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Opportunities and obstacles for deep learning in biology and medicine.
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. Ching T, et al. J R Soc Interface. 2018 Apr;15(141):20170387. doi: 10.1098/rsif.2017.0387. J R Soc Interface. 2018. PMID: 29618526 Free PMC article. Review.
Ten quick tips for deep learning in biology.
Lee BD, Gitter A, Greene CS, Raschka S, Maguire F, Titus AJ, Kessler MD, Lee AJ, Chevrette MG, Stewart PA, Britto-Borges T, Cofer EM, Yu KH, Carmona JJ, Fertig EJ, Kalinin AA, Signal B, Lengerich BJ, Triche TJ Jr, Boca SM. Lee BD, et al. PLoS Comput Biol. 2022 Mar 24;18(3):e1009803. doi: 10.1371/journal.pcbi.1009803. eCollection 2022 Mar. PLoS Comput Biol. 2022. PMID: 35324884 Free PMC article. No abstract available.
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.
Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL; Clinical Genome Resource Somatic Working Group and Clinical Interpretation of Variants in Cancer team members. Danos AM, et al. Hum Mutat. 2018 Nov;39(11):1721-1732. doi: 10.1002/humu.23651. Hum Mutat. 2018. PMID: 30311370 Free PMC article.
A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients.
Pishvaian MJ, Blais EM, Bender RJ, Rao S, Boca SM, Chung V, Hendifar AE, Mikhail S, Sohal DPS, Pohlmann PR, Moore KN, He K, Monk BJ, Coleman RL, Herzog TJ, Halverson DD, DeArbeloa P, Petricoin EF 3rd, Madhavan S. Pishvaian MJ, et al. JAMIA Open. 2019 Oct 7;2(4):505-515. doi: 10.1093/jamiaopen/ooz045. eCollection 2019 Dec. JAMIA Open. 2019. PMID: 32025647 Free PMC article.