Publications by Year: 2016

Caicedo JC, Singh S, and Carpenter AE. 2016. “Applications in image-based profiling of perturbations. .” Current Opinion in Biotechnology 39:134-142. Publisher's Version
Pawlowski N, Caicedo JC, Singh S, Carpenter AE, and Storkey A. 2016. “Automating Morphological Profiling with Generic Deep Convolutional Networks.” In . Publisher's Version
Bray MA, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, and Carpenter AE. 2016. “Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.” Nature Protocols. 11(9):1757-74. Publisher's Version
Uhlmann V, Singh S, and Carpenter AE. 2016. “CP-CHARM: segmentation-free image classification made accessible.” BMC Bioinformatics 17(1):51. Publisher's Version
Goodman A and Carpenter AE. 2016. “High-Throughput, Automated Image Processing for Large-Scale Fluorescence Microscopy Experiments.” Microscopy and Microanalysis. 22(S3):538–539. Publisher's Version
Shan J, Logan DJ, Root DE, Carpenter AE, and Bhatia SN. 2016. “High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro.” Journal of Biomolecular Screening. 21(9):897-911. Publisher's Version
Meijering E, Carpenter AE, Peng H, Hamprecht F, Olivo-Marin, and JC. 2016. “Imagining the future of bioimage analysis.” Nature Biotechnology. 34(12)1250-55. Publisher's Version
Dordea AC, Bray M-A, Allen K, Logan D, Fei F, Malhotra R, Gregory M, Carpenter AE, and Buys ES. 2016. “An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells.” Experimental Eye Research. 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, and Andrade CH. 2016. “QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni.” Journal of Chemical Information and Modeling. 56(7):1357-72. Publisher's Version
Neves BJ, Dantas RF, Senger MR, Goes Valente WC, Mello Rezende-Neto de J, Chaves WT, Kamentsky L, Carpenter AE, Silva-Jr FP, and Andrade CH. 2016. “The Antidepressant Drug Paroxetine as a New Lead Candidate in Schistosome Drug Discovery.” MedChemComm . Publisher's Version
Dao D, Fraser AN, Hung J, Ljosa V, Singh S, and Carpenter AE. 2016. “CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.” Bioinformatics. 32(20):3210-3212. 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, 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