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Predicting tumor cell line response to drug pairs with deep learning.
Xia F, Shukla M, Brettin T, Garcia-Cardona C, Cohn J, Allen JE, Maslov S, Holbeck SL, Doroshow JH, Evrard YA, Stahlberg EA, Stevens RL. Xia F, et al. Among authors: shukla m. BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):486. doi: 10.1186/s12859-018-2509-3. BMC Bioinformatics. 2018. PMID: 30577754 Free PMC article.
PATRIC, the bacterial bioinformatics database and analysis resource.
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW. Wattam AR, et al. Among authors: shukla m. Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91. doi: 10.1093/nar/gkt1099. Epub 2013 Nov 12. Nucleic Acids Res. 2014. PMID: 24225323 Free PMC article.
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. Overbeek R, et al. Among authors: shukla m. Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14. doi: 10.1093/nar/gkt1226. Epub 2013 Nov 29. Nucleic Acids Res. 2014. PMID: 24293654 Free PMC article.
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA 3rd, Stevens R, Vonstein V, Wattam AR, Xia F. Brettin T, et al. Among authors: shukla m. Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365. Sci Rep. 2015. PMID: 25666585 Free PMC article.
Antimicrobial Resistance Prediction in PATRIC and RAST.
Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R. Davis JJ, et al. Among authors: shukla m. Sci Rep. 2016 Jun 14;6:27930. doi: 10.1038/srep27930. Sci Rep. 2016. PMID: 27297683 Free PMC article.
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL. Wattam AR, et al. Among authors: shukla m. Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29. Nucleic Acids Res. 2017. PMID: 27899627 Free PMC article.
PATRIC as a unique resource for studying antimicrobial resistance.
Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H. Antonopoulos DA, et al. Among authors: shukla m. Brief Bioinform. 2019 Jul 19;20(4):1094-1102. doi: 10.1093/bib/bbx083. Brief Bioinform. 2019. PMID: 28968762 Free PMC article.
KBase: The United States Department of Energy Systems Biology Knowledgebase.
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. Arkin AP, et al. Among authors: shukla m. Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. Nat Biotechnol. 2018. PMID: 29979655 Free PMC article. No abstract available.
887 results