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Items: 20

1.

Draft Genome Sequence of Pseudomonas aeruginosa Strain LMG 1272, an Atypical White Line Reaction Producer.

Salari F, Zare-Mirakabad F, Alavi MH, Girard L, Ghafari M, De Mot R, Rokni-Zadeh H.

Microbiol Resour Announc. 2020 Feb 13;9(7). pii: e01363-19. doi: 10.1128/MRA.01363-19.

2.

A Stochastic Model of DNA Double-Strand Breaks Repair Throughout the Cell Cycle.

Mohseni-Salehi FS, Zare-Mirakabad F, Sadeghi M, Ghafouri-Fard S.

Bull Math Biol. 2020 Jan 14;82(1):11. doi: 10.1007/s11538-019-00692-z.

PMID:
31933029
3.

The assessment of efficient representation of drug features using deep learning for drug repositioning.

Moridi M, Ghadirinia M, Sharifi-Zarchi A, Zare-Mirakabad F.

BMC Bioinformatics. 2019 Nov 14;20(1):577. doi: 10.1186/s12859-019-3165-y.

4.

Assessing the impact of exact reads on reducing the error rate of read mapping.

Salari F, Zare-Mirakabad F, Sadeghi M, Rokni-Zadeh H.

BMC Bioinformatics. 2018 Nov 6;19(1):406. doi: 10.1186/s12859-018-2432-7.

5.

The effect of stochasticity on repair of DNA double strand breaks throughout non-homologous end joining pathway.

Mohseni-Salehi FS, Zare-Mirakabad F, Ghafouri-Fard S, Sadeghi M.

Math Med Biol. 2018 Dec 5;35(4):517-539. doi: 10.1093/imammb/dqx017.

PMID:
29237014
6.

Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction.

Montaseri S, Zare-Mirakabad F, Ganjtabesh M.

J Bioinform Comput Biol. 2017 Dec;15(6):1750023. doi: 10.1142/S0219720017500238. Epub 2017 Oct 19.

PMID:
29113564
7.

S-FLN: A sequence-based hierarchical approach for functional linkage network construction.

Jalilvand A, Akbari B, Zare Mirakabad F.

J Theor Biol. 2018 Jan 21;437:149-162. doi: 10.1016/j.jtbi.2017.10.021. Epub 2017 Oct 26.

PMID:
29080781
8.

RNA design using simulated SHAPE data.

Lotfi M, Zare-Mirakabad F, Montaseri S.

Genes Genet Syst. 2018 May 3;92(6):257-265. doi: 10.1266/ggs.16-00067. Epub 2017 Jul 28.

9.

Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data.

Montaseri S, Ganjtabesh M, Zare-Mirakabad F.

PLoS One. 2016 Nov 28;11(11):e0166965. doi: 10.1371/journal.pone.0166965. eCollection 2016.

10.

Evaluating the accuracy of protein design using native secondary sub-structures.

Movahedi M, Zare-Mirakabad F, Arab SS.

BMC Bioinformatics. 2016 Sep 5;17(1):353. doi: 10.1186/s12859-016-1199-y.

11.

Corrigendum: MWCOACH: Protein complex prediction in weighted PPI networks [Genes Genet. Syst. (2015) 90, p. 317-324].

Kouhsar M, Zare-Mirakabad F, Jamali Y.

Genes Genet Syst. 2016;91(1):47. doi: 10.1266/ggs.91.47.

12.

WCOACH: Protein complex prediction in weighted PPI networks.

Kouhsar M, Zare-Mirakabad F, Jamali Y.

Genes Genet Syst. 2015;90(5):317-24. doi: 10.1266/ggs.15-00032. Epub 2016 Jan 15. Erratum in: Genes Genet Syst. 2016;91(1):47.

13.

RNA secondary structure prediction based on SHAPE data in helix regions.

Lotfi M, Zare-Mirakabad F, Montaseri S.

J Theor Biol. 2015 Sep 7;380:178-82. doi: 10.1016/j.jtbi.2015.05.026. Epub 2015 May 30.

PMID:
26037307
14.

Using temperature effects to predict the interactions between two RNAs.

Ganjtabesh M, Montaseri S, Zare-Mirakabad F.

J Theor Biol. 2015 Jan 7;364:98-102. doi: 10.1016/j.jtbi.2014.09.001. Epub 2014 Sep 10.

PMID:
25218429
15.

RNA-RNA interaction prediction using genetic algorithm.

Montaseri S, Zare-Mirakabad F, Moghadam-Charkari N.

Algorithms Mol Biol. 2014 Jun 29;9:17. doi: 10.1186/1748-7188-9-17. eCollection 2014.

16.

Transcription factor binding sites prediction based on modified nucleosomes.

Talebzadeh M, Zare-Mirakabad F.

PLoS One. 2014 Feb 21;9(2):e89226. doi: 10.1371/journal.pone.0089226. eCollection 2014.

17.

Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method.

Ganjtabesh M, Zare-Mirakabad F, Nowzari-Dalini A.

EXCLI J. 2013 Jun 17;12:546-55. eCollection 2013.

18.

A heuristic approach to RNA-RNA interaction prediction.

Montaseri S, Moghadam-Charkari N, Zare-Mirakabad F.

J Theor Biol. 2012 May 7;300:206-11. doi: 10.1016/j.jtbi.2012.01.025. Epub 2012 Jan 26.

PMID:
22300797
19.

Genetic algorithm for dyad pattern finding in DNA sequences.

Zare-Mirakabad F, Ahrabian H, Sadeghi M, Hashemifar S, Nowzari-Dalini A, Goliaei B.

Genes Genet Syst. 2009 Feb;84(1):81-93.

20.

New scoring schema for finding motifs in DNA Sequences.

Zare-Mirakabad F, Ahrabian H, Sadeghi M, Nowzari-Dalini A, Goliaei B.

BMC Bioinformatics. 2009 Mar 20;10:93. doi: 10.1186/1471-2105-10-93.

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