prof. dr. sc. Mile Šikić

External associate, Department of Electronic Systems and Information Processing

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

Supervised learning approach to long read classification

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

RNA Splice Aware Mapper

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

Approaches to metagenomic classification and assembly

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

Disentangling Sources of Influence in Online Social Networks

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

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

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

Informatics

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

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

Differentiating between Exogenous and Endogenous Information Propagation in Social Networks

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

Unsupervised Learning of Sequencing Read Types

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

Algorithms for Layout Phase of De Novo Genome Assembly

Vaser, Robert ; 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

De Novo Assembly using Unsupervised Read Categorization

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

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

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

Ra – Rapid de novo genome assembler

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

Rala - Rapid layout module for de novo genome assembly

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

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

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

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

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

Inference of influence in social networks

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

RNA Transcriptome Mapping with GraphMap

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

Fast and accurate de novo genome assembly from long uncorrected reads

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

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

Šošić, Martin ; Šikić, Mile
2017.
Bioinformatics

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

SWORD—a highly efficient protein database search

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

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.
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

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

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

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

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

SIFT missense predictions for genomes

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

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

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

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

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))

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

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

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

Aspects of DNA Assembly Acceleration on Reconfigurable Platforms

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

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

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

Protein database search optimization based on CUDA and MPI

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

SW#–GPU-enabled exact alignments on genome scale

Korpar, Matija ; Šikić, Mile
2013.
Bioinformatics

From Short to Long Reads: Benchmarking Assembly Tools

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

Approaches to DNA de novo Assembly

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

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

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

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

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

Prediction of interacting protein residues using sequence and structure data.

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

Epidemic centrality – identifying “superspreaders” in complex networks

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

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

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

Computational method for prediction of protein-protein interaction sites

Šikić, Mile
2008.

Comparison of the RADIUS and Diameter Protocols

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

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

Mobile content efficiency and business model

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

WLAN securtiy

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

The content charging model in mobile packet networks

Šikić, Mile
2003.
MIPRO-2003

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.