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Article

Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203

Alchikh, M. and Conrad, T. O. F. and Hoppe, Ch. and Ma, X. and Broberg, E. and Penttinen, P. and Reiche, J. and Biere, B. and Schweiger, B. and Rath, B. (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). 380.e9-380.e16. ISSN 1469-0691

Alchikh, Maren and Conrad, T. O. F. and Obermeier, Patrick E. and Ma, Xiaolin and Schweiger, Brunhilde and Opota, Onya and Rath, Barbara A. (2024) 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).

Bielow, C. and Aiche, S. and Andreotti, S. and Reinert, K. (2011) MSSimulator: Simulation of Mass Spectrometry Data. Journal of Proteome Research, 10 (7). pp. 2922-2929.

Bittracher, Andreas and Koltai, Péter and Junge, Oliver (2015) Pseudogenerators of spatial transfer operators. SIAM Journal on Applied Dynamical Systems, 14 (3). pp. 1478-1517. ISSN 1536-0040

Bleich, Amnon and Linnemann, Antje and Benjamin, Jaidi and Bjoern, H. Diem and Conrad, T. O. F. (2023) Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification. Machine Learning and Knowledge Extraction, 5 (4). ISSN 2504-4990

Bostanci, Inan and Conrad, T. O. F. (2024) Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach. Journal of Artificial Societies and Social Simulation . (Submitted)

Bruckner, S. and Kayser, B. and Conrad, T. O. F. (2013) Finding Modules in Networks with Non-modular Regions. Lecture Notes in Computer Science (Proceedings of SEA 2013), 7933 . pp. 188-199. ISSN 0302-9743

Conrad, T. O. F. (2004) New Approaches for Visualizing and Analyzing Metabolic Pathways. Proceedings of the Second Australian Undergraduate Students’ Computing Conference .

Conrad, T. O. F. and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Schütte, Ch. (2017) Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. BMC Bioinformatics, 18 (160). ISSN 1471-2105

Conrad, T. O. F. and Ferrer, Eloi and Mietchen, Daniel and Pusch, Larissa and Stegmüller, Johannes and Schubotz, Moritz (2024) Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing. Nature Scientific Data, 11 (1).

Conrad, T. O. F. and Leichtle, A. and Hagehülsmann, A. and Diederichs, E. and Baumann, S. and Thiery, J. and Schütte, Ch. (2006) Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level. Lecture Notes in Computer Science, 4216 . pp. 119-128.

Cvetkovic, Nada and Conrad, T. O. F. and Lie, Han Cheng (2021) A convergent discretisation method for transition path theory for diffusion processes. Multiscale Modeling & Simulation, 19 (1). ISSN 15403467

Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2012) Random Walks on Complex Modular Networks. Journal of Numerical Analysis, Industrial and Applied Mathematics, 6 (1-2). pp. 29-50. ISSN 1790–8140

Fiedler, G. M. and Leichtle, A. and Kase, J. and Baumann, S. and Ceglarek, U. and Felix, K. and Conrad, T. O. F. and Witzigmann, H. and Weimann, A. and Schütte, Ch. and Hauss, J. and Büchler, M. and Thiery, J. (2009) Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer. Clinical Cancer Research, 15 (11). pp. 3812-3819. ISSN 1078-0432

Fürst, Steffen and Conrad, T. O. F. and Jaeger, Carlo and Wolf, S. (2024) Vahana.jl - A framework (not only) for large-scale agent-based models. Social Simulation Conference 2024 . (In Press)

Gaskin, Thomas and Conrad, T. O. F. and Pavliotis, Grigorios A. and Schütte, Ch. (2024) Neural parameter calibration and uncertainty quantification for epidemic forecasting. PLoS ONE, 19 (10). ISSN 1932-6203

Gupta, Pooja and Reinsch , Norbert and Spötter, Andreas and Conrad, T. O. F. and Bienefeld, Kaspar (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).

Gupta, Pooja and Conrad, T. O. F. and Spötter, Andreas and Reinsch, Norbert and Bienefeld, Kaspar (2012) Simulating a base population in honey bee for molecular genetic studies. Genetics Selection Evolution, 44 . p. 14.

Hoppe, C. and Obermeier, P. and Muehlhans, S. and Alchikh, M. and Seeber, L. and Tief, F. and Karsch, K. and Chen, X. and Boettcher, S. and Diedrich, S. and Conrad, T. O. F. and Kisler, B. and Rath , B. (2016) Article: 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. ISSN 1179-1942

Iravani, Sahar and Conrad, T. O. F. (2019) Deep Learning for Proteomics Data for Feature Selection and Classification. Lecture Notes in Computer Science, 11713 .

Iravani, Sahar and Conrad, T. O. F. (2021) An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20 (1). ISSN 1545-4963

Iravani, Sahar and Conrad, T. O. F. (2024) Towards More Effective Table-to-Text Generation: Assessing In-Context Learning and Self-Evaluation with Open-Source Models. Computational Linguistics . (Submitted)

Jayrannejad, Fahrnaz and Conrad, T. O. F. (2017) Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining. Springer Lecture Notes in Artificial Intelligence .

Juds, Carmen and Schmidt, Johannes and Weller, Michael and Lange, Thorid and Conrad, T. O. F. and Boerner, Hans (2020) 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). ISSN 0002-7863

Karsch, K. and Obermeier, P. and Seeber, L. and Chen, X. and Tief, F. and Muehlhans, S. and Hoppe, Ch. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2015) Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children. The Pediatric Infectious Disease Journal, 34 (10).

Kork, F. and Spies, C. and Conrad, T. O. F. and Weiss, B. and Roenneberg, T. and Wernecke, K.-D. and Balzer, F. (2018) Associations of postoperative mortality with the time of day, week and year. Anaesthesia, 73 (6). pp. 711-718. ISSN 0959-2962

Krah, A. and Schmidt, F. and Becher, D. and Schmid, M. and Albrecht, D. and Rack, A. and Büttner, K. and Jungblut, P. (2003) Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis. Molecular & Cellular Proteomics, 2 (12). pp. 1271-1283.

Leichtle, A. and Ceglarek, U. and Weinert, P. and Nakas, C. T. and Nuoffer, J.-M. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2013) Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma. Metabolomics, 9 (3). pp. 677-687. ISSN 1573-3890

Leichtle, A. and Nuoffer, J.-M. and Ceglarek, U. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2012) Serum amino acid profiles and their alterations in colorectal cancer. Metabolomics . ISSN 1573-3890

Liang, YongTian and Piao, Chengji and B. Beuschel, Christine and Toppe, David and Kollipara, Laxmikanth and Bogdanow, Boris and Maglione, Marta and Lützkendorf, Janine and See, Jason Chun Kit and Huang, Sheng and Conrad, T. O. F. and Kintscher, Ulrich and Madeo, Frank and Liu, Fan and Sickmann, Albert and Sigrist, Stephan J. (2021) eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction. Cell Reports, 35 (2). ISSN 2211-1247

Ma, X. and Conrad, T. O. F. and Alchikh, M. and Reiche, J. and Schweiger, B. and Rath, B. (2018) Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review. Reviews in Medical Virology, 28 (5). ISSN 1099-1654

Maier, Kristina and Weiser, Martin and Conrad, T. O. F. (2024) Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology. arXiv . (Submitted)

Marzban, Forough and Conrad, T. O. F. and Marzban, Pouria and Sodoudi, Sahar (2018) 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). ISSN 2320-0243

Melnyk, Kateryna and Klus, S. and Montavon, Grègoire and Conrad, T. O. F. (2020) Graph Kernel Koopman Embedding for Human Microbiome Analysis. Applied Network Science, 5 (96). ISSN 2364-8228

Melnyk, Kateryna and Weimann, K. and Conrad, T. O. F. (2023) Understanding microbiome dynamics via interpretable graph representation learning. Scientific Reports, 13 (2058). ISSN 2045-2322

Mireles, Victor and Conrad, T. O. F. (2015) Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrices. Procedia Computer Science, 51 . pp. 2967-2971. ISSN 1877-0509

Mireles, Victor and Conrad, T. O. F. (2018) Reusable building blocks in biological systems. Journal of the Royal Society Interface, 15 (149). ISSN 1742-5662

Müller, Sebastian and Paltra, Sydney and Rehmann, Jakob and Nagel, Kai and Conrad, T. O. F. (2023) Explicit Modelling of Antibody Levels for Infectious Disease Simulations in the Context of SARS-CoV-2. iScience, 26 (9). ISSN 2589-0042

Obermeier, P. and Muehlhans, S. and Hoppe, Ch. and Karsch, K. and Tief, F. and Seeber, L. and Chen, X. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2016) Enabling Precision Medicine With Digital Case Classification at the Point-of-Care. EBioMedicine, 4 . pp. 191-196.

Obermeier, P. and Heim, A. and Biere, B. and Hage, E. and Alchikh, M. and Conrad, T. O. F. and Schweiger, B. and Rath, B. (2022) Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations. iScience, 25 (5). ISSN 25890042

Paltra, Sydney and Conrad, T. O. F. (2024) Clinical Effectiveness of Ritonavir-Boosted Nirmatrelvir—A Literature Review. Advances in Respiratory Medicine, 92 (1). ISSN 2543-6031

Pusch, Larissa and Conrad, T. O. F. (2024) Combining LLMs and Knowledge Graphs to Reduce Hallucinations in Question Answering. Bioinformatics . ISSN 1367-4803 (Submitted)

Rams, Mona and Conrad, T. O. F. (2022) Sparse dictionary learning allows model-free pseudotime estimation of transcriptomics data. BMC Genomics, 23 (56). ISSN 1471-2105

Rath , B. and Conrad, T. O. F. and Myles, P. and Alchikh, M. and Ma, X. and Hoppe, Ch. and Tief, F. and Obermeier, P. and Reiche, J. and Kisler, B. and Schweiger, B. (2017) Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials. Expert Review of Anti-infective Therapy (IERZ), 15 (6). pp. 545-568.

Rath , B. and Tief, F. and Karsch, K. and Muehlhans, S. and Obermeier, P. and Adamou, E. and Chen, X. and Seeber, L. and Peiser, Ch. and Hoppe, Ch. and von Kleist, M. and Conrad, T. O. F. and Schweiger, B. (2013) 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. ISSN 2212-3989

Sarich, M. and Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2014) Modularity revisited: A novel dynamics-based concept for decomposing complex networks. Journal of Computational Dynamics, 1 (1). pp. 191-212. ISSN 2158-2491

Seeber, L. and Conrad, T. O. F. and Hoppe, Ch. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Tief, F. and Boettcher, S. and Diedrich, S. and Schweiger, B. and Rath , B. (2017) Educating parents about the vaccination status of their children: A user-centered mobile application. Preventive Medicine Reports, 5 . pp. 241-250.

Shao, Borong and Carlo, Cannistraci and Conrad, T. O. F. (2017) Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data. Genomics and Computational Biology, 3 (3). ISSN 2365-7154

Shao, Borong and Conrad, T. O. F. (2015) 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. ISSN 2321-8169

Shao, Borong and Conrad, T. O. F. (2016) Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction. Lecture Notes in Computer Science (LNCS): Proceeding of IWBBIO 2016, 9656 .

Shao, Borong and Bjaanæs, Maria and Helland, Åslaug and Schütte, Ch. and Conrad, T. O. F. (2019) EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma. PLoS ONE, 14 (1). ISSN 1932-6203

Sherratt, Katharine and Srivastava, Ajitesh and Ainslie, Kylie and Singh, David E. and Cublier, Aymar and Marinescu, Maria Cristina and Carretero, Jesus and Garcia, Alberto Cascajo and Franco, Nicolas and Willem, Lander and Abrams, Steven and Faes, Christel and Beutels, Philippe and Hens, Niel and Müller, Sebastian and Charlton, Billy and Ewert, Ricardo and Paltra, Sydney and Rakow, Christian and Rehmann, Jakob and Conrad, T. O. F. and Schütte, Christof and Nagel, Kai and Abbott, Sam and Grah, Rok and Niehus, Rene and Prasse, Bastian and Sandmann, Frank and Funk, Sebastian (2024) Characterising information gains and losses when collecting multiple epidemic model outputs. Epidemics, 47 . ISSN 1755-4365

Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Lingnau, A. and Lein, M. and Miller, K. and Schrader, M. (2008) Serum proteomic profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry in testicular germ cell cancer patients. European Urology Supplements, 7 (3). p. 83.

Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Miller, K. and Schrader, M. (2009) Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry: serum protein profiling in seminoma patients. World J of Urology, 28 (2). pp. 193-197.

Tief, F. and Hoppe, Ch. and Seeber, L. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Adamou, E. and Conrad, T. O. F. and Schweiger, B. and Adam, T. and Rath , B. (2016) 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, 21 (5). pp. 413-424. ISSN 1359-6535 (print); 2040-2058 (online)

Tuncay, E. G. and Erdur, R. C. and Conrad, T. O. F. (2022) Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA. IEEE Transactions on Computational Biology and Bioinformatics . ISSN 1557-9964 (In Press)

Vega del Valle, I. and Schütte, Ch. and Conrad, T. O. F. (2016) Finding metastable states in real-world time series with recurrence networks. Physica A, 445 .

Weimann, K. and Conrad, T. O. F. (2024) FELRec: Efficient Handling of Item Cold-Start With Dynamic Representation Learning in Recommender Systems. International Journal of Data Science and Analytics, 19 (1).

Weimann, K. and Conrad, T. O. F. (2024) Federated Learning with Deep Neural Networks: A Privacy-Preserving Approach to Enhanced ECG Classification. IEEE Journal of Biomedical and Health Informatics, 28 (11). ISSN 2168-2194

Weimann, K. and Conrad, T. O. F. (2023) Predicting Coma Recovery After Cardiac Arrest With Residual Neural Networks. Computing in Cardiology (CinC) 2023, 50 .

Weimann, K. and Conrad, T. O. F. (2024) Self-Supervised Pre-Training with Joint-Embedding Predictive Architecture Boosts ECG Classification Performance. IEEE . (Submitted)

Weimann, K. and Conrad, T. O. F. (2021) Transfer Learning for ECG Classification. Scientific Reports, 11 (5251). ISSN 2045-2322

Wulkow, Hanna and Conrad, T. O. F. and Djurdjevac Conrad, Natasa and Mueller, Sebastian Alexander and Nagel, Kai and Schütte, Ch. (2021) Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts. PLoS ONE, 16 (4). ISSN 1932-6203

You, Xintian Arthur and Conrad, T. O. F. (2016) Acfs: accurate circRNA identification and quantification from NGS data. Nature Scientific Reports, 6 . ISSN 2045-2322

You, Xintian Arthur (2015) Hastings: An R pipeline for large-scale RNA-Seq data analysis. Technical Report . (Unpublished)

Zhang, W. and Klus, S. and Conrad, T. O. F. and Schütte, Ch. (2019) Learning chemical reaction networks from trajectory data. SIAM Journal on Applied Dynamical Systems, 18 (4). ISSN 1536-0040

Book Section

Conrad, T. O. F. and Reinert, K. and Kohlbacher, O. (2008) Bioinformatics Support for Mass Spectrometry Quality Control. In: Proteomics Sample Preparation. Wiley-Vch, p. 485.

Conference or Workshop Item

Schubotz, Moritz and Ferrer, Eloi and Stegmüller, Johannes and Mietchen, Daniel and Teschke, Olaf and Pusch, Larissa and Conrad, T. O. F. (2023) Bravo MaRDI: A Wikibase Knowledge Graph on Mathematics. In: Proceedings of the 4th Wikidata Workshop 2022 co-located with the 22st International Semantic Web Conference (ISWC2023), Athens, Greece, November 2023. (In Press)

Book

Huang, Y. and Kornhuber, R. and Widlund, O. and Xu, J., eds. (2011) Domain decomposition methods in science and engineering XIX. Lecture Notes in Computational Science and Engineering, 78 . Springer Berlin Heidelberg. ISBN 978-3-642-11303-1

Thesis

Conrad, T. O. F. (2003) Berechnung von freien Energie Flächen am Beispiel des Alanin-Dipeptides. Other thesis, Freie Universität Berlin.

Conrad, T. O. F. (2004) Metabolic Pathways. Other thesis, Monash University Melbourne.

Ozdoba, Christopher (2015) Ensemble Machine Learning Techniques for Analyzing Large Biological Datasets Using the SAP In-Memory Database HANA. Masters thesis, Freie Universität Berlin.

Rack, A. (2005) Prediction of Post-translational Modifications of Proteins from 2-DE/MS Data. Masters thesis, Freie Universität Berlin.

Rams, Mona (2016) A new approach for biomarker detection using fusion networks. Masters thesis, Freie Universität Berlin.