Publications 
A.  Articles 
1.  Markovic  S,  Rodic  A,  Salom  I,  Milicevic  O,  Djordjevic  M,  Djordjevic  M,  COVID-19  severity 
determinants inferred through ecological and epidemiological modeling, arXiv:2109.00038. 
2.  Milicevic O, Salom I, Tumbas M, Rodic A, Markovic S, Zigic D, Djordjevic M, Djordjevic M, PM
2.5
 as 
a major predictor of COVID-19 basic reproduction number in the USA, Environmental Research 201, 
111526, 2021. 
3.  Djordjevic M, Salom I, Markovic S, Rodic A, Milicevic O, Djordjevic M, Inferring the main drivers of 
SARS-CoV-2 transmissibility, GeoHealth, 2021 (in press). 
4.  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 5, 2000101, 2021 
(featured as journal’s Cover page). 
5.  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. 
6.  Djordjevic M,Rodic A, Salom I, Zigic D, Milicevic O, Ilic B, Djordjevic M, A systems biology approach 
to COVID-19 progression in population, Advances in Protein Chemistry and Structural Biology 127, 291, 
2021. 
7.  Stojku S, Ilic B, Djordjevic M, Djordjevic M,Extracting the temperature dependence in high-p
⊥
 particle 
energy loss, Physics Review C 103, 024908, 2021. 
8.  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. 
9.  Zigic D, Ilic B, Djordjevic M, Djordjevic M, Exploring the initial stages in heavy-ion collisions with high-
p
⊥
 R
AA
and v
2
 theory and data, Physics Review C 101, 064909, 2020. 
10. Milicevic O, Repac J, Bozic B, Djordjevic Mand Djordjevic M, A Simple Criterion for Inferring CRISPR 
Array Direction. Front. Microbiol. 10, 2054, 2019. 
11. Djordjevic M, Rodic A, Graovac S, From biophysics to 'omics and systems biology, European Biophys 
Journal. 48, 413, 2019 
12. 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. 
13. 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. 
14. 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). 
15. Zigic D, Salom I, Auvinen J, Djordjevic M, Djordjevic M, DREENA-B framework: first predictions of 
R
AA
 and v
2
 within dynamical energy loss formalism in evolving QCD medium, Physics Letters B 791, 236, 
2019.   
16. 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. 
17. 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. 
18. 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. 
19. Zigic  D,  Salom  I,  Auvinen  J,  Djordjevic  M,  Djordjevic  M,  Joint  R
AA
  and  v
2
predictions  for  Pb+Pb 
collisions at the LHC within DREENA-C framework, Journal of Physics G 46, 085101, 2019. 
20. 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. 

21. 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. 
22. 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. 
23. 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. 
24. Djordjevic M, Djordjevic M and Zdobnov E, Scoring Targets of Transcription in Bacteria Rather than 
Focusing on Individual Binding Sites, Frontiers in  Microbiology8, 2314, 2017. 
25. 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  
Microbiology8, 2139, 2017. 
26. Rodic  A,  Blagojevic  B,  Zdobnov  E,  Djordjevic  M  andDjordjevic  M,  Understanding  key  features of 
bacterial restriction-modification systems through quantitative modeling, BMC Systems Biology, 11:377, 
2017. 
27. Guzina J and Djordjevic M, Mix-and-matching as a promoter recognition mechanism by ECF σ factors, 
BMC Evolutionary Biology, 17:12, 2017. 
28. Nikolic M, Stankovic T, Djordjevic M, Contribution of bacterial promoter elements to transcription start 
site detection accuracy, J of Bioinformatics and Computational Biology15: 1650038, 2017. 
29. Guzina J, Djordjevic M, Promoter recognition by ECF σ factors: analyzing DNA and protein interaction 
motifs, Journal of Bacteriology 198:1927, 2016.  
30. 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.  
31. Guzina  J,  Djordjevic  M,  Bioinformatics  as  a  first-line  approach  for  understanding  bacteriophage 
transcription, Bacteriophage5:e1062588, 2015 (invited review paper). 
32. 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.  
33. 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. 
34. 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.  
35. Djordjevic M, Integrating sequence analysis with biophysical modelling for accurate transcription start 
site prediction, Journal of Integrative Bioinformatics 11(2):240, 2014 (invited review paper). 
36. Djordjevic M, Djordjevic M and Blagojevic B, RHIC and LHC jet suppression in non-central collisions, 
Physics Letters B737:298, 2014.  
37. Djordjevic  M  аnd  Djordjevic M, LHC jet suppression of light and heavy flavor observables, Physics 
Letters B 734:286, 2014.  
38. 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.  
39. Djordjevic  M  аnd  Djordjevic  M,  Understanding the  strong  suppression patterns at  RHIC  and LHC, 
Modern Physics Letters A 29: 1430035, 2014 (invited review paper).  
40. 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.  
41. Djordjevic  M,  Efficient  transcription  initiation  in  bacteria:  an  interplay  of  protein-DNA  interaction 
parameters, Integrative Biology 5(5):796, 2013. 

42. Djordjevic  M,  Modeling  bacterial  immune  systems:  strategies  for  expression  of  toxic  -  but  useful  - 
molecules, Biosystems 112(2):139, 2013. 
43. Djordjevic M, Djordjevic M, A simple biosynthetic pathway for large product generation from small 
substrate amounts, Physical Biology 9(5): 056004, 2012.  
44. Djordjevic M, Djordjevic M, Severinov K, CRISPR transcript processing: a mechanism for generating a 
large number of small interfering RNAs, Biology Direct7(1): 24, 2012.  
45. 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(3): 389, 2012. 
46. Djordjevic M, Djordjevic M,  Generalization of radiative jet energy loss to non-zero magnetic mass, 
Physics Letters B 709:229, 2012. 
47. Djordjevic M, Redefining Escherichia coli σ
70
 promoter elements: -15 motif as a complement of the -10 
motif, Journal of Bacteriology, 193(22): 6305, 2011.  
48. 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(6): 1367, 2010  
49. Djordjevic  M,  Inferring  protein-DNA  interaction  parameters  from  SELEX  experiments.  Methods  in 
Molecular Biology, 674: 195, 2010 (invited book chapter).  
50. Djordjevic M and Bundschuh R, Open complex formation by bacterial RNA polymerase – a quantitative 
model, Biophysical Journal, 94(11): 4233, 2008.  
51. 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(5): 1429, 2008.  
52. Djordjevic  M,  SELEX  experiments:  novel  prospects  applications  and  data  analysis  for  inferring 
regulatory pathways, Biomolecular Engineering 24(2):179, 2007 (invited review paper).  
53. 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(2):420, 2007.  
54. Djordjevic M, Semenova E, Shraiman B and Severinov K, Quantitative analysis of transcription strategy 
by a virulent bacteriophage, Virology, 354(2):240, 2006.  
55. Djordjevic M, Sengupta A M, Quantitative modeling and data analysis of SELEX experiments, Physical 
Biology 3:13, 2006.  
56. 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 Microbiology55:764, 2005.  
57. Djordjevic M, Sengupta A M and Shraiman B, A biophysical approach to transcription factor binding site 
discovery, Genome Research 13(11):2381, 2003.  
58. Sengupta A M, Djordjevic M, Shraiman B, Specificity and robustness in transcription control networks, 
Proceedings of the National Academy of Science 99:2072, 2002.  
59. Mendas I, Djordjevic M and Markovic M, Properties of the nonclassical maximum-entropy states, Journal 
of Physics A: Mathematical and General 33:921, 2000. 