prof. dr. sc. Mile Šikić

Full professor, Department of Electronic Systems and Information Processing

Location:
Public phone number:
6129-781
Internal phone number:
281

Time- and memory-efficient genome assembly with Raven

Vaser, Robert ; Šikić, Mile
2021.
Nature Computational Science

Efficacy of next-generation sequencing in bacterial zoonoses diagnostics

Duvnjak, Sanja ; Pavlinec, Željko ; Vaser, Robert ; Križanović, Krešimir ; Šikić, Mile ; Zdelar-Tuk, Maja ; Reil, Irena ; Spičić, Silvio
2021.
Veterinarska stanica

Detecting Base Modifications in DNA Sequences

Stanojević Dominik ; Šikić Mile
2020.
Fifth International Workshop on Data Science

A step towards neural genome assembly

Vrček, Lovro ; Veličković, Petar ; Šikić, Mile
2020.
NeurIPS 2020 Learning Meets Combinatorial Algorithms Workshop

Deep learning approach to determining the type of long reads

Vrček, Lovro ; Huang, Megan Hong Hui ; Vaser, Robert ; Šikić, Mile
2020.
International Conference on Intelligent Systems for Molecular Biology 2020

Benchmarking metagenomic classification tools for long read sequencing data

Josip Marić ; Sylvain Riondet ; Krešimir Križanović ; Niranjan Nagarajan ; Mile Šikić
2020.
28th International Conference on Intelligent Systems for Molecular Biology (ISMB) 2020

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
2019.
Nature Biotechnology

Disentangling Sources of Influence in Online Social Networks

Piškorec, Matija ; Šmuc, Tomislav ; Šikić, Mile
2019.
IEEE access

Approaches to metagenomic classification and assembly

Marić, Josip ; Šikić, Mile
2019.
42nd International Convention on Information, Communication and Electronic Technology

Supervised learning approach to long read classification

Vrček, Lovro ; Šikić, Mile
2019.
Fourth International Workshop on Data Science

Yet another de novo genome assembler

Vaser, Robert ; Šikić, Mile
2019.
2019 11th International Symposium on Image and Signal Processing and Analysis (ISPA)

RNA Splice Aware Mapper

Marić, Josip ; Križanović, Krešimir ; Šikić, Mile
2019.
Fourth International Workshop on Data Science

Horizontal silicon nanowires for surface-enhanced Raman spectroscopy

Gebavi, Hrvoje ; Ristić, Davor ; Baran, Nikola ; Mikac, Lara ; Mohaček-Grošev, Vlasta ; Gotić, Marijan ; Šikić, Mile ; Ivanda, Mile
2018.
Materials research express

Silicon Nanowires Substrates Fabrication for Ultra-Sensitive Surface Enhanced Raman Spectroscopy Sensors

Gebavi, Hrvoje ; Mikac, Lara ; Marciuš, Marijan ; Šikić, Mile ; Mohaček-Grošev, Vlasta ; Janči, Tibor ; Vidaček, Sanja ; Hasanspahić, Emina ; Omanović Miklićanin, Enisa ; Ivanda, Mile
2017.
Croatica chemica acta

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

Šošić, Martin ; Šikić, Mile
2017.
Bioinformatics

Fast and accurate de novo genome assembly from long uncorrected reads

Vaser, Robert ; Sović, Ivan ; Nagaranjan, Niranjan ; Šikić, Mile
2017.
Genome research

Inference of influence in social networks

Matija Piškorec, Nino Antulov-Fantulin, Iva Miholić, Tomislav Šmuc, Mile Šikić
2017.
CompleNet 2017

Rala - Rapid layout module for de novo genome assembly

Vaser, Robert ; Šikić, Mile
2017.
ISMB/ECCB 2017

Ra – Rapid de novo genome assembler

Vaser, Robert ; Šikić, Mile
2017.
ISMB/ECCB 2017

Read classification using semi-supervised deep learning

Šebrek, Tomislav ; Tomljanović, Jan ; Krapac, Josip ; Šikić, Mile
2017.
2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017

MinCall | MinION end2end convolutional deep learning basecaller

Miculinić, Neven ; Ratković, Marko ; Šikić, Mile
2017.
2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017

De Novo Assembly using Unsupervised Read Categorization

Tomljanović, Jan ; Šebrek, Tomislav ; Šikić, Mile
2017.
Second International Workshop on Data Science

De Novo Assembly using Semi-Supervised Read Categorization

Šebrek, Tomislav ; Tomljanović, Jan ; Šikić, Mile
2017.
Second International Workshop on Data Science

Algorithms for Layout Phase of De Novo Genome Assembly

Vaser, Robert ; Šikić, Mile
2017.
Second International Workshop on Data Science

Unsupervised Learning of Sequencing Read Types

Tomljanović, Jan ; Šebrek, Tomislav ; Šikić, Mile
2017.
ICCBB 2017

Differentiating between Exogenous and Endogenous Information Propagation in Social Networks

Piškorec, Matija ; Šmuc, Tomislav ; Šikić, Mile
2017.
Second International Workshop on Data Science

Modeling Peer and External Influence in Online Social Networks: Case of 2013 Referendum in Croatia

Piškorec, Matija ; Antulov-Fantulin, Nino ; Miholić, Iva ; Šmuc, Tomislav ; Šikić, Mile
2017.
Complex Networks 2017

Trade-offs in query and target indexing for the selection of candidates in protein homology searches

Ristov, Strahil ; Vaser, Robert ; Šikić, Mile
2017.
The Prague Stringology Conference

Informatics

Džapo, Hrvoje ; Podobnik, Vedran ; Pribanić, Tomislav ; Seder, Marija ; Šikić, Mile
2017.

RNA Transcriptome Mapping with GraphMap

Križanović, Krešimir ; Sović, Ivan ; Krpelnik, Ivan ; Šikić, Mile
2017.
13th International Symposium, ISBRA 2017

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

Križanović, Krešimir ; Echchiki, Amina ; Roux, Julien ; Šikić, Mile
2017.
Bioinformatics

SIFT missense predictions for genomes

Vaser, Robert ; Adusumalli, Swarnaseetha ; Ngak Leng, Sim ; Šikić, Mile ; Ng, Pauline C.
2016.
Nature Protocols

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Sović, Ivan ; Šikić, Mile ; Wilm Andreas ; Fenlon, Shannon Nicole ; Chen, Swaine
2016.
Nature Communications

SWORD—a highly efficient protein database search

Vaser, Robert ; Pavlović, Dario ; Šikić, Mile
2016.
Bioinformatics

Big data in the age of genomics

Šikić, Mile
2016.
Data Science Monetization 2016 Conference

SWORD—a highly efficient protein database search

Vaser, Robert ; Pavlović, Dario ; Šikić, Mile
2016.
ECCB 2016: THE 15TH EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY

Racon - Rapid consensus module for raw de novo genome assembly of long uncorrected reads

Vaser, Robert ; Sović, Ivan ; Nagarajan, Niranjan ; Šikić, Mile
2016.
London calling conference 2016

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

Sović, Ivan ; Križanović, Krešimir ; Skala, Karolj ; Šikić, Mile
2016.
Bioinformatics

TGTP-DB – a database for extracting genome, transcriptome and proteome data using taxonomy

Križanović, Krešimir ; Marinović, Mladen ; Bulović, Ana ; Vaser, Robert ; Šikić, Mile
2016.
39th International Convention Mipro 2016, Distributed Computing, Visualization and Biomedical Engineering /DC VIS

Statistical Inference Framework for Source Detection of Contagion Processes on Arbitrary Network Structures

Antulov-Fantulin, Nino ; Lančić, Alen ; Štefančić, Hrvoje ; Šikić, Mile ; Šmuc, Tomislav
2015.
IEEE Eighth International Conference on Self-Adaptive and Self-Organizing Systems Workshops

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

Antulov-Fantulin, Nino ; Lančić, Alen ; Šmuc, Tomislav ; Štefančić, Hrvoje ; Šikić, Mile
2015.
Physical Review Letters

Continuum model of gene expression

Novak, Andrej, Racz, Gabriela C. ; Sedmak, Goran ; Šikić, Mile
2015.
Thirteenth International Seminar: Mathematical Models & Modeling in Laser Plasma Processes & Advanced Science Technologies

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

Korpar, Matija ; Šošić, Martin ; Blažeka, Dino ; Šikić, Mile
2015.
PLoS One

Some new results on assessment of Q-gram filter efficiency

Novak, Andrej ; Križanović, Krešimir ; Lančić, Alen ; Šikić, Mile
2015.
International Symposium on Image and Signal Processing and Analysis (9 ; 2015))

ExoLocator—an online view into genetic makeup of vertebrate proteins

Khoo, Aik-Aun ; Ogrizek-Tomaš, Mario ; Bulović, Ana ; Korpar, Matija ; Gurler, Ece ; Slijepčević, Ivan ; Šikić, Mile ; Mihalek, Ivana
2014.
Nucleic acids research

FastSIR algorithm : A fast algorithm for the simulation of the epidemic spread in large networks by using the susceptible–infected–recovered compartment model

Antulov-Fantulin, Nino ; Lančić, Alen ; Štefančić, Hrvoje ; Šikić, Mile
2013.
Information sciences

Approaches to DNA de novo Assembly

Sović, Ivan ; Skala, Karolj ; Šikić, Mile
2013.
MIPRO

From Short to Long Reads: Benchmarking Assembly Tools

Sović, Ivan ; Skala, Karolj ; Šikić, Mile
2013.
ISMB/ECCB 2013

SW#–GPU-enabled exact alignments on genome scale

Korpar, Matija ; Šikić, Mile
2013.
Bioinformatics

Protein database search optimization based on CUDA and MPI

Pavlović, Dario ; Vaser, Robert ; Korpar, Matija ; Šikić, Mile
2013.
The 36th international ICT convention MIPRO

Epidemic centrality — is there an underestimated epidemic impact of network peripheral nodes?

Šikić, Mile ; Lančić, Alen ; Antulov-Fantulin, Nino ; Štefančić, Hrvoje
2013.
European physical journal B : condensed matter physics

Proteins and Nucleic Acids in Space and Time

Tomić, Sanja ; Brkić, Hrvoje ; Grabar Branilović, Marina ; Tomić, Antonija ; Branimir, Bertoša ; Mile, Šikić
2013.
Bioinformatics and biological physics

Aspects of DNA Assembly Acceleration on Reconfigurable Platforms

Sović, Ivan ; Šikić, Mile ; Skala, Karolj
2013.
IT SYSTEMS 2013

Prediction of interacting protein residues using sequence and structure data.

Franke, Vedran ; Šikić, Mile ; Vlahoviček, Kristian
2012.

CUDA implementation of the algorithm for simulating the epidemic spreading over large networks

Šošić, Matija ; Šikić, Mile
2012.
35. međunarodni skup MIPRO

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

Sandhu, Kuljeet Singh ; Li, Guoliang ; Poh, Huay Mei ; Quek , Yu Ling Kelly ; Sia , Yee Yen ; Peh, Su Qin ; Mulawadi, Fabianus Hendriyan ; Lim , Joanne ; Šikić, Mile ; Menghi, Francesca ; Thalamuthu, Anbupalam ; Sung , Wing Kin ; Ruan, Xiaoan ; Fullwood, Melissa Jane ; Liu, Edison ; Csermely , Peter ; Ruan, Yijun
2012.
Cell reports

BioMe : biologically relevant metals

Tus, Alan ; Rakipović, Alen ; Peretin, Goran ; Tomić, Sanja ; Šikić, Mile
2012.
Nucleic acids research

Phase diagram of epidemic spreading — unimodal vs. bimodal probability distributions

Lančić, Alen ; Antulov-Fantulin, Nino ; Šikić, Mile ; Štefančić, Hrvoje
2011.
Physica. A, Statistical mechanics and its applications

Epidemic centrality – identifying “superspreaders” in complex networks

Šikić, Mile ; Lančić, Alen ; Antulov-Fantulin, Nino ; Štefančić, Hrvoje
2011.
European Conference on Complex Systems 2011

Parallel Protein Docking Tool

Sović, Ivan ; Antulov-Fantulin, Nino ; Čanadi, Igor ; Šikić, Mile
2010.
International Convention on Information and Communication Technology, Electronics and Microelectronics (33 ; 2010)

Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests

Šikić, Mile ; Tomić, Sanja ; Vlahoviček, Kristian
2009.
Plos computational biology

Comparison of the RADIUS and Diameter Protocols

Stanke, Mladen ; Šikić, Mile
2008.
Information Technology Interfaces, 2008. ITI 2008. 30th International Conference on

Computational method for prediction of protein-protein interaction sites

Šikić, Mile
2008.

PSAIA - Protein Structure and Interaction Analyzer

Mihel, Josip ; Šikić, Mile ; Tomić, Sanja ; Jeren Branko ; Vlahoviček, Kristian
2008.
BMC STRUCTURAL BIOLOGY

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination

Dokmanić, Ivan ; Šikić, Mile ; Tomić, Sanja
2008.
Acta Crystallographica Section D - Biological Crystallography

Prediction of protein-protein hetero interaction sites from local sequence information using Random Forest

Šikić, Mile ; Jeren, Branko ; Vlahoviček, Kristian
2007.
The 2nd Opatija Meeting on Computational Solutions in the Life Sciences

Correlating protein surface shape and hydrophobicity using spherical harmonical expansions

Dokmanić, Ivan ; Šikić, Mile ; Tomić, Sanja
2007.
The 2nd Opatija Meeting on Computational Solutions in the Life Sciences

Protecting and controlling Virtual LANs by Linux router-firewall

Katić, Tihomir ; Šikić, Mile ; Šikić, Krešimir
2005.
Information Technology Interfaces

Guidline to maintain an efficient email working environment

Šikić, Mile
2004.
E-biz 2004

The content charging model in mobile packet networks

Šikić, Mile
2003.
MIPRO-2003

WLAN securtiy

Šikić, Mile
2003.
KOM 2003, Komunikacijske tehnologije i norme u informatici

Mobile content efficiency and business model

Šikić, Mile
2003.
Major Cities of Europe IT User's Group

Content charging models in mobile packet networks

Šikić, Mile
2002.

Teaching duties

University undergraduate

University graduate

Postgraduate doctoral study programme

Competences

  • Computational and artificial intelligence
    Artificial intelligence Computation theory
  • Computers and information processing
    Network theory (graphs) DNA computing

Personal data

Graduation year:
1996.
mr.sc. graduation year:
2002.
PhD graduation year:
2008.
Employed in this institution since:
1997.