Publications

2017
Bray MA, Gustafsdottir SM, Ljosa V, Singh S, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancík V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, and Carpenter AE. 2017. “A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay.” Gigascience. Publisher's Version
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Vasilevich AS, Carlier A, Boer de J, and Singh S. 2017. “How Not To Drown in Data: A Guide for Biomaterial Engineers.” Trends in Biotechnology, 35(9):743-755. Publisher's Version
Hulshof FFB, Papenburg B, Vasilevich A, Hulsman M, Zhao Y, Levers M, Fekete N, Boer de M, Yuan H, Singh S, Beijer N, Bray MA, Logan DJ, Reinders M, Carpenter AE, Blitterswijk van C, Stamatialis D, and Boer de J. 2017. “Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration.” Biomaterials 137:49-60. Publisher's Version
Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE, and Carpenter AE. 2017. “An open-source solution for advanced imaging flow cytometry data analysis using machine learning.” Methods. pii: S1046-2023(16)30291-2. Publisher's Version
Barczak AK, Avraham R, Singh S, Luo SS, Zhang WR, Bray MA, Hinman AE, Thompson M, Nietupski RM, Golas A, Montgomery P, Fitzgerald M, Smith RS, White DW, Tischler AD, Carpenter AE, and Hung DT. 2017. “Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence.” PLoS Pathog. 15;13(5):e1006363. Publisher's Version
Doan M. 2017. “Zooming in on adipocytes: High and deep.” Cytometry A.;91(11):1051–1054. Publisher's Version
Hung J, Goodman A, Lopes S, Rangel G, Ravel D, Costa F, Duraisingh M, Marti M, and Carpenter AE. 2017. “Applying Faster R-CNN for Object Detection on Malaria Images.” In 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)., Pp. 808–813. IEEE.
Caicedo JC, Cooper S, Heigwer F, Warchal S, Qiu P, Molnar C, Vasilevich AS, Barry JD, Bansal HS, Kraus O, Wawer M, Paavolainen L, Herrmann MD, Rohban M, Hung J, Hennig H, Concannon J, Smith I, Clemons PA, Singh S, Rees P, Horvath P, Linington RG, and Carpenter AE. 2017. “Data-analysis strategies for image-based cell profiling.” Nat Methods 14(9):849-863. Publisher's Version
Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, and Wolf FA. 2017. “Reconstructing cell cycle and disease progression using deep learning.” Nat Commun 8(1):463. Publisher's Version
2016
Caicedo JC, Singh S, and Carpenter AE. 2016. “Applications in image-based profiling of perturbations. .” Current Opinion in Biotechnology 39:134-142. Publisher's Version
Pawlowski N, Caicedo JC, Singh S, Carpenter AE, and Storkey A. 2016. “Automating Morphological Profiling with Generic Deep Convolutional Networks.” In . Publisher's Version
Bray MA, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, and Carpenter AE. 2016. “Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.” Nature Protocols. 11(9):1757-74. Publisher's Version
Uhlmann V, Singh S, and Carpenter AE. 2016. “CP-CHARM: segmentation-free image classification made accessible.” BMC Bioinformatics 17(1):51. Publisher's Version
Goodman A and Carpenter AE. 2016. “High-Throughput, Automated Image Processing for Large-Scale Fluorescence Microscopy Experiments.” Microscopy and Microanalysis. 22(S3):538–539. Publisher's Version
Shan J, Logan DJ, Root DE, Carpenter AE, and Bhatia SN. 2016. “High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro.” Journal of Biomolecular Screening. 21(9):897-911. Publisher's Version
Meijering E, Carpenter AE, Peng H, Hamprecht F, Olivo-Marin, and JC. 2016. “Imagining the future of bioimage analysis.” Nature Biotechnology. 34(12)1250-55. Publisher's Version
Dordea AC, Bray M-A, Allen K, Logan D, Fei F, Malhotra R, Gregory M, Carpenter AE, and Buys ES. 2016. “An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells.” Experimental Eye Research. Publisher's Version
Melo-Filho CC, Dantas RF, Braga RC, Neves BJ, Senger MR, Valente WC, Rezende-Neto JM, Chaves WT, Muratov EN, Paveley RA, Furnham N, Kamentsky L, Carpenter AE, Silva-Junior FP, and Andrade CH. 2016. “QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni.” Journal of Chemical Information and Modeling. 56(7):1357-72. Publisher's Version
Neves BJ, Dantas RF, Senger MR, Goes Valente WC, Mello Rezende-Neto de J, Chaves WT, Kamentsky L, Carpenter AE, Silva-Jr FP, and Andrade CH. 2016. “The Antidepressant Drug Paroxetine as a New Lead Candidate in Schistosome Drug Discovery.” MedChemComm . Publisher's Version
Dao D, Fraser AN, Hung J, Ljosa V, Singh S, and Carpenter AE. 2016. “CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.” Bioinformatics. 32(20):3210-3212. Publisher's Version

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