Bioinformatics:

Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šilić; Fast and accurate de novo genome assembly from long uncorrected reads // Genome Research (2017)

Robert Vaser, Dario Pavlović, Mile Šikić;  SWORD - a higly efficient protein database search // Bioinformatics (2016) 32 (17)

Ivan Sović, Krešimir Križanović, Karolj Skala, and Mile Šikić: Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads, Bioinformatics (2016) 32 (17)

Ivan Sović, Mile Šikić, Andreas Wilm, Shannon Nicole Fenlon, Swaine Chen, Niranjan Nagarajan;  Fast and sensitive mapping of nanopore sequencing reads with GraphMap // Nature Communications 7, 2016

Robert Vaser, Swarnaseetha Adusumalli,Sim Ngak Leng, Mile Šikić; Pauline C. Ng, SIFT missense predictions for genomes . // Nature Protocols. 11 (2016) , 1; 1-9

Mirjana Domazet-Lošo, Tomislav Domazet-Lošo; gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances // PLoS One (2016)

Matija Korpar, Martin Šošić, Dino Blažeka, Mile Šikić. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search . // PLoS One. 10 (2015)

Khoo, Aik Aun;  Ogrizek-Tomaš, Mario; Bulović, Ana; Korpar, Matija; Gurler, Ece; Slijepčević, Ivan; Šikić, Mile; Mihalek, Ivana. ExoLocator - an online view into genetic makeup of vertebrate proteins, // Nucl. Acids Res./(2014) 42

Korpar, Matija, Šikić, Mile.:SW#–GPU-enabled exact alignments on genome scale  // Bioinformatics (2013) 29 (19): 2494-2495.

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,. Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks . // Cell reports. 2 (2012)

Tus, Alan; Rakipović, Alen; Peretin Goran; Tomić Sanja; Šikić, Mile. BioMe: biologically relevant metals . // Nucleic acids research. v40 (Web Server Issue) (2012),

Franke, Vedran; Šikić, Mile, Kristian Vlahoviček. Prediction of interacting protein residues using sequence and structure data. // Methods in Molecular Biology, Computer-Aided Drug Design. (2012) 819 , pp. 233-251

Mirjana Domazet-Lošo, Bernard Haubold; Alignment-free detection of local similarity among viral and bacterial genomes // Bioinformatics (2011)

Mirjana Domazet-Lošo, Bernard Haubold; Alignment-free detection of horizontal gene transfer between closely related bacterial genomes // Mobile Genetic Elements (2011)

Ivan Sović, Nino Antulov-Fantulin, Igor Čanadi Igor, Matija Piškorec, Mile Šikić. Parallel Protein Docking Tool // 33rd International Convention on Information and Communication Technology, Electronics and Microelectronics, MIPRO 2010; Opatija; 

Šikić, M., Tomić, S. and Vlahoviček, K.  Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests PLOS Computational Biology: 5(1), 2009 (pdf)

Mirjana Domazet-Lošo, Bernard Haubold; Efficient Estimation of Pairwise Distances between Genomes // Bioinformatics (2009)

Bernard Haubold, Peter Pfaffelhuber, Mirjana Domazet-Lošo, Thomas Wiehe; Estimating Mutation Distances from Unaligned Genomes // Journal of Computational Biology (2009)

Mihel, J., Šikić, M., Tomić, S., Jeren, B. and Vlahoviček, K. PSAIA - Protein structure and interaction analyser BMC Structural Biology: 8:21, 2008 (pdf)

Bernard Haubold, Mirjana Domazet-Lošo, Thomas Wiehe; Estimating Mutation Distances from Unaligned Genomes // Lecture Notes in Computer Science (2008)

Dokmanić, I., Šikić, M. and Tomić, S. Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination Acta Crystallographica Section D: Biological Crystallography, D64, 257-263, 2008 (pdf

Dokmanić, I., Šikić, M. and Tomić, S. Correlating protein surface shape and hydrophobicity using spherical harmonic expansions The 2nd Opatija Meeting on Computational Solutions in the Life Sciences, Opatija September 2007 (pdf)  

Šikić, M., Vlahoviček, K. and Jeren, B. Prediction of protein-protein hetero interaction sites from local sequence information using Random Forest The 2nd Opatija Meeting on Computational Solutions in the Life Sciences, Opatija September 2007 (pdf)

 

Complex networks:

Nino Antulov-Fantulin, Alen Lančić, Tomislav Šmuc, Hrvoje Štefančić, and Mile Šikić. Identification of Patient Zero in Static and Temporal Networks: Robustness and Limitations. Physical Review Letters 114, 248701 (2015).

Mile Šikić, Alen Lančić; Nino Antulov-Fantulin, Hrvoje Štefančić. Epidemic centrality - is there an underestimated epidemic impact of network peripheral nodes, European physical journal B : condensed matter physics (1434-6028) 86 (2013), 10; 1-13. 

Nino Antulov-Fantulin, Alen Lančić, Hrvoje Štefančić, Mile Šikić. FastSIR Algorithm: A Fast Algorithm for simulation of epidemic spread in large networks by using SIR compartment model, Information Sciences. Volume 239, 1 August 2013, Pages 226–240

Lančić, Alen; Antulov-Fantulin, Nino; Šikić, Mile; Štefančić, Hrvoje. Phase diagram of epidemic spreading — unimodal vs. bimodal probability distributions. // Physica. A, Statistical mechanics and its applications. 390 (2011).

Matija Šošić, Mile Šikić. CUDA implementation of the algorithm for simulation of the epidemic spread in large networks// 35th International Convention on Information and Communication Technology, Electronics andMicroelectronics, MIPRO 2012; Opatija;

Lančić, A., Antulov-Fantulin, N. Rektorova nagrada: Širenje epidemija na kompleksnim mrežama-teorijski modeli i računalne simulacije, 2009 (pdf)