prof. dr. sc. Mile Šikić

Full professor, Department of Electronic Systems and Information Processing

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

1. Franke, Vedran; Šikić, Mile; Vlahoviček, Kristian.
Prediction of interacting protein residues using sequence and structure data. // Computational Drug Discovery and Design / Riccardo Baron, editor(s).
New York, Dordrecht, Heidelberg, London : Springer, 2012. Str. 233-251.
 
  Journal articles and review articles in CC journals
 

1. Gebavi, Hrvoje; Ristić, Davor; Baran, Nikola; Mikac, Lara; Mohaček-Grošev, Vlasta; Gotić, Marijan; Šikić, Mile; Ivanda, Mile.
Horizontal silicon nanowires for surface-enhanced Raman spectroscopy. // Materials research express. 15 (2018) , 1; (journal article).

2. Gebavi, Hrvoje; Mikac, Lara; Marciuš, Marijan; Šikić, Mile; Mohaček-Grošev, Vlasta; Janči, Tibor; Vidaček, Sanja; Hasanspahić, Emina; Omanović Miklićanin, Enisa; Ivanda, Mile.
Silicon Nanowires Substrates Fabrication for Ultra-Sensitive Surface Enhanced Raman Spectroscopy Sensors. // Croatica chemica acta. 90 (2017) , 2; 259-262 (journal article).

3. Križanović, Krešimir; Echchiki, Amina; Roux, Julien; Šikić, Mile.
Evaluation of tools for long read RNA-seq splice- aware alignment. // Bioinformatics. btx668 (2017) ; (journal article).

4. Šošić, Martin; Šikić, Mile.
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. // Bioinformatics. 33 (2017) , 9; 1394-1395 (journal article).

5. Vaser, Robert; Sović, Ivan; Nagaranjan, Niranjan; Šikić, Mile.
Fast and accurate de novo genome assembly from long uncorrected reads. // Genome research. 27 (2017) ; 737-746 (journal article).

6. Sović, Ivan; Križanović, Krešimir; Skala, Karolj; Šikić, Mile.
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads. // Bioinformatics. 32 (2016) , 17; 2582-2589 (journal article).

7. Sović, Ivan; Šikić, Mile; Wilm Andreas; Fenlon, Shannon Nicole; Chen, Swaine.
Fast and sensitive mapping of nanopore sequencing reads with GraphMap. // Nature Communications. 7 (2016) ; 11307-1-11307-11 (journal article).

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

9. Vaser, Robert; Pavlović, Dario; Šikić, Mile.
SWORD—a highly efficient protein database search. // Bioinformatics. 32 (2016) , 17; 680-684 (journal article).

10. Antulov-Fantulin, Nino; Lančić, Alen; Šmuc, Tomislav; Štefančić, Hrvoje; Šikić, Mile.
Identification of Patient Zero in Static and Temporal Networks : Robustness and Limitations. // Physical Review Letters. 114 (2015) ; 248701-1-248701-5 (journal article).

11. 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. // Nucleic acids research. 42 (2014) , D1; 879-881 (journal article).

12. Antulov-Fantulin, Nino; Lančić, Alen; Štefančić, Hrvoje; Šikić, Mile.
FastSIR algorithm : A fast algorithm for the simulation of the epidemic spread in large networks by using the susceptible–infected–recovered compartment model. // Information sciences. 239 (2013) ; 226-240 (journal article).

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

14. Šikić, Mile; Lančić, Alen; Antulov-Fantulin, Nino; Štefančić, Hrvoje.
Epidemic centrality — is there an underestimated epidemic impact of network peripheral nodes?. // European physical journal B : condensed matter physics. 86 (2013) , 10; 440-1-440-13 (journal article).

15. Tus, Alan; Rakipović, Alen; Peretin, Goran; Tomić, Sanja; Šikić, Mile.
BioMe : biologically relevant metals. // Nucleic acids research. 40 (2012) ; W352-W357 (journal article).

16. 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) , 1; 65-76 (journal article).

17. Dokmanić, Ivan; Šikić, Mile; Tomić, Sanja.
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. 64 (2008) , 3; 257-263 (journal article).
 
  Scientific papers in other journals
 

1. Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile.
SW#db: GPU-Accelerated Exact Sequence Similarity Database Search. // PLoS One. 10 (2015) , 12; (journal article).

2. 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) ; 1-13 (journal article).

3. Šikić, Mile; Tomić, Sanja; Vlahoviček, Kristian.
Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests. // Plos computational biology. 5 (2009) , 1; e1000278-1-e1000278-9 (journal article).

4. Mihel, Josip; Šikić, Mile; Tomić, Sanja; Jeren Branko; Vlahoviček, Kristian.
PSAIA - Protein Structure and Interaction Analyzer. // Bmc structural biology. 8 (2008) ; (journal article).
 
  Conference reports (abstracts) in other journals
 

1. Križanović, Krešimir; Sović, Ivan; Krpelnik, Ivan; Šikić, Mile.
RNA Transcriptome Mapping with GraphMap // Bioinformatics Research and Applications 13th International Symposium, ISBRA 2017 / Cai, Zhipeng ; Daescu, Ovidiu ; Li, Min, editor(s).
Springer, 2017. (lecture,international peer-review,abstract,scientific).
 
  Published invited lectures
 

1. Tomić, Sanja; Brkić, Hrvoje; Grabar Branilović, Marina; Tomić, Antonija; Branimir, Bertoša; Mile, Šikić.
Proteins and Nucleic Acids in Space and Time // Bioinformatics and biological physics: proceedings of the scientific meeting / Paar, Vladimir, editor(s).
Zagreb : Hrvatska akademija znanosti i umjetnosti, 2013. 149-157 (invited talk,domestic peer-review,published).

2. Šikić, Mile.
Mobile content efficiency and business model // Major Cities of Europe IT User's Group, Zagreb 2003.
2003. (invited talk,published).
 
  Scientific conference papers with international peer-review
 

1. Piškorec, Matija; Antulov-Fantulin, Nino; Miholić, Iva; Šmuc, Tomislav; Šikić, Mile.
Modeling Peer and External Influence in Online Social Networks: Case of 2013 Referendum in Croatia // Complex Networks and Their Applications VI: Proceedings of Complex Networks 2017 (The Sixth International Conference on Complex Networks and Their Applications) / Cherifi, Chantal ; Cherifi, Hocine ; Karsai, Marton ; Musolesi, Mirco, editor(s).
Springer International Publishing, 2017. 1015-1027 (lecture,international peer-review,published,scientific).

2. Ristov, Strahil; Vaser Robert; Šikić Mile.
Trade-offs in query and target indexing for the selection of candidates in protein homology searches // Proceedings of The Prague Stringology Conference 2017 / Jan Holub and Jan Ždarek, editor(s).
Prag : Czech Technical University in Prague, 2017. 118-125 (lecture,international peer-review,published,scientific).

3. Tomljanović, Jan; Šebrek, Tomislav; Šikić, Mile.
Unsupervised Learning of Sequencing Read Types // Proceedings of the 2017 International Conference on Computational Biology and Bioinformatics.
2017. 12-17 (lecture,international peer-review,published,scientific).

4. Križanović, Krešimir; Marinović, Mladen; Bulović, Ana; Vaser, Robert; Šikić, Mile.
TGTP-DB – a database for extracting genome, transcriptome and proteome data using taxonomy // Proceedings of the 39th International Convention Mipro 2016, Distributed Computing, Visualization and Biomedical Engineering /DC VIS / Biljanović, Petar, editor(s).
Rijeka : Croatian Society for Information and Communication Technology, Electronics and Microelectronics - MIPRO, 2016. 472-476 (lecture,international peer-review,published,scientific).

5. Vaser, Robert; Pavlović, Dario; Šikić, Mile.
SWORD—a highly efficient protein database search // ECCB 2016: THE 15TH EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY.
2016. 680-684 (lecture,international peer-review,published,scientific).

6. Antulov-Fantulin, Nino; Lančić, Alen; Štefančić, Hrvoje; Šikić, Mile; Šmuc, Tomislav.
Statistical Inference Framework for Source Detection of Contagion Processes on Arbitrary Network Structures // Proceedings of 2014 IEEE Eighth International Conference on Self-Adaptive and Self-Organizing Systems Workshops.
2015. 78-83 (international peer-review,published,scientific).

7. Novak, Andrej; Križanović, Krešimir; Lančić, Alen; Šikić, Mile.
Some new results on assessment of Q-gram filter efficiency // 9th International Symposium on Image and Signal Processing and Analysis (ISPA) 2015 . proceedings.
IEEE, 2015. 294-297 (lecture,international peer-review,published,scientific).

8. Pavlović, Dario; Vaser, Robert; Korpar, Matija; Šikić, Mile.
Protein database search optimization based on CUDA and MPI // .
(lecture,international peer-review,published,scientific).

9. Sović, Ivan; Skala, Karolj; Šikić, Mile.
Approaches to DNA de novo Assembly // Mipro 2013, Proceedings of the 36th International Convention.
(lecture,international peer-review,published,scientific).

10. Sović, Ivan; Šikić, Mile; Skala, Karolj.
Aspects of DNA Assembly Acceleration on Reconfigurable Platforms // PROCEEDINGS IT SYSTEMS 2013 / Žagar, Martin ; Knezović, Josip ; Mlinarić, Hrvoje ; Hofman Daniel, Kovač Mario, editor(s).
Bol, Brač, Hrvatska : University of Zagreb, Faculty of Electrical Engineering and Computing, 2013. 289-292 (lecture,international peer-review,published,scientific).

11. Šošić, Matija; Šikić, Mile.
CUDA implementation of the algorithm for simulating the epidemic spreading over large networks // .
(lecture,international peer-review,published,scientific).

12. Sović, Ivan; Antulov-Fantulin, Nino; Čanadi, Igor; Šikić, Mile.
Parallel Protein Docking Tool // 33rd International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO 2010) : Proceedings.
Opatija, 2010. 1333-1338 (lecture,international peer-review,published,scientific).

13. Stanke, Mladen; Šikić, Mile.
Comparison of the RADIUS and Diameter Protocols // Information Technology Interfaces, 2008. ITI 2008. 30th International Conference on.
Dubrovnik, 2008. 893-898 (lecture,international peer-review,published,scientific).

14. Katić, Tihomir; Šikić, Mile; Šikić, Krešimir.
Protecting and controlling Virtual LANs by Linux router-firewall // Proceedings of the 27th International Conference on Information Technology Interfaces / Lužar - Stiffler, Vesna ; Hljuz Dobrić, Vesna ; Dobrenić, Nataša, editor(s).
Zagreb : SRCE University Computing Centre, University of Zagreb, 2005. 549-554 (lecture,international peer-review,published,scientific).

15. Šikić, Mile.
The content charging model in mobile packet networks // Computer in telecommunications.
Zagreb, 2003. 68-73 (lecture,international peer-review,published,scientific).
 
  Other refereed conference papers
 

1. Šikić, Mile.
WLAN securtiy // KOM 2003, Komunikacijske tehnologije i norme u informatici / Polonijo, Mislav, editor(s).
Rijeka : CASE d.o.o., 2003. III-41 - III-55 (lecture,domestic peer-review,published,expert).
 
  Non-refereed conference paper
 

1. Šikić, Mile.
Guidline to maintain an efficient email working environment // E-biz 2004 / Mislav Polonijo, editor(s).
Rijeka : CASE, 2004. (lecture,published,expert).
 
  Abstracts in Book of abstracts
 

1. Piškorec, Matija; Šmuc, Tomislav; Šikić, Mile.
Differentiating between Exogenous and Endogenous Information Propagation in Social Networks // Second International Workshop on Data Science.
39-41 (poster,international peer-review,abstract).

2. Matija Piškorec, Nino Antulov-Fantulin, Iva Miholić, Tomislav Šmuc, Mile Šikić.
Inference of influence in social networks // CompleNet 2017.
2017. (lecture,international peer-review,abstract,scientific).

3. Miculinić, Neven; Ratković, Marko; Šikić, Mile.
MinCall | MinION end2end convolutional deep learning basecaller // 2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017.
2017. 1-8 (lecture,international peer-review,scientific).

4. Šebrek, Tomislav; Tomljanović, Jan; Šikić, Mile.
De Novo Assembly using Semi-Supervised Read Categorization // Second International Workshop on Data Science / Lončarić, Sven ; Šmuc, Tomislav, editor(s).
2017. 73-75 (poster,international peer-review,scientific).

5. Tomljanović, Jan; Šebrek, Tomislav; Šikić, Mile.
De Novo Assembly using Unsupervised Read Categorization // Second International Workshop on Data Science / Lončarić, Sven ; Šmuc, Tomislav, editor(s).
Zagreb, 2017. 69-72 (poster,international peer-review,scientific).

6. Vaser, Robert; Šikić, Mile.
Rala - Rapid layout module for de novo genome assembly // ISMB/ECCB 2017.
2017. 1-1 (poster,international peer-review,abstract,scientific).

7. Vaser, Robert; Šikić, Mile.
Ra – Rapid de novo genome assembler // ISMB/ECCB 2017.
2017. 1-1 (poster,international peer-review,abstract,scientific).

8. Vaser, Robert; Šikić, Mile.
Algorithms for Layout Phase of De Novo Genome Assembly // Second International Workshop on Data Science.
2017. 86-87 (poster,international peer-review,scientific).

9. Novak, Andrej, Racz, Gabriela C.; Sedmak, Goran; Šikić, Mile.
Continuum model of gene expression // Thirteenth International Seminar: Mathematical Models & Modeling in Laser Plasma Processes & Advanced Science Technologies.
2015. 75-75 (lecture,international peer-review,abstract,scientific).

10. Sović, Ivan; Skala, Karolj; Šikić, Mile.
From Short to Long Reads: Benchmarking Assembly Tools // ISMB/ECCB 2013.
2013. 1-1 (poster,international peer-review,abstract,scientific).

11. Šikić, Mile; Lančić, Alen; Antulov-Fantulin, Nino; Štefančić, Hrvoje.
Epidemic centrality – identifying “superspreaders” in complex networks // Book of Abstracts ECCS'11 Vienna / Thurner, Stefan ; Szell, Michael, editor(s).
Beč, Austrija, 2011. 124-125 (poster,abstract,scientific).

12. Dokmanić, Ivan; Šikić, Mile; Tomić, Sanja.
Correlating protein surface shape and hydrophobicity using spherical harmonical expansions // Book of abstracts, The 2nd Opatija Meeting on Computational Solutions in the Life Sciences / Babić, Darko ; Došlić, Nađa ; Smith, David ; Tomić, Sanja ; Vlahoviček, Kristian, editor(s).
Zagreb : Ruđer Bošković Institute, 2007. 69-69 (poster,international peer-review,abstract,scientific).

13. Šikić, Mile; Jeren, Branko; Vlahoviček, Kristian.
Prediction of protein-protein hetero interaction sites from local sequence information using Random Forest // Book of abstracts, The 2nd Opatija Meeting on Computational Solutions in the Life Sciences / Babić, Darko ; Došlić, Nađa ; Smith, David ; Tomić, Sanja, Vlahoviček, Kristian, editor(s).
Opatija : Centre for Computational Solutions in the Life Sciences, IRB, 2007. 87-87 (poster,international peer-review,abstract,scientific).
 
  Unpublished papers
 

1. Šebrek, Tomislav; Tomljanović, Jan; Krapac, Josip; Šikić, Mile.
Read classification using semi-supervised deep learning // 2nd International workshop on deep learning for precision medicine, ECML-PKDD 2017.
2017. 1-8 (lecture,international peer-review,unpublished,scientific).

2. Šikić, Mile.
Big data in the age of genomics // .
2016. (invited talk,ppt presentation).

3. Vaser, Robert; Sović, Ivan; Nagarajan, Niranjan; Šikić, Mile.
Racon - Rapid consensus module for raw de novo genome assembly of long uncorrected reads // London calling conference 2016.
2016. (poster,international peer-review,unpublished,scientific).
 
  Dissertations
 

1. Šikić, Mile.
Computational method for prediction of protein-protein interaction sites / doctoral thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.09. 2008, 123 pages. Mentor: Jeren, Branko.
 
  Master thesis
 

1. Šikić, Mile.
Content charging models in mobile packet networks / pre-Bologna master thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 18.09. 2002, 118 pages. Mentor: Kos, Mladen.
 
  Mentoring
 

1. Babojelić, Dario.
Fast protein sequence similarity search / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2018, 22 pages. Mentor: Šikić, Mile.

2. Baksa, Mirna.
Mobile application for collecting user activity data / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2018, 29 pages. Mentor: Šikić, Mile.

3. Fureš, Matej.
The assessment of the expected genome assembly completeness from available reads / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2018, 21 pages. Mentor: Šikić, Mile.

4. Jurić, Antonio.
Scaffolding Assembled Genomes with Long Reads / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 20.09. 2018, 49 pages. Mentor: Šikić, Mile.

5. Krpelnik, Ivan.
Scaffolding Assembled Genomes with Long Reads / pre-Bologna graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 05.07. 2018, 44 pages. Mentor: Šikić, Mile.

6. Miculinić, Neven.
End-to-End Deep Learning Model for Base Calling of MinION Nanopore Reads / pre-Bologna graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 05.07. 2018, 47 pages. Mentor: Šikić, Mile.

7. Paulinović, Mate.
Learned index structures / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2018, 35 pages. Mentor: Šikić, Mile.

8. Šaravanja, Matej.
A service for DNA backup / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2018, 32 pages. Mentor: Šikić, Mile.

9. Selak, Ana Marija.
Hidden Markov Model for Base Calling of MinION Nanopore Reads / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 02.03. 2018, 20 pages. Mentor: Šikić, Mile.

10. Škugor, Luka.
De Novo Metagenome Assembly Using Read Clustering / pre-Bologna graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 05.07. 2018, 34 pages. Mentor: Šikić, Mile.

11. Sodić, Filip.
Approximate Algorithm for Computing Alignment Between Two Long Sequences / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2018, 36 pages. Mentor: Šikić, Mile.

12. Vršnak, Donik.
Landau-Vishkin-Nussinov Algorithm for Pair-wise Sequence Alignment / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2018, 39 pages. Mentor: Šikić, Mile.

13. Žuljević, Petar.
Protein Database Search Using Partial Order Alignment / pre-Bologna graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 05.07. 2018, 37 pages. Mentor: Šikić, Mile.

14. Baćac, Adriano.
Classification of Large-Scale Biological Annotations Using Word Embeddings Derived from Corpora of Biomedical Research Literature / graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 10.7. 2017, 45 pages. Mentor: Šikić, Mile.

15. Bradač, Mislav.
Algorithm for the Alignment of Two Partial Order Alignment Graphs / baccalaureus graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 04.07. 2017, 27 pages. Mentor: Šikić, Mile.

16. Floreani, Filip.
Manual detection of false overlaps occurring during genome assembly / baccalaureus graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 4.7. 2017, 31 pages. Mentor: Šikić, Mile.

17. Kutnjak, Mateo.
dna2vec: vector representation of variable length k-mers / baccalaureus graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 4.7. 2017, 31 pages. Mentor: Šikić, Mile.

18. Megla, Lucija.
Computing the Error Profiles of Third Generation Sequencing Technologies / graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 10.07. 2017, 38 pages. Mentor: Šikić, Mile.

19. Ratković, Marko.
Deep Learning Model for Base Calling of MinION Nanopore Reads / graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 10.7. 2017, 48 pages. Mentor: Šikić, Mile.

20. Rupe, Marina.
Analysis of a Metagenomic Sample Obtained by Third Generation Sequencing Technology / baccalaureus graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 4.7. 2017, 35 pages. Mentor: Šikić, Mile.

21. Šebrek, Tomislav.
Classification of 1D-Signal Types Using Semi- Supervised Deep Learning / graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 10.7. 2017, 60 pages. Mentor: Šikić, Mile.

22. Tomljanović, Jan.
Identification of 1D-Signal Types Using Unsupervised Deep Learning / graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 10.7. 2017, 65 pages. Mentor: Šikić, Mile.

23. Jurić, Antonio.
Long RNA-Seq Alignment / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 5.7. 2016., 39 pages. Mentor: Šikić, Mile.

24. Kostelac, Mario.
De novo assembly using long error-prone reads / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.2. 2016., 59 pages. Mentor: Šikić, Mile.

25. Krpelnik, Ivan.
RNA-seq Alignment Using Existing Gene Annotations / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 5.7. 2016., 29 pages. Mentor: Šikić, Mile.

26. Miholić, Iva.
Detectability of Patient Zero Depending on its Position in the Network / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 5.7. 2016., 92 pages. Mentor: Šikić, Mile.

27. Škugor, Luka.
Tree of Bloom Filters / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 5.7. 2016., 28 pages. Mentor: Šikić, Mile.

28. Sović, Ivan.
ALGORITHMS FOR DE NOVO GENOME ASSEMBLY FROM THIRD GENERATION SEQUENCING DATA / doctoral thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 04.10. 2016., 185 pages. Mentor: Šikić, Mile.

29. Vujević, Ivan.
Real-Time Analysis of a Metagenomic Sample Obtained by Nanopore Based Sequencing Technology / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 5.7. 2016., 45 pages. Mentor: Šikić, Mile.

30. Antulov-Fantulin, Nino.
Statistical inference algorithms for epidemic processes on complex networks / doctoral thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 7.4. 2015, 107 pages. Mentor: Šikić, Mile ; Šmuc, Tomislav.

31. Baćac, Adriano.
Generating consensus sequence using partially ordered multiple sequence alignment graphs / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 2.5. 2015, 37 pages. Mentor: Šikić, Mile.

32. Čulinović, Marko.
Scaffolding using long error-prone reads / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 3.6 2015, 44 pages. Mentor: Šikić, Mile.

33. Hadviger, Antea.
Enhanced suffix array / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 3.6. 2015, 41 pages. Mentor: Šikić, Mile.

34. Humski, Dorija.
A reduced gene database for precision species detection / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 3.6. 2015., 27 pages. Mentor: Šikić, Mile.

35. Marić, Josip.
Long Read RNA-seq Mapper / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 3.6. 2015, 62 pages. Mentor: Šikić, Mile.

36. Megla, Lucija.
Reconstruction of a phylogenetic tree using a neighbor-joining method / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 2.5. 2015, 34 pages. Mentor: Šikić, Mile.

37. Pavlović, Dario.
Splice isoform identification from transcript graphs / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 3.6. 2015., 48 pages. Mentor: Šikić, Mile.

38. Ratković, Marko.
Long read aligner / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 2.6. 2015, 42 pages. Mentor: Šikić, Mile.

39. Šebrek, Tomislav.
Suffix Tree / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 2.5. 2015, 40 pages. Mentor: Šikić, Mile.

40. Selak, Ana Marija.
Phylogenetic tree reconstruction using maximum parsimony branch-and-bound algorithm / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 2.5. 2015, 33 pages. Mentor: Šikić, Mile.

41. Šterbić, Luka.
EAGLER - Eliminating Assembly Gaps by Long Extending Reads / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.12. 2015, 57 pages. Mentor: Šikić, Mile.

42. Vaser, Robert.
De novo transcriptome assembly / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 3.6. 2015., 43 pages. Mentor: Šikić, Mile.

43. Žužić, Goran.
Global sequence alignment tool / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 5.2. 2015, 30 pages. Mentor: Šikić, Mile.

44. Dvorničić, Mirta.
De novo metagenomic assembly using Bayesian model-based clustering / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.7. 2014, 46 pages. Mentor: Šikić, Mile.

45. Jerković, Igor.
RNA-seq mapper / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.7. 2014., 38 pages. Mentor: Šikić, Mile.

46. Miholić, Iva.
Information propagation in online social networks / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 12.6. 2014, 39 pages. Mentor: Šikić, Mile.

47. Osrečki, Matija.
Finding overlapping DNA reads / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.2. 2014, 28 pages. Mentor: Šikić, Mile.

48. Rahle, Bruno.
Simplification of the Overlap Graph / graduate thesis.
Zagreb : Sveučilište u Zagrebu, 1.7. 2014., 47 pages. Mentor: Šikić, Mile.

49. Šošić, Martin.
An SIMD dynamic programming C/C++ library / graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 24.9 2014, 49 pages. Mentor: Šikić, Mile.

50. Šošić, Matija.
Identify pathogen organisms from a stream of RNA sequences / graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 29.06. 2014, 33 pages. Mentor: Šikić, Mile.

51. Vujević, Ivan.
Tool for fast searching of protein sequences in databases / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.6. 2014, 32 pages. Mentor: Šikić, Mile.

52. Žuljević, Petar.
Genome alignment tool / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.6. 2014, 31 pages. Mentor: Šikić, Mile.

53. Županović, Vanessa.
Computational approaches for refinement and validation of genome assemblies / graduate thesis.
Zagreb : Fakultet elektrorehnike i računarstva, 1.7. 2014, 65 pages. Mentor: Šikić, Mile.

54. Blažeka, Dino.
Web interface for sequence alignment / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 09.07. 2013., 48 pages. Mentor: Šikić, Mile.

55. Humski, Dorija.
Alternative splicing / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.07. 2013., 30 pages. Mentor: Šikić, Mile.

56. Korpar, Matija.
SW# - Sequence alignment library utilizing graphics processing units / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 09.07. 2013., 85 pages. Mentor: Šikić, Mile.

57. Kušević, Katarina.
Computing method for determing protein interactions / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 09.07. 2013, 53 pages. Mentor: Šikić, Mile.

58. Mikulić, Marija.
GPU implementation of a space and time optimal parallel sequence alignment algorithm / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.7. 2013., 32 pages. Mentor: Šikić, Mile.

59. Pavetić, Filip.
Tool for aligning long DNA reads / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 27.09. 2013, 37 pages. Mentor: Šikić, Mile.

60. Pavlović, Dario.
Evaluation of a method for long read error correction / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 01.07. 2013, 20 pages. Mentor: Šikić, Mile.

61. Šterbić, Luka.
Optical map assembly: graph correction module / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 1.7. 2013., 42 pages. Mentor: Šikić, Mile.

62. Vaser, Robert.
The evaluation of protein database searching tools / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 01.07. 2013, 32 pages. Mentor: Šikić, Mile.

63. Bulović, Ana.
Application for automatic analysis of protein coding genes / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 09.07 2012, 59 pages. Mentor: Šikić, Mile.

64. Hucaljuk, Josip.
GPU implementation of time efficient linear space local alignment algorithm / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.6. 2012., 43 pages. Mentor: Šikić, MIle.

65. Jerković, Igor.
Make Me Move – didactic computer game for learning structural molecular biology / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2012, 31 pages. Mentor: Šikić, Mile.

66. Ogrizek-Tomaš, Mario.
Web application for comparative analysis of protein paralogs / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 07.07. 2012, 59 pages. Mentor: Šikić, Mile.

67. Rahle, Bruno.
SWIG - Aligning structures using iterative application of Smith-Waterman algorithm / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2012., 38 pages. Mentor: Šikić, Mile.

68. Rakipović, Alen.
BioMe - statistical analyzer for biologically relevant metals / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2012., 34 pages. Mentor: Šikić, Mile.

69. Slijepčević, Ivan.
Orhobalancer: web application for creation of taxonomically balanced sets of orthologous protein sequences / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2012, 37 pages. Mentor: Šikić, Mile.

70. Šošić, Martin.
Implementation of compressed data structure for text searching based on FMindex / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2012., 41 pages. Mentor: Šikić, Mile.

71. Šošić, Matija.
FM index implementation / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06 2012, 32 pages. Mentor: Šikić, Mile.

72. Županović, Vanessa.
A tool for simulating sequence reads / baccalaureus graduate thesis.
Zagreb : Fakultet Elektrotehnike i Računarstva, 29.06 2012, 41 pages. Mentor: Šikić, Mile.

73. Žužić, Goran.
GPU implementation of an efficient linear-memory algorithm for local sequence alignment / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.6. 2012, 27 pages. Mentor: Šikić, Mile.

74. Blažeka, Dino.
Detecting epistasis using ant colony optimization algorithm / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2011, 27 pages. Mentor: Šikić, Mile.

75. Katić, Tihomir.
Optimisation of firewall security rules / pre-Bologna master thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 13.12. 2011, 123 pages. Mentor: Šikić, Mile.

76. Korpar, Matija.
Smith-Waterman algorithm implementation using graphic cards with CUDA architecture / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2011, 31 pages. Mentor: Šikić, Mile.

77. Kušević, Katarina.
Implementation of algorithm for computing protein interactions / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06. 2011, 30 pages. Mentor: Šikić, Mile.

78. Osrečki, Matija.
Adaptive wavelet transform implemented on CUDA platform / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.06 2011, 36 pages. Mentor: Šikić, Mile.

79. Papeš Šokčević, Lidija.
Improved algorithm for selection and validation of best multivariate structure-property molecular models / pre-Bologna master thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 26.10. 2011., 72 pages. Mentor: Šikić, Mile ; Lučić, Bono.

80. Pavetić, Filip.
Electrostatic charge distribution calculation in CUDA / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 29.6 2011, 28 pages. Mentor: Šikić, Mile.

81. Popović, Irena.
Prediction of solvent accessible surface area from protein sequence / pre-Bologna graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 22.04. 2011., 43 pages. Mentor: Šikić, Mile.

82. Sović, Ivan.
Protein docking tool: visualization module / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 06.07. 2011., 89 pages. Mentor: Šikić, Mile.

83. Antulov-Fantulin, Nino.
Protein Docking tool: rotation and scoring modules / graduate thesis.
Zagreb : Fakultet elektrotehike i računarstva, 06.07. 2010., 64 pages. Mentor: Šikić, Mile.

84. Bilić, Ivan.
A solution for accessing to servers that are inside of mobile networks / pre-Bologna graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 23.10 2010, 89 pages. Mentor: Šikić, Mile.

85. Čanadi, Igor.
Protein Docking Tool: Steric Scan module / baccalaureus graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 11.07. 2010, 27 pages. Mentor: Šikić, Mile.

86. Čolić, Dragana.
Protein Docking Tool: Module For Interaction Detection / graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 06.07. 2010, 52 pages. Mentor: Šikić, Mile.

87. Ćurić, Jura.
Secondary protein structure analysis by the method of signal processing / graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 06.07. 2010, 49 pages. Mentor: Šikić, Mile.

88. Janjić, Saša.
Secondary structure prediction using only sequence data / pre-Bologna graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 03. 2010, 68 pages. Mentor: Šikić, Mile.

89. Matija Piškorec.
Multiresolution analysis of macromolecular structures / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 6.7. 2010., 38 pages. Mentor: Šikić, Mile.

90. Ogrizek-Tomaš, Mario.
Influence of quarantine on epidemic spread / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 16.07. 2010., 64 pages. Mentor: Šikić, Mile.

91. Peretin, Goran.
Representation of metals in proteins / graduate thesis.
Zagreb : Fakultet Elektrotehnike i računarstva, 06.07. 2010, 32 pages. Mentor: Šikić, Mile.

92. Petrović, Juraj.
Prediction of protein-protein interactions using Random Forests / graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2010., 49 pages. Mentor: Šikić, Mile.

93. Rakipović, Alen.
Simulation of the impact organizing parties on propagation of viruses at spreading the infection / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 11.07. 2010., 30 pages. Mentor: Šikić, Mile.

94. Tus, Alan.
Database of metals in proteins / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 07.07. 2010, 33 pages. Mentor: Šikić, Mile.

95. Bokšić, Mirna.
Genome coding regions analysis / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 17.07. 2009, 52 pages. Mentor: Seršić, Damir.

96. Štimac, Maja.
Classification of coding regions in the genome / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 17.7. 2009, 37 pages. Mentor: Seršić, Damir.

97. Antulov-Fantulin, Nino.
Influence of epidemic spread on network structure / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehike i računarstva, 11.07. 2008, 43 pages. Mentor: Jeren, Branko.

98. Matija Piškorec.
Identification of key players in complex networks of blogs / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 11.7. 2008., 39 pages. Mentor: Jeren, Branko.

99. Petrović, Juraj.
The automated construction of a testing set for predicting of protein interactions / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 03.07. 2008., 38 pages. Mentor: Jeren, Branko.

100. Sović, Ivan.
Visualization of macromolecules / baccalaureus graduate thesis.
Zagreb : Fakultet elektrotehnike i računarstva, 11.07. 2008., 49 pages. Mentor: Jeren, Branko.
 

Teaching duties

University undergraduate

University graduate

Postgraduate doctoral study programme

Personal data

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