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Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data.
P E de Souza C, Andronescu M, Masud T, Kabeer F, Biele J, Laks E, Lai D, Ye P, Brimhall J, Wang B, Su E, Hui T, Cao Q, Wong M, Moksa M, Moore RA, Hirst M, Aparicio S, Shah SP. P E de Souza C, et al. Among authors: andronescu m. PLoS Comput Biol. 2020 Sep 23;16(9):e1008270. doi: 10.1371/journal.pcbi.1008270. eCollection 2020 Sep. PLoS Comput Biol. 2020. PMID: 32966276 Free PMC article.
Clonal fitness inferred from time-series modelling of single-cell cancer genomes.
Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, O'Flanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA; IMAXT Consortium; McPherson A, Bouchard-Côté A, Aparicio S, Shah SP. Salehi S, et al. Among authors: andronescu m. Nature. 2021 Jul;595(7868):585-590. doi: 10.1038/s41586-021-03648-3. Epub 2021 Jun 23. Nature. 2021. PMID: 34163070 Free PMC article.
Accurate determination of CRISPR-mediated gene fitness in transplantable tumours.
Eirew P, O'Flanagan C, Ting J, Salehi S, Brimhall J, Wang B, Biele J, Algara T, Lee SR, Hoang C, Yap D, McKinney S, Bates C, Kong E, Lai D, Beatty S, Andronescu M, Zaikova E, Funnell T, Ceglia N, Chia S, Gelmon K, Mar C, Shah S, Roth A, Bouchard-Côté A, Aparicio S. Eirew P, et al. Among authors: andronescu m. Nat Commun. 2022 Aug 4;13(1):4534. doi: 10.1038/s41467-022-31830-2. Nat Commun. 2022. PMID: 35927228 Free PMC article.
Thermodynamically based DNA strand design.
Tulpan D, Andronescu M, Chang SB, Shortreed MR, Condon A, Hoos HH, Smith LM. Tulpan D, et al. Among authors: andronescu m. Nucleic Acids Res. 2005 Sep 6;33(15):4951-64. doi: 10.1093/nar/gki773. Print 2005. Nucleic Acids Res. 2005. PMID: 16145053 Free PMC article.
To heuristically search for good strand sets, our algorithm uses a conflict-driven stochastic local search approach, which is known to be effective in solving comparable search problems. The PairFold program of Andronescu et al. [M. Andronescu, Z. C. Zhang an …
To heuristically search for good strand sets, our algorithm uses a conflict-driven stochastic local search approach, which is known to be ef …
A new algorithm for RNA secondary structure design.
Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon A. Andronescu M, et al. J Mol Biol. 2004 Feb 20;336(3):607-24. doi: 10.1016/j.jmb.2003.12.041. J Mol Biol. 2004. PMID: 15095976
A thermodynamic approach to designing structure-free combinatorial DNA word sets.
Shortreed MR, Chang SB, Hong D, Phillips M, Campion B, Tulpan DC, Andronescu M, Condon A, Hoos HH, Smith LM. Shortreed MR, et al. Among authors: andronescu m. Nucleic Acids Res. 2005 Sep 2;33(15):4965-77. doi: 10.1093/nar/gki812. Print 2005. Nucleic Acids Res. 2005. PMID: 16284197 Free PMC article.
Free energy estimation of short DNA duplex hybridizations.
Tulpan D, Andronescu M, Leger S. Tulpan D, et al. Among authors: andronescu m. BMC Bioinformatics. 2010 Feb 24;11:105. doi: 10.1186/1471-2105-11-105. BMC Bioinformatics. 2010. PMID: 20181279 Free PMC article.
40 results