Drugst.One – A plug-and-play solution for online systems medicine and network-based drug repurposing
Andreas Maier1*, Michael Hartung1, The Drugst.One Initiative, and Jan Baumbach1,2
1Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
2Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
Single cell 3` transcriptome profiling
Nevena Milivojević1*, Uršula Prosenc Zmrzljak2, Biljana Ljujić3, Valentina Đorđević4, Marina Gazdić Janković3, Marko Živanović1,5, Feđa Puač6, Miloš Ivanović7, and Nenad Filipović5,8
1Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
2BIA Separations CRO Laboratory, Teslova ulica 30, 1000 Ljubljana, Slovenia
3Faculty of Medical Sciences, University of Kragujevac, Svetozara Markovića 69, 34000 Kragujevac, Serbia
4Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
5BioIRC – Bioengineering Research and Development Center, University of Kragujevac, Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia
6Labena d.o.o. Serbia, Bulevar Zorana Đinđića 123G, 11070 Belgrade, Serbia
7Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia
8Faculty of Engineering, University of Kragujevac, Sestre Janjić 6, 34000 Kragujevac, Serbia
The use of Active Machine Learning for Protospacer-Adjacent Motif recovery in Class 2 CRISPR-Cas systems
Bogdan Kirillov*1,2, Aleksandra Vasileva3,4, Oleg Fedorov5, Maxim Panov6, and Konstantin Severinov7
1Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld 1, 121205 Moscow, Russia
2Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, 119334 Moscow, Russia
3Peter the Great St. Petersburg Polytechnic Universitsy, Politekhnicheskaya St 29, 195251 St. Petersburg, Russia
4Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, 123182 Moscow, Russia
5Research Institute for Systems Biology and Medicine, Department of Mathematical Biology and Bioinformatics, Nauchny Proezd 18, 117246 Moscow, Russia
6Artificial Intelligence Cross Center Unit, Technology Innovation Institute, PO Box: 9639, Masdar City, Abu Dhabi, United Arab Emirates
7Waksman Institute of Microbiology,, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
Newest Advances on the FeatureCloud Platform for Federated Learning in Biomedicine
Niklas Probul1*, Mohammad Bakhtiari1, Mohammad Kazemi Majdabadi1, Balázs Orbán3, Sándor Fejér3, Supratim Das1, Julian Klemm1, Christina C Saak1, Nina K Wenke1, and Jan Baumbach1,2
1 Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
2 Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
3 Gnome Design SRL, Sfântu Gheorghe, Romania
Echocardiography-based Left Ventricle Cardiac Hypertrophy Simulations
Bogdan Milićević*1,2, Miljan Milošević2,3,4, Vladimir Simić2,3, Danijela Trifunović5, Goran Stanković5,6, Nenad Filipović1,2, and Miloš Kojić2,6,7
1Faculty of Engineering, University of Kragujevac, Kragujevac 34000, Serbia
2Bioengineering Research and Development Center (BioIRC), Kragujevac 34000, Serbia
3Institute for Information Technologies, University of Kragujevac, Kragujevac 34000, Serbia
4Belgrade Metropolitan University, Belgrade 11000, Serbia
5Cardiology Department, University Clinical Center of Serbia, Visegradska 26, 11000 Belgrade, Serbia
6Serbian Academy of Sciences and Arts, Belgrade 11000, Serbia
7Houston Methodist Research Institute, Houston TX 77030, USA
From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome
Olga Tsoy1*, Zakaria Louadi2, Chit Tong Lio2, Jan Baumbach1, Olga Kalinina3,4, Alexander Gress3,4, Tim Kacprowski5,6, and Markus List2
1University of Hamburg, Notkestrasse 9, Hamburg, Germany
2Technical University of Munich, Maximus-von-Imhof-Forum 3, Freising, Germany
3Helmholtz Centre for Infection Research, Inhoffenstraße 7, Saarbrücken, Germany.
4Saarland University, Homburg, Germany
5PLRI of TU Braunschweig and MHH, Rebenring 56, Brunswick, Germany
6BRICS, TU Braunschweig, Rebenring 56, Brunswick, Germany
Fatty Acid Data Analysis Unravels Skeletal Site and Age-Specific Features of Human Bone Marrow Adiposity
Drenka Trivanović1*, Jovana Kovačević2, Aleksandra Arsić1, Marko Vujačić3, Nikola Bogosavljević3, Ivana Okić Djordjević1, Milena Živanović1, Slavko Mojsilović1, Mirjana Maljković2, and Aleksandra Jauković1
1Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Dr. Subotića 4, 11000 Belgrade, Serbia
2Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
3Institute for Orthopedy Banjica, Mihaila Avramovića 28, 11000, Belgrade, Serbia
Clustering and classification of SARS-COV-2 isolates using RSCU
S. Malkov1*, M. Beljanski1, G. Pavlović Lažetić1, B. Stojanović2, M. Maljković1, A. Veljković1, S. Kapunac1, and N. Mitić1
1Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
2Mathematical Institute SASA, Knez Mihaila 36, 11000 Belgrade, Serbia
Using whole exome sequencing to explore genetic basis of unicuspid aortic valve disease
Martina Mia Mitić1, Dušan Ušjak1*, Maja Milošević2, Marija Cumbo1, Sofija Dunjić Manevski1, Branko Tomić1, Ivana Petrović2, Petar Otašević2, Slobodan Micović2, Milovan Bojić2, and Valentina Đorđević1
1Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444a, Belgrade, Serbia
2Institute for Cardiovascular Diseases Dedinje, Heroja Milana Tepića 1, Belgrade, Serbia
Machine learning approach in inferring main population-level COVID-19 risk factors
Sofija Marković1*, Anđela Rodić1, Ognjen Milićević2, Igor Salom3, Magdalena Đorđević3, and Marko Đorđević1
1Faculty of Biology, University of Belgrade, Studentski trg 6, 11000 Belgrade, Serbia
2School of Medicine, University of Belgrade, dr Subotića starijeg 8, 11000 Belgrade, Serbia
3Institute of Physics Belgrade, National Institute of the Republic of Serbia, University of Belgrade, Pregrevica 118, 11000 Belgrade, Serbia
Using AI to design antibodies
Goran Rakočević1,2
1Absci, Vancouver, Washington, USA
2School of computing, Union University, Belgrade
Exploration of Pharmacogenomic Biomarkers in Chronic Immune Diseases Using Single-Cell RNA Sequencing
Mario Gorenjak1, Larisa Goričan1, Boris Gole1, Uršula Prosenc*2, Erik Melén3, Michael Kabesch4, Anke H Maitland-van der Zee5,6, Susanne Reinartz7, Susanne J H Vijverberg5,6, Uroš Potočnik1,8,9 and the PERMEABLE consortium
1University of Maribor, Faculty of Medicine, Centre for Human Molecular Genetics and Pharmacogenomics, Slovenia
2BIA Separations CRO – Labena d.o.o., Teslova 30, 1000 Ljubljana, Slovenia
3Karolinska Institutet, Department of Clinical Sciences and Education Södersjukhuset, Stockholm, Sweden
4University Children’s Hospital Regensburg (KUNO), Department of Pediatric Pneumology and Allergy, Regensburg, Germany
5University of Amsterdam, Amsterdam University Medical Centers, Department of Respiratory Medicine, Amsterdam, The Netherlands
6University of Amsterdam, Amsterdam University Medical Centers, Department of Pediatric Pulmonology, Amsterdam, The Netherlands
7Tergooi Medical Center, Department of Otorhinolaryngology, Hilversum, The Netherlands
8University of Maribor, Faculty for Chemistry and Chemical Engineering, Laboratory for Biochemistry, Molecular Biology and Genomics, Maribor, Slovenia
9Maribor University Medical Centre, Department for Science and Research, Maribor, Slovenia
AI-powered framework to predict the toxicity of microplastics
Junli Xu1,2,3
1School of Biosystems and Food Engineering, University College of Dublin, Belfield, Dublin 4, Ireland.
2Institute of Food and Health, University College Dublin, Belfield, Dublin 4, Ireland.
3Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
Mapping of Disease Names to Disease Codes based on Natural Language Processing Techniques
Anđelka Zečević1*, Jovana Kovačević2, and Radoslav Davidović3
1Mathematical Institute, Serbian Academy of Sciences and Arts
2Faculty of Mathematics, University of Belgrade
3Institute of Nuclear Sciences Vinča
Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST
Klaudia Adamowicz1*, Andreas Maier1, Jan Baumbach1,2 and David B. Blumenthal3
1Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
2Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
3Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU), Erlangen, Germany
Computational Modelling of Drug Effects on Cardiomyopathy and Analysis of Myocardial Work
Smiljana Tomasevic1,2*, Miljan Milosevic2,3, Bogdan Milicevic1,2, Vladimir Simic2,3, Momcilo Prodanovic2,3,4, Srboljub M. Mijailovich4,5, Nenad Filipovic1,2
1Faculty of Engineering, University of Kragujevac, Sestre Janjic 6, 34000 Kragujevac, Serbia
2Bioengineering Research and Development Center (BioIRC), Prvoslava Stojanovica 6, 34000 Kragujevac, Serbia
3Institute for Information Technologies, University of Kragujevac, Jovana Cvijica bb, 34000 Kragujevac, Serbia
4FilamenTech, Inc., Newton, MA 02458, USA
5BioCAT, Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA
Alternative splicing impacts microRNA regulation within coding regions
Lena Maria Hackl1*, Amit Fenn1,2, Zakaria Louadi1,2, Jan Baumbach1,3, Tim Kacprowski4,5, Markus List2 and Olga Tsoy1
1Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
2Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Arcisstraße 21, 80333 Munich, Germany
3Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark
4Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
5Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
Analytical Framework for Social Distancing Impact on Epidemic Outbursts: Insights from COVID-19 Dynamics
Magdalena Djordjevic1*, Bojana Ilic1, Stefan Stojku1, Igor Salom1, and Marko Đorđević2
1Institute of Physics Belgrade, National Institute of the Republic of Serbia, Serbia
2Faculty of Biology, University of Belgrade, Serbia
Integration of differential transcriptomic and proteomic data in hydrated and desiccated leaves of Ramonda serbica Panc.
Marija Vidović1*, Ilaria Battisti2,3, Ana Pantelić1, Dejana Milic1, Giorgio Arrigoni2,3, Antonio Masi4, and Sonja Veljović Jovanović5
1Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
2Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
3Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129 Padova, Italy
4DAFNAE, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
5Institute for Multidisciplinary Research, University of Belgrade, Kneza Viseslava 1, 11000 Belgrade, Serbia
Modulating Horizontal Gene Transfer through Bistability in the Dynamics of Bacterial Restriction-Modification Systems
Marko Djordjevic1*, Lidija Zivkovic2, and Magdalena Djordjevic2
1Faculty of Biology, University of Belgrade, Serbia
2Institute of Physics Belgrade, National Institute of the Republic of Serbia, Serbia
Semantic unification and search of bioinformatics databases
A. Veljković1*, and N. Mitić1
1Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
Deciphering key regulatory networks and drug repurposing candidates through scRNAseq data analysis using SCANet
Mhaned Oubounyt1*, Jan Baumbach1, and Maria L. Elkjaer1
1 Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
Decoding Cystic Fibrosis Phenotype
Aleksandra Divac Rankov1*, Dušan Ušjak1, Martina Mia Mitić1, and Jelena Kusic Tisma1
1Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, Belgrade, Serbia
CADDIE – An online knowledge base for network-based mechanism exploration and drug repurposing in oncology
Michael Hartung1*, Elisa Anastasi2, Zeinab M. Mamdouh3,4, Cristian Nogales3, Harald HHW Schmidt3, Jan Baumbach1,5, Olga Zolotareva1,6, and Markus List6
1Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
2School of Computing, Newcastle University, Newcastle upon Tyne, UK
3Department of Pharmacology and Personalised Medicine, Maastricht University, Maastricht, Netherlands
4Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
5Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
6Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
Application of classification algorithms for hip implant surface topographies
Aleksandra Vulović*1,2, Tijana Geroski1,2, and Nenad Filipović1,2
1Faculty of Engineering University of Kragujevac, Sestre Janjić 6, 34000 Kragujevac, Serbia
2Bioengineering Research and Development Center (BioIRC), Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia
Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD)
Milan Senćanski1*, Ivana Prodić1, Ana Pantelić1, and Marija Vidović1
1Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
Beyond the Global Health Security Index: A Machine Learning Approach to Analyzing the Official COVID-19 Deaths and Excess Deaths Data
Andjela Rodic1*, Sofija Markovic1, Igor Salom2, and Marko Djordjevic1
1Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
2Institute of Physics, National Institute of the Republic of Serbia, Pregrevica 118, University of Belgrade, 11000 Belgrade, Serbia
Zero- and Few-Shot Machine Learning for Named Entity Recognition in Biomedical Texts
Miloš Košprdić1*, Nikola Prodanović1, Adela Ljajić1, Bojana Bašaragin1, and Nikola Milošević1,2
1Institute for Artificial Intelligence Research and Development of Serbia, Fruškogorska 1, Novi Sad, Serbia
2Bayer A.G., Reaserch and Development, Mullerstrasse 173, Berlin, Germany
