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Cytoscape.js: a graph theory library for visualisation and analysis.
Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD. Franz M, et al. Among authors: sumer o. Bioinformatics. 2016 Jan 15;32(2):309-11. doi: 10.1093/bioinformatics/btv557. Epub 2015 Sep 28. Bioinformatics. 2016. PMID: 26415722 Free PMC article.
Using biological pathway data with paxtools.
Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C. Demir E, et al. Among authors: sumer os. PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19. PLoS Comput Biol. 2013. PMID: 24068901 Free PMC article.
Author Correction: The evolution of RET inhibitor resistance in RET-driven lung and thyroid cancers.
Rosen EY, Won HH, Zheng Y, Cocco E, Selcuklu D, Gong Y, Friedman ND, de Bruijn I, Sumer O, Bielski CM, Savin C, Bourque C, Falcon C, Clarke N, Jing X, Meng F, Zimel C, Shifman S, Kittane S, Wu F, Ladanyi M, Ebata K, Kherani J, Brandhuber BJ, Fagin J, Sherman EJ, Rekhtman N, Berger MF, Scaltriti M, Hyman DM, Taylor BS, Drilon A. Rosen EY, et al. Among authors: sumer o. Nat Commun. 2022 Apr 5;13(1):1936. doi: 10.1038/s41467-022-29700-y. Nat Commun. 2022. PMID: 35383193 Free PMC article. No abstract available.
The evolution of RET inhibitor resistance in RET-driven lung and thyroid cancers.
Rosen EY, Won HH, Zheng Y, Cocco E, Selcuklu D, Gong Y, Friedman ND, de Bruijn I, Sumer O, Bielski CM, Savin C, Bourque C, Falcon C, Clarke N, Jing X, Meng F, Zimel C, Shifman S, Kittane S, Wu F, Ladanyi M, Ebata K, Kherani J, Brandhuber BJ, Fagin J, Sherman EJ, Rekhtman N, Berger MF, Scaltriti M, Hyman DM, Taylor BS, Drilon A. Rosen EY, et al. Among authors: sumer o. Nat Commun. 2022 Mar 18;13(1):1450. doi: 10.1038/s41467-022-28848-x. Nat Commun. 2022. PMID: 35304457 Free PMC article.
Comparison of clinical geneticist and computer visual attention in assessing genetic conditions.
Duong D, Johny AR, Ledgister Hanchard S, Fortney C, Flaharty K, Hellmann F, Hu P, Javanmardi B, Moosa S, Patel T, Persky S, Sümer Ö, Tekendo-Ngongang C, Lesmann H, Hsieh TC, Waikel RL, André E, Krawitz P, Solomon BD. Duong D, et al. Among authors: sumer o. PLoS Genet. 2024 Feb 27;20(2):e1011168. doi: 10.1371/journal.pgen.1011168. eCollection 2024 Feb. PLoS Genet. 2024. PMID: 38412177 Free PMC article.
Human and computer attention in assessing genetic conditions.
Duong D, Johny AR, Hanchard SL, Fortney C, Hellmann F, Hu P, Javanmardi B, Moosa S, Patel T, Persky S, Sümer Ö, Tekendo-Ngongang C, Hsieh TC, Waikel RL, André E, Krawitz P, Solomon BD. Duong D, et al. Among authors: sumer o. medRxiv [Preprint]. 2023 Jul 28:2023.07.26.23293119. doi: 10.1101/2023.07.26.23293119. medRxiv. 2023. PMID: 37577564 Free PMC article. Updated. Preprint.
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