Curriculum Vitae PERSONAL INFORMATION Name and surname Academic title Year and institution of PhD obtained Address Phone Fax E-mail Personal web page Citizenship Date and place of birth Mile Šikić PhD 2008, University of Zagreb, Faculty of Electrical Engineering and Computing Kutnjački put 12, 10000 Zagreb, Croatia (385) 98 3872 943 (385) 6129 652 [email protected] http://complex.zesoi.fer.hr/msikic.html Croatian 18.11.1972, Zagreb, Croatia WORK EXPERIENCE1 (CHRONOLOGICALLY∗) Date (from – until) Institution Position Work field Date (from – until) Institution Position Work field Date (from – until) Institution Position Work field Date (from – until) Institution Position Work field ,, 1 2 3 1997-2005 University of Zagreb, Faculty of Electrical Engineering and Computing Scientific Assistant Computer and mobile networks, network security 2005-2009 University of Zagreb, Faculty of Electrical Engineering and Computing Teaching Assistant bioinformatics, complex networks 2009University of Zagreb, Faculty of Electrical Engineering and Computing Assistant Professor bioinformatics, complex networks, GPU programming 1.5.2011-1.9.2012 A*STAR Bioinformatics Institute, Singapore Senior postdoc, visiting scientist bioinformatics, complex networks, GPU programming Please add rows to enter all required information all information in the document should be entered chronologically – from the most recent to the oldest EDUCATION2 (CHRONOLOGICALLY) Date Place Institution Title of qualification awarded Date Place Institution Title of qualification awarded Date Place Institution Title of qualification awarded 1996 Zagreb University of Zagreb, Faculty of Electrical Engineering and Computing Ms EE 2002 Zagreb University of Zagreb, Faculty of Electrical Engineering and Computing Ms sc EE 2008 Zagreb University of Zagreb, Faculty of Electrical Engineering and Computing Phd TRAINING (CHRONOLOGICALLY) Year Place Institution Subject and skills covered Year Place Institution Subject and skills covered 2001 Zagreb Management centre Europe, Brussels PMI approved Project management curse specialized for IT managers. The curse included the following subjects: creating interactive project teams, implementing effective Planning and Control of project teams, project organizing, establishing effective communication across the project team, empowering project team members. 2006 Zagreb Business Management Consultants (PMI registered Education Provider) PMP Certification Test Preparation Curse . LANGUAGES MOTHER TONGUE ENGLISH LANGUAGE Speaking Writing Reading CROATIAN Cambridge CAE Excellent Excellent Excellent RESEARCH GRANTS IN THE LAST 3 YEARS (CHRONOLOGICALLY ; LEADER AND ASSOCIATES; FUNDING SOURCE) Title: Epidemiological models and dynamics of spreading on complex networks Project leader: Dr. Hrvoje Štefančić Lead investigator: Dr. Mile Šikić Founding source: Croatian Science Foundation Status: In evaluation Title: Complex network analysis of cis and trans chromatin interactions Project leader:Dr. Kuljeet Singh Sandhu (Genome Institute of Singapore) Lead investigator: Dr. Mile Šikić Status: Awarded (April 2012) Amount awarded: Project (176,700.00 SGD), Mile Šikić (8,000 SGD) Project aims. Using in-house genome-wide chromatin interaction data, we aim: 1. To analyze the complex network properties of chromatin interactions. Topological descriptors like scale-freeness, modularity, transitivity, local and global centralities, rich-club/VIP-club 2 phenomenon etc of interacting genomic elements like promoters, terminators, enhancers, silencers, locus control regions and imprinting control regions would be analyzed. We would particularly focus on exploring the complexity of enhancer-promoter and promoter-promoter interactions and study genetic (sequence), epigenetic (chromatin) and functional (expression) traits underlying this complexity. 2. To analyze the disease associated Single Nucleotide Polymorphisms (SNPs) with respect to network topology. We will overlay the SNPs uncovered by Genome Wide Association Studies (GWAS) onto our chromatin interaction network. The objective is to explain the mechanism of previously un-annotated disease causing SNPs, especially those in the non-coding regions, with the help of long range chromatin interaction networks. 3.To explore the interdependency of chromatin interaction network with other regulatory networks like gene co-regulatory and protein interaction network. Evidences suggest that chromatin interactions could associate with co-regulation of interacting gene and, moreover, protein products of co-regulated genes are more likely to interact downstream. Thus, we would study the extent these networks are coupled together and functional consequences of their co-oscillations. The project would not only advance our understanding of genome regulation and perturbations therein, but would also help designing novel medical strategies to keep the cellular networks healthy and robust. Project progress: We have already finished our work on the first aim and this work has been submitted to Cell reports. RESEARCH AND OTHER PROJECTS (CHRONOLOGICALLY; LEADER AND ASSOCIATES; FUNDING SOURCE) 1997 – I have been worked as member of a project team or a leader on tens of various projects with companies and institutions in the following fields: • Consulting services in ICT and network security • Network security and Linux projects • Project management for software programming • e-learning, home automation, wireless LAN security, spam) • Consulting in the GPRS/UMTS aggregation and mediation • Consulting in the content charging and M-commerce • SMS and WAP design • videoconferencing rooms projects • feasibility studies for optical communication networks Some of Reference Clients were: • Kapsch Carrier Com, Austria • Orange Austria • Croatian Academic and Research Network, • Croatian government, • "Privredna banka Zagreb" (bank, Unicredito group) • “Croatia osiguranje” (the biggest insurance company in Croatia) 2005 - Metronet Croatia (www.metronet.hr), (initiator and member of start-up team), today company has around 200 employees 2002 – 2007 Project: Digital speech processing in contemporary information technologies Leader: Davor Petrinović Founding source: MZOS, Republic of Croatia 2003 Project: Open office referral centre Leader: Mile Šikić Founding source: MZOS, Republic of Croatia 2003 Project: Open archives referral centre Leader: Mile Šikić Founding source: MZOS, Republic of Croatia 2007 – Project: Computational study of bio-macromolecules and development of new algorithms Leader: Sanja Tomić Founding source: MZOS, Republic of Croatia 2007 – Project: Complex Systems Modelling Leader: Branko Jeren Founding source: MZOS, Republic of Croatia REFEREES (NAMES,ADDRESSES,E-MAIL ADDRESSES, FAX NUMBERS) Dr. Chandra Verna A*STAR, Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671 (65) 6478 8273 [email protected] (65) 6478 9047 Prof. Kristian Vlahoviček University of Zagreb, Faculty of Science, Division of Biology Horvatovac 102a, 10000 Zagreb, Croatia (385) 1 4606 306 [email protected] (385) 1 4605 286 Hrvoje Supić IBM Global Technology Services Central and Eastern Europe, Russia and Turkey Managed Services Leader Miramarska 23, 10000 Zagreb, Croatia (385) 1 6308 111 [email protected] (385) 1 6308 111 TEACHING RECORD (CHRONOLOGICALLY ; UNDERGRADUATE , GRADUATE , POSTGRADUATE STUDY PROGRAMMES 2005 – 2009 Systems and Signals (undergraduate course), teaching assistant and lecturer student evaluation of teaching for 2009 (4.47, scale 1 – 5 ) 2009 – 2011 Programming and Software Engineering (undergraduate course), lecturer student evaluation of teaching for 2009 (4.68, scale 1 – 5 ) student evaluation of teaching for 2010 (4.85, scale 1 – 5 ) Algorithms and Data Structures (undergraduate course), lecturer student evaluation of teaching for 2010 (4.85, scale 1 – 5 ) student evaluation of teaching for 2011 (4.68, scale 1 – 5 ) MENTORSHIP OF DEFENDED DOCTORAL AND MASTER DISSERTATIONS AND TRAINING OF YOUNG RESEARCHERS AND SCIENTISTS (CHRONOLOGICALLY) Mentorship of two defended master of science(Ms. sc) dissertations and two doctoral dissertation (in progress). Supervised 14 master and 19 bachelor degree thesis. MEMBERSHIP IN SCIENCE ORGANIZATIONS AND BODIES (CHRONOLOGICALLY; HOME AND INTERNATIONAL ORGANIZATIONS AND BODIES) IEEE PUBLIC AND PROFESSIONAL SERVICE (CHRONOLOGICALLY; HOME AND INTERNATIONAL) Science and society Synergy Institute, Croatia http://www.iszd.hr/ (steering committee), 2010 Artes Calculi, Croatia http://www.artcalc.com/ (supervisory board), 2010 - MOST SIGNIFICANT PUBLICATIONS (CHRONOLOGICALLY; HOME AND INTERNATIONAL) Mile Šikić, Sanja Tomić, Kristian Vlahoviček. Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests // Plos computational biology. (2009) impact factor 2010 – 5.515; 38 citations; Alan Tus, Alen Rakipović, Goran Peretin, Sanja Tomić, Mile Šikić. BioMe: biologically relevant metals // Nucl. Acids Res. Web server issue (2012), impact factor 2010 – 7.836; Mile Šikić, Alen Lančić; Nino Antulov-Fantulin, Hrvoje Štefančić. Epidemic centrality and the underestimated epidemic impact of network peripheral nodes // http://arxiv.org/abs/1110.2558v1(2011 ) – under review. ALL PAPERS (CHRONOLOGICALLY; RESEARCH BOOKS, HOME AND INTERNATIONAL RESEARCH JOURNALS, HOME AND INTERNATIONAL CONFERENCE PROCEEDINGS ; PLEASE WRITE THEIR IMPACT FACTOR ) Journal papers: Ivan Dokmanić, Mile Šikić, Sanja Tomić. 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, impact factor 2010 – 6.326; 37 citations Josip Mihel, Mile Šikić, Sanja Tomić, Branko Jeren, Kristian Vlahoviček. PSAIA - Protein Structure and Interaction Analyzer. // Bmc structural biology. 8 (2008) impact factor 2010 – 2.26; 27 citations; Mile Šikić, Sanja Tomić, Kristian Vlahoviček. Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests // Plos computational biology. (2009) impact factor 2010 – 5.515; 38 citations; Alen Lančić, Nino Antulov-Fantulin, Mile Šikić, Hrvoje Štefančić. Phase diagram of epidemic spreading - unimodal vs. bimodal probability distributions // Physica A 390 (1) (2011), impact factor 2010 – 1.52; Alan Tus, Alen Rakipović, Goran Peretin, Sanja Tomić, Mile Šikić. BioMe: biologically relevant metals // Nucl. Acids Res. Web server issue (2012), impact factor 2010 – 7.836; Kuljeet Singh Sandhu, Guoliang Li, Huay Mei Poh, Yu Ling Kelly Quek, Yee Yen Sia, Su Qin Peh, Fabianus Hendriyan Mulawadi, Mile Šikić, Francesca Menghi, Anbupalam Thalamuthu, Wing Kin Sung, Xiaoan Ruan, Melissa Jane Fullwood, Edison Liu, Peter Csermely, Yijun Ruan. Large scale functional organization of long-range chromatin interaction networks (2012). Papers under review: Matija Korpar, Mile Šikić Back to basis: GPU enabled exact alignments on genome scale (2012) Mile Šikić, Alen Lančić; Nino Antulov-Fantulin, Hrvoje Štefančić. Epidemic centrality and the underestimated epidemic impact of network peripheral nodes // http://arxiv.org/abs/1110.2558v1(2011). 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 //http://arxiv.org/abs/1202.1639 (2012). Ivan Slijepčević, Mile Šikić, Ivana Mihalek. OrthoBalancer- a tool for creation of taxonomicaly balanced sets of orthologous protein sequence (2012) Book chapters: Vedran Franke, Mile Šikić, Kristian Vlahoviček. Prediction of interacting protein residues using sequence and structure data //Methods in Molecular Biology, Volume 819, (2012), Pages 233-251 Conference papers: 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 and Microelectronics, MIPRO 2012; Opatija; 21 May 2012 through 25 May 2012 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; 24 May 2010 through 28 May 2010 Mladen Stanke, Mile Šikić Comparison of the RADIUS and Diameter Protocols // Information Technology Interfaces, 2008. ITI 2008. 30th International Conference on. Dubrovnik, 2008. 893-898 . Tihomir Katić, Mile Šikić, Krešimir Šikić. Protecting and controlling Virtual LANs by Linux router-firewall // Proceedings of the 27th International Conference on Information Technology Interfaces / Dubrovnik, 2005. 549-554 Ivan Dokmanić, Mile Šikić, Sanja Tomić. Correlating protein surface shape and hydrophobicity using spherical harmonical expansions // Book of abstracts, The 2nd Opatija Meeting on Computational Solutions in the Life Sciences : Opatija, 2007. 69 Mile Šikić, Branko Jeren, Kristian Vlahoviček. 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, Opatija, 20
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