMGA1, CCNB1, CDK4, and Lin28A protein, decreases sphere formation, and inhibits colony formation. Our results suggest a previously unknown structural feature of Lin28 targets and a new strategy for manipulating Lin28 function.
V Kulikov, SM Guo, M Stone, A Goodman, AE Carpenter, M Bathe, and V Lempitsky. 2019. “DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images.” PLoS Computational Biology, 15, 5, Pp. e1007012. Publisher's Version
JC Caicedo, J Roth, A Goodman, T Becker, KW Karhohs, M Broisin, C Molnar, C McQuin, S Singh, F Theis, and Carpenter AE. 2019. “Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images.” Cytometry, 95: 952-965.
E Shlevkov, H Basu, MA Bray, Z Sun, W Wei, K Apaydin, KW Karhohs, PF Chen, JLM Smith, O Wiskow, K Roet, X Huang, K Eggan, Carpenter AE, RJ Kleiman, and TL Schwarz. 2019. “A High-Content Screen Identifies TPP1 and Aurora B as Regulators of Axonal Mitochondrial Transport.” Cell Reports, 28, 12, Pp. 3224-3237.e5. Publisher's Version
M Nassar, M Doan, A Filby, O Wolkenhauer, DK Fogg, J Piasecka, CA Thornton, AE Carpenter, HD Summers, P Rees, and H Hennig. 2019. “Label-Free Identification of White Blood Cells Using Machine Learning.” Cytometry A, 95, 8, Pp. 836-842. Publisher's Version
M Doan and AE Carpenter. 2019. “Leveraging machine vision in cell-based diagnostics to do more with less.” Nature Materials, 18, Pp. 414-418. Publisher's Version
JC Caicedo, A Goodman, KW Karhohs, BA Cimini, J Ackerman, M Haghighi, C Heng, T Becker, M Doan, C McQuin, M Rohban, S Singh, and Carpenter AE. 2019. “Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl.” Nature Methods, 16, Pp. 1247–1253. Publisher's Version
CT Rueden, J Ackerman, ET Arena, J Eglinger, BA Cimini, A Goodman, AE Carpenter, and KW Eliceiri. 2019. “Scientific Community Image Forum: A discussion forum for scientific image software.” PLoS Biology.
2018
SJ Yang, M Berndl, D Michael Ando, M Barch, A Narayanaswamy, E Christiansen, S Hoyer, C Roat, J Hung, CT Rueden, A Shankar, S Finkbeiner, and P Nelson. 2018. “Assessing microscope image focus quality with deep learning.” BMC Bioinformatics 19(1):28962. Publisher's Version
[Github page]
C McQuin, A Goodman, V Chernyshev, L Kamentsky, BA Cimini, KW Karhohs, M Doan, L Ding, SM Rafelski, D Thirstrup, W Wiegraebe, S Singh, T Becker, JC Caicedo, and AE Carpenter. 2018. “CellProfiler 3.0: Next-generation image processing for biology.” PLoS Biol. 16(7):e2005970. Publisher's Version
[Github page]
T Becker, JC Caicedo, S Singh, M Weckmann, and AE Carpenter. 2018. “Combining morphological and migration profiles of in vitro time-lapse data.” 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), Pp. 965–968.
P Goldsborough, N Pawlowski, JC Caicedo, S Singh, and AE Carpenter. 2018. “CytoGAN: Generative Modeling of Cell Images”. Publisher's Version
[link to biorxiv preprint]
AS Vasilevich, F Mourcin, A Mentink, F Hulshof, N Beijer, Y Zhao, M Levers, B Papenburg, S Singh, AE Carpenter, D Stamatialis, C van Blitterswijk, K Tarte, and J DeBoer. 2018. “Designed Surface Topographies Control ICAM-1 Expression in Tonsil-Derived Human Stromal Cells.” Front Bioeng Biotechnol. 6:87. Publisher's Version
M Doan, I Vorobjev, P Rees, A Filby, O Wolkenhauer, AE Goldfeld, J Lieberman, N Barteneva, AE Carpenter, and H Hennig. 2018. “Diagnostic Potential of Imaging Flow Cytometry.” Trends Biotechnol 112:39-45. Publisher's Version
U Ben-David, B Siranosian, G Ha, H Tang, Y Oren, K Hinohara, CA Strathdee, J Dempster, NJ Lyons, R Burns, A Nag, G Kugener, BA Cimini, P Tsvetkov, YE Maruvka, R O’Rourke, A Garrity, AA Tubelli, P Bandopadhayay, A Tsherniak, F Vazquez, B Wong, C Birger, M Ghandi, A Thorner, J Bittker, M Meyerson, G Getz, R Beroukhim, and TR Golub. 2018. “Genetic and transcriptional evolution alters cancer cell line drug response.” Nature, 560, 7718, Pp. 325-330. Publisher's Version
[Carpenter lab paper: Carpenter not co-author]
J Simm, G Klambauer, A Arany, M Steijaert, JK Wegner, E Gustin, V Chupakhin, YT Chong, J Vialard, P Buijnsters, I Velter, A Vapirev, S Singh, AE Carpenter, R Wuyts, S Hochreiter, and CH Moreau. 2018. “Repurposed High-Throughput Images Enable Biological Activity Prediction For Drug Discovery.” Cell Chem Biol. Publisher's Version
JC Caicedo, C McQuin, A Goodman, S Singh, and AE Carpenter. 2018. “Weakly supervised learning of single-cell feature embeddings.” 2018 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) bioRxiv, Pp. 293431. Publisher's Version
[Github page]
2017
J Hung, A Goodman, S Lopes, G Rangel, D Ravel, F Costa, M Duraisingh, M Marti, and AE Carpenter. 2017. “Applying Faster R-CNN for Object Detection on Malaria Images.” 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)., Pp. 808–813.
[link to arxiv page]

Pages