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Home Members Conrad, Tim, PD Dr.

Conrad, Tim, PD Dr.

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Contact

Room
4008
Phone
+49 30 84185-250
Email
Email
Division
Mathematics of Complex Systems
Department
Visual and Data-Centric Computing
Group
Bioinformatics in Medicine

Projects

Projects as Head

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Fluoromath - Unsupervised Deep Learning to assess Hand Diseases

Inflammatory auto-immune diseases are highly prevalent and have limited treatment opportunities. Fluorescence optical imaging (FOI) is a new method that enables radiation...

Fluoromath - Unsupervised Deep Learning to assess Hand Diseases
MODAL

Research Campus MODAL

The Forschungscampus ("Research Campus") MODAL is a platform for a public-private innovation partnership established by ZIB and Freie Universität Berlin together with...

Research Campus MODAL
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MODAL-MedLab

Changes in cells while they are undergoing transformation from "normal" to malignant cells (e.g. during infections) happen on many biological levels, such as genome... MODAL-MedLab
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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

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, 2017 (in press) Fahrnaz Jayrannejad, Tim Conrad BibTeX
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
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