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Metrics reloaded: recommendations for image analysis validation.
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. Maier-Hein L, et al. Among authors: saez rodriguez j. Nat Methods. 2024 Feb;21(2):195-212. doi: 10.1038/s41592-023-02151-z. Epub 2024 Feb 12. Nat Methods. 2024. PMID: 38347141 Free article. Review.
BIAS: Transparent reporting of biomedical image analysis challenges.
Maier-Hein L, Reinke A, Kozubek M, Martel AL, Arbel T, Eisenmann M, Hanbury A, Jannin P, Müller H, Onogur S, Saez-Rodriguez J, van Ginneken B, Kopp-Schneider A, Landman BA. Maier-Hein L, et al. Med Image Anal. 2020 Dec;66:101796. doi: 10.1016/j.media.2020.101796. Epub 2020 Aug 21. Med Image Anal. 2020. PMID: 32911207 Free PMC article.
Understanding metric-related pitfalls in image analysis validation.
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. Reinke A, et al. Among authors: saez rodriguez j. Nat Methods. 2024 Feb;21(2):182-194. doi: 10.1038/s41592-023-02150-0. Epub 2024 Feb 12. Nat Methods. 2024. PMID: 38347140 Review.
Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium; Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Hill SM, et al. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22. Nat Methods. 2016. PMID: 26901648 Free PMC article.
Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.
Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MG, Rajeeve V, Cardaci S, Foster S, Yun H, Cutillas P, Warren A, Gnanapragasam V, Gottlieb E, Franze K, Huntly B, Maher ER, Maxwell PH, Saez-Rodriguez J, Frezza C. Sciacovelli M, et al. Nature. 2016 Aug 31;537(7621):544-547. doi: 10.1038/nature19353. Nature. 2016. PMID: 27580029 Free PMC article.
Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.
Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, Santos R, Rao Y, Sassi F, Pinnelli M, Ansari R, Harper S, Jackson DA, McRae R, Pooley R, Wilkinson P, van der Meer D, Dow D, Buser-Doepner C, Bertotti A, Trusolino L, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. Behan FM, et al. Nature. 2019 Apr;568(7753):511-516. doi: 10.1038/s41586-019-1103-9. Epub 2019 Apr 10. Nature. 2019. PMID: 30971826 Free article.
SREBP1-induced fatty acid synthesis depletes macrophages antioxidant defences to promote their alternative activation.
Bidault G, Virtue S, Petkevicius K, Jolin HE, Dugourd A, Guénantin AC, Leggat J, Mahler-Araujo B, Lam BYH, Ma MK, Dale M, Carobbio S, Kaser A, Fallon PG, Saez-Rodriguez J, McKenzie ANJ, Vidal-Puig A. Bidault G, et al. Nat Metab. 2021 Sep;3(9):1150-1162. doi: 10.1038/s42255-021-00440-5. Epub 2021 Sep 16. Nat Metab. 2021. PMID: 34531575 Free PMC article.
The spatial transcriptomic landscape of the healing mouse intestine following damage.
Parigi SM, Larsson L, Das S, Ramirez Flores RO, Frede A, Tripathi KP, Diaz OE, Selin K, Morales RA, Luo X, Monasterio G, Engblom C, Gagliani N, Saez-Rodriguez J, Lundeberg J, Villablanca EJ. Parigi SM, et al. Nat Commun. 2022 Feb 11;13(1):828. doi: 10.1038/s41467-022-28497-0. Nat Commun. 2022. PMID: 35149721 Free PMC article.
Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment.
Schneider KM, Mohs A, Gui W, Galvez EJC, Candels LS, Hoenicke L, Muthukumarasamy U, Holland CH, Elfers C, Kilic K, Schneider CV, Schierwagen R, Strnad P, Wirtz TH, Marschall HU, Latz E, Lelouvier B, Saez-Rodriguez J, de Vos W, Strowig T, Trebicka J, Trautwein C. Schneider KM, et al. Nat Commun. 2022 Jul 8;13(1):3964. doi: 10.1038/s41467-022-31312-5. Nat Commun. 2022. PMID: 35803930 Free PMC article.
285 results