Pesquisa | BVS Violência e Saúde

1.

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

Nguyen, Tram Anh; Heng, Jia Wei Joel; Kaewsapsak, Pornchai; Kok, Eng Piew Louis; Stanojevic, Dominik; Liu, Hao; Cardilla, Angelysia; Praditya, Albert; Yi, Zirong; Lin, Mingwan; Aw, Jong Ghut Ashley; Ho, Yin Ying; Peh, Kai Lay Esther; Wang, Yuanming; Zhong, Qixing; Heraud-Farlow, Jacki; Xue, Shifeng; Reversade, Bruno; Walkley, Carl; Ho, Ying Swan; Sikic, Mile; Wan, Yue; Tan, Meng How.

Nat Methods ; 19(7): 833-844, 2022 07.

Artigo em Inglês | MEDLINE | ID: mdl-35697834

2.

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

Maric, Josip; Krizanovic, Kresimir; Riondet, Sylvain; Nagarajan, Niranjan; Sikic, Mile.

BMC Bioinformatics ; 25(1): 15, 2024 Jan 11.

Artigo em Inglês | MEDLINE | ID: mdl-38212694

3.

Facilitating genome structural variation analysis.

Sikic, Mile.

Nat Methods ; 20(4): 491-492, 2023 04.

Artigo em Inglês | MEDLINE | ID: mdl-36959321

4.

Fast and accurate de novo genome assembly from long uncorrected reads.

Vaser, Robert; Sovic, Ivan; Nagarajan, Niranjan; Sikic, Mile.

Genome Res ; 27(5): 737-746, 2017 05.

Artigo em Inglês | MEDLINE | ID: mdl-28100585

5.

Evaluation of tools for long read RNA-seq splice-aware alignment.

Krizanovic, Kresimir; Echchiki, Amina; Roux, Julien; Sikic, Mile.

Bioinformatics ; 34(5): 748-754, 2018 03 01.

Artigo em Inglês | MEDLINE | ID: mdl-29069314

6.

The Applied Genomics Development Strategy by the Croatian Academy of Sciences and Arts paves the way for the future development of applied genomics in Croatia.

Sedlic, Filip; Sertic, Jadranka; Markotic, Alemka; Primorac, Dragan; Slavica, Anita; Zibar, Lada; Vlahovicek, Kristian; Kusec, Vesna; Baric, Ivo; Paar, Vladimir; Borovecki, Fran; Zmak, Ljiljana; Kurolt, Ivan-Christian; Canki-Klain, Nina; Roksandic, Suncana; Rincic, Iva; Juric, Hrvoje; Skaro, Vedrana; Marjanovic, Damir; Projic, Petar; Primorac, Damir; Starcevic, Antonio; Vujaklija, Dusica; Sikic, Mile; Krizanovic, Kresimir; Gamulin, Stjepan.

Croat Med J ; 65(3): 297-302, 2024 Jun 13.

Artigo em Inglês | MEDLINE | ID: mdl-38868976

7.

Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.

Sosic, Martin; Sikic, Mile.

Bioinformatics ; 33(9): 1394-1395, 2017 05 01.

Artigo em Inglês | MEDLINE | ID: mdl-28453688

8.

SWORD-a highly efficient protein database search.

Vaser, Robert; Pavlovic, Dario; Sikic, Mile.

Bioinformatics ; 32(17): i680-i684, 2016 09 01.

Artigo em Inglês | MEDLINE | ID: mdl-27587689

9.

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

Sovic, Ivan; Krizanovic, Kresimir; Skala, Karolj; Sikic, Mile.

Bioinformatics ; 32(17): 2582-9, 2016 09 01.

Artigo em Inglês | MEDLINE | ID: mdl-27162186

10.

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

Khoo, Aik Aun; Ogrizek-Tomas, Mario; Bulovic, Ana; Korpar, Matija; Gürler, Ece; Slijepcevic, Ivan; Sikic, Mile; Mihalek, Ivana.

Nucleic Acids Res ; 42(Database issue): D879-81, 2014 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-24271393

11.

Identification of Patient Zero in Static and Temporal Networks: Robustness and Limitations.

Antulov-Fantulin, Nino; Lancic, Alen; Smuc, Tomislav; Stefancic, Hrvoje; Sikic, Mile.

Phys Rev Lett ; 114(24): 248701, 2015 Jun 19.

Artigo em Inglês | MEDLINE | ID: mdl-26197016

12.

SW#-GPU-enabled exact alignments on genome scale.

Korpar, Matija; Sikic, Mile.

Bioinformatics ; 29(19): 2494-5, 2013 Oct 01.

Artigo em Inglês | MEDLINE | ID: mdl-23864730

13.

BioMe: biologically relevant metals.

Tus, Alan; Rakipovic, Alen; Peretin, Goran; Tomic, Sanja; Sikic, Mile.

Nucleic Acids Res ; 40(Web Server issue): W352-7, 2012 Jul.

Artigo em Inglês | MEDLINE | ID: mdl-22693222

14.

Genome assembly and chemogenomic profiling of National Flower of Singapore Papilionanthe Miss Joaquim 'Agnes' reveals metabolic pathways regulating floral traits.

Lim, Abner Herbert; Low, Zhen Jie; Shingate, Prashant Narendra; Hong, Jing Han; Chong, Shu Chen; Ng, Cedric Chuan Young; Liu, Wei; Vaser, Robert; Sikic, Mile; Sung, Wing-Kin Ken; Nagarajan, Niranjan; Tan, Patrick; Teh, Bin Tean.

Commun Biol ; 5(1): 967, 2022 09 15.

Artigo em Inglês | MEDLINE | ID: mdl-36109650

15.

Time- and memory-efficient genome assembly with Raven.

Vaser, Robert; Sikic, Mile.

Nat Comput Sci ; 1(5): 332-336, 2021 May.

Artigo em Inglês | MEDLINE | ID: mdl-38217213

16.

Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.

Sikic, Mile; Tomic, Sanja; Vlahovicek, Kristian.

PLoS Comput Biol ; 5(1): e1000278, 2009 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-19180183

17.

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes.

Bertrand, Denis; Shaw, Jim; Kalathiyappan, Manesh; Ng, Amanda Hui Qi; Kumar, M Senthil; Li, Chenhao; Dvornicic, Mirta; Soldo, Janja Paliska; Koh, Jia Yu; Tong, Chengxuan; Ng, Oon Tek; Barkham, Timothy; Young, Barnaby; Marimuthu, Kalisvar; Chng, Kern Rei; Sikic, Mile; Nagarajan, Niranjan.

Nat Biotechnol ; 37(8): 937-944, 2019 08.

Artigo em Inglês | MEDLINE | ID: mdl-31359005

18.

PSAIA - protein structure and interaction analyzer.

Mihel, Josip; Sikic, Mile; Tomic, Sanja; Jeren, Branko; Vlahovicek, Kristian.

BMC Struct Biol ; 8: 21, 2008 Apr 09.

Artigo em Inglês | MEDLINE | ID: mdl-18400099

19.

SIFT missense predictions for genomes.

Vaser, Robert; Adusumalli, Swarnaseetha; Leng, Sim Ngak; Sikic, Mile; Ng, Pauline C.

Nat Protoc ; 11(1): 1-9, 2016 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-26633127

20.

Fast and sensitive mapping of nanopore sequencing reads with GraphMap.

Sovic, Ivan; Sikic, Mile; Wilm, Andreas; Fenlon, Shannon Nicole; Chen, Swaine; Nagarajan, Niranjan.

Nat Commun ; 7: 11307, 2016 Apr 15.

Artigo em Inglês | MEDLINE | ID: mdl-27079541

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