Publications

2016
Caicedo JC, Singh S, Carpenter AE. Applications in image-based profiling of perturbations. [Internet]. Current Opinion in Biotechnology 39:134-142 2016; Publisher's Version
Uhlmann V, Singh S, Carpenter AE. CP-CHARM: segmentation-free image classification made accessible [Internet]. BMC Bioinformatics 2016;17(1):51. Publisher's Version
Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, Rees P. Label-free cell cycle analysis for high-throughput imaging flow cytometry [Internet]. Nat Commun 7:10256 2016; Publisher's Version
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. A Genome-wide RNAi screen for microtubule network formation and lysosome motility regulation in Drosophila S2 cells [Internet]. Cell Reports 14(3):611-20 2016; Publisher's Version
Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS. High-throughput Phenotyping of Lung Cancer Somatic Mutations. [Internet]. Cancer Cell, 30(2):214-28 2016; Publisher's Version
2015
Logan DJ, Shan J, Bhatia SN, Carpenter AE. Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. [Internet]. Methods pii: S1046-2023(15)30170-5 2015; Publisher's Version
Bray MA, Carpenter AE. CellProfiler Tracer: Exploring and Validating High-Throughput, Time-Lapse Microscopy Image Data [Internet]. BMC Bioinformatics 16:368 2015; Publisher's Version
Arbelle A, Drayman N, Bray M, Alon U, Carpenter AE, Riklin Raviv T. Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics [Internet]. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015. 2015;:218–225. Publisher's Version
Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE. Morphological profiles of RNAI-induced gene knockdown are highly reproducible but dominated by seed effects. [Internet]. PLoS One 10(7): e(0131370) 2015; Publisher's Version
Bray MA, Vokes MS, Carpenter AE. Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images [Internet]. Current Protocols in Molecular Biology 2015;(109):14.17.1-14.17.13. Publisher's Version
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, Iliopoulous O. Pharmacological HIF2α inhibition improves VHL disease-associated phenotypes in zebrafish model. [Internet]. Journal of Clinical Investigation. 125(5):1987-1997 2015; Publisher's Version
Gilad T, Bray MA, Carpenter AE, Riklin Raviv T. Symmetry-Based Mitosis Detection in Time-Lapse Microscopy. Paper presented at ISBI 2015 2015 International Symposium on Biomedical Imaging: From Nano to Macro. 2015;14:40-16.
Jeong YM, Duanting Z, Hennig H, Samanta A, Agrawalla BK, Bray MA, Carpenter AE, Chang YT. CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells. [Internet]. Chemistry and Biology.22(2):299-307 2015; Publisher's Version
Arganda-Carreras I, Turaga SC, Berger DR, Cireşan D, Giusti A, Gambardella LM, Schmidhuber J, Laptev D, Dwivedi S, Buhmann JM. Crowdsourcing the creation of image segmentation algorithms for connectomics. Frontiers in Neuroanatomy 9:00142 2015;
2014
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. Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma [Internet]. Oncotarget 6(7):4704-16 2014; Publisher's Version PDF
Singh S, Bray MA, Jones TR, Carpenter AE. Pipeline for illumination correction of images for high-throughput microscopy [Internet]. Journal of Microscopy 256(3):231-236 2014; Publisher's Version
Rees P, Wills JW, Brown MR, Tonkin J, Holton MD, Hondow N, Brown AP, Brydson R, Millar V, Carpenter AE, Summers HD. Nanoparticle vesicle encoding for imaging and tracking cell populations. [Internet]. Nature Methods 11:1177-1181 2014; Publisher's Version
Sheik-Khalil E, Bray MA, Ozkaya S, Scarlatti G, Jansson M, Carpenter AE, Fenyo EM. Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition [Internet]. BMC Infectious Diseases 14:472 2014; Publisher's Version
Khan IA, Fraser A, Bray MA, Smith PJ, White NS, Carpenter AE, Errington RJ. ProtocolNavigator: emulation based software for the design, documentation and reproduction biological experiments. [Internet]. Bioinformatics 30(23):344--3442 2014; Publisher's Version
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 CSY, Duvall JR, Wilson JA, Bittker JA, Dančík V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, Clemons PA. Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. [Internet]. PNAS. 111(30):10911-10916 2014; Publisher's Version

Pages