@ARTICLE{
author={Markovic Sofija,Djordjevic Magdalena R,Ou Hong-Yu,Djordjevic Marko J},
year={2025},
title={Bistability in type I toxin-antitoxin systems may lead to stress-induced persister formation},
journal={NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
volume={12},
number={1},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Zivkovic Lidija M,Ou Hong Yu,Djordjevic Marko J},
year={2025},
title={Nonlinear regulatory dynamics of bacterial restriction-modification systems modulates horizontal gene transfer susceptibility},
journal={NUCLEIC ACIDS RESEARCH},
volume={53},
number={2},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Karmakar Bithika,Zigic Dusan,Djordjevic Magdalena R,Huovinen Pasi,Djordjevic Marko J,Auvinen Jussi},
year={2024},
title={Probing the shape of the quark-gluon plasma droplet via event-by-event quark-gluon plasma tomography},
journal={PHYSICAL REVIEW C},
volume={110},
number={4},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Ilic Bojana N,Salom Igor,Djordjevic Marko J,Djordjevic Magdalena R},
year={2023},
title={An analytical framework for understanding infection progression under social mitigation measures},
journal={NONLINEAR DYNAMICS},
volume={111},
number={23},
pages={22033-22053},
document_type={Article},
} 

@ARTICLE{
author={Karmakar Bithika,Zigic Dusan,Salom Igor,Djordjevic Magdalena R,Auvinen Jussi,Huovinen Pasi,Djordjevic Marko J},
year={2023},
title={Constraining η/s through high-p⊥ theory and data},
journal={PHYSICAL REVIEW C},
volume={108},
number={4},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Ilic Bojana N,Salom Igor,Djordjevic Marko J,Djordjevic Magdalena R},
year={2023},
title={An analytical framework for understanding infection progression under social mitigation measures},
journal={NONLINEAR DYNAMICS},
volume={111},
number={23},
pages={22033-22053},
document_type={Article},
} 

@ARTICLE{
author={Stojku Stefan,Auvinen Jussi,Djordjevic Magdalena R,Djordjevic Marko J,Huovinen Pasi},
year={2023},
title={Initial Time Τ0 Constrained by High-P⊥ Data},
journal={ACTA PHYSICA POLONICA B PROCEEDINGS SUPPLEMENT},
volume={16},
number={1},
pages={-},
document_type={Proceedings Paper},
} 

@ARTICLE{
author={Tumbas Marko,Markovic Sofija,Salom Igor,Djordjevic Marko J},
year={2023},
title={A large-scale machine learning study of sociodemographic factors contributing to COVID-19 severity},
journal={FRONTIERS IN BIG DATA},
volume={6},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Li Peifei,Goh Ying-Xian,Ilic Bojana N,Tai Cui,Deng Zixin,Chen Zhaoyan,Djordjevic Marko J,Ou Hong-Yu},
year={2023},
title={Antibiotic-induced degradation of antitoxin enhances the transcription of acetyltransferase-type toxin-antitoxin operon},
journal={JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY},
volume={78},
number={4},
pages={1066-1075},
document_type={Article},
} 

@ARTICLE{
author={Zhang Jianfeng,Guan Jiahao,Wang Meng,Li Gang,Djordjevic Marko J,Tai Cui,Wang Hui,Deng Zixin,Chen Zhaoyan,Ou Hong-Yu},
year={2023},
title={SecReT6 update: a comprehensive resource of bacterial Type VI Secretion Systems},
journal={SCIENCE CHINA-LIFE SCIENCES},
volume={66},
number={3},
pages={626-634},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J,Markovic Sofija,Salom Igor,Djordjevic Magdalena R},
year={2023},
title={Understanding risk factors of a new variant outburst through global analysis of Omicron transmissibility},
journal={ENVIRONMENTAL RESEARCH},
volume={216},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Markovic Sofija,Salom Igor,Rodic Andjela M,Djordjevic Marko J},
year={2022},
title={Analyzing the GHSI puzzle of whether highly developed countries fared worse in COVID-19},
journal={SCIENTIFIC REPORTS},
volume={12},
number={1},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Goh Ying-Xian,Li Peifei,Wang Meng,Djordjevic Marko J,Tai Cui,Wang Hui,Deng Zixin,Chen Zhaoyan,Ou Hong-Yu},
year={2022},
title={Comparative Analysis of Diverse Acetyltransferase-Type Toxin-Antitoxin Loci in Klebsiella pneumoniae},
journal={MICROBIOLOGY SPECTRUM},
volume={10},
number={4},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Stojku Stefan,Auvinen Jussi,Djordjevic Marko J,Huovinen Pasi,Djordjevic Magdalena R},
year={2022},
title={Early evolution constrained by high-p perpendicular to quark-gluon plasma tomography},
journal={PHYSICAL REVIEW C},
volume={105},
number={2},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Ilic Bojana N,Zigic Dusan,Djordjevic Marko J,Djordjevic Magdalena R},
year={2021},
title={Utilizing high-p(perpendicular to) theory and data to constrain the initial stages of quark-gluon plasma},
journal={INTERNATIONAL JOURNAL OF MODERN PHYSICS E},
volume={30},
number={11},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Markovic Sofija,Rodic Andjela M,Salom Igor,Milicevic Ognjen S,Djordjevic Magdalena R,Djordjevic Marko J},
year={2021},
title={COVID-19 severity determinants inferred through ecological and epidemiological modeling},
journal={ONE HEALTH},
volume={13},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Milicevic Ognjen S,Salom Igor,Rodic Andjela M,Markovic Sofija,Tumbas Marko,Zigic Dusan,Djordjevic Magdalena R,Djordjevic Marko J},
year={2021},
title={PM2.5 as a major predictor of COVID-19 basic reproduction number in the USA},
journal={ENVIRONMENTAL RESEARCH},
volume={201},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J,Salom Igor,Markovic Sofija,Rodic Andjela M,Milicevic Ognjen S,Djordjevic Magdalena R},
year={2021},
title={Inferring the Main Drivers of SARS-CoV-2 Global Transmissibility by Feature Selection Methods},
journal={GEOHEALTH},
volume={5},
number={9},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Rodic Andjela M,Salom Igor,Zigic Dusan,Milicevic Ognjen S,Ilic Bojana N,Djordjevic Marko J},
year={2021},
title={A systems biology approach to COVID-19 progression in population},
journal={PROTEOMICS AND SYSTEMS BIOLOGY},
volume={127},
number={},
pages={291-314},
document_type={Review; Book Chapter},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J,Ilic Bojana N,Stojku Stefan,Salom Igor},
year={2021},
title={Understanding Infection Progression under Strong Control Measures through Universal COVID-19 Growth Signatures},
journal={GLOBAL CHALLENGES},
volume={5},
number={5},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Stojku Stefan,Ilic Bojana N,Djordjevic Marko J,Djordjevic Magdalena R},
year={2021},
title={Extracting the temperature dependence in high-p(perpendicular to) particle energy loss},
journal={PHYSICAL REVIEW C},
volume={103},
number={2},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Salom Igor,Rodic Andjela M,Milicevic Ognjen S,Zigic Dusan,Djordjevic Magdalena R,Djordjevic Marko J},
year={2021},
title={Effects of Demographic and Weather Parameters on COVID-19 Basic Reproduction Number},
journal={FRONTIERS IN ECOLOGY AND EVOLUTION},
volume={8},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Stojku Stefan,Zigic Dusan,Ilic Bojana N,Auvinen Jussi,Salom Igor,Djordjevic Marko J,Huovinen Pasi},
year={2021},
title={From high p(perpendicular to) theory and data to inferring anisotropy of Quark-Gluon Plasma},
journal={NUCLEAR PHYSICS A},
volume={1005},
number={},
pages={-},
document_type={Article; Proceedings Paper},
} 

@ARTICLE{
author={Zigic Dusan,Ilic Bojana N,Djordjevic Marko J,Djordjevic Magdalena R},
year={2020},
title={Exploring the initial stages in heavy-ion collisions with high-p(perpendicular to) theory and data},
journal={PHYSICAL REVIEW C},
volume={101},
number={6},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Stojku Stefan,Djordjevic Marko J,Huovinen Pasi},
year={2019},
title={Shape of the quark gluon plasma droplet reflected in the high-p(perpendicular to) data},
journal={PHYSICAL REVIEW C},
volume={100},
number={3},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Milicevic Ognjen S,Repac Jelena,Bozic Bojan Dj,Djordjevic Magdalena R,Djordjevic Marko J},
year={2019},
title={A Simple Criterion for Inferring CRISPR Array Direction},
journal={FRONTIERS IN MICROBIOLOGY},
volume={10},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J,Rodic Andjela M,Graovac Stefan},
year={2019},
title={From biophysics to "omics and systems biology},
journal={EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS},
volume={48},
number={5},
pages={413-424},
document_type={Review},
} 

@ARTICLE{
author={Zigic Dusan,Salom Igor,Auvinen Jussi,Djordjevic Marko J,Djordjevic Magdalena R},
year={2019},
title={DREENA-C framework: joint R(AA )and v(2) predictions and implications to QGP tomography},
journal={JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS},
volume={46},
number={8},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Zigic Dusan,Djordjevic Marko J,Auvinen Jussi},
year={2019},
title={How to test path-length dependence in energy-loss mechanisms: Analysis leading to a new observable},
journal={PHYSICAL REVIEW C},
volume={99},
number={6},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Zigic Dusan,Salom Igor,Auvinen Jussi,Djordjevic Marko J,Djordjevic Magdalena R},
year={2019},
title={DREENA-B framework: First predictions of R-AA and v(2) within dynamical energy loss formalism in evolving QCD medium},
journal={PHYSICS LETTERS B},
volume={791},
number={},
pages={236-241},
document_type={Article},
} 

@ARTICLE{
author={Bozic Bojan Dj,Repac Jelena,Djordjevic Marko J},
year={2019},
title={Endogenous Gene Regulation as a Predicted Main Function of Type I-E CRISPR/Cas System in E. coli},
journal={MOLECULES},
volume={24},
number={4},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Blagojevic Bojana N,Djordjevic Magdalena R,Djordjevic Marko J},
year={2019},
title={Calculating hard probe radiative energy loss beyond the soft-gluon approximation: Examining the approximation validity},
journal={PHYSICAL REVIEW C},
volume={99},
number={2},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Zigic Dusan,Blagojevic Bojana N,Auvinen Jussi,Salom Igor,Djordjevic Marko J},
year={2019},
title={Dynamical energy loss formalism: from describing suppression patterns to implications for future experiments},
journal={NUCLEAR PHYSICS A},
volume={982},
number={},
pages={699-702},
document_type={Article; Proceedings Paper},
} 

@ARTICLE{
author={Graovac Stefan,Rodic Andjela M,Djordjevic Magdalena R,Severinov Konstantin,Djordjevic Marko J},
year={2019},
title={Effects of Population Dynamics on Establishment of a Restriction-Modification System in a Bacterial Host},
journal={MOLECULES},
volume={24},
number={1},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Klimuk Evgeny,Bogdanova Ekaterina,Nagornykh Max,Rodic Andjela M,Djordjevic Marko J,Medvedeva Sofia,Pavlova Olga,Severinov Konstantin},
year={2018},
title={Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock},
journal={NUCLEIC ACIDS RESEARCH},
volume={46},
number={20},
pages={10810-10826},
document_type={Article},
} 

@ARTICLE{
author={Musharova Olga,Vyhovskyi Danylo,Medvedeva Sofia,Guzina Jelena,Zhitnyuk Yulia,Djordjevic Marko J,Severinov Konstantin,Savitskaya Ekaterina},
year={2018},
title={Avoidance of Trinucleotide Corresponding to Consensus Protospacer Adjacent Motif Controls the Efficiency of Prespacer Selection during Primed Adaptation},
journal={MBIO},
volume={9},
number={6},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Guzina Jelena,Chen Wei-Hua,Stankovic Tamara,Djordjevic Magdalena R,Zdobnov Evgeny,Djordjevic Marko J},
year={2018},
title={In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence},
journal={FRONTIERS IN GENETICS},
volume={9},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J,Djordjevic Magdalena R,Zdobnov Evgeny},
year={2017},
title={Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites},
journal={FRONTIERS IN MICROBIOLOGY},
volume={8},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Rodic Andjela M,Blagojevic Bojana N,Djordjevic Magdalena R,Severinov Konstantin,Djordjevic Marko J},
year={2017},
title={Features of CRISPR-Cas Regulation Key to Highly Efficient and Temporally-Specific crRNA Production},
journal={FRONTIERS IN MICROBIOLOGY},
volume={8},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Rodic Andjela M,Blagojevic Bojana N,Zdobnov Evgeny,Djordjevic Magdalena R,Djordjevic Marko J},
year={2017},
title={Understanding key features of bacterial restriction-modification systems through quantitative modeling},
journal={BMC SYSTEMS BIOLOGY},
volume={11},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Guzina Jelena,Djordjevic Marko J},
year={2017},
title={Mix-and-matching as a promoter recognition mechanism by ECF sigma factors},
journal={BMC EVOLUTIONARY BIOLOGY},
volume={17},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Nikolic Milos,Stankovic Tamara,Djordjevic Marko J},
year={2017},
title={Contribution of bacterial promoter elements to transcription start site detection accuracy},
journal={JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY},
volume={15},
number={2},
pages={-},
document_type={Article; Proceedings Paper},
} 

@ARTICLE{
author={Guzina Jelena,Djordjevic Marko J},
year={2016},
title={Promoter Recognition by Extracytoplasmic Function sigma Factors: Analyzing DNA and Protein Interaction Motifs},
journal={JOURNAL OF BACTERIOLOGY},
volume={198},
number={14},
pages={1927-1938},
document_type={Article},
} 

@ARTICLE{
author={Morozova Natalia,Sabantsev Anton,Bogdanova Ekaterina,Fedorova Yana,Maikova Anna,Vedyaykin Alexey,Rodic Andjela M,Djordjevic Marko J,Khodorkovskii Mikhail,Severinov Konstantin},
year={2016},
title={Temporal dynamics of methyltransferase and restriction endonuclease accumulation in individual cells after introducing a restriction-modification system},
journal={NUCLEIC ACIDS RESEARCH},
volume={44},
number={2},
pages={790-800},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J},
year={2015},
title={Predictions of heavy-flavor suppression at 5.1 TeV Pb+Pb collisions at the CERN Large Hadron Collider},
journal={PHYSICAL REVIEW C},
volume={92},
number={2},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Guzina Jelena,Djordjevic Marko J},
year={2015},
title={Inferring bacteriophage infection strategies from genome sequence: analysis of bacteriophage 7-11 and related phages},
journal={BMC EVOLUTIONARY BIOLOGY},
volume={15},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Zukher Inna,Novikova Maria,Tikhonov Anton,Nesterchuk Mikhail V,Osterman Ilya A,Djordjevic Marko J,Sergiev Petr V,Sharma Cynthia M,Severinov Konstantin},
year={2014},
title={Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C},
journal={NUCLEIC ACIDS RESEARCH},
volume={42},
number={19},
pages={11891-11902},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J},
year={2014},
title={Heavy flavor puzzle from data measured at the BNL Relativistic Heavy Ion Collider: Analysis of the underlying effects},
journal={PHYSICAL REVIEW C},
volume={90},
number={3},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J},
year={2014},
title={Understanding the unexpected suppression patterns at RHIC and LHC},
journal={MODERN PHYSICS LETTERS A},
volume={29},
number={31},
pages={-},
document_type={Review},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J,Blagojevic Bojana N},
year={2014},
title={RHIC and LHC jet suppression in non-central collisions},
journal={PHYSICS LETTERS B},
volume={737},
number={},
pages={298-302},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J},
year={2014},
title={LHC jet suppression of light and heavy flavor observables},
journal={PHYSICS LETTERS B},
volume={734},
number={},
pages={286-289},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J},
year={2014},
title={Explaining the fine hierarchy in pion and kaon suppression at LHC: importance of fragmentation functions},
journal={JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS},
volume={41},
number={5},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J},
year={2013},
title={Modeling bacterial immune systems: Strategies for expression of toxic - but useful - molecules},
journal={BIOSYSTEMS},
volume={112},
number={2},
pages={139-144},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J},
year={2013},
title={Efficient transcription initiation in bacteria: an interplay of protein-DNA interaction parameters},
journal={INTEGRATIVE BIOLOGY},
volume={5},
number={5},
pages={796-806},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J,Djordjevic Magdalena R,Severinov Konstantin},
year={2012},
title={CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs},
journal={BIOLOGY DIRECT},
volume={7},
number={},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J,Djordjevic Magdalena R},
year={2012},
title={A simple biosynthetic pathway for large product generation from small substrate amounts},
journal={PHYSICAL BIOLOGY},
volume={9},
number={5},
pages={-},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Magdalena R,Djordjevic Marko J},
year={2012},
title={Generalization of radiative jet energy loss to non-zero magnetic mass},
journal={PHYSICS LETTERS B},
volume={709},
number={3},
pages={229-233},
document_type={Article},
} 

@ARTICLE{
author={Pavlova Olga,Lavysh Dania,Klimuk Evgeny,Djordjevic Marko J,Liavcheev Dmitry A,Gelfand Mikhail S,Severinov Konstantin,Akulenko Natalja},
year={2012},
title={Temporal Regulation of Gene Expression of the Escherichia coli Bacteriophage phiEco32},
journal={JOURNAL OF MOLECULAR BIOLOGY},
volume={416},
number={3},
pages={389-399},
document_type={Article},
} 

@ARTICLE{
author={Djordjevic Marko J},
year={2011},
title={Redefining Escherichia coli sigma(70) Promoter Elements: -15 Motif as a Complement of the -10 Motif},
journal={JOURNAL OF BACTERIOLOGY},
volume={193},
number={22},
pages={6305-6314},
document_type={Article},