Comparison of the RADIUS and Diameter protocols. - Mladen Stanke; Mile Sikic (ITI, 2008)

Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests. - Mile Sikic; Sanja Tomic; Kristian Vlahovicek (PLoS Comput. Biol., 2009)

Epidemic centrality and the underestimated epidemic impact on network peripheral nodes - Mile Sikic; Alen Lancic; Nino Antulov-Fantulin; Hrvoje Stefancic (CoRR, 2011)

CUDA implementation of the algorithm for simulating the epidemic spreading over large networks. - Matija Sosic; Mile Sikic (MIPRO, 2012)

FastSIR Algorithm: A Fast Algorithm for simulation of epidemic spread in large networks by using SIR compartment model - Nino Antulov-Fantulin; Alen Lancic; Hrvoje Stefancic; Mile Sikic (CoRR, 2012)

BioMe: biologically relevant metals. - Alan Tus; Alen Rakipovic; Goran Peretin; Sanja Tomic; Mile Sikic (Nucleic Acids Res., 2012)

SW#-GPU-enabled exact alignments on genome scale. - Matija Korpar; Mile Sikic (Bioinform., 2013)

FastSIR algorithm: A fast algorithm for the simulation of the epidemic spread in large networks by using the susceptible-infected-recovered compartment model. - Nino Antulov-Fantulin; Alen Lancic; Hrvoje Stefancic; Mile Sikic (Inf. Sci., 2013)

Statistical Inference Framework for Source Detection of Contagion Processes on Arbitrary Network Structures. - Nino Antulov-Fantulin; Alen Lancic; Hrvoje Stefancic; Mile Sikic; Tomislav Smuc (SASO Workshops, 2014)

Detectability limits of epidemic sources in networks. - Nino Antulov-Fantulin; Alen Lancic; Tomislav Smuc; Hrvoje Stefancic; Mile Sikic (CoRR, 2014)

$LCSk$++: Practical similarity metric for long strings. - Filip Pavetic; Goran Zuzic; Mile Sikic (CoRR, 2014)

ExoLocator - an online view into genetic makeup of vertebrate proteins. - Aik Aun Khoo; Mario Ogrizek-Tomas; Ana Bulovic; Matija Korpar; Ece Gürler; Ivan Slijepcevic; Mile Sikic; Ivana Mihalek (Nucleic Acids Res., 2014)

Some new results on assessment of Q-gram filter efficiency. - Andrej Novák; Kresimir Krizanovic; Alen Lancic; Mile Sikic (ISPA, 2015)

Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads. - Ivan Sovic; Kresimir Krizanovic; Karolj Skala; Mile Sikic (Bioinform., 2016)

SWORD - a highly efficient protein database search. - Robert Vaser; Dario Pavlovic; Mile Sikic (Bioinform., 2016)

Modeling peer and external influence in online social networks. - Matija Piskorec; Nino Antulov-Fantulin; Iva Miholic; Tomislav Smuc; Mile Sikic (CoRR, 2016)

Modeling Peer and External Influence in Online Social Networks: Case of 2013 Referendum in Croatia. - Matija Piskorec; Nino Antulov-Fantulin; Iva Miholic; Tomislav Smuc; Mile Sikic (COMPLEX NETWORKS, 2017)

Unsupervised Learning of Sequencing Read Types. - Jan Tomljanovic; Tomislav Sebrek; Mile Sikic (ICCBB, 2017)

Trade-offs in Query and Target Indexing for the Selection of Candidates in Protein Homology Searches. - Strahil Ristov; Robert Vaser; Mile Sikic (Stringology, 2017)

Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. - Martin Sosic; Mile Sikic (Bioinform., 2017)

Fast and simple algorithms for computing both $LCS_{k}$ and $LCS_{k+}$. - Filip Pavetic; Ivan Katanic; Gustav Matula; Goran Zuzic; Mile Sikic (CoRR, 2017)

Fast and Simple Algorithms for Computing both LCSk and LCSk+. - Filip Pavetic; Ivan Katanic; Gustav Matula; Goran Zuzic; Mile Sikic (Stringology, 2018)

Evaluation of tools for long read RNA-seq splice-aware alignment. - Kresimir Krizanovic; Amina Echchiki; Julien Roux; Mile Sikic (Bioinform., 2018)

Yet another de novo genome assembler. - Robert Vaser; Mile Sikic (ISPA, 2019)

Approaches to metagenomic classification and assembly. - Josip Maric; Mile Sikic (MIPRO, 2019)

Disentangling Sources of Influence in Online Social Networks. - Matija Piskorec; Tomislav Smuc; Mile Sikic (IEEE Access, 2019)

MinCall - MinION end2end convolutional deep learning basecaller. - Neven Miculinic; Marko Ratkovic; Mile Sikic (CoRR, 2019)

Read classification using semi-supervised deep learning. - Tomislav Sebrek; Jan Tomljanovic; Josip Krapac; Mile Sikic (CoRR, 2019)

A step towards neural genome assembly. - Lovro Vrcek; Petar Velickovic; Mile Sikic (CoRR, 2020)

Time- and memory-efficient genome assembly with Raven. - Robert Vaser; Mile Sikic (Nat. Comput. Sci., 2021)

Learning to Untangle Genome Assembly with Graph Convolutional Networks. - Lovro Vrcek; Xavier Bresson; Thomas Laurent 001; Martin Schmitz 002; Mile Sikic (CoRR, 2022)

Finding Hamiltonian Cycles with Graph Neural Networks. - Filip Bosnic; Mile Sikic (ISPA, 2023)

Graph Neural Network Meets de Bruijn Genome Assembly. - Marijo Simunovic; Lovro Vrcek; Mile Sikic (ISPA, 2023)

Reconstruction of short genomic sequences with graph convolutional networks. - Lovro Vrcek; Xavier Bresson; Thomas Laurent 001; Martin Schmitz 002; Mile Sikic (MIPRO, 2023)

Comparative Analysis of Nanopore-based Unsupervised Learning Methods in Epitranscriptomics. - Ivan Vujaklija; Sinisa Bidin; Mile Sikic (MIPRO, 2024)

RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks. - Rafael Josip Penic; Tin Vlasic; Roland G. Huber; Yue Wan; Mile Sikic (CoRR, 2024)

Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction". - Ivona Martinovic; Tin Vlasic; Yang Li 107; Bryan Hooi; Yang Zhang 040; Mile Sikic (Zenodo, 2024)

Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction". - Ivona Martinovic; Tin Vlasic; Yang Li 107; Bryan Hooi; Yang Zhang 040; Mile Sikic (Zenodo, 2024)

Comparative analysis of metagenomic classifiers for long-read sequencing datasets. - Josip Maric; Kresimir Krizanovic; Sylvain Riondet; Niranjan Nagarajan; Mile Sikic (BMC Bioinform., 2024)