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Dr. Beth Cimini's CV
54. Lacoste J, Haghighi M, Haider S, Reno C, Lin Z, Segal D, Qian WW, Xiong X, Teelucksingh T, Miglietta E, Shafqat-Abbasi H, Ryder PV, Senft R, Cimini BA, Murray RR, Nyirakanani C, Hao T, McClain GG, Roth FP, Calderwood MA, Hill DE, Vidal M, Yi SS, Sahni N, Peng J, Gingras A, Singh S, Carpenter AE, Taipale M. Pervasive mislocalization of pathogenic coding variants underlying human disorders. Cell. 2024. doi: 10.1016/j.cell.2024.09.003 (Research article)
53. IGVF Consortium. Deciphering the impact of genomic variation on function. Nature 2024. doi: 10.1038/s41586-024-07510-0 (Research article) doi.
52. Weisbart, E, Kumar, A, Arevalo, J, Carpenter AE, Cimini BA, Singh S. Cell Painting Gallery: an open resource for image-based profiling. Nat Methods. 2024. doi: 10.1038/s41592-024-02399-z (Research article) doi. pdf
51. Cimini BA+, Tromans-Coia C, Stirling DR, Sivagurunathan S, Senft RA, Ryder PV, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz MC, Weisbart E, Carpenter AE. A postdoctoral training program in bioimage analysis. Mol Biol Cell. 2024. 35, e2. doi: 10.1091/mbc.E24-05-0214 (Research article) doi. pdf.
50. Rakic M, Wong HE, Ortiz JJG, Cimini B, Guttag J, Dalca AV. Tyche: Stochastic In-Context Learning for Medical Image Segmentation. IEEE / CVF Computer Vision and Pattern Recognition Conference (CVPR) 2024. doi: 10.48550/arXiv.2401.13650 (Conference paper) doi. pdf.
49. De Niz M, Escobedo García R, Terán Ramirez C, Pakowski Y, Abonza Y, Bialy N, Orr VL, Olivera A, Abonza V, Alleva K, Allodi S, Almeida MF, B49ecerril Cuevas AR, Bonnet F, Burgos Solorio A, Chew T, Chiabrando G, Cimini B, Cleret-Buhot A, Contreras Jiménez G, Daza L, De Sá V, De Val N, Delgado-Álvarez DL, Eliceiri K, Fiolka R, Grecco H, Hanein D, Hernández Herrera P, Hockberger P, Hernandez HO, Hernandez Guadarrama Y, Itano M, Jacobs CA, Jiménez-García LF, Jiménez Sabinina V, Kamaid A, Keppler A, Kumar A, Lacoste J, Lovy A, Luby-Phelps K, Mahadevan-Jansen A, Malacrida L, Mehta SB, Miller C, Miranda K, Moore JA, North A, O'Toole P, Olivares Urbano M, Pietrasanta LI, Portugal RV, Rossi AH, Sanchez Contreras J, Strambio-De-Castilla C, Soldevila G, Vale B, Vazquez D, Wood C, Brown CM, Guerrero A. Building momentum through networks: Bioimaging across the Americas’, J Microsc. 2024. doi. pdf. (Commentary)
48. Chandrasekaran SN, Cimini BA, Goodale A, Miller L, Kost-Alimova M, Jamali N, Doench JG, Fritchman B, Skepner A, Melanson M, Kalinin AA, Arevalo J, Haghighi M, Caicedo JC, Kuhn D, Hernandez D, Berstler J, Abbasi HS, Root DE, Swalley SE, Singh S, Carpenter AE. Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nat Methods. 2024. doi. pdf. (Research article)
47. Cimini BA. Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. J Microsc. 2024. doi. pdf. (Review)
46. Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, Wang Y, Han L, Yang X, Labagnara M, Gligorovski V, Scheder M, Rahi SJ, Kempster C, Pollitt A, Espinosa L, Mignot T, Middeke JM, Eckardt J, Li W, Li Z, Cai X, Bai B, Greenwald NF, Van Valen D, Weisbart E, Cimini BA, Cheung T, Brück O, Bader GD, Wang B. (2024). The multimodality cell segmentation challenge: toward universal solutions. Nat Methods. 2024. doi. pdf. (Research article)
45. Moshkov N, Bornholdt M, Benoit S, Smith M, McQuin C, Goodman A, Senft R, Han Y, Babadi M, Horvath P, Cimini BA, Carpenter AE, Singh S, Caicedo JC. Learning representations for image-based profiling of perturbations. Nat Commun. 2024. 15: 1594. doi. pdf. (Research article)
44. Maier-Hein L, Reinke A, Godau P, Tizabi MD, Buettner F, Christodoulou E, Glocker B, Isensee F, Kleesiek J, Kozubek M, Reyes M, Riegler MA, Wiesenfarth M, Kavur AE, Sudre CH, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Rädsch T, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Blaschko MB, Cardoso MJ, Cheplygina V, Cimini BA, Collins GS, Farahani K, Ferrer L, Galdran A, van Ginneken B, Haase R, Hashimoto DA, Hoffman MM, Huisman M, Jannin P, Kahn CE, Kainmueller D, Kainz B, Karargyris A, Karthikesalingam A, Kofler F, Kopp-Schneider A, Kreshuk A, Kurc T, Landman BA, Litjens G, Madani A, Maier-Hein K, Martel AL, Mattson P, Meijering E, Menze B, Moons KGM, Müller H, Nichyporuk B, Nickel F, Petersen J, Rajpoot N, Rieke N, Saez-Rodriguez J, Sánchez CI, Shetty S, van Smeden M, Summers RM, Taha AA, Tiulpin A, Tsaftaris SA, Van Calster B, Varoquaux G, Jäger PF. Metrics reloaded: recommendations for image analysis validation. Nat Methods. 2024. 21: 195–212. doi. pdf. (Research article)
43. Reinke A, Tizabi MD, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Kavur AE, Rädsch T, Sudre CH, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Buettner F, Cardoso MJ, Cheplygina V, Chen J, Christodoulou E, Cimini BA, Farahani K, Ferrer L, Galdran A, van Ginneken B, Glocker B, Godau P, Hashimoto DA, Hoffman MM, Huisman M, Isensee F, Jannin P, Kahn CE, Kainmueller D, Kainz B, Karargyris A, Kleesiek J, Kofler F, Kooi T, Kopp-Schneider A, Kozubek M, Kreshuk A, Kurc T, Landman BA, Litjens G, Madani A, Maier-Hein K, Martel AL, Meijering E, Menze B, Moons KGM, Müller H, Nichyporuk B, Nickel F, Petersen J, Rafelski SM, Rajpoot N, Reyes M, Riegler MA, Rieke N, Saez-Rodriguez J, Sánchez CI, Shetty S, Summers RM, Taha AA, Tiulpin A, Tsaftaris SA, Van Calster B, Varoquaux G, Yaniv ZR, Jäger PF, Maier-Hein L. Understanding metric-related pitfalls in image analysis validation. Nat Methods. 2024. 21: 182–194. doi. pdf. (Research article)
42. Tegtmeyer M*, Arora J*, Asgari S*, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Conner L, Carpenter AE, Singh S+, Nehme R+, Raychaudhuri S+. High-dimensional phenotyping to define the genetic basis of cellular morphology. Nat Commun. 2024. 15: 347. doi. pdf. (Research article)
41. Gogoberidze N, Cimini BA, Defining the boundaries: challenges and advances in identifying cells in microscopy images. Curr Opin Biotechnol. 2023;85: 103055. doi. pdf. (Review)
40. Tromans-Coia C*,Jamali N*, Abbasi HS, Giuliano KA, Hagimoto M, Jan K, Kaneko E, Letzsch S, Schreiner A, Sexton JZ, Suzuki M, Trask OJ, Yamaguchi M, Yanagawa F, Yang M, Carpenter AE, Cimini BA. Assessing the performance of the Cell Painting assay across different imaging systems. Cytometry A. 2023. doi. pdf. (Research article)
39. Kelley ME, Berman AY, Stirling DR, Cimini BA, Han Y, Singh S, Carpenter AE, Kapoor TM, Way GP. High-content microscopy reveals a morphological signature of bortezomib resistance. eLife. 2023. doi. pdf. (Research article)
38. Sivagurunathan S, Marcotti S, Nelson CJ, Jones ML, Barry DJ, Slater TJA, Eliceiri KW, Cimini BA. Bridging Imaging Users to Imaging Analysis - A community survey. J Microsc. 2023 Sep 20. doi. pdf. (Research article)
37. Weisbart E*, Tromans-Coia C*, Diaz-Rohrer B*, Stirling DR*, Garcia-Fossa F*, Senft RA*, Hiner MC, de Jesus MB, Eliceiri KW, Cimini BA. CellProfiler plugins -- an easy image analysis platform integration for containers and Python tools. J Microsc. 2023 Sep 10. doi. pdf. (Research article)
36. Haghighi M, Cruz MC, Weisbart E, Cimini BA, Singh A, Bauman J, Lozada ME, Kavari SL, Neal JT, Blainey PC, Carpenter AE, Singh S. Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. In: Elkind E, editor. Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence. 2023. IJCAI-23. p. 4775–4784. doi. pdf. (Conference paper)
35. Schmied C, Nelson M, Avilov S, Bakker G, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho M, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Dévédec SL, Guyader SL, Liu P, Martins G, Mathur A, Miura K, Llopis PM, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Rizwan A, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio De Castillia C, Taatjes D, Tischer C, Jambor HK. Community-developed checklists for publishing images and image analysis. Nat Methods. 2023. doi. pdf. (Research article)
34. Ouyang W, Eliceiri KW, Cimini BA. Moving beyond the desktop: Prospects for Practical Bioimage Analysis via the Web. Front Bioinf. 2023. doi. pdf. (Commentary)
33. Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel J, Moreno XC, Medeiros Gd, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Küpcü Yoldaş A, Kyoda K, Villegeorges AT, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochem. Cell Biol. 2023. doi. pdf. (Research article)
32. Senft RA*, Diaz-Rohrer B*, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL, Eliceiri KW, Cimini BA. A biologist’s guide to planning and performing quantitative bioimaging experiments. PLoS Biol. 2023. 21(6): e3002167. doi. pdf. (Research article)
31. Laber S, Strobel S, Mercader JM, Dashti H, R.C. dos Santos F, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, Kost-Alimova M, Deodato G, Harney A, Way GP, Saadat A, Harken S, Reibe-Pal S, Ebert H, Zhang Y, Calabuig-Navarro V, McGonagle E, Stefek A, Dupuis JE, Cimini BA, Hauner H, Udler MS, Carpenter AE, Florez JC, Lindgren C, Jacobs, Claussnitzer M (2023). Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell Genomics. 3, 100346. PMID: 37492099; PMCID: PMC10363917. doi. pdf. (Research Article)
30. Glunk V, Laber S, Sinnott-Armstrong N, Sobreira DR, Strobel SM, Batista TM, Kubitz P, Moud BN, Ebert H, Huang Y, Brandl B, Garbo G, Honecker J, Stirling DR, Abdennur N, Calabuig-Navarro V, Skurk T, Ocvirk S, Stemmer K, Cimini BA, Carpenter AE, Dankel SN, Lindgren CM, Hauner H, Nobrega MA, Claussnitzer M (2023). A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nature Metabolism. 5, 861–879. PMID: 37253881. doi. pdf. (Research Article)
29. Cimini BA, Eliceiri KW. The Twenty Questions of Bioimage Object Analysis. Nat Methods. 2023; 20:976–8. doi. pdf. (Commentary)
28. Carpenter AE, Cimini BA, Eliceiri KW (2023). Smart microscopes of the future. Nature Methods. 20, 962-964. PMID: 37434001. doi. pdf. (Commentary)
27. Berryer MH, Rizki G, Nathanson A, Klein JA, Trendafilova D, Susco SG, Lam D, Messana A, Holton KM, Karhohs KW, Cimini BA, Pfaff K, Carpenter AE, Rubin LL, Barrett LE (2023). High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. Elife. 21;12:e80168. PMID: 37083703; PMCID: PMC10121225. doi. pdf. (Research Article)
26. Weisbart E, Cimini BA. Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale. Nat Methods. 2023. doi. pdf. (Research article)
25. Cimini BA, Chandrasekaran SN, Kost-Alimova M, Miller L, Goodale A, Fritchman B, Byrne P, Garg S, Jamali N, Logan D, Concannon JB, Lardeau CH, Mouchet E, Singh S, Abbasi HS, Aspesi P Jr, Boyd JD, Gilbert T, Gnutt D, Hariharan S, Hernandez D, Hormel G, Juhani K, Melanson M, Mervin LH, Monteverde T, Pilling JE, Skepner A, Skepner SE, Vrcic A, Weisbart E, Williams G, Yu S, Zapiec B, Carpenter AE (2023). Optimizing the Cell Painting assay for image-based profiling. Nature Protocols. 18, 1981–2013. PMID: 37344608. doi. pdf. (Research Article)
24. Garcia-Fossa F, Cruz MC, Haghighi M, Bispo de Jesus M, Singh S, Carpenter AE, Cimini BA (2023). Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization. Current Protocols, 3(3):e713. PMID: 36921124 PMCID: PMC10027367. doi. pdf. (Research Article)
23. Haghighi M, Caicedo JC, Cimini BA, Carpenter AE, Singh S. High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nat Methods. 2022. doi. pdf. PMID: 36344834 (Research article)
22. Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban M, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, Haghighi M, Weisbart E, Singh S, Subramanian A, Carpenter AE. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Systems. 2022;13: 911–923.e9. doi. author_version. PMID: 36395727 (Research article)
21. Rueden CT, Hiner MC, Evans EL, Pinkert MA, Lucas AM, Carpenter AE, Cimini BA, Eliceiri KW. PyImageJ: A library for integrating ImageJ and Python. Nat Methods. 2022;19: 1326–1327. doi. pdf. PMID: 36253645 (Research article)
20. Cimini, BA. Improved tracking via cell region fingerprints. Nat Methods (2022). doi. redcube. PMID: 36138172 (Commentary)
19. Jamali N, Dobson ETA, Eliceiri KW, Carpenter AE, Cimini BA (2021). 2020 BioImage Analysis Survey: Community experiences and needs for the future. Biological Imaging, 1–28. / doi. pdf. GitHub. PMID: 35387317 PMCID: PMC8982832 (Research article)
18. Wang JS, Kamath T, Mazur CM, Mirzamohammadi F, Rotter D, Hojo H, Castro CD, Tokavanich N, Patel R, Govea N, Enishi T, Wu Y, da Silva Martins J, Bruce M, Brooks DJ, Bouxsein ML, Tokarz D, Lin CP, Abdul A, Macosko EZ, Fiscaletti M, Munns CF, Ryder P, Kost-Alimova M, Byrne P, Cimini B, Fujiwara M, Kronenberg HM, Wein MN. Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin. Nat Commun. 2021 Nov 1;12(1):6271. doi. PMID: 34725346 PMCID: PMC8560803 (Research article)
17. Stirling DR, Carpenter AE, Cimini BA (2021). CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. Bioinformatics. / doi. pdf. PMID: 34478488. PMCID: in process (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. / doi. pdf. GitHub. 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. PMID: 34168275. PMCID: PMC8225800. doi. pdf. (Research article)
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. PMID: 34038030. PMCID: PMC8450896. doi. pdf. (Research article)
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. PMID: 33872058 PMCID: PMC8108523. doi. pdf. (Review article)
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. PMID: 33355295. PMCID: PMC7877457. doi. pdf. (Research article)
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. PMID: 31636459. PMCID: PMC6919559. doi. pdf. (Research article)
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. PMID: 31216269. PMCID: PMC6602289. doi. pdf. (PLoS Biology Community page)
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. PMID: 29969450. PMCID: PMC6029841. doi. pdf. (Research article)
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.