Umarov R - Search Results

1

Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics.

Maddirevula S, Kuwahara H, Ewida N, Shamseldin HE, Patel N, Alzahrani F, AlSheddi T, AlObeid E, Alenazi M, Alsaif HS, Alqahtani M, AlAli M, Al Ali H, Helaby R, Ibrahim N, Abdulwahab F, Hashem M, Hanna N, Monies D, Derar N, Alsagheir A, Alhashem A, Alsaleem B, Alhebbi H, Wali S, Umarov R, Gao X, Alkuraya FS. Maddirevula S, et al. Among authors: umarov r. Genome Biol. 2020 Jun 17;21(1):145. doi: 10.1186/s13059-020-02053-9. Genome Biol. 2020. PMID: 32552793 Free PMC article. Clinical Trial.

2

Promoter analysis and prediction in the human genome using sequence-based deep learning models.

Umarov R, Kuwahara H, Li Y, Gao X, Solovyev V. Umarov R, et al. Bioinformatics. 2019 Aug 15;35(16):2730-2737. doi: 10.1093/bioinformatics/bty1068. Bioinformatics. 2019. PMID: 30601980

3

ACRE: Absolute concentration robustness exploration in module-based combinatorial networks.

Kuwahara H, Umarov R, Almasri I, Gao X. Kuwahara H, et al. Among authors: umarov r. Synth Biol (Oxf). 2017 Mar 1;2(1):ysx001. doi: 10.1093/synbio/ysx001. eCollection 2017 Jan. Synth Biol (Oxf). 2017. PMID: 32995502 Free PMC article.

4

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.

Dai H, Umarov R, Kuwahara H, Li Y, Song L, Gao X. Dai H, et al. Among authors: umarov r. Bioinformatics. 2017 Nov 15;33(22):3575-3583. doi: 10.1093/bioinformatics/btx480. Bioinformatics. 2017. PMID: 28961686 Free PMC article.

5

SBOLme: a Repository of SBOL Parts for Metabolic Engineering.

Kuwahara H, Cui X, Umarov R, Grünberg R, Myers CJ, Gao X. Kuwahara H, et al. Among authors: umarov r. ACS Synth Biol. 2017 Apr 21;6(4):732-736. doi: 10.1021/acssynbio.6b00278. Epub 2017 Jan 25. ACS Synth Biol. 2017. PMID: 28076956

6

DEEPre: sequence-based enzyme EC number prediction by deep learning.

Li Y, Wang S, Umarov R, Xie B, Fan M, Li L, Gao X. Li Y, et al. Among authors: umarov r. Bioinformatics. 2018 Mar 1;34(5):760-769. doi: 10.1093/bioinformatics/btx680. Bioinformatics. 2018. PMID: 29069344 Free PMC article.

7

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.

Umarov R, Li Y, Arakawa T, Takizawa S, Gao X, Arner E. Umarov R, et al. PLoS Comput Biol. 2021 Sep 7;17(9):e1009376. doi: 10.1371/journal.pcbi.1009376. eCollection 2021 Sep. PLoS Comput Biol. 2021. PMID: 34491989 Free PMC article.

8

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes.

Li Y, Xu Z, Han W, Cao H, Umarov R, Yan A, Fan M, Chen H, Duarte CM, Li L, Ho PL, Gao X. Li Y, et al. Among authors: umarov r. Microbiome. 2021 Feb 8;9(1):40. doi: 10.1186/s40168-021-01002-3. Microbiome. 2021. PMID: 33557954 Free PMC article.

9

A deep learning framework to predict binding preference of RNA constituents on protein surface.

Lam JH, Li Y, Zhu L, Umarov R, Jiang H, Héliou A, Sheong FK, Liu T, Long Y, Li Y, Fang L, Altman RB, Chen W, Huang X, Gao X. Lam JH, et al. Among authors: umarov r. Nat Commun. 2019 Oct 30;10(1):4941. doi: 10.1038/s41467-019-12920-0. Nat Commun. 2019. PMID: 31666519 Free PMC article.

10

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks.

Umarov RK, Solovyev VV. Umarov RK, et al. PLoS One. 2017 Feb 3;12(2):e0171410. doi: 10.1371/journal.pone.0171410. eCollection 2017. PLoS One. 2017. PMID: 28158264 Free PMC article.

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