Publications

2018
Yang SJ, Berndl M, Michael Ando D, Barch M, Narayanaswamy A, Christiansen E, Hoyer S, Roat C, Hung J, Rueden CT, Shankar A, Finkbeiner S, Nelson P. Assessing microscope image focus quality with deep learning. [Internet]. BMC Bioinformatics 19(1):28962 2018; Publisher's Version
2017
Hung J, Goodman A, Lopes S, Rangel G, Ravel D, Costa F, Duraisingh M, Marti M, Carpenter AE. Applying Faster R-CNN for Object Detection on Malaria Images. 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). 2017;:808–813.
Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, Wolf FA. Reconstructing cell cycle and disease progression using deep learning [Internet]. Nat Commun 8(1):463 2017; Publisher's Version
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, Carpenter AE. Data-analysis strategies for image-based cell profiling [Internet]. Nat Methods 2017;14(9):849-863. Publisher's Version
Hulshof FFB, Papenburg B, Vasilevich A, Hulsman M, Zhao Y, Levers M, Fekete N, de Boer M, Yuan H, Singh S, Beijer N, Bray MA, Logan DJ, Reinders M, Carpenter AE, van Blitterswijk C, Stamatialis D, de Boer J. Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration. [Internet]. Biomaterials 137:49-60 2017; 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, Hung DT. Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence. [Internet]. PLoS Pathog. 15;13(5):e1006363 2017; Publisher's Version
Rohban MH, Singh S, Wu X, Berthet JB, Bray MA, Shrestha Y, Varelas X, Boehm JS, Carpenter AE. Systematic morphological profiling of human gene and allele function via Cell Painting [Internet]. eLife. 10.7554/eLife.24060 2017; Publisher's Version
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, Carpenter AE. A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay. [Internet]. Gigascience 2017; Publisher's Version PDF
Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE. An open-source solution for advanced imaging flow cytometry data analysis using machine learning. [Internet]. Methods. pii: S1046-2023(16)30291-2 2017; Publisher's Version
Doan M. Zooming in on adipocytes: High and deep. [Internet]. Cytometry A.;91(11):1051–1054 2017; Publisher's Version
Vasilevich AS, Carlier A, de Boer J, Singh S. How Not To Drown in Data: A Guide for Biomaterial Engineers [Internet]. Trends in Biotechnology 2017;35(9):743-755. Publisher's Version
2016
Pawlowski N, Caicedo JC, Singh S, Carpenter AE, Storkey A. Automating Morphological Profiling with Generic Deep Convolutional Networks. [Internet]. 2016; Publisher's Version
Meijering E, Carpenter AE, Peng H, Hamprecht F, Olivo-Marin JC. Imagining the future of bioimage analysis. [Internet]. Nature Biotechnology. 34(12)1250-55 2016; Publisher's Version
Bray MA, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, Carpenter AE. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. [Internet]. Nature Protocols. 11(9):1757-74 2016; Publisher's Version
Goodman A, Carpenter AE. High-Throughput, Automated Image Processing for Large-Scale Fluorescence Microscopy Experiments. [Internet]. Microscopy and Microanalysis. 22(S3):538–539 2016; 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, Andrade CH. QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. [Internet]. Journal of Chemical Information and Modeling. 56(7):1357-72 2016; Publisher's Version
Dao D, Fraser AN, Hung J, Ljosa V, Singh S, Carpenter AE. CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets [Internet]. Bioinformatics. 32(20):3210-3212 2016; Publisher's Version
Shan J, Logan DJ, Root DE, Carpenter AE, Bhatia SN. High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro. [Internet]. Journal of Biomolecular Screening. 21(9):897-911 2016; Publisher's Version
Neves BJ, Dantas RF, Senger MR, Goes Valente WC, de Mello Rezende-Neto J, Chaves WT, Kamentsky L, Carpenter AE, Silva-Jr FP, Andrade CH. The Antidepressant Drug Paroxetine as a New Lead Candidate in Schistosome Drug Discovery [Internet]. MedChemComm 2016; Publisher's Version
Dordea AC, Bray MA, Allen K, Logan D, Fei F, Malhotra R, Gregory M, Carpenter AE, Buys ES. An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells. [Internet]. Experimental Eye Research 2016; Publisher's Version

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