Šikić M - Search Results

1

Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering.

Vujaklija I, Biđin S, Volarić M, Bakić S, Li Z, Foo R, Liu J, Šikić M. Vujaklija I, et al. Among authors: sikic m. Nucleic Acids Res. 2024 Dec 10:gkae1168. doi: 10.1093/nar/gkae1168. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39658045

2

Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing.

Stanojević D, Li Z, Bakić S, Foo R, Šikić M. Stanojević D, et al. Among authors: sikic m. Nat Commun. 2024 Jul 3;15(1):5580. doi: 10.1038/s41467-024-49847-0. Nat Commun. 2024. PMID: 38961062 Free PMC article.

3

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references.

Sarashetti P, Lipovac J, Tomas F, Šikić M, Liu J. Sarashetti P, et al. Among authors: sikic m. Genome Biol. 2024 Dec 18;25(1):312. doi: 10.1186/s13059-024-03452-y. Genome Biol. 2024. PMID: 39696427 Free PMC article.

4

BioMe: biologically relevant metals.

Tus A, Rakipovic A, Peretin G, Tomic S, Sikic M. Tus A, et al. Among authors: sikic m. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W352-7. doi: 10.1093/nar/gks514. Epub 2012 Jun 12. Nucleic Acids Res. 2012. PMID: 22693222 Free PMC article.

5

ExoLocator--an online view into genetic makeup of vertebrate proteins.

Khoo AA, Ogrizek-Tomas M, Bulovic A, Korpar M, Gürler E, Slijepcevic I, Šikic M, Mihalek I. Khoo AA, et al. Among authors: sikic m. Nucleic Acids Res. 2014 Jan;42(Database issue):D879-81. doi: 10.1093/nar/gkt1164. Epub 2013 Nov 23. Nucleic Acids Res. 2014. PMID: 24271393 Free PMC article.

6

Fast and sensitive mapping of nanopore sequencing reads with GraphMap.

Sović I, Šikić M, Wilm A, Fenlon SN, Chen S, Nagarajan N. Sović I, et al. Among authors: sikic m. Nat Commun. 2016 Apr 15;7:11307. doi: 10.1038/ncomms11307. Nat Commun. 2016. PMID: 27079541 Free PMC article.

7

Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads.

Sović I, Križanović K, Skala K, Šikić M. Sović I, et al. Among authors: sikic m. Bioinformatics. 2016 Sep 1;32(17):2582-9. doi: 10.1093/bioinformatics/btw237. Epub 2016 May 9. Bioinformatics. 2016. PMID: 27162186

8

Direct identification of A-to-I editing sites with nanopore native RNA sequencing.

Nguyen TA, Heng JWJ, Kaewsapsak P, Kok EPL, Stanojević D, Liu H, Cardilla A, Praditya A, Yi Z, Lin M, Aw JGA, Ho YY, Peh KLE, Wang Y, Zhong Q, Heraud-Farlow J, Xue S, Reversade B, Walkley C, Ho YS, Šikić M, Wan Y, Tan MH. Nguyen TA, et al. Among authors: sikic m. Nat Methods. 2022 Jul;19(7):833-844. doi: 10.1038/s41592-022-01513-3. Epub 2022 Jun 13. Nat Methods. 2022. PMID: 35697834

9

Comparative analysis of metagenomic classifiers for long-read sequencing datasets.

Marić J, Križanović K, Riondet S, Nagarajan N, Šikić M. Marić J, et al. Among authors: sikic m. BMC Bioinformatics. 2024 Jan 11;25(1):15. doi: 10.1186/s12859-024-05634-8. BMC Bioinformatics. 2024. PMID: 38212694 Free PMC article.

10

Time- and memory-efficient genome assembly with Raven.

Vaser R, Šikić M. Vaser R, et al. Among authors: sikic m. Nat Comput Sci. 2021 May;1(5):332-336. doi: 10.1038/s43588-021-00073-4. Epub 2021 May 20. Nat Comput Sci. 2021. PMID: 38217213

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