prof. dr. sc. Mile Šikić

Full professor, Department of Electronic Systems and Information Processing

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

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

Sedlić, Filip; Sertić, Jadranka; Markotić, Alemka; Primorac, Dragan; Slavica, Anita; Zibar, Lada; Vlahoviček, Kristian; Kušec, Vesna; Barić, Ivo; Paar, Vladimir; Borovečki, Fran; Žmak, Ljiljana; Kurolt, Ivan-Christian; Canki-Klain, Nina; Roksandić, Sunčana; Rinčić, Iva; Jurić, Hrvoje; Škaro, Vedrana; Marjanović, Damir; Projić, Petar; Primorac, Damir; Starčević, Antonio; Vujaklija, Dušica; Šikić, Mile; Križanović, Krešimir; Gamulin, Stjepan
2024.
Croatian medical journal

Telomere-to-telomere phased genome assembly using error-corrected Simplex nanopore reads

Stanojević, Dominik; Lin, Dehui; Florez De Sessions, Paola; Sikić, Mile
2024.

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

Stanojević, Dominik; Li, Zhe; Bakić, Sara; Foo, Roger; Šikić, Mile
2024.
Nature communications

The Hitchhiker’s Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction

Sarashetti, Prasad; Lipovac, Josipa; Tomas, Filip; Šikic, Mile; Liu, Jianjun
2024.

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

Vujaklija, Ivan; Biđin, Siniša; Volarić, Marin; Bakić, Sara; Li, Zhe; Foo, Roger; Liu, Jianjun; Šikić, Mile
2024.
Nucleic acids research

Comparative Analysis of Nanopore-based Unsupervised Learning Methods in Epitranscriptomics

Vujaklija, Ivan; Biđin, Siniša; Šikić, Mile
2024.

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

Sarashetti, Prasad; Lipovac, Josipa; Tomas, Filip; Šikić, Mile; Liu, Jianjun
2024.
Genome biology

RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks

Penić, Rafael Josip; Vlašić, Tin; Huber, Roland G.; Wan, Yue; Šikić, Mile
2024.

Reconstruction of short genomic sequences with graph convolutional networks

Vrček, Lovro; Bresson, Xavier; Laurent, Thomas; Schmitz, Martin; Šikić, Mile
2023.

Utilizing parental data in trio binning diploid de novo genome assembly

Lipovac,Josipa;Križanović,Krešimir;Šikić,Mile
2023.

Facilitating genome structural variation analysis

Šikić, Mile
2023.
Nature methods

Reconstruction of short genomic sequences with graph convolutional networks

Vrček, Lovro; Bresson, Xavier; Thomas, Laurent; Schmitz, Martin; Šikić, Mile
2023.

Improving Metagenomic Classification Accuracy through Metagenome Assembly-driven Database Reduction

Lipovac,Josipa;Friganović,Krešimir;Šikić,Mile;Križanović,Krešimir
2023.

Harnessing the Power of Language Models to Predict RNA Structure

Penić, Rafael Josip; Vlašić, Tin; Šikić, Mile
2023.

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 ; Stanojević, 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 ; Šikić, Mile ; Wan, Yue ; Tan, Meng How
2022.
Nature methods

Asian Reference Genome Project

Šikić, Mile
2022.

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 ; Jing, Han Hong ; Chong, Shu Chen ; Ng, Cedric Chuan Young ; Liu, Wei ; Vaser, Robert ; Šikić, Mile ; Sung, Wing-Kin Ken ; Nagarajan, Niranjan ; Tan, Patrick ; Tean Teh, Bin
2022.
Communications biology

Combining protein and RNA structures information in developing new scoring functions

Martinović, Ivona
2022.

Evaluation of RNA Atom Distance Prediction Models

Šarić, Jelena
2022.

Removing chimeric reads improves metagenome assembly

Lipovac,Josipa;Huang,Meghan;Šikić,Mile;Bakić,Sara;Požega,Luka;Križanović,Krešimir
2022.

Detection of Modified Nucleotide Clusters in Nanopore Sequenced RNA Reads

Lipovac, Josipa
2021.

Whole genome comparison of Vibrio harveyi strains from the Mediterranean Sea

Pavlinec, Željko ; Vaser, Robert ; Zupičić, Ivana Giovanna ; Zrnčić, Snježana ; Oraić, Dražen ; Šikić, Mile
2021.

Data Structure for Efficient Storage of Genome Sequencing Data

Klabučar, Ivan
2021.

Generalization of partial order alignment

Rašić, Marin
2021.

Rapid alignment of high-fidelity seqeuncing data

Staver, Mauro
2021.

Time- and memory-efficient genome assembly with Raven

Vaser, Robert ; Šikić, Mile
2021.
Nature computational science

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

Chen, Ying; Davidson, Nadia M.; Wan, Yuk Kei; Patel, Harshil; Yao, Fei; Low, Hwee Meng; Hendra, Christopher; Watten, Laura; Sim, Andre; Sawyer, Chelsea; Iakovleva, Viktoriia; Lee, Puay Leng; Xin, Lixia; Ng, Hui En Vanessa; Loo, Jia Min; Ong, Xuewen; Ng, Hui Qi Amanda; Wang, Jiaxu; Koh, Wei Qian Casslynn; Poon, Suk Yeah Polly; Stanojević, Dominik; Tran, Hoang-Dai; Lim, Kok Hao Edwin; Toh, Shen Yon; Ewels, Philip Andrew; Ng, Huck-Hui; Iyer, N.Gopalakrishna; Thiery, Alexandre; Chng, Wee Joo; Chen, Leilei; DasGupta, Ramanuj; Sikić, Mile; Chan, Yun-Shen; Tan, Boon Ooi Patrick; Wan, Yue; Tam, Wai Leong; Yu, Qiang; Khor, Chiea Chuan; Wüstefeld, Torsten; Pratanwanich, Ploy N.; Love, Michael I.; Goh, Wee Siong Sho; Ng, Sarah B.; Oshlack, Alicia; Göke, Jonathan
2021.

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

DNA Nanopore Sequencing Basecaller

Pavlić, Stanislav
2021.

Deep learning model of nanopore sequencing pore

Penić, Rafael Josip
2021.

Whole genome comparison of Vibrio harveyi strains from the Mediterranean Sea

Pavlinec, Željko ; Vaser, Robert ; Zupičić, Ivana Giovanna ; Zrnčić, Snježana ; Oraić, Dražen ; Šikić, Mile
2021.

Detection of Modified Nucleotide Clusters in Nanopore Sequenced RNA Reads

Lipovac Josipa
2021.

Rapid Microbe Detection Using Deep Learning

Bakić, Sara
2021.

Detection of Modified Nucleotides Using Nanopore Sequencing and Deep Learning Methods

Deur, Sanja
2021.

Deep Learning Model of Nanopore Sequencing Pore

Penić, Rafael Josip
2021.

Rapid overlapping of Single Molecule High-Fidelity Sequencing Data

Pratljačić, Suzana
2021.

Deep Learning Model of Nanopore Sequencing Pore

Penić, Rafael Josip
2021.

De Novo Diploid Assembly Using Third-Generation Sequencing Data

Yatsukha, Roman
2020.

Microbe Detection Using Signal Processing and Locality Sensitive Hashing

Paulinović, Mate
2020.

System For Monitoring a Subject During Google Search

Šaravanja, Matej
2020.

De Novo Metagenome Assembly Using Third Generation Sequencing Dana

Brekalo, Tvrtko
2020.

Pipeline for Detection Clusters of Modified Nucleotides in Nanopore Sequenced RNA Reads

Martinović, Ivona
2020.

Deep learning approach to determining the type of long reads

Vrček, Lovro ; Huang, Megan Hong Hui ; Vaser, Robert ; Šikić, Mile
2020.

A step towards neural genome assembly

Vrček, Lovro ; Veličković, Petar ; Šikić, Mile
2020.

Overlapping Single Molecule High-Fidelity Sequencing Data

Babojelić, Dario
2020.

Microbe Detection Using Deep Learning

Baksa, Mirna
2020.

Benchmarking metagenomic classification tools for long read sequencing data

Josip Marić ; Sylvain Riondet ; Krešimir Križanović ; Niranjan Nagarajan ; Mile Šikić
2020.

Genome Scaffolding Using Hi-C Sequencing

Wolf, Filip
2020.

Detecting Base Modifications in DNA Sequences

Stanojević Dominik ; Šikić Mile
2020.

Upper bound in genome assembly

Požega, Luka
2019.

Reference-Guided de novo Genome Assembly

Bakić, Sara
2019.

Read classification using deep learning methods

Relić, Borna
2019.

Discovering gene variants from sequencing data

Kosier, Sanja
2019.

A Programming Library for Mapping Long RNA Reads

Penić, Rafael Josip
2019.

Short Reads Mapping

Pavlić, Stanislav
2019.

Long Reads Mapping

Pongračić, Kristijan
2019.

A Benchmark of Tools for Metagenomic Species Identification

Lipovac, Josipa
2019.

Early Screening for Preeclampsia

Rupe, Marina
2019.

Statistical inference of exogenous and endogenous information propagation in social networks

Piškorec, Matija
2019.

Algorithms for de novo assembly of large genomes

Vaser, Robert
2019.

A Programming Library for Mapping Long RNA Reads

Penić, Rafael Josip
2019.

Classification of 1D-Signal Types Using Deep Learning

Floreani, Filip
2019.

Sequence to graph mapping

Batić, Dominik
2019.

Using Reference Database for Plasmid Prediction

Deur, Sanja
2019.

A Benchmark of Tools for Metagenomic Species Identification

Lipovac, Josipa
2019.

Approaches to metagenomic classification and assembly

Marić, Josip ; Šikić, Mile
2019.

Yet another de novo genome assembler

Vaser, Robert ; Šikić, Mile
2019.

Supervised learning approach to long read classification

Vrček, Lovro ; Šikić, Mile
2019.

RNA Splice Aware Mapper

Marić, Josip ; Križanović, Krešimir ; Šikić, Mile
2019.

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

Polishing of a DNA sequence using deep learning methods

Vrček, Lovro
2019.

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

Hidden Markov Model for Base Calling of MinION Nanopore Reads

Selak, Ana Marija
2018.

Fast protein sequence similarity search

Babojelić, Dario
2018.

Landau-Vishkin-Nussinov Algorithm for Pair-wise Sequence Alignment

Vršnak, Donik
2018.

Approximate Algorithm for Computing Alignment Between Two Long Sequences

Sodić, Filip
2018.

The assessment of the expected genome assembly completeness from available reads

Fureš, Matej
2018.

A service for DNA backup

Šaravanja, Matej
2018.

Learned index structures

Paulinović, Mate
2018.

Mobile application for collecting user activity data

Baksa, Mirna
2018.

Scaffolding Assembled Genomes with Long Reads

Krpelnik, Ivan
2018.

End-to-End Deep Learning Model for Base Calling of MinION Nanopore Reads

Miculinić, Neven
2018.

De Novo Metagenome Assembly Using Read Clustering

Škugor, Luka
2018.

Scaffolding Assembled Genomes with Long Reads

Jurić, Antonio
2018.

Protein Database Search Using Partial Order Alignment

Žuljević, Petar
2018.

Classification of Large-Scale Biological Annotations Using Word Embeddings Derived from Corpora of Biomedical Research Literature

Baćac, Adriano
2017.

Read classification using semi-supervised deep learning

Šebrek, Tomislav ; Tomljanović, Jan ; Krapac, Josip ; Šikić, Mile
2017.

MinCall | MinION end2end convolutional deep learning basecaller

Miculinić, Neven ; Ratković, Marko ; Šikić, Mile
2017.

De Novo Assembly using Semi-Supervised Read Categorization

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

Algorithms for Layout Phase of De Novo Genome Assembly

Vaser, Robert ; Šikić, Mile
2017.

Unsupervised Learning of Sequencing Read Types

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

Differentiating between Exogenous and Endogenous Information Propagation in Social Networks

Piškorec, Matija ; Šmuc, Tomislav ; Šikić, Mile
2017.

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

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

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

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

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.
Studies in computational intelligence

Ra – Rapid de novo genome assembler

Vaser, Robert ; Šikić, Mile
2017.

Rala - Rapid layout module for de novo genome assembly

Vaser, Robert ; Šikić, Mile
2017.

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

Ristov, Strahil ; Vaser, Robert ; Šikić, Mile
2017.

Computing the Error Profiles of Third Generation Sequencing Technologies

Megla, Lucija
2017.

Classification of 1D-Signal Types Using Semi- Supervised Deep Learning

Šebrek, Tomislav
2017.

Deep Learning Model for Base Calling of MinION Nanopore Reads

Ratković, Marko
2017.

Identification of 1D-Signal Types Using Unsupervised Deep Learning

Tomljanović, Jan
2017.

Informatics

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

De Novo Assembly using Unsupervised Read Categorization

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

Inference of influence in social networks

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

Algorithm for the Alignment of Two Partial Order Alignment Graphs

Bradač, Mislav
2017.

Manual detection of false overlaps occurring during genome assembly

Floreani, Filip
2017.

dna2vec: vector representation of variable length k-mers

Kutnjak, Mateo
2017.

Analysis of a Metagenomic Sample Obtained by Third Generation Sequencing Technology

Rupe, Marina
2017.

RNA Transcriptome Mapping with GraphMap

Križanović, Krešimir ; Sović, Ivan ; Krpelnik, Ivan ; Šikić, Mile
2017.
Lecture notes in computer science

De novo assembly using long error-prone reads

Kostelac, Mario
2016.

Tree of Bloom Filters

Škugor, Luka
2016.

RNA-seq Alignment Using Existing Gene Annotations

Krpelnik, Ivan
2016.

Long RNA-Seq Alignment

Jurić, Antonio
2016.

Real-Time Analysis of a Metagenomic Sample Obtained by Nanopore Based Sequencing Technology

Vujević, Ivan
2016.

Detectability of Patient Zero Depending on its Position in the Network

Miholić, Iva
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

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

SWORD—a highly efficient protein database search

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

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

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

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

Križanović, Krešimir ; Marinović, Mladen ; Bulović, Ana ; Vaser, Robert ; Šikić, Mile
2016.

Big data in the age of genomics

Šikić, Mile
2016.

SWORD—a highly efficient protein database search

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

ALGORITHMS FOR DE NOVO GENOME ASSEMBLY FROM THIRD GENERATION SEQUENCING DATA

Sović, Ivan
2016.

Phylogenetic tree reconstruction using maximum parsimony branch-and-bound algorithm

Selak, Ana Marija
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

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

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

A reduced gene database for precision species detection

Humski, Dorija
2015.

Splice isoform identification from transcript graphs

Pavlović, Dario
2015.

EAGLER - Eliminating Assembly Gaps by Long Extending Reads

Šterbić, Luka
2015.

Generating consensus sequence using partially ordered multiple sequence alignment graphs

Baćac, Adriano
2015.

Long read aligner

Ratković, Marko
2015.

Global sequence alignment tool

Žužić, Goran
2015.

Reconstruction of a phylogenetic tree using a neighbor-joining method

Megla, Lucija
2015.

Suffix Tree

Šebrek, Tomislav
2015.

Continuum model of gene expression

Novak, Andrej, Racz, Gabriela C. ; Sedmak, Goran ; Šikić, Mile
2015.

Statistical inference algorithms for epidemic processes on complex networks

Antulov-Fantulin, Nino
2015.

Enhanced suffix array

Hadviger, Antea
2015.

Scaffolding using long error-prone reads

Čulinović, Marko
2015.

De novo transcriptome assembly

Vaser, Robert
2015.

Long Read RNA-seq Mapper

Marić, Josip
2015.

Some new results on assessment of Q-gram filter efficiency

Novak, Andrej ; Križanović, Krešimir ; Lančić, Alen ; Šikić, Mile
2015.

Simplification of the Overlap Graph

Rahle, Bruno
2014.

Information propagation in online social networks

Miholić, Iva
2014.

Genome alignment tool

Žuljević, Petar
2014.

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

Antulov-Fantulin, Nino ; Lančić, Alen ; Štefančić, Hrvoje ; Šikić, Mile ; Šmuc, Tomislav
2014.

De novo metagenomic assembly using Bayesian model-based clustering

Dvorničić, Mirta
2014.

RNA-seq mapper

Jerković, Igor
2014.

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

An SIMD dynamic programming C/C++ library

Šošić, Martin
2014.

Tool for fast searching of protein sequences in databases

Vujević, Ivan
2014.

Identify pathogen organisms from a stream of RNA sequences

Šošić, Matija
2014.

Finding overlapping DNA reads

Osrečki, Matija
2014.

Computational approaches for refinement and validation of genome assemblies

Županović, Vanessa
2014.

The evaluation of protein database searching tools

Vaser, Robert
2013.

Tool for aligning long DNA reads

Pavetić, Filip
2013.

SW#–GPU-enabled exact alignments on genome scale

Korpar, Matija ; Šikić, Mile
2013.
Bioinformatics

Web interface for sequence alignment

Blažeka, Dino
2013.

GPU implementation of a space and time optimal parallel sequence alignment algorithm

Mikulić, Marija
2013.

Optical map assembly: graph correction module

Šterbić, Luka
2013.

Alternative splicing

Humski, Dorija
2013.

Evaluation of a method for long read error correction

Pavlović, Dario
2013.

SW# - Sequence alignment library utilizing graphics processing units

Korpar, Matija
2013.

Computing method for determing protein interactions

Kušević, Katarina
2013.

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

Approaches to DNA de novo Assembly

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

From Short to Long Reads: Benchmarking Assembly Tools

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

Protein database search optimization based on CUDA and MPI

Pavlović, Dario ; Vaser, Robert ; Korpar, Matija ; Šikić, Mile
2013.

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

Proteins and Nucleic Acids in Space and Time

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

Aspects of DNA Assembly Acceleration on Reconfigurable Platforms

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

BioMe - statistical analyzer for biologically relevant metals

Rakipović, Alen
2012.

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

GPU implementation of time efficient linear space local alignment algorithm

Hucaljuk, Josip
2012.

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.

BioMe : biologically relevant metals

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

GPU implementation of an efficient linear-memory algorithm for local sequence alignment

Žužić, Goran
2012.

FM index implementation

Šošić, Matija
2012.

SWIG - Aligning structures using iterative application of Smith-Waterman algorithm

Rahle, Bruno
2012.

Application for automatic analysis of protein coding genes

Bulović, Ana
2012.

Implementation of compressed data structure for text searching based on FMindex

Šošić, Martin
2012.

A tool for simulating sequence reads

Županović, Vanessa
2012.

Web application for comparative analysis of protein paralogs

Ogrizek-Tomaš, Mario
2012.

Orhobalancer: web application for creation of taxonomically balanced sets of orthologous protein sequences

Slijepčević, Ivan
2012.

Make Me Move – didactic computer game for learning structural molecular biology

Jerković, Igor
2012.

Epidemic centrality – identifying “superspreaders” in complex networks

Šikić, Mile ; Lančić, Alen ; Antulov-Fantulin, Nino ; Štefančić, Hrvoje
2011.

Optimisation of firewall security rules

Katić, Tihomir
2011.

Adaptive wavelet transform implemented on CUDA platform

Osrečki, Matija
2011.

Protein docking tool: visualization module

Sović, Ivan
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

Electrostatic charge distribution calculation in CUDA

Pavetić, Filip
2011.

Detecting epistasis using ant colony optimization algorithm

Blažeka, Dino
2011.

Improved algorithm for selection and validation of best multivariate structure-property molecular models

Papeš Šokčević, Lidija
2011.

Smith-Waterman algorithm implementation using graphic cards with CUDA architecture

Korpar, Matija
2011.

Implementation of algorithm for computing protein interactions

Kušević, Katarina
2011.

Prediction of solvent accessible surface area from protein sequence

Popović, Irena
2011.

Multiresolution analysis of macromolecular structures

Matija Piškorec
2010.

Influence of quarantine on epidemic spread

Ogrizek-Tomaš, Mario
2010.

Representation of metals in proteins

Peretin, Goran
2010.

Parallel Protein Docking Tool

Sović, Ivan ; Antulov-Fantulin, Nino ; Čanadi, Igor ; Piškorec, Matija ; Šikić, Mile
2010.

A solution for accessing to servers that are inside of mobile networks

Bilić, Ivan
2010.

Protein Docking Tool: Steric Scan module

Čanadi, Igor
2010.

Secondary structure prediction using only sequence data

Janjić, Saša
2010.

Secondary protein structure analysis by the method of signal processing

Ćurić, Jura
2010.

Protein Docking tool: rotation and scoring modules

Antulov-Fantulin, Nino
2010.

Prediction of protein-protein interactions using Random Forests

Petrović, Juraj
2010.

Simulation of the impact organizing parties on propagation of viruses at spreading the infection

Rakipović, Alen
2010.

Protein Docking Tool: Module For Interaction Detection

Čolić, Dragana
2010.

Database of metals in proteins

Tus, Alan
2010.

Classification of coding regions in the genome

Štimac, Maja
2009.

Genome coding regions analysis

Bokšić, Mirna
2009.

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

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

PSAIA - Protein Structure and Interaction Analyzer

Mihel, Josip ; Šikić, Mile ; Tomić, Sanja ; Jeren Branko ; Vlahoviček, Kristian
2008.
BMC structural biology

The automated construction of a testing set for predicting of protein interactions

Petrović, Juraj
2008.

Visualization of macromolecules

Sović, Ivan
2008.

Computational method for prediction of protein-protein interaction sites

Šikić, Mile
2008.

Influence of epidemic spread on network structure

Antulov-Fantulin, Nino
2008.

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

Comparison of the RADIUS and Diameter Protocols

Stanke, Mladen ; Šikić, Mile
2008.

Identification of key players in complex networks of blogs

Piškorec, Matija
2008.

Correlating protein surface shape and hydrophobicity using spherical harmonical expansions

Dokmanić, Ivan ; Šikić, Mile ; Tomić, Sanja
2007.

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

Šikić, Mile ; Jeren, Branko ; Vlahoviček, Kristian
2007.

Protecting and controlling Virtual LANs by Linux router-firewall

Katić, Tihomir ; Šikić, Mile ; Šikić, Krešimir
2005.

Guidline to maintain an efficient email working environment

Šikić, Mile
2004.

The content charging model in mobile packet networks

Šikić, Mile
2003.

WLAN securtiy

Šikić, Mile
2003.

Mobile content efficiency and business model

Šikić, Mile
2003.

Content charging models in mobile packet networks

Šikić, Mile
2002.

Teaching

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.