MARKO DJORDJEVIC
Faculty of Biology
Birthplace:
Belgrade, Serbia
University of Belgrade
Citizenship:
Serbia
Studentski Trg 16
E-mail:
dmarko@bio.bg.ac.rs
11000 Belgrade, Serbia
Tel:
(+381 11) 3033-356
Research Fields:
Quantitative and systems biology, Bioinformatics
Education
Sept. 2005-
Aug. 2008
Mathematical Biosciences Institute; The Ohio State University, USA.
Postdoc quantitative biology, supervisor Prof. Avner Friedman, NAS (National Academy of
Sciences of USA) member.
Sept. 2000-
Oct. 2005:
PhD, Columbia U. Dept. of Physics, NY, USA
Thesis research in theoretical biophysics and bioinformatics; Thesis title: “Biophysics and
Bioinformatics of Transcription Regulation in Bacteria and Bacteriophages”; PhD thesis
advisor: Prof. Boris Shraiman (NAS member).
Feb 2004:
M. Phil. in Physics, Columbia University, NY.
May 2002:
M. A. in Physics, Columbia University, NY.
June 2000:
Diploma in Physics, Belgrade University, Faculty of Physics, Serbia.
One of the two best students in generation; Diploma thesis research in Quantum statistical
physics, Institute of Physics Belgrade (Thesis title: “Mixed states of quantum harmonic
oscillator”); advisor Dr. Istok Mendas (PhD, Queen’s University, Belfast, UK).
Positions
Dec 2014 – present:
Associate Professor of Biophysics, Head of Quantitative Biology Group,
University of Belgrade, Faculty of Biology
Sept 2010 – Dec 2014:
Assistant Professor of Biophysics, U. of Belgrade, Faculty of Biology
Sept 2008 – June 2010:
Assistant Prof. of Physics, Arkansas State U. & The Arkansas Biosciences
Institute.
Apr 2008:
Offer of Assistant Professorship in Biophysics at NORDITA (Nordic Institute
for Theoretical Physics), Stockholm (declined).
Oct 2005 – Aug 2008:
Postdoctoral Fellow, Mathematical Biosciences Institute, Ohio State U.
Sept 2000 – Aug 2005:
Faculty fellow and Research Assistant, Dept. of Physics, Columbia U.
Jun 1999 – Jun 2000 :
Diploma Thesis Research, Institute of Theoretical Physics, Belgrade.
Awards and recognitions
March 2011:
Feb 2005
Jan 2005:
Nov 1998:
Marie Curie Fellowship, European Commission - REA, Brussels, Belgium
Keystone Symposia scholarship, Taos, New Mexico.
Feinberg Postdoctoral Fellowship, Weizmann Institute of Science, Israel (declined).
'Prof. Dr. Djordje Zivanovic' Fellowship, awarded to two best students in
generation, Faculty of Physics, Belgrade, Serbia.
1995 -2000
'Department of Science' Fellowship (awarded five times), Serbia.
1996-1999
'Madlena Jankovic' Fellowship, for success in diploma studies, Belgrade, Serbia.
July 1995:
The bronze medal, XXVI International Physics Olympiad, Canberra, Australia.
Awarded Grants
Research (including international collaboration)
PI, Science Fund of the Republic of Serbia, The Program IDEAS, 7750294, “Biophysics and
Bioinformatics of CRISPR/Cas and Toxin-Antitoxin Regulation”, from 2022-2025.
PI, Science Fund of the Republic of Serbia, The Serbian Science and Diaspora Collaboration Program,
6417603, “Quantitative modeling of regulatory dynamics of CRISPR/Cas systems”, from 2020-2021.
Co-PI (Faculty of Biology coordinator): Science, Technology and Innovation Action Plan “One Belt And
One Road” International Cooperation Projects, China, 19430750600, “Shanghai-Islamabad-Belgrade
joint innovation center on Antibacterial Resistance”, from 2019-2022.
Co-PI (Faculty of Biology coordinator): Swiss National Science Foundation, SCOPES project,
IZ73Z0_152297, “Bioinformatics and modeling of bacterial immune systems - understanding control of
CRISPR/Cas”, from 2014-2017.
PI (Scientist in charge): FP7 Marie Curie International Reintegration grant, PIRG08-GA-2010-276996,
"Bioinformatics analysis of transcription regulation: a modeling approach", European Commission -
Research Executive Agency, from 2011-2015.
PI (Project leader): Basic Science Research Grant, OI173052, "Bioinformatic promoter predictions and
theoretical modeling of gene circuits in bacteria", Ministry of Science and Technology - Republic of
Serbia, 2011-2019.
Infrastructure (Education)
PI (Project leader): Development of Higher Education Grant, "Infrastructure for computational biology
laboratory at University of Biology, Faculty of Biology", Ministry of Science and Technology - Republic
of Serbia, 2017-2018.
Teaching experience
Molecular Biophysics (Fall 2012 – Fall 2020), Multidisciplinary PhD Biophysics program, U. of
Belgrade, Serbia.
Bioinformatics and Computational Biology (Fall 2019-2021), Computational Systems Biology (co-
teach Fall 2020), Neuroinformatics (co-teach, Fall 2013, Fall 2019), Computational Immunobiology
(Fall 2013 - Fall 2014), PhD program, Faculty of Biology, U. of Belgrade, Serbia.
Bioinformatics (Fall 2012 – Fall 2021); Fundamentals of molecular biophysics (co-teach, Fall 2016-
2021); MSc program, Faculty of Biology, U. of Belgrade, Serbia.
Fundamentals of Bioinformatics (Fall 2012 – Fall 2021); Physics in Biology (Fall 2010 – Fall 2021);
Faculty of Biology, U. of Belgrade, Serbia.
Electricity and Magnetism (Spring 2010); Thermal Physics (Fall 2009); General Physics I (Spring
2009); Physics for health science professionals (Fall 2008); Arkansas State U, AR.
Tutorial on ChIP-chip data analysis (Spring 2007); VIGRE working group in mathematical biology
(Fall 2006), The Ohio State U, Columbus, Ohio.
Introduction to experimental physics laboratory (Fall 2001); Introduction to physics laboratory (Fall
2000 - Spring 2001), Columbia U, New York.
Academic supervision
Postdocs: dr Bojan Bozic (2017-2019), dr Jelena Repac (2017-2019)
PhD Students: Andjela Rodic (2015 – 2022), Jelena Guzina (2013 – 2017), Miodrag Stokic (2011 –
2015), Ognjen Milicevic (2016 – current), Marko Tumbas (2019 – current), Sofija Markovic (2020 –
current).
MSc Students: Jelena Guzina (2013), Djordje Markovic (2014), Marija Basic (2014), Andjela Rodic
(2015), Nikola Dragic (2015), Ivona Tomic (2017), Stefan Graovac (2018), Aleksa Ratarac (2019),
Marko Tumbas (2019), Sofija Markovic (2020), Anica Brzakovic (2020), Stefan Djordjevic (2022),
Milica Jokovic (2022).
PhD students’ awards
“2016. Young scientist research award”, awarded to Jelena Guzina by the Faculty of Biology,
University of Belgrade, Serbia, Sept 2016.
Award for the best oral presentation at the 8th Inter. Young Scientists School of Systems Biology
and Bioinformatics, awarded to Andjela Rodic, Novosibirsk, Russia, Sept 2016
Fellowship for the Advanced Lecture Course on Systems Biology, awarded by SYSBIO 2016 to
Andjela Rodic, Innsbruck, Austria, Jan 2016
Annual award for the best master thesis in Molecular Biology, awarded to Andjela Rodic by the
Foundation "Goran Ljubijankic", Belgrade, Serbia, Dec 2015
Community service:
Journal Editor
Associate Editor: Frontiers in Ecology and Evolution, Frontiers Journals (IF 4.5).
Associate Editor: Frontiers in Genetics, Frontiers Journals (IF 4.8).
Academic Editor: PLOS ONE, PLOS Journals (IF 3.8, from 2018-2021).
Editorial Board: Combinatorial Chemistry & High Throughput Screening, Bentham Science (IF 1.7).
Review Editor: Frontiers in Molecular Biosciences, Frontiers Journals (IF 6.1).
Journal Referee
Biochemistry (American Chemical Society), Bioinformatics (Oxford Journals), BMC Bioinformatics
(BioMed Central), BMC Biotechnology (BioMed Central), BioTechniques (Informa Life Sciences),
Bulletin of Mathematical Biology (The Society for Mathematical Biology), DNA Research (Oxford
Journals), Environmental research, Mathematical Biosciences (ScienceDirect), Frontiers in Big Data,
Frontiers in Genetics, Frontiers in Ecology and Evolution, Frontiers in Medicine, Frontiers in
Molecular Biosciences, Frontiers in Public Health (Frontiers Journals), Journal of Bacteriology
(American Society for Microbiology), Journal of Urban Health (Springer), Nucleic Acids Research
(Oxford University Press), Pacific Symposium on Biocomputing, Physical Biology (Institute of
Physics), PLoS Computational Biology, PLoS ONE, Proceedings of the National Academy of Sciences
of USA, Physical Review E, Physical Review Letters (American Physical Society), Scientific Reports
(Nature).
Reviewer of International Projects
‒ The Netherlands Organization for Scientific Research (NWO, the Dutch Research Council), KLEIN
Research Proposals
‒ Austrian Science Fund (FWN), Erwin Schrödinger Fellowships
‒ ERA-Chemistry Open Initiative, European Commission (trilateral Germany-Austria-Hungary)
‒ Dmitry Zimin Dynasty Foundation (Russia).
International Faculty Search Committee
‒ Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia. A member of the
Subcommittee on Biomedicine, invited by Interim Provost Prof. Keith Stevenson, 2015 – 2017.
Conference Organization
- BELBI 2021, BELBI 2018 and BELBI 2016 (Belgrade Bioinformatics Conference), Belgrade, Serbia.
- TABIS2013 (Theoretical Approaches to BioInformation Systems), Belgrade, Serbia, Sept 2013
- 2nd and 3rd Young Researchers Workshop in Mathematical Biology, Columbus, OH, Mar 2007, 2008
Programe Committee
IWBBIO 2022 (9th International Conference on Bioinformatics and Biomedical Engineering), Gran
Cnaria, Spain
BIOMESIP 2021 (International Conference on Bioengineering, Biomedical Signal and Image
Processing), Granada, Spain.
Scientific society/board
- Vice President of the Serbian Society for Bioinformatics and Computational Biology
- Member: Council for multidisciplinary studies, University of Belgrade
- Board member: Multidisciplinary PhD program in Biophysics, University of Belgrade
Scientific Programs and Schools
Lecturer:
Quantitative Biology School, Pazmany Peter Catholic University (PPCU, Hungary) and the FIRC
Institute of Molecular Oncology (IFOM, Italy), Budapest, Hungary, May 2022.
"APS & ICTP-SAIFR Young Physicists Forum on Biological Physics: from Molecular to
Macroscopic Scale", co-organized by the American Physical Society, Sao Paulo, Brazil, March 2020.
Participant (during PhD and Postdoc studies):
Evolution of Molecular Networks, Kavli Institute for Theoretical Physics, Santa Barbara, California,
Jan 2007.
Networks in Growth, Death and Aging, Kavli Institute for Theoretical Physics, Santa Barbara,
California, February 2005.
The 22nd Jerusalem Winter School in Theoretical Physics, Biological Networks and Evolution,
Jerusalem, Israel, January 2005.
Bio-Molecular Networks, Kavli Institute for Theoretical Physics, Santa Barbara, California, Spring
2003.
Publications
A. Articles
M. Djordjevic published 65 peer reviewed papers with average impact factor of 4.5, cited >2100 times per
Google Scholar, h-index 20. The first or the corresponding author on 33 papers, and the main author
responsible for quantitative analysis on 10 collaborative (experiment) papers.
1. Djordjevic M, Markovic S, Salom I, Djordjevic M. Understanding risk factors of a new variant outburst
through global analysis of Omicron transmissibility, Environmental Research 216, 114446, 2023.
2. Markovic S, Salom I, Rodic A, Djordjevic M, Analyzing the GHSI puzzle of whether highly developed
countries fared worse in COVID-19, Nature Scientific Reports 12, 1. 2022.
3. Zhang J, Guan J, Wang M, Li G, Djordjevic M, Tai C, Wang H, Deng Z, Chen Z, Ou HY, SecReT6 update:
a comprehensive resource of bacterial Type VI Secretion Systems, Science China Life Sciences, 1 (2022).
4. Goh YX, Li P, Wang M, Djordjevic M, Tai C, Wang H, Deng Z, Chen Z, Ou HY, Comparative Analysis
of Diverse Acetyltransferase-Type Toxin-Antitoxin Loci in Klebsiella pneumoniae, Microbiology
spectrum 10, e00320, 2022.
5. Stojku S, Auvinen J, Djordjevic M, Huovinen P, Djordjevic M, Early evolution constrained by high-pt
quark-gluon plasma tomography, Phys. Rev. C 105, L021901, 2022.
6. Markovic S, Rodic A, Salom I, Milicevic O, Djordjevic M, Djordjevic M, COVID-19 severity
determinants inferred through ecological and epidemiological modelling, One Health 13, 100355, 2021.
7. Milicevic O, Salom I, Markovic S, Rodic A, Tumbas M, Zigic D, Djordjevic M, Djordjevic M, PM2.5 as
a major predictor of COVID-19 basic reproduction number in the USA, Environmental Research Res 201,
111526, 2021.
8. Djordjevic M, Salom I, Markovic S, Rodic A, Milicevic O, Djordjevic M, Inferring the main drivers of
SARS-CoV-2 transmissibility, Geohealth 5, e2021GH000432, 2021.
9. Djordjevic M, Djordjevic M, Ilic B, Stojku S, Salom I, Understanding Infection Progression under Strong
Control Measures through Universal COVID-19 Growth Strategies, Global Challenges (Advanced
Science News Communication) 5, 2000101, 2021 (featured as journal’s Cover page).
10. Salom I, Rodic A, Milicevic O, Zigic D, Djordjevic M, Djordjevic M, Effects of demographic and weather
parameters on COVID-19 basic reproduction number, Frontiers in Ecology and Evolution 8, 524, 2021.
11. Djordjevic M, Rodic A, Salom I, Zigic D, Milicevic O, Ilic B, Djordjevic M, A systems biology approach
to COVID-19 progression in population, Adv Protein Chem Struct Biol. 127, 291, 2021.
12. Stojku S, Ilic B, Djordjevic M, Djordjevic M, Extracting the temperature dependence in high-p
⊥
particle
energy loss, Physics Review C 103, 024908, 2021.
13. Djordjevic M, Stojku S, Zigic D, Ilic B, Auvinen J, Salom I, Djordjevic M and Huovinen P, From high p
⊥
theory and data to inferring anisotropy of Quark-Gluon Plasma, Nuclear Physics A 1005, 121900, 2021.
14. Ilic B, Zigic D, Djordjevic M, Djordjevic M, Utilizing high- theory and data to constrain the initial stages
of quark-gluon plasma, Int. J. Mod. Phys. E 30, 2141007, 2021.
15. Zigic D, Ilic B, Djordjevic M, Djordjevic M, Exploring the initial stages in heavy-ion collisions with high-
p
⊥ RAA
and v2 theory and data, Physics Review C 101, 064909, 2020.
16. Milicevic O, Repac J, Bozic B, Djordjevic M and Djordjevic M, A Simple Criterion for Inferring CRISPR
Array Direction. Front. Microbiol. 10, 2054, 2019.
17. Djordjevic M, Rodic A, Graovac S, From biophysics to 'omics and systems biology, European Biophys
Journal. 48, 413, 2019.
18. Bozic B, Repac J, Djordjevic M, Endogenous Gene Regulation as a Predicted Main Function of Type I-
E CRISPR/Cas System in E. coli, Molecules 24, E784, 2019.s
19. Graovac S, Rodic A, Djordjevic M, Severinov K, Djordjevic M, Effects of Population Dynamics on
Establishment of a Restriction-Modification System in a Bacterial Host, Molecules 24, E198, 2019.
20. Djordjevic M, Stojku S, Djordjevic M and Huovinen P, How to infer the shape of the QGP droplet from
the data, Phys. Rev. C Rapid Communications 100, 031901, 2019.
21. Zigic D, Salom I, Auvinen J, Djordjevic M, Djordjevic M, DREENA-B framework: first predictions of
RAA and v2 within dynamical energy loss formalism in evolving QCD medium, Phys. Lett. B 791, 236,
2019.
22. Djordjevic M, Zigic D, Djordjevic M, Auvinen J, How to test path-length dependence in energy loss
mechanisms: analysis leading to a new observable, Physical Review C 99, 061902(R), 2019.
23. Blagojevic B, Djordjevic M, Djordjevic M, Calculating hard probe radiative energy loss beyond the soft-
gluon approximation: Examining the approximation validity, Physical Rev C 99, 024901, 2019.
24. Djordjevic M, Zigic D, Blagojevic B, Auvinen J, Salom I, Djordjevic M, Dynamical energy loss
formalism: from describing suppression patterns to implications for future experiments, Nuclear Physics
A 982, 699, 2019.
25. Zigic D, Salom I, Auvinen J, Djordjevic M, Djordjevic M, Joint RAA and v2 predictions for Pb+Pb
collisions at the LHC within DREENA-C framework, Journal of Physics G 46, 085101, 2019.
26. Musharova O, Vyhovskyi D, Medvedeva S, Guzina J, Zhitnyuk Y, Djordjevic M, Severinov K, Savitskaya
E, Avoidance of Trinucleotide Corresponding to Consensus Protospacer Adjacent Motif Controls the
Efficiency of Prespacer Selection during Primed Adaptation, mBio 9, e02169, 2018.
27. Guzina J, Chen WH, Stankovic T, Djordjevic M, Zdobnov E, Djordjevic M, In silico Analysis Suggests
Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence,
Frontiers in Genetics 9,474, 2018.
28. Klimuk E, Bogdanova E, Nagornykh M, Rodic A, Djordjevic M, Medvedeva S, Pavlova O, Severinov K,
Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as
a transcription elongation roadblock, Nucleic Acids Research 46,10810, 2018.
29. Rodic A., Blagojevic B., Djodjevic, M. Systems biology of bacterial immune systems: regulation of
restriction-modification and CRISPR-Cas systems, p. 37-58, In: Rajewsky N., Jurga S., Barciszewski J.
(eds) Systems Biology. RNA Technologies. Springer, Cham (invited book chapter), 2018.
30. Djordjevic M, Djordjevic M and Zdobnov E, Scoring Targets of Transcription in Bacteria Rather than
Focusing on Individual Binding Sites, Frontiers in Microbiology 8, 2314, 2017.
31. Rodic A, Blagojevic B, Severinov K, Djordjevic M and Djordjevic M, Features of CRISPR-Cas
Regulation Key to Highly Efficient and Temporally-Specific crRNA Production, Frontiers in
Microbiology 8, 2139, 2017.
32. Rodic A, Blagojevic B, Zdobnov E, Djordjevic M and Djordjevic M, Understanding key features of
bacterial restriction-modification systems through quantitative modeling, BMC Syst. Biol. 11, 377, 2017.
33. Guzina J and Djordjevic M, Mix-and-matching as a promoter recognition mechanism by ECF σ factors,
BMC Evolutionary Biology, 17, 12, 2017.
34. Nikolic M, Stankovic T, Djordjevic M, Contribution of bacterial promoter elements to transcription start
site detection accuracy, J of Bioinformatics and Computational Biology 15, 1650038, 2017.
35. Guzina J, Djordjevic M, Promoter recognition by ECF σ factors: analyzing DNA and protein interaction
motifs, Journal of Bacteriology 198, 1927, 2016.
36. Morozova N, Sabantsev A, Bogdanova E, Fedorova Y, Maikova A, Vedyaykin A, Rodic A, Djordjevic
M, Khodorkovskii M, Severinov K, Temporal dynamics of methyltransferase and restriction
endonuclease accumulation in individual cells after introducing a restriction-modification system,
Nucleic Acids Research 44, 790, 2016.
37. Guzina J, Djordjevic M, Bioinformatics as a first-line approach for understanding bacteriophage
transcription, Bacteriophage 5, e1062588, 2015 (invited review paper).
38. Guzina J, Djordjevic M, Inferring bacteriophage infection strategies from genome sequence: analysis of
bacteriophage 7-11 and related phages, BMC Evolutionary Biology 15, S1, 2015.
39. Djordjevic M аnd Djordjevic M, Predictions of heavy-flavor suppression at 5.1 TeV Pb+Pb collisions at
the CERN Large Hadron Collider, Physical Review C 92, 024918, 2015.
40. Zukher I, Novikova M, Tikhonov A, Nesterchuk M, Osterman I, Djordjevic M, Sergiev P, Sharma C,
Severinov K, Ribosome-controlled transcription termination is essential for the production of antibiotic
microcin C, Nucleic Acids Research 42, 11891, 2014.
41. Djordjevic M, Integrating sequence analysis with biophysical modelling for accurate transcription start
site prediction, Journal of Integrative Bioinformatics 11, 240, 2014 (invited review paper).
42. Djordjevic M, Djordjevic M and Blagojevic B, RHIC and LHC jet suppression in non-central collisions,
Physics Letters B 737, 298, 2014.
43. Djordjevic M аnd Djordjevic M, LHC jet suppression of light and heavy flavor observables, Physics
Letters B 734, 286, 2014.
44. Djordjevic M аnd Djordjevic M, Heavy flavor puzzle from data measured at the BNL Relativistic Heavy
Ion Collider: Analysis of the underlying effects, Physical Review C 90, 034910, 2014.
45. Djordjevic M аnd Djordjevic M, Understanding the strong suppression patterns at RHIC and LHC,
Modern Physics Letters A 29, 1430035, 2014 (invited review paper).
46. Djordjevic M, Djordjevic M, Explaining the fine hierarchy in pion and kaon suppression at LHC:
Importance of fragmentation functions, Journal of Physics G 41, 055104, 2014.
47. Djordjevic M, Efficient transcription initiation in bacteria: an interplay of protein-DNA interaction
parameters, Integrative Biology 5, 796, 2013.
48. Djordjevic M, Modeling bacterial immune systems: strategies for expression of toxic - but useful -
molecules, Biosystems 112, 139, 2013.
49. Djordjevic M, Djordjevic M, A simple biosynthetic pathway for large product generation from small
substrate amounts, Physical Biology 9, 056004, 2012.
50. Djordjevic M, Djordjevic M, Severinov K, CRISPR transcript processing: a mechanism for generating a
large number of small interfering RNAs, Biology Direct 7, 24, 2012.
51. Pavlova O, Lavysh D, Klimik E, Djordjevic M, Ravcheev DA, Gelfand MS, Severinov K, Akulenko N,
Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32, Journal of
Molecular Biology 416, 389, 2012.
52. Djordjevic M, Djordjevic M, Generalization of radiative jet energy loss to non-zero magnetic mass,
Physics Letters B 709, 229, 2012.
53. Djordjevic M, Redefining Escherichia coli σ70 promoter elements: -15 motif as a complement of the -10
motif, Journal of Bacteriology 193, 6305, 2011.
54. Pougach K, Semenova E, Bogdanova E, Datsenko KA, Djordjevic M, Wanner BL, and Severinov K,
Transcription, transcripts processing and function of E. coli CRISPR locus, Molecular Microbiology 77,
1367, 2010
55. Djordjevic M, Inferring protein-DNA interaction parameters from SELEX experiments. Methods in
Molecular Biology 674, 195, 2010 (invited book chapter).
56. Djordjevic M and Bundschuh R, Open complex formation by bacterial RNA polymerase – a quantitative
model, Biophysical Journal 94, 4233, 2008.
57. Bogdanova E, Djordjevic M, Papapanagiotou I, Heyduk T, Kneale G and Severinov K, Transcription
regulation of the type II restriction-modification system AhdI, Nuclear Acids Research 36, 1429, 2008.
58. Djordjevic M, SELEX experiments: novel prospects applications and data analysis for inferring
regulatory pathways, Biomolecular Engineering 24, 179, 2007 (invited review paper).
59. Sevostyanova A, Djordjevic M, Kuznedelov K, Naryshkina T, Gelfand M, Severinov K and Minakhin L,
Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage
phiYS40, Journal of Molecular Biology 366, 420, 2007.
60. Djordjevic M, Semenova E, Shraiman B and Severinov K, Quantitative analysis of transcription strategy
by a virulent bacteriophage, Virology, 354, 240, 2006.
61. Djordjevic M, Sengupta A M, Quantitative modeling and data analysis of SELEX experiments, Physical
Biology 3, 13, 2006.
62. Semenova E, Djordjevic M, Shraiman B and Severinov K, The tale of two RNA polymerases: transcription
profiling and gene expression strategy of bacteriophage Xp10, Molecular Microbiology 55, 764, 2005.
63. Djordjevic M, Sengupta A M and Shraiman B, A biophysical approach to transcription factor binding site
discovery, Genome Research 13, 2381, 2003.
64. Sengupta A M, Djordjevic M, Shraiman B, Specificity and robustness in transcription control networks,
Proceedings of the National Academy of Science 99, 2072, 2002.
65. Mendas I, Djordjevic M and Markovic M, Properties of the nonclassical maximum-entropy states, Journal
of Physics A: Mathematical and General 33, 921, 2000.
B. Books
1. Grbic B, Djordjevic M, Popovic-Bozic M and Stosic M, International physics olympiads 1967-1996,
Collected problems and solutions (in Serbian), Serbian Physical Society Press (2000) [ISBN 86-17-08245-
3].
2. Djordjevic M, Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages,
PhD Thesis (2005) [ISBN 05-42-23846-2].
3. Djordjevic M and Djordjevic M, Fundamentals of physics for biologists: Collected problems and solutions
(in Serbian), University of Belgrade – Faculty of Biology press (2014) [ISBN 978-867078-112-2
Talks, seminars and science popularization
M. Djordjevic presented his research as 63 talks at international conferences (29 plenary) and 37 seminars at
major research centers (see http://www.bio.bg.ac.rs/Marko_Djordjevic_web_site for full list). His research
was featured in “Vecernje novosti” (Serbian highest-circulation newspaper), on Radio Television of Serbia
1st channel (“Jutarnji program”), in popular science magazine “Elementi” (issued by Serbian center for
promotion of science.
A. Conferences and Workshops
1. Using mathematical modeling and feature selection techniques to infer the predictors of the SARS-CoV-2
transmissibility. The Eighth International Conference on Mathematical Modeling and Analysis of
Populations in Biological Systems (ICMA-VIII), Lafayette, LA, USA, Oct 2022 (given by Dr. Andjela
Rodic).
2. Biophysical modeling and analysis of the predictors of the COVID-19 transmission and clinical severity
(invited talk), RBC 2022 – Regional Biophysics Conference, Pеcs, Hungary, Aug 2022 (given by Dr.
Andjela Rodic).
3. Inferring environmental drivers of COVID-19 severity by machine learning. FEMS Conference on
Microbiology, Belgrade, Serbia, Jul 2022 (given by PhD student Sofija Markovic).
4. Estimating parameter values, analyzing the role, and identifying predictors of the SARS-CoV-2 inherent
transmissibility, FEMS Conference on Microbiology, Belgrade, Serbia, Jul 2022 (given by PhD student
Andjela Rodic).
5. Analytical study of infection outburst under strong mitigation measures. FEMS Conference on
Microbiology, Belgrade, Serbia, Jul 2022 (given by Dr. Bojana Ilic).
6. Combining machine learning and non-linear dynamics modeling to understand COVID-19 risk factors,
13th International Multiconference on Bioinformatics of Genome Regulation and Structure/Systems
Biology -BGRS/SB 2022, Novosibirsk, Russia, Jun 2022.
7. Analytical and numerical study of infection progression under social distancing measures. 13th
International Multiconference on Bioinformatics of Genome Regulation and Structure/Systems Biology -
BGRS/SB 2022, Novosibirsk, Russia, Jun 2022 (given by Dr. Bojana Ilic).
8. Modeling the COVID-19 transmission dynamics and identifying meteorological and sociodemographic
predictors. 13th International Multiconference on Bioinformatics of Genome Regulation and
Structure/Systems Biology -BGRS/SB 2022, Novosibirsk, Russia, Jun 2022 (given by PhD student
Andjela Rodic).
9. Understanding infectious disease spread by dynamical modeling and machine learning, Quantitative
Biology School, Pazmany Peter Catholic University, Budapest, Hungary, May 2022.
10. Investigating the SARS-CoV-2 virus transmission using a non-linear compartmental epidemiological
model, 2nd Conference on Nonlinearity, Belgrade, Serbia, Oct 2021 (given by PhD student Andjela
Rodic).
11. Inferring COVID-19 severity determinants by combining epidemiological modeling and machine
learning. 2nd Conference on Nonlinearity, Belgrade, Serbia, Oct 2021 (given by PhD student Sofija
Markovic).
12. Global COVID-19 growth signatures used to characterize COVID-19 nonlinear infection dynamics, 2nd
Conference on Nonlinearity, Belgrade, Serbia, Oct 2021 (given by Dr. Bojana Ilic).
13. A systems biology approach to understanding SARS-CoV-2 transmissibility in population. Moscow
Conference of Computational Molecular Biology (MCCMB 2021), Moscow, Russia, Jul 2021 (given by
PhD student Sofija Markovic).
14. Biophysical and bioinformatics approach to study socio-demographic and weather impacts on the SARS-
CoV-2 virus transmissibility (invited talk), Belgrade Bioinformatics Conference - BELBI 2021, Belgrade,
Serbia, Jun 2021 (given by PhD student Andjela Rodic).
15. A bioinformatics approach to inferring environmental drivers of SARS-CoV-2 transmissibility. Belgrade
Bioinformatics Conference - BELBI 2021, Belgrade, Serbia, Jun 2021 (given by PhD student Sofija
Markovic).
16. Understanding Infection Progression under Strong Control Measures through Universal COVID-19
Growth Signatures. Belgrade Bioinformatics Conference - BELBI 2021, Belgrade, Serbia, Jun 2021
(given by Dr. Bojana Ilic).
17. A biophysical approach to modeling biological systems and bioinformatics (3 lectures + 3 working
sessions), APS & ICTP-SAIFR Young Physicists Forum on Biological Physics: from Molecular to
Macroscopic Scale, co-organized by the American Physical Society, Sao Paulo, Brazil, March 2020.
18. Analysis of CRISPR/Cas non-canonical functions, International Moscow Conference on Computational
Molecular Biology (MCCMB19), Moscow, Russia, Jul 2019
19. Biophysics and Bioinformatics of CRISPR/Cas and restriction-modification systems in bacteria, Second
Congress of Biologists in Serbia, Kladovo, Serbia, Sept 2018.
20. Assessing CRISPR-Cas design principles by biophysical modeling, 14th International Conference on
21. Fundamental and Applied Aspects of Physical Chemistry (Physical Chemistry 2018), Belgrade, Serbia,
Sept 2018 (given by PhD student Andjela Rodic).
22. Including population dynamics effects in modeling regulation of bacterial restriction modification
systems, Physical Chemistry 2018, Belgrade, Serbia, Sept 2018 (given by PhD student Stefan Graovac).
23. Integrating computational systems biology and bioinformatics in research and education, Neuronet
Initiative Project, International experience in education programs, Novosibirsk, Russia, Aug 2018.
24. A Kolmogorov-Smirnov based approach for predicting targets of transcription, WIBSB 2018, First Sino-
Russian Workshop on Integrative Bioinformatics and Systems Biology, Novosibirsk, Russia, Aug 2018.
25. CRISPR-Cas regulation: a systems biology approach, BGRS/SB2018, 11th International Multiconference
on Bioinformatics of Genome Regulation and Structure/Systems Biology Novosibirisk, Russia, Aug 2018.
26. A Kolmogorov-Smirnov based approach for predicting bacterial transcription targets, BelBI2018 -
Belgrade Bioinformatics Conference, Belgrade, Serbia, Jun 2018.
27. Biophysical modeling of bacterial immune systems: analyzing regulation of CRISPR-Cas and restriction-
modification systems, RBC2018, Zrece, Slovenia, May 2018.
28. Understanding key features of CRISPR/Cas system induction through modeling, International Moscow
Conference on Computational Molecular Biology (MCCMB17), Moscow, Russia, Jul 2017.
29. Modelling Expression Dynamics of Bacterial Immune Systems, First Congress of Molecular Biologists of
Serbia (CoMBoS2017), Belgrade, Serbia, Sept 2017.
30. CRISPR/Cas: from bacterial immune system to new biotechnology applications, JRC-ICGEB joint
workshop genome editing and related technologies, Trieste, Italy, Nov 2016.
31. CRISPR/Cas and restriction-modification systems: from bacterial immune systems to biotechnology
applications, CRISPR Biotechnology Workshop, Belgrade City Library, Dec 2016 (given by PhD students
Andjela Rodic and Tamara Stankovic).
32. Transcription initiation by alternative σ factors: revising the rigidness paradigm, 10th International
Multiconference: BGRS/SB2016, Novosibirisk, Russia, Sept 2016 (given by PhD student Jelena Guzina).
33. Modeling CRISPR/Cas system induction: the significance of cooperative transcription regulation,
BGRS/SB2016, Novosibirsk, Russia, Sept 2016 (given by PhD student Andjela Rodic).
34. Transcription initiation by alternative σ factors, BELBI2016 - Belgrade Bioinformatics Conference,
Belgrade, Serbia, June 2016 (given by PhD student Jelena Guzina).
35. Examining regulation of restriction-modification systems by quantitative modeling, BELBI2016 -
Belgrade, Serbia, June 2016 (given by PhD student Andjela Rodic).
36. Achieving a rapid expression of toxic (but useful) molecules within cell, BELBI2016 - Belgrade, Serbia,
June 2016 (given by PhD student Bojana Blagojevic).
37. From biophysical modeling to bioinformatics, Belgrade International Molecular Life Science Conference
for Students, Belgrade, Serbia, Jan 2015.
38. Inferring bacteriophage infection strategies from genome sequence: analysis of acteriophage 7-11 and
related phages, Bacteriophages 2015, London, UK, Jan 2016 (given by PhD student Jelena Guzina).
39. Towards Accurate Transcription Start Site Prediction: a modelling approach, German Conference on
Bioinformatics (GCB2014), Bielefeld, Germany, September 2014.
40. Modeling bacterial immune systems: CRISPR/CAS regulation, The 9th international Conference on
Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2014), Novosibirsk,
Russia, June 2014.
41. A biophysical approach to bacterial transcription start site prediction, The 9th international Conference
on Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2014), Novosibirsk,
Russia, June 2014.
42. Integrating Sequence Analysis with Biophysical Modelling for Accurate Transcription Start Site
Prediction, 10th International Symposium on Integrative Bioinformatics (IB2014), Newcastle, UK, May
2014.
43. Bioinformatic analysis of bacterial promoters, TABIS 2013 - Theoretical Approaches to BioInformation
Systems 2013, Belgrade, Serbia, September 2013.
44. Bioinformatics analysis of gene expression strategies of bacterial viruses, TABIS 2013, Belgrade, Serbia,
September 2013 (given by PhD student Jelena Guzina).
45. CRISPR transcript processing: an unusual mechanism for rapid production of small RNAs, ICSB 2012 -
The 13th International Conference on Systems Biology, Toronto, CA, Aug 2012.
46. Predictions of bacterial transcription start sites - a biophysical approach, RBC 2012 - The 5th Regional
biophysics conference, Kladovo, Serbia, Sept 2012.
47. Transcription Start Site Prediction in Bacteria, DMBI 2012 - International Meeting on Data Mining in
Bioinformatics, Belgrade, Serbia, Jun 2012.
48. CRISPR transcript processing: an unusual mechanism for rapid production of desired molecules, IPCAT
2012 - 9th International Conference on Information Processing in Cells and Tissues, Trinity College,
Cambridge, UK, Apr 2012.
49. A Genome-wide Analysis of Poised Promoters in Bacteria, 7th Annual Rocky Mountains Bioinformatics
Conference, Snowmass Village, Colorado, Dec 2009.
50. Biophysical modeling of transcription initiation in bacteria, 8th International conf. on Information
Processing in Cells and Tissues (IPCAT 2009), Franscini Ascona, Switzerland, Apr 2009.
51. Quantitative modeling of transcription initiation in bacteria, BioSysBio Conference 2009, Cambridge,
UK, Mar 2009.
52. Using biophysics to investigate engineering principles behind transcription initiation, Engineering
principles in Biological Systems, Cold Spring Harbor, NY, Dec 2008.
53. Biophysical modeling of transcription initiation, 2008 APS March Meeting, New Orleans, Louisiana, Mar
2008.
54. Theoretical modeling of transcription initiation by bacterial RNA polymerase, Partners Meeting, OSU
MBI, Columbus, Ohio, Nov 2007.
55. The open complex formation by bacterial RNA polymerase, poster spotlight at Q-bio Conference on
Cellular Information Processing, Santa Fe, Aug 2007.
56. Using in vitro selection to infer transcription regulatory networks, Evolution of Molecular Networks,
KITP, Santa Barbara, California, Feb 2007.
57. Computational analysis of gene regulation, Partners Meeting, OSU, Columbus, Ohio, Nov 2006.
58. Computational search for transcription factor binding sites, 9th Annual Conference on Computational
Genomics, Baltimore, Maryland, Oct 2006.
59. Quantitative modeling and data analysis of SELEX experiments, 2006 APS March Meeting, Baltimore,
Maryland, Mar 2006.
60. Biophysics and bioinformatics of transcription, Partners Meeting, OSU, Columbus, OH, Nov 2005.
61. Quantitative modeling and analysis of data for SELEX experiments, 91st Statistical Mechanics
Conference, Piscataway, New Jersey, May 2004.
62. Biophysical approach to identification of transcription factor binding sites, 5th General Conference of the
Balkan Physical Union, Vrnjacka Banja, Serbia, Aug 2003.
63. A biophysical approach to transcription factor binding site discovery, 88th Statistical Mechanics
Conference, Piscataway, New Jersey, Dec 2002.
B. Colloquia and Seminars
1. Biophysical and bioinformatics approach in the study of SARS-CoV-2 virus transmission in the
population, Bioinformatics Seminar, Faculty of Mathematics, University of Belgrade, Belgrade, Feb 2021
(given by PhD student Andjela Rodic).
2. Biophysical and bioinformatics approach in the study of SARS-CoV-2 virus transmission in the
population, World Biophysics Week, Ilija M. Kolarac Endowment, Belgrade, Serbia, Jan 2021 (given by
PhD student Andjela Rodic).
3. A biophysical approach to understanding gene expression regulation in bacteria, Theoretical Physics
Seminar, Jozef Stefan Institute, Ljubljana, Slovenia, Sept 2019.
4. Regulatory dynamics of restriction-modification systems in bacteria: from biophysics models to synthetic
biology, Bioinformatics Seminar, Faculty of Mathematics, University of Belgrade, Belgrade, May 2019
(given by PhD students Andjela Rodic and Stefan Graovac).
5. From protein-DNA interactions to systems biology. Lecture Series in Honor of 2017 Nobel Prizes in
Physiology or Medicine, Faculty of Physical Chemistry, University of Belgrade, Belgrade, Mar 2018.
6. CRISPR/Cas and restriction-modification systems: modeling dynamics of bacterial immune system
expression, Bioinformatics Seminar, Faculty of Mathematics, University of Belgrade, Belgrade, Dec 2016
(given by PhD students Andjela Rodic and Bojana Blagojevic).
7. Biophysical Modeling and Bioinformatics, International Biophysics Week, Kolarac Foundation, Belgrade,
Belgrade, March 2016 (given by PhD student Jelena Guzina).
8. Modeling bacterial immune systems, Seminar of Bioinformatics, Faculty of Mathematics, University of
Belgrade, Belgrade, Nov 2015 (given by PhD student Andjela Rodic).
9. Bioinformatics analysis of transcription regulation in bacteria and bacteriophages, Bioinformatics
seminar, Faculty of Mathematics, University of Belgrade, March 2015, Belgrade (given by PhD student
Jelena Guzina).
10. Biophysical Modeling and Bioinformatics of Gene Expression Regulation, Colloquium at Faculty of
Physics, University of Belgrade, Belgrade, Serbia, June 2014.
11. Bioinformatics and Biological System Modeling, Lecture Series in Honor of 150 Years of Faculty of
Biology, University of Belgrade, Belgrade, Serbia, Nov 2013.
12. Modeling the open complex formation by bacterial RNA polymerase, NORDITA (Nordic Institute for
Theoretical Physics) Seminar, Stockholm, Sweden, Mar 2008.
13. Theoretical modeling of Gene Regulation, ISU Mathematics Colloquium, Iowa State University, Ames,
Iowa, Feb 2008.
14. Modeling and Bioinformatics of Gene Transcription, Frontiers in Systems and Integrative Biology,
UCLA, Los Angeles, California, Feb 2008.
15. Gene Regulation: Biophysical Modeling and Bioinformatics Applications, Biophysics Seminar, Brown
University, Providence, Rhode Island, Feb 2008.
16. Biophysics and Bioinformatics of Gene Regulation, Physics Colloquium, Western Kentucky
University, Bowling Green, Kentucky, Feb 2008.
17. Quantitative Modeling of Gene Regulation, Mathematics Colloquium, West Virginia
University, Morgantown, West Virginia, Feb 2008.
18. Biophysical modeling of the open complex formation by bacterial RNA polymerase, Physics Colloquium,
National Central University, Taipei, Taiwan, Jan 2008.
19. Theoretical modeling of transcription initiation in bacteria, Center for Nonlinear Studies Seminar, LANL,
Los Alamos, Dec 2007.
20. Biophysics and bioinformatics approaches to gene expression regulation, Iowa State University
Mathematics Colloquium, Iowa State University, Ames, Nov 2007.
21. Theoretical modeling of the open complex formation in bacteria, Computational and Applied Mathematics
Seminar, Iowa State University, Ames, Iowa, Nov 2007.
22. Quantitative modeling of transcription initiation by bacterial RNA polymerase, Applied Mathematics
Colloquium, Columbia University, New York, Oct 2007.
23. Quantitative modeling of transcription initiation in bacteria, Brookhaven National Laboratory, Upton,
New York, Oct 2007.
24. Theoretical modeling of the open complex formation in bacteria, Lunch Seminar, University of California
at San Francisco, San Francisco, Oct 2007.
25. Biophysics and bioinformatics of gene transcription, Department of Biology Colloquium, Institute for
Physiology and Biochemistry, Belgrade, Serbia, Sept 2007.
26. Biophysics and bioinformatics of gene transcription, Physics Colloquium, Faculty of Natural Sciences
and Mathematics, Novi Sad, Serbia, Sept 2007.
27. Quantitative modeling of transcription initiation in bacteria, Theoretical Physics Seminar, Jozef Stefan
Institute, Ljubljana, Slovenia, Aug 2007.
28. Transcription factor binding energy vs. biological function, Plant Biotechnology Seminar, Columbus,
Ohio, Jan 2007.
29. Search for transcription factor binding sites in eukaryotes: a principal limit and a novel method, Plant
Biotechnology Seminar, Columbus, Ohio, Jan 2006.
30. Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages, Postdoctoral
Seminar, OSU MBI, Columbus, Ohio, Oct 2005.
31. Bioinformatics of transcription regulation in bacteria and bacteriophages, Computational Biology &
Medical Informatics Seminar, IBM T. J. Watson Res. Center, Yorktown Heights, NY, Jan 2005.
32. Quantitative analysis of gene expression regulation: a biophysical approach, Rockefeller University, New
York, New York, Jan 2005.
33. Quantitative analysis of gene expression regulation: a biophysical approach, Princeton University,
Princeton, New Jersey, Jan 2005.
34. Biophysics and bioinformatics of transcription regulation, Computational Physics and Bioinformatics
Group Seminar, Weizmann Institute of Science, Rehovot, Israel, Dec 2004.
35. Computational analysis of gene expression regulation in bacteria and bacteriophages, Brookhaven
National Laboratory, Upton, New York, Dec 2004.
36. Computational analysis of gene expression regulation in bacteria and bacteriophages, Columbia
University, New York, New York, Dec 2004.
37. Computational approaches to transcription regulation, Colloquium at Faculty of Physics, Belgrade,
Serbia, Sept 2004.
