Conrad, Tim, PD Dr.

Contact

Room

4008

Phone

+49 30 84185-250

Projects

Projects as Head

Model-Regularized Learning Of Complex Dynamical Behavior

This project is planned to couple machine learning approaches, especially from the field of Deep Learning, with (reduced) ODE models in the sense that the model becomes... Model-Regularized Learning Of Complex Dynamical Behavior

$MATH+ AA1-20$

Geometric Learning for Single-Cell RNA Velocity Modeling

Recent advances in Single-Cell RNA sequencing allow to infer both the gene expression of a cell and the so-called "velocity vector" initializing the changes in that... Geometric Learning for Single-Cell RNA Velocity Modeling

Mobilitätsmodelle zur Eindämmung von COVID-19 in Berlin

Die Ausbreitung von SARS-CoV-2 stellt die Welt, und auch Deutschland, vor erhebliche Probleme. Um eine Überlastung des Gesundheitssystems abzuwenden, wurden bekanntlich...

Mobilitätsmodelle zur Eindämmung von COVID-19 in Berlin

BIFOLD

Big Data (BD) and Machine Learning (ML) -together with decision-making- are the key pillars of Artificial Intelligence (AI). The analysis of very large and heterogeneous...

BIFOLD

Projects as Member

High-throughput Analysis of Large Medical Data

Data is growing and moving faster than healthcare organizations can consume it; 80% of medical data is unstructured and is clinically relevant. Getting access to this...

High-throughput Analysis of Large Medical Data

Sparse Compressed Sensing Based Classifiers for -Omics Mass-Data

Tumor diseases rank among the most frequent causes of death in Western countries coinciding with an incomplete understanding of the underlying pathogenic mechanisms and a...

Sparse Compressed Sensing Based Classifiers for -Omics Mass-Data

Publications

2025

How did we get there? AI applications to biological networks and sequences Computers in Biology and Medicine, Vol.190, 2025 Marco Anteghini, Francesco Gualdi, Baldo Oliva BibTeX
DOI

Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach Journal of Artificial Societies and Social Simulation, 28(1), 2025 Inan Bostanci, Tim Conrad BibTeX
DOI

2024

Characterising information gains and losses when collecting multiple epidemic model outputs Epidemics, Vol.47, 2024 Katharine Sherratt, Ajitesh Srivastava, Kylie Ainslie, David E. Singh, Aymar Cublier, Maria Cristina Marinescu, Jesus Carretero, Alberto Cascajo Garcia, Nicolas Franco, Lander Willem, Steven Abrams, Christel Faes, Philippe Beutels, Niel Hens, Sebastian Müller, Billy Charlton, Ricardo Ewert, Sydney Paltra, Christian Rakow, Jakob Rehmann, Tim Conrad, Christof Schütte, Kai Nagel, Sam Abbott, Rok Grah, Rene Niehus, Bastian Prasse, Frank Sandmann, Sebastian Funk BibTeX
DOI

Clinical Effectiveness of Ritonavir-Boosted Nirmatrelvir—A Literature Review Advances in Respiratory Medicine, 92(1), 2024 Sydney Paltra, Tim Conrad BibTeX
DOI

Clustering Time-Snapshots of Temporal Networks: From Synthetic Data to Real-World Applications 2024 (under review) Filip Blaskovic, Tim Conrad, Stefan Klus, Natasa Djurdjevac Conrad BibTeX
arXiv

Disease Burden and Inpatient Management of Children with Acute Respiratory Viral Infections during the Pre-COVID Era in Germany: A Cost-of-Illness Study Viruses, 16(4), 2024 Maren Alchikh, Tim Conrad, Patrick Obermeier, Xiaolin Ma, Brunhilde Schweiger, Onya Opota, Barbara Rath BibTeX
DOI

FELRec: Efficient Handling of Item Cold-Start With Dynamic Representation Learning in Recommender Systems International Journal of Data Science and Analytics, 2024 Kuba Weimann, Tim Conrad BibTeX
DOI

Federated Learning with Deep Neural Networks: A Privacy-Preserving Approach to Enhanced ECG Classification IEEE Journal of Biomedical and Health Informatics, 28(11), 2024 Kuba Weimann, Tim Conrad BibTeX
DOI

Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology Proceedings of the Royal Society A, Vol.481, 2024 Kristina Maier, Martin Weiser, Tim Conrad BibTeX
arXiv
DOI

Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing Scientific Data, Vol.11, 2024 Tim Conrad, Eloi Ferrer, Daniel Mietchen, Larissa Pusch, Johannes Stegmuller, Moritz Schubotz BibTeX
DOI

Neural parameter calibration and uncertainty quantification for epidemic forecasting PLOS ONE, 19(10), 2024 Thomas Gaskin, Tim Conrad, Grigorios A. Pavliotis, Christof Schütte BibTeX
arXiv
DOI

Vahana.jl - A framework (not only) for large-scale agent-based models Proceedings of Social Simulation Conference 2024 (SSC24), 2024 (accepted for publication) Steffen Fürst, Tim Conrad, Carlo Jaeger, Sarah Wolf BibTeX

2023

An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(1), pp. 151-161, 2023 Sahar Iravani, Tim Conrad BibTeX
DOI

Bravo MaRDI: A Wikibase Knowledge Graph on Mathematics Proceedings of the 4th Wikidata Workshop 2022 co-located with the 22st International Semantic Web Conference (ISWC2023), 2023 (accepted for publication) Moritz Schubotz, Eloi Ferrer, Johannes Stegmüller, Daniel Mietchen, Olaf Teschke, Larissa Pusch, Tim Conrad BibTeX

Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification Machine Learning and Knowledge Extraction, 5(4), 2023 Amnon Bleich, Antje Linnemann, Benjamin Jaidi, Bjoern H Diem, Tim Conrad BibTeX
DOI

Explicit modeling of antibody levels for infectious disease simulations in the context of SARS-CoV-2 iScience, 26(9), 2023 Sebastian Müller, Sydney Paltra, Jakob Rehmann, Kai Nagel, Tim Conrad BibTeX
DOI

Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(3), pp. 2064-2077, 2023 Erhun Giray Tuncay, Rıza Cenk Erdur, Tim Conrad BibTeX
DOI

Predicting Coma Recovery After Cardiac Arrest With Residual Neural Networks Computing in Cardiology (CinC) 2023, Vol.50, 2023 Kuba Weimann, Tim Conrad BibTeX
DOI

Understanding microbiome dynamics via interpretable graph representation learning Scientific Reports, Vol.13, p. 2058, 2023 Kateryna Melnyk, Kuba Weimann, Tim Conrad BibTeX
DOI

2022

Dictionary learning allows model-free pseudotime estimation of transcriptomics data BMC Genomics, Vol.23, 2022 Mona Rams, Tim Conrad BibTeX
DOI

Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations iScience, 25(5), 2022 Patrick E Obermeier, Albert Heim, Barbara Biere, Elias Hage, Maren Alchikh, Tim Conrad, Brunhilde Schweiger, Barbara A Rath BibTeX
DOI

2021

A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes Multiscale Modeling & Simulation, 19(1), pp. 242-266, 2021 Nada Cvetkovic, Tim Conrad, Han Cheng Lie BibTeX
DOI

Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts PLOS One, 16(4), 2021 Hanna Wulkow, Tim Conrad, Natasa Djurdjevac Conrad, Sebastian A. Müller, Kai Nagel, Christof Schütte BibTeX
DOI

Transfer Learning for ECG Classification Scientific Reports, Vol.11, 2021 K. Weimann, Tim Conrad BibTeX
DOI

eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction Cell Reports, 35(2), 2021 YongTian Liang, Chengji Piao, Christine B. Beuschel, David Toppe, Laxmikanth Kollipara, Boris Bogdanow, Marta Maglione, Janine Lützkendorf, Jason Chun Kit See, Sheng Huang, Tim Conrad, Ulrich Kintscher, Frank Madeo, Fan Liu, Albert Sickmann, Stephan J. Sigrist BibTeX
DOI

2020

A light-weight and highly flexible software system for analyzing large bio-medical datasets Future Generation Computer Systems, 2020 (under review) Huy Le Duc, Tim Conrad BibTeX

Combining Phage Display and Next-generation Sequencing for Materials Sciences: A Case Study on Probing Polypropylene Surfaces Journal of the American Chemical Society, 142(24), pp. 10624-10628, 2020 Carmen Juds, Johannes Schmidt, Michael Weller, Thorid Lange, Tim Conrad, Hans Boerner BibTeX
DOI

Dictionary Learning for transcriptomics data reveals type-specific gene modules in a multi-class setting it - Information Technology, 62(3-4), 2020 Mona Rams, Tim Conrad BibTeX
DOI

Graph Kernel Koopman Embedding for Human Microbiome Analysis Applied Network Science, 5(96), 2020 Kateryna Melnyk, Grègoire Montavon, Stefan Klus, Tim Conrad BibTeX
DOI

2019

Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care Clinical Microbiology and Infection, 25(3), pp. 380.e9-380.e16, 2019 Maren Alchikh, Tim Conrad, Xiaolin Ma, Eeva K. Broberg, P. Penttinen, J. Reiche, Barbara Biere, Brunhilde Schweiger, Barbara Rath, Christian Hoppe BibTeX
DOI

Comparison of 2D and 3D CNNs for Classification of Knee MRI Bachelor's thesis, Freie Universität Berlin, Alexander Tack, Felix Ambellan (Advisors), 2019 Mona Prendke PDF
BibTeX
URN

Deep Learning for Proteomics Data for Feature Selection and Classification Machine Learning and Knowledge Extraction. CD-MAKE 2019, A. Holzinger, P. Kieseberg, A. Tjoa, E. Weippl (Eds.), Vol.11713, Lecture Notes in Computer Science, 2019 Sahar Iravani, Tim Conrad BibTeX
DOI

EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma PLOS ONE, 14(1), 2019 Borong Shao, Maria Bjaanaes, Aslaug Helland, Christof Schütte, Tim Conrad BibTeX
DOI

Learning chemical reaction networks from trajectory data SIAM Journal on Applied Dynamical Systems (SIADS), 18(4), pp. 2000-2046, 2019 Wei Zhang, Stefan Klus, Tim Conrad, Christof Schütte BibTeX
arXiv
DOI

2018

Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care. Clinical Microbiology and Infection Clinical Microbiology and Infection, pp. 1-1, 2018 (accepted for publication) Maren Alchikh, Tim Conrad, Christian Hoppe, Xiaolin Ma, Eeva K. Broberg, P. Penttinen, J. Reiche, Barbara Biere, Brunhilde Schweiger, Barbara Rath BibTeX
DOI

Associations of postoperative mortality with the time of day, week and year Anaesthesia, 73(6), pp. 711-718, 2018 F. Kork, Tim Conrad, B. Weiss, T. Roenneberg, K.-D. Wernecke, Felix Balzer BibTeX

Associations of postoperative mortality with the time of day, week and year Anaesthesia, 2018 (accepted for publication) F. Kork, Claudia Spies, Tim Conrad, B. Weiss, T. Roenneberg, K.-D. Wernecke, Felix Balzer BibTeX

Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review Medical Virology, 28(5), pp. 1-12, 2018 (accepted for publication) Xiaolin Ma, Tim Conrad, Maren Alchikh, J. Reiche, Brunhilde Schweiger, Barbara Rath BibTeX
DOI

Clinical characteristics and disease severity associated with adenovirus infections in infants and children - discovery of a novel adenovirus, HAdV-D80 Clinical Infectious Diseases, 2018 (under review) Patrick Obermeier, A. Heim, Barbara Biere, E. Hage, Maren Alchikh, Tim Conrad, Brunhilde Schweiger, Barbara Rath BibTeX

Estimation of the Near-Surface Air Temperature during the Day and Nighttime from MODIS in Berlin, Germany International Journal of Advanced Remote Sensing and GIS, 7(1), pp. 2478-2517, 2018 Forough Marzban, Tim Conrad, Pouria Marban, Sahar Sodoudi BibTeX
DOI

Reusable building blocks in biological systems Journal of the Royal Society Interface, 15(149), pp. 1-10, 2018 (accepted for publication) Victor Mireles, Tim Conrad BibTeX
DOI

2017

Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining Springer Lecture Notes in Artificial Intelligence, p. studi, 2017 (accepted for publication) Fahrnaz Jayrannejad, Tim Conrad BibTeX

Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining Springer Lecture Notes in Artificial Intelligence, 2017 (in press) Fahrnaz Jayrannejad, Tim Conrad BibTeX

Educating parents about the vaccination status of their children: A user-centered mobile application Preventive Medicine Reports, Vol.5, pp. 241-250, 2017 (accepted for publication) L. Seeber, Tim Conrad, Christian Hoppe, Patrick Obermeier, X. Chen, K. Karsch, S. Muehlhans, Franziska Tief, Sindy Boettcher, S. Diedrich, Brunhilde Schweiger, Barbara Rath BibTeX
DOI

Epithelial Mesenchymal Transition Network-Based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data Genomics and Computational Biology, 3(3), p. e57, 2017 Borong Shao, Carlo Vittorio Cannistraci, Tim Conrad BibTeX
DOI

Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data Genomics and Computational Biology, 3(3), pp. 1-13, 2017 (accepted for publication) Shao Borong, Carlo Cannistraci, Tim Conrad BibTeX
DOI

Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials Expert Review of Anti-infective Therapy, 15(6), pp. 545-568, 2017 Barbara Rath, Tim Conrad, Puja Myles, Maren Alchikh, Xiaolin Ma, Christian Hoppe, Franziska Tief, Xi Chen, Patrick Obermeier, Bron Kisler, Brunhilde Schweiger BibTeX
DOI

Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data BMC Bioinfomatics, 18(160), 2017 Tim Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Alexander Benedikt Leichtle, Jan Vybiral, Gitta Kytyniok, Christof Schütte BibTeX
DOI

Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data BMC Bioinformatics, 18(160), pp. 1-20, 2017 Tim Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Jan Vybiral, Gitta Kutyniok, Christof Schütte BibTeX
DOI

2016

Acfs: accurate circRNA identification and quantification from NGS data Nature Scientific Reports, Vol.6, 2016 Tim Conrad, Xintian You BibTeX
DOI

An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use Antiviral Therapy, Vol.21, pp. 413-424, 2016 Franziska Tief, Christian Hoppe, L. Seeber, Patrick Obermeier, X. Chen, K. Karsch, S. Muehlhans, E. Adamou, Tim Conrad, Brunhilde Schweiger, T. Adam, Barbara Rath BibTeX
DOI

Decomposing biological systems into reusable modules reveals characteristic module size distributions 2016 (under review) Victor Mireles, Tim Conrad BibTeX

Enabling Precision Medicine With Digital Case Classification at the Point-of-Care EBioMedicine, Vol.4, pp. 191-196, 2016 Patrick Obermeier, S. Muehlhans, Christian Hoppe, K. Karsch, Franziska Tief, L. Seeber, X. Chen, Tim Conrad, Sindy Boettcher, S. Diedrich, Barbara Rath BibTeX
DOI

Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction Lecture Notes in Computer Science (LNCS), pp. 1235-146, Vol.9656, 2016 Borong Shao, Tim Conrad BibTeX
DOI

Finding metastable states in real-world time series with recurrence networks Physica A: Statistical Mechanics and its Applications, Vol.445, pp. 1-17, 2016 Iliusi Vega, Christof Schütte, Tim Conrad BibTeX
DOI

Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study Drug Safety, 39(10), pp. 977-988, 2016 Christian Hoppe, Patrick Obermeier, S. Mehlhans, Maren Alchikh, L. Seeber, Franziska Tief, K. Karsch, X. Chen, Sindy Boettcher, S. Diedrich, Tim Conrad BibTeX
DOI

2015

Analyzing the Influence of Filaggrin on Other Skin Associated Genes in a Filaggrin Deficient Skin Model Using the Core Network Approach Technical Report, 2015 Tim Conrad, Leonie Wallmeyer, Mona Rams, Stefan Börno, Bernd Timmermann, Sarah Hedtrich BibTeX

Are NoSQL data stores useful for bioinformatics researchers? International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), 3(3), pp. 1704-1708, 2015 Tim Conrad, Borong Shao BibTeX
DOI

Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children The Pediatric Infectious Disease Journal, 34(10), 2015 Tim Conrad, K. Karsch, Patrick Obermeier, L. Seeber, X. Chen, Franziska Tief, S. Muehlhans, Christian Hoppe, Sindy Boettcher, S. Diedrich, Barbara Rath BibTeX

Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrics Procedia Computer Science, Vol.51, pp. 2967-2971, 2015 Tim Conrad, Victor Mireles BibTeX
DOI

Non-convex regularization for supervised learning Technical Report, 2015 Tim Conrad, Matthias Lenga PDF
BibTeX

2014

Modularity revisited: A novel dynamics-based concept for decomposing complex networks Journal of Computational Dynamics, 1(1), pp. 191-212, 2014 Marco Sarich, Natasa Djurdjevac Conrad, Sharon Bruckner, Tim Conrad, Christof Schütte PDF
BibTeX
DOI

SAIMeR: Self-adapted method for the identification of metastable states in real-world time series ZIB-Report 14-16 Iliusi Vega, Christof Schütte, Tim Conrad PDF
BibTeX
URN

Showcase 3: Information-based medicine MATHEON-Mathematics for Key Technologies, Vol.1, pp. 66-67, Peter Deuflhard, Martin Grötschel, Dietmar Hömberg, Ulrich Horst, Jürg Kramer, Volker Mehrmann, Konrad Polthier, Frank Schmidt, Martin Skutella, Jürgen Sprekels (Eds.), European Mathematical Society, 2014 Christof Schütte, Tim Conrad BibTeX

2013

Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera) BMC Genetics, 14(36), 2013 Pooja Gupta, Norbert Reinsch, Andreas Spötter, Tim Conrad, Kaspar Bienefeld BibTeX
DOI

Finding Modules in Networks with Non-modular Regions Lecture Notes in Computer Science (Proceedings of SEA 2013), Vol.7933, pp. 188-199, 2013 Tim Conrad, Sharon Bruckner, Bastian Kayser BibTeX
DOI

Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma Metabolomics, 9(3), pp. 677-687, 2013 Tim Conrad, Alexander Benedikt Leichtle, Uta Ceglarek, P. Weinert, C.T. Nakas, Jean-Marc Nuoffer, Julia Kase, Helmut Witzigmann, Joachim Thiery, Georg Martin Fiedler BibTeX
DOI

Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir Infectious Disorders - Drug Targets, 13(1), pp. 25-33, 2013 Tim Conrad, Barbara Rath, Franziska Tief, K. Karsch, S. Muehlhans, Patrick Obermeier, E. Adamou, X. Chen, L. Seeber, Ch. Peiser, Christian Hoppe, Max von Kleist, Brunhilde Schweiger BibTeX

2012

Random Walks on Complex Modular Networks Journal of Numerical Analysis, Industrial and Applied Mathematics, 6(1-2), pp. 29-50, 2012 Natasa Djurdjevac Conrad, Stefanie Bruckner, Tim Conrad, Christof Schütte BibTeX

Serum amino acid profiles and their alterations in colorectal cancer Metabolomics, 2012 Tim Conrad, Alexander Benedikt Leichtle, Jean-Marc Nuoffer, Uta Ceglarek, Julia Kase, Helmut Witzigmann, Joachim Thiery, Georg Martin Fiedler BibTeX
DOI

Simulating a base population in honey bee for molecular genetic studies Genetics Selection Evolution, 2012 Pooja Gupta, Tim Conrad, Andreas Spötter, Norbert Reinsch, Kaspar Bienefeld BibTeX
DOI

2004

Metabolic Pathways Doctoral thesis, Monash University Melbourne, unknown (Advisor), 2004 Tim Conrad BibTeX

New Appraches for Visualizing and Analyzing Metabolic Pathways Proceedings of the Second Australian Undergraduate Students? Computing Conference, 2004 Tim Conrad BibTeX