Publications

2016
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, and Gelfand VI. 2016. “A Genome-wide RNAi screen for microtubule network formation and lysosome motility regulation in Drosophila S2 cells.” Cell Reports 14(3):611-20. 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, and Boehm JS. 2016. “High-throughput Phenotyping of Lung Cancer Somatic Mutations.” Cancer Cell, 30(2):214-28. Publisher's Version
Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, and Rees P. 2016. “Label-free cell cycle analysis for high-throughput imaging flow cytometry.” Nat Commun 7:10256. Publisher's Version
Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, and Carpenter AE. 2016. “Systematic morphological profiling of human gene and allele function via Cell Painting.” eLife. 10.7554/eLife.24060. Publisher's Version
2015
Jeong Y-M, Duanting Z, Hennig H, Samanta A, Agrawalla BK, Bray M-A, Carpenter AE, and Chang Y-T. 2015. “CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells.” Chemistry and Biology.22(2):299-307. Publisher's Version
Arganda-Carreras I, Turaga SC, Berger DR, Cireşan D, Giusti A, Gambardella LM, Schmidhuber J, Laptev D, Dwivedi S, and Buhmann JM. 2015. “Crowdsourcing the creation of image segmentation algorithms for connectomics.” Frontiers in Neuroanatomy 9:00142.
Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, and Carpenter AE. 2015. “Morphological profiles of RNAI-induced gene knockdown are highly reproducible but dominated by seed effects.” PLoS One 10(7): e(0131370). Publisher's Version
Metelo AM, Noonan HR, Li X, Jin Y, Baker R, Kamentsky L, Zhang Y, Rooijen van E, Shin J, Carpenter AE, Yeh JR, Peterson RT, and Iliopoulous O. 2015. “Pharmacological HIF2α inhibition improves VHL disease-associated phenotypes in zebrafish model.” Journal of Clinical Investigation. 125(5):1987-1997. Publisher's Version
Logan DJ, Shan J, Bhatia SN, and Carpenter AE. 2015. “Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification.” Methods pii: S1046-2023(15)30170-5 . Publisher's Version
Gilad T, Bray MA, Carpenter AE, and Riklin Raviv T. 2015. “Symmetry-Based Mitosis Detection in Time-Lapse Microscopy. Paper presented at ISBI 2015 2015 International Symposium on Biomedical Imaging: From Nano to Macro.” In , 10th ed., 14: Pp. 40-16. Brooklyn Bridge, NY.
Arbelle A, Drayman N, Bray M, Alon U, Carpenter AE, and Riklin Raviv T. 2015. “Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics.” In Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015., Pp. 218–225. Springer International Publishing. Publisher's Version
Bray M-A, Vokes MS, and Carpenter AE. 2015. “Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images.” Current Protocols in Molecular Biology. 109:14.17.1-14.17.13. Publisher's Version
2014
Nieland TJF, Logan DJ, Saulnier J, Lam D, Johnson C, Root DE, Carpenter AE, and Sabatini BL. 2014. “High Content Image Analysis Identifies Novel Regulators of Synaptogenesis in a High-Throughput RNAi Screen of Primary Neurons.” PLoS ONE 9(3):e91744. Publisher's Version
Rees P, Wills JW, Brown MR, Tonkin J, Holton MD, Hondow N, Brown AP, Brydson R, Millar V, Carpenter AE, and Summers HD. 2014. “Nanoparticle vesicle encoding for imaging and tracking cell populations.” Nature Methods 11:1177-1181. Publisher's Version
Khan IA, Fraser A, Bray M-A, Smith PJ, White NS, Carpenter AE, and Errington RJ. 2014. “ProtocolNavigator: emulation based software for the design, documentation and reproduction biological experiments.” Bioinformatics 30(23):344--3442. Publisher's Version
Majithia AR, Flannick J, Shahinian P, Guo M, Bray MA, Fontanillas P, Gabriel SE, GoT2D Consortium, and NHGRI/FHS Allelic Spectrum Pr. 2014. “Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes.” PNAS 111(36):13127-13132 . Publisher's Version
Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray M-A, 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, and Clemons PA. 2014. “Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling.” PNAS. 111(30):10911-10916 . Publisher's Version
Chudnovsky Y, Kim D, Zheng S, Whyt WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Mitalipova M, Muffat J, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, and Chheda MG. 2014. “ZFHX4 is a master regulator of NuRD core member CHD4 and regulates the glioblastoma tumor initiating cell state.” Cell Reports 6(2):313-324. Publisher's Version
Sheik-Khalil E, Bray M-A, Ozkaya S, Scarlatti G, Jansson M, Carpenter AE, and Fenyo EM. 2014. “Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition.” BMC Infectious Diseases 14:472. Publisher's Version

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