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High-throughput translational medicine: challenges and solutions.
Sulakhe D, Balasubramanian S, Xie B, Berrocal E, Feng B, Taylor A, Chitturi B, Dave U, Agam G, Xu J, Börnigen D, Dubchak I, Gilliam TC, Maltsev N. Sulakhe D, et al. Among authors: xu j. Adv Exp Med Biol. 2014;799:39-67. doi: 10.1007/978-1-4614-8778-4_3. Adv Exp Med Biol. 2014. PMID: 24292961 Review.
Lynx: a database and knowledge extraction engine for integrative medicine.
Sulakhe D, Balasubramanian S, Xie B, Feng B, Taylor A, Wang S, Berrocal E, Dave U, Xu J, Börnigen D, Gilliam TC, Maltsev N. Sulakhe D, et al. Among authors: xu j. Nucleic Acids Res. 2014 Jan;42(Database issue):D1007-12. doi: 10.1093/nar/gkt1166. Epub 2013 Nov 21. Nucleic Acids Res. 2014. PMID: 24270788 Free PMC article.
An integrative computational approach for prioritization of genomic variants.
Dubchak I, Balasubramanian S, Wang S, Cem M, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC. Dubchak I, et al. Among authors: xu j. PLoS One. 2014 Dec 15;9(12):e114903. doi: 10.1371/journal.pone.0114903. eCollection 2014. PLoS One. 2014. PMID: 25506935 Free PMC article.
Disease gene prioritization using network and feature.
Xie B, Agam G, Balasubramanian S, Xu J, Gilliam TC, Maltsev N, Börnigen D. Xie B, et al. Among authors: xu j. J Comput Biol. 2015 Apr;22(4):313-23. doi: 10.1089/cmb.2015.0001. J Comput Biol. 2015. PMID: 25844670 Free PMC article.
Lynx: a knowledge base and an analytical workbench for integrative medicine.
Sulakhe D, Xie B, Taylor A, D'Souza M, Balasubramanian S, Hashemifar S, White S, Dave UJ, Agam G, Xu J, Wang S, Gilliam TC, Maltsev N. Sulakhe D, et al. Among authors: xu j. Nucleic Acids Res. 2016 Jan 4;44(D1):D882-7. doi: 10.1093/nar/gkv1257. Epub 2015 Nov 20. Nucleic Acids Res. 2016. PMID: 26590263 Free PMC article.
Low-homology protein threading.
Peng J, Xu J. Peng J, et al. Among authors: xu j. Bioinformatics. 2010 Jun 15;26(12):i294-300. doi: 10.1093/bioinformatics/btq192. Bioinformatics. 2010. PMID: 20529920 Free PMC article.
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. Among authors: xu j. 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.
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