Papers

For CellProfiler citations, visit the CellProfiler website!

Google Scholar page (with citation metrics): broad.io/CiminiGoogleScholar

Dr. Beth Cimini's CV: broad.io/Cimini_CV

17. Stirling DR, Carpenter AE, Cimini BA (2021). CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. Bioinformatics. / doipdf. PMID: 34478488. (Research article)

16. Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A (2021). CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics, 22 (1), 433. / doipdf. PMID: 34507520 PMCID: PMC8431850. (Research article)

15. Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M (2021). Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging.Communications Biology, 24:4, 786 /  doi: 10.1038/s42003-021-02276-x

14. Dobson ET, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW (2021). ImageJ and CellProfiler: Complements in open-source bioimage analysis. Current Protocols, 1, e89. doi: 10.1002/cpz1.89

13. Lucas AM, Ryder PV, Li B, Cimini BA, Eliceiri KW, Carpenter AE. Open-source deep-learning software for bioimage segmentation. Molecular Biology of the Cell, 2021 Apr 19;32(9):823-829. doi: 10.1091/mbc.E20-10-0660

12. Danielson E, Perez de Arce K, Cimini B, Wamhoff EC, Singh S, Cottrell JR, Carpenter AE, Bathe M. (2020). Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging. eNeuro, 21 December 2020. doi: 10.1523/ENEURO.0286-20.2020 

11. Cimini BA, Nørrelykke SF, Louveaux M et al. (2020) The NEUBIAS Gateway: a hub for bioimage analysis methods and materials. F1000Research. 9:613 doi: 10.12688/f1000research.24759.1  (Editorial, not peer reviewed)

10. Ravindranathan A, Diolaiti ME, Cimini BA, Stohr BA. (2019) In Situ Visualization of Telomere Length, Telomere Elongation, and TERT Expression in Single Cells. Current Protocols in Cell Biology. 2019 Dec;85(1):e97. doi: 10.1002/cpcb.97

9. Caicedo JC, Goodman A, Karhohs KW, Cimini BA, Ackerman J, Haghighi M, Heng C, Becker T, Doan M, McQuin C, Rohban M, Singh S, Carpenter AE (2019) Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods, 2019 Dec;16(12):1247-1253. doi: 10.1038/s41592-019-0612-7

8. Rueden CT, Ackerman J, Arena ET, Eglinger J, Cimini BA, Goodman A, Carpenter AE, Eliceiri KW. (2019) Scientific Community Image Forum: A discussion forum for scientific image software. PLoS Biology, 2019 Jun 19;17(6):e3000340. doi: 10.1371/journal.pbio.3000340. 

7. Ravindranathan A, Cimini B, Diolaiti ME, Stohr BA. (2018). Preliminary development of an assay for detection of TERT expression, telomere length, and telomere elongation in single cells. PLoS One, 2018 Dec 5;13(12):e0206525. doi: 10.1371/journal.pone.0206525.

6. Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR. (2018). Genetic and transcriptional evolution alters cancer cell line drug response. Nature, 560(7718), 325-330. doi: 10.1038/s41586-018-0409-3. 

5. 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. (2018) CellProfiler 3.0: Next-generation image processing for biology. PLoS Biology, 16(7), e2005970. doi: 10.1371/journal.pbio.2005970.

4. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li G-W, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B (2013). Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System, Cell, 155(7), 1479-1491. doi: 10.1016/j.cell.2013.12.001

3. Diolaiti ME, Cimini BA, Kageyama R, Charles F, Stohr BA. (2013).  In Situ Visualization of Telomere Elongation Patterns in Human Cells. Nucleic Acids Research, 41(18):e176. doi:10.1093/nar/gkt689.

2. Belin BJ, Cimini BA, Blackburn EH, Mullins RD.  (2013). Visualization of Actin Filaments and Monomers in Somatic Cell Nuclei. Molecular Biology of the Cell, 24(7), 982-94. doi: 10.1091/mbc.E12-09-0685

1. Cimini BA, Strang CE, Wotring VE, Keyser KT, Eldred WD. (2008). The Role of Acetylcholine in Nitric Oxide Production in the Salamander Retina.  Journal of Comparative Neurology, 507(6), 1952-1963. doi: 10.1002/cne.21655.