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Items: 1 to 20 of 103

1.

Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler.

Bray MA, Carpenter AE.

Methods Mol Biol. 2018;1683:89-112. doi: 10.1007/978-1-4939-7357-6_7.

PMID:
29082489
2.

Reconstructing cell cycle and disease progression using deep learning.

Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, Wolf FA.

Nat Commun. 2017 Sep 6;8(1):463. doi: 10.1038/s41467-017-00623-3.

3.

Data-analysis strategies for image-based cell profiling.

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.

Nat Methods. 2017 Aug 31;14(9):849-863. doi: 10.1038/nmeth.4397.

PMID:
28858338
4.

Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration.

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.

Biomaterials. 2017 Aug;137:49-60. doi: 10.1016/j.biomaterials.2017.05.020. Epub 2017 May 12.

PMID:
28535442
5.

Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence.

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.

PLoS Pathog. 2017 May 15;13(5):e1006363. doi: 10.1371/journal.ppat.1006363. eCollection 2017 May.

6.

High-Throughput, Automated Image Processing for Large-Scale Fluorescence Microscopy Experiments.

Goodman A, Carpenter AE.

Microsc Microanal. 2016 Jul;22(Suppl 3):538-539. doi: 10.1017/S1431927616003548. Epub 2016 Jul 25. No abstract available.

7.

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay.

Bray MA, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, 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.

Gigascience. 2017 Dec 1;6(12):1-5. doi: 10.1093/gigascience/giw014.

8.

Systematic morphological profiling of human gene and allele function via Cell Painting.

Rohban MH, Singh S, Wu X, Berthet JB, Bray MA, Shrestha Y, Varelas X, Boehm JS, Carpenter AE.

Elife. 2017 Mar 18;6. pii: e24060. doi: 10.7554/eLife.24060.

9.

Imagining the future of bioimage analysis.

Meijering E, Carpenter AE, Peng H, Hamprecht FA, Olivo-Marin JC.

Nat Biotechnol. 2016 Dec 7;34(12):1250-1255. doi: 10.1038/nbt.3722. No abstract available.

PMID:
27926723
10.

High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro.

Shan J, Logan DJ, Root DE, Carpenter AE, Bhatia SN.

J Biomol Screen. 2016 Oct;21(9):897-911. doi: 10.1177/1087057116660277. Epub 2016 Aug 4.

PMID:
27650791
11.

An open-source solution for advanced imaging flow cytometry data analysis using machine learning.

Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE, Filby A.

Methods. 2017 Jan 1;112:201-210. doi: 10.1016/j.ymeth.2016.08.018. Epub 2016 Sep 2.

12.

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.

Bray MA, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, Carpenter AE.

Nat Protoc. 2016 Sep;11(9):1757-74. doi: 10.1038/nprot.2016.105. Epub 2016 Aug 25.

13.

Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening.

Neves BJ, Dantas RF, Senger MR, Melo-Filho CC, Valente WC, de Almeida AC, Rezende-Neto JM, Lima EF, Paveley R, Furnham N, Muratov E, Kamentsky L, Carpenter AE, Braga RC, Silva-Junior FP, Andrade CH.

J Med Chem. 2016 Aug 11;59(15):7075-88. doi: 10.1021/acs.jmedchem.5b02038. Epub 2016 Jul 22.

PMID:
27396732
14.

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.

Dao D, Fraser AN, Hung J, Ljosa V, Singh S, Carpenter AE.

Bioinformatics. 2016 Oct 15;32(20):3210-3212. Epub 2016 Jun 26.

15.

QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni.

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.

J Chem Inf Model. 2016 Jul 25;56(7):1357-72. doi: 10.1021/acs.jcim.6b00055. Epub 2016 Jun 16.

16.

An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells.

Dordea AC, Bray MA, Allen K, Logan DJ, Fei F, Malhotra R, Gregory MS, Carpenter AE, Buys ES.

Exp Eye Res. 2016 Jun;147:50-6. doi: 10.1016/j.exer.2016.04.012. Epub 2016 Apr 24.

17.

Applications in image-based profiling of perturbations.

Caicedo JC, Singh S, Carpenter AE.

Curr Opin Biotechnol. 2016 Jun;39:134-42. doi: 10.1016/j.copbio.2016.04.003. Epub 2016 Apr 17. Review.

18.

CP-CHARM: segmentation-free image classification made accessible.

Uhlmann V, Singh S, Carpenter AE.

BMC Bioinformatics. 2016 Jan 27;17:51. doi: 10.1186/s12859-016-0895-y.

19.

A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells.

Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding M, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Sharma M, Dean D, Cohen AR, Gelfand VI.

Cell Rep. 2016 Jan 26;14(3):611-620. doi: 10.1016/j.celrep.2015.12.051. Epub 2016 Jan 7.

20.

Label-free cell cycle analysis for high-throughput imaging flow cytometry.

Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, Rees P.

Nat Commun. 2016 Jan 7;7:10256. doi: 10.1038/ncomms10256.

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