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* NOTE - Complex Network and Bioinformatics Group

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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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