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Items: 1 to 50 of 112

1.

Label-Free Identification of White Blood Cells Using Machine Learning.

Nassar M, Doan M, Filby A, Wolkenhauer O, Fogg DK, Piasecka J, Thornton CA, Carpenter AE, Summers HD, Rees P, Hennig H.

Cytometry A. 2019 May 13. doi: 10.1002/cyto.a.23794. [Epub ahead of print]

PMID:
31081599
2.

Capturing single-cell heterogeneity via data fusion improves image-based profiling.

Rohban MH, Abbasi HS, Singh S, Carpenter AE.

Nat Commun. 2019 May 7;10(1):2082. doi: 10.1038/s41467-019-10154-8.

3.

Leveraging machine vision in cell-based diagnostics to do more with less.

Doan M, Carpenter AE.

Nat Mater. 2019 May;18(5):414-418. doi: 10.1038/s41563-019-0339-y. No abstract available.

PMID:
31000804
4.

Weakly Supervised Learning of Single-Cell Feature Embeddings.

Caicedo JC, McQuin C, Goodman A, Singh S, Carpenter AE.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2018 Jun;2018:9309-9318. doi: 10.1109/CVPR.2018.00970. Epub 2018 Dec 17.

5.

Designed Surface Topographies Control ICAM-1 Expression in Tonsil-Derived Human Stromal Cells.

Vasilevich AS, Mourcin F, Mentink A, Hulshof F, Beijer N, Zhao Y, Levers M, Papenburg B, Singh S, Carpenter AE, Stamatialis D, van Blitterswijk C, Tarte K, de Boer J.

Front Bioeng Biotechnol. 2018 Jun 28;6:87. doi: 10.3389/fbioe.2018.00087. eCollection 2018.

6.

CellProfiler 3.0: Next-generation image processing for biology.

McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE.

PLoS Biol. 2018 Jul 3;16(7):e2005970. doi: 10.1371/journal.pbio.2005970. eCollection 2018 Jul.

7.

Opportunities and obstacles for deep learning in biology and medicine.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS.

J R Soc Interface. 2018 Apr;15(141). pii: 20170387. doi: 10.1098/rsif.2017.0387. Review.

8.

Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery.

Simm J, Klambauer G, Arany A, Steijaert M, Wegner JK, Gustin E, Chupakhin V, Chong YT, Vialard J, Buijnsters P, Velter I, Vapirev A, Singh S, Carpenter AE, Wuyts R, Hochreiter S, Moreau Y, Ceulemans H.

Cell Chem Biol. 2018 May 17;25(5):611-618.e3. doi: 10.1016/j.chembiol.2018.01.015. Epub 2018 Mar 1.

9.

Diagnostic Potential of Imaging Flow Cytometry.

Doan M, Vorobjev I, Rees P, Filby A, Wolkenhauer O, Goldfeld AE, Lieberman J, Barteneva N, Carpenter AE, Hennig H.

Trends Biotechnol. 2018 Jul;36(7):649-652. doi: 10.1016/j.tibtech.2017.12.008. Epub 2018 Jan 31.

10.

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.

11.

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.

12.

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
13.

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
14.

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.

15.

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.

16.

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.

17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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;147:50-56. doi: 10.1016/j.exer.2016.04.012. Epub 2016 Apr 24.

26.

Applications in image-based profiling of perturbations.

Caicedo JC, Singh S, Carpenter AE.

Curr Opin Biotechnol. 2016 Jun;39:134-142. doi: 10.1016/j.copbio.2016.04.003. Epub 2016 Apr 17. Review.

27.

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.

28.

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.

29.

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.

30.

Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification.

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

Methods. 2016 Mar 1;96:6-11. doi: 10.1016/j.ymeth.2015.12.002. Epub 2015 Dec 11.

31.

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.

Bray MA, Carpenter AE.

BMC Bioinformatics. 2015 Nov 4;16:368. doi: 10.1186/s12859-015-0759-x.

32.

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects.

Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE.

PLoS One. 2015 Jul 21;10(7):e0131370. doi: 10.1371/journal.pone.0131370. eCollection 2015.

33.

Synthesis and protonation of an encumbered iron tetraisocyanide dianion.

Mokhtarzadeh CC, Margulieux GW, Carpenter AE, Weidemann N, Moore CE, Rheingold AL, Figueroa JS.

Inorg Chem. 2015 Jun 1;54(11):5579-87. doi: 10.1021/acs.inorgchem.5b00730. Epub 2015 May 12.

PMID:
25965161
34.

Pharmacological HIF2α inhibition improves VHL disease-associated phenotypes in zebrafish model.

Metelo AM, Noonan HR, Li X, Jin Y, Baker R, Kamentsky L, Zhang Y, van Rooijen E, Shin J, Carpenter AE, Yeh JR, Peterson RT, Iliopoulos O.

J Clin Invest. 2015 May;125(5):1987-97. doi: 10.1172/JCI73665. Epub 2015 Apr 13.

35.

Comparative measure of the electronic influence of highly substituted aryl isocyanides.

Carpenter AE, Mokhtarzadeh CC, Ripatti DS, Havrylyuk I, Kamezawa R, Moore CE, Rheingold AL, Figueroa JS.

Inorg Chem. 2015 Mar 16;54(6):2936-44. doi: 10.1021/ic5030845. Epub 2015 Feb 20.

PMID:
25700244
36.

Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma.

Du Z, Abedalthagafi M, Aizer AA, McHenry AR, Sun HH, Bray MA, Viramontes O, Machaidze R, Brastianos PK, Reardon DA, Dunn IF, Freeman GJ, Ligon KL, Carpenter AE, Alexander BM, Agar NY, Rodig SJ, Bradshaw EM, Santagata S.

Oncotarget. 2015 Mar 10;6(7):4704-16.

37.

CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells.

Jeong YM, Duanting Z, Hennig H, Samanta A, Agrawalla BK, Bray MA, Carpenter AE, Chang YT.

Chem Biol. 2015 Feb 19;22(2):299-307. doi: 10.1016/j.chembiol.2014.11.018. Epub 2015 Jan 15.

38.

Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images.

Bray MA, Vokes MS, Carpenter AE.

Curr Protoc Mol Biol. 2015 Jan 5;109:14.17.1-13. doi: 10.1002/0471142727.mb1417s109.

39.

Direct observation of β-chloride elimination from an isolable β-chloroalkyl complex of square-planar nickel.

Carpenter AE, McNeece AJ, Barnett BR, Estrada AL, Mokhtarzadeh CC, Moore CE, Rheingold AL, Perrin CL, Figueroa JS.

J Am Chem Soc. 2014 Nov 5;136(44):15481-4. doi: 10.1021/ja508956q. Epub 2014 Oct 21.

PMID:
25317481
40.

Pipeline for illumination correction of images for high-throughput microscopy.

Singh S, Bray MA, Jones TR, Carpenter AE.

J Microsc. 2014 Dec;256(3):231-6. doi: 10.1111/jmi.12178. Epub 2014 Sep 16.

41.

Nanoparticle vesicle encoding for imaging and tracking cell populations.

Rees P, Wills JW, Brown MR, Tonkin J, Holton MD, Hondow N, Brown AP, Brydson R, Millar V, Carpenter AE, Summers HD.

Nat Methods. 2014 Nov;11(11):1177-81. doi: 10.1038/nmeth.3105. Epub 2014 Sep 14.

PMID:
25218182
42.

Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition.

Sheik-Khalil E, Bray MA, Özkaya Şahin G, Scarlatti G, Jansson M, Carpenter AE, Fenyö EM.

BMC Infect Dis. 2014 Aug 30;14:472. doi: 10.1186/1471-2334-14-472.

43.

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

Khan IA, Fraser A, Bray MA, Smith PJ, White NS, Carpenter AE, Errington RJ.

Bioinformatics. 2014 Dec 1;30(23):3440-2. doi: 10.1093/bioinformatics/btu554. Epub 2014 Aug 22.

44.

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling.

Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray MA, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CS, Duvall JR, Wilson JA, Bittker JA, Dančík V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, Clemons PA.

Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):10911-6. doi: 10.1073/pnas.1410933111. Epub 2014 Jul 14.

45.

High- and low-throughput scoring of fat mass and body fat distribution in C. elegans.

Wählby C, Conery AL, Bray MA, Kamentsky L, Larkins-Ford J, Sokolnicki KL, Veneskey M, Michaels K, Carpenter AE, O'Rourke EJ.

Methods. 2014 Aug 1;68(3):492-9. doi: 10.1016/j.ymeth.2014.04.017. Epub 2014 Apr 28.

46.

Increasing the Content of High-Content Screening: An Overview.

Singh S, Carpenter AE, Genovesio A.

J Biomol Screen. 2014 Jun;19(5):640-50. doi: 10.1177/1087057114528537. Epub 2014 Apr 7. Review.

47.

High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons.

Nieland TJ, Logan DJ, Saulnier J, Lam D, Johnson C, Root DE, Carpenter AE, Sabatini BL.

PLoS One. 2014 Mar 14;9(3):e91744. doi: 10.1371/journal.pone.0091744. eCollection 2014.

48.

Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth.

Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Moore CB, Siddiqi N, Rubin EJ, Hung DT.

PLoS Pathog. 2014 Feb 20;10(2):e1003946. doi: 10.1371/journal.ppat.1003946. eCollection 2014 Feb.

49.

ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state.

Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RG, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG.

Cell Rep. 2014 Jan 30;6(2):313-24. doi: 10.1016/j.celrep.2013.12.032. Epub 2014 Jan 16.

50.

Multiplex cytological profiling assay to measure diverse cellular states.

Gustafsdottir SM, Ljosa V, Sokolnicki KL, Anthony Wilson J, Walpita D, Kemp MM, Petri Seiler K, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, Shamji AF.

PLoS One. 2013 Dec 2;8(12):e80999. doi: 10.1371/journal.pone.0080999. eCollection 2013.

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