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Home  |  Members  |  Conrad, PD Dr. Tim

Conrad, PD Dr. Tim

Position: 
Head of Department
Room: 
4008
Division: 
Mathematics of Complex Systems
Department: 
Visual and Data-Centric Computing
Research group: 
Bioinformatics in Medicine
Mail: 
conradzib.de
Phone: 
+49 30 841 85 - 250
Fax: 
+49 30 841 85 - 107

Projects

Head

BIFOLD
Mobilitätsmodelle zur Eindämmung von COVID-19 in Berlin
Sparse Compressed Sensing Based Classifiers for -Omics Mass-Data
MODAL-MedLab
Research Campus MODAL
Fluoromath - Unsupervised Deep Learning to assess Hand Diseases

Member

Sparse Compressed Sensing Based Classifiers for -Omics Mass-Data
High-throughput Analysis of Large Medical Data

Publications

2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2004

2023

Kateryna Melnyk, Kuba Weimann, Tim Conrad Understanding microbiome dynamics via interpretable graph representation learning Nature Scientific Reports, 2023 (accepted for publication) BibTeX

2022

Mona Rams, Tim Conrad Dictionary learning allows model-free pseudotime estimation of transcriptomics data BMC Genomics, Vol.23, 2022 BibTeX
DOI
Patrick E Obermeier, Albert Heim, Barbara Biere, Elias Hage, Maren Alchikh, Tim Conrad, Brunhilde Schweiger, Barbara A Rath Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations iScience, 25(5), 2022 BibTeX
DOI
Erhun Giray Tuncay, Rıza Cenk Erdur, Tim Conrad Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022 BibTeX
DOI

2021

Nada Cvetkovic, Tim Conrad, Han Cheng Lie A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes Multiscale Modeling & Simulation, 19(1), pp. 242-266, 2021 BibTeX
DOI
Sahar Iravani, Tim Conrad An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021 (epub ahead of print) BibTeX
DOI
Hanna Wulkow, Tim Conrad, Natasa Djurdjevac Conrad, Sebastian A. Müller, Kai Nagel, Christof Schütte Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts PLOS One, 16(4), 2021 BibTeX
DOI
K. Weimann, Tim Conrad Transfer Learning for ECG Classification Scientific Reports, Vol.11, 2021 BibTeX
DOI
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 eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction Cell Reports, 35(2), 2021 BibTeX
DOI

2020

Huy Le Duc, Tim Conrad A light-weight and highly flexible software system for analyzing large bio-medical datasets Future Generation Computer Systems, 2020 (under review) BibTeX
Carmen Juds, Johannes Schmidt, Michael Weller, Thorid Lange, Tim Conrad, Hans Boerner Combining Phage Display and Next-generation Sequencing for Materials Sciences: A Case Study on Probing Polypropylene Surfaces Journal of the American Chemical Society, 2020 BibTeX
DOI
Mona Rams, Tim Conrad Dictionary Learning for transcriptomics data reveals type-specific gene modules in a multi-class setting it - Information Technology, 62(3-4), 2020 BibTeX
DOI
Kateryna Melnyk, Grègoire Montavon, Stefan Klus, Tim Conrad Graph Kernel Koopman Embedding for Human Microbiome Analysis Applied Network Science, 5(96), 2020 BibTeX
DOI

2019

Maren Alchikh, Tim Conrad, Xiaolin Ma, Eeva K. Broberg, P. Penttinen, J. Reiche, Barbara Biere, Brunhilde Schweiger, Barbara Rath, Christian Hoppe 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 BibTeX
Mona Prendke Comparison of 2D and 3D CNNs for Classification of Knee MRI Bachelor's thesis, Freie Universität Berlin, Alexander Tack, Felix Ambellan (Advisors), 2019 PDF
BibTeX
URN
Sahar Iravani, Tim Conrad Deep Learning for Proteomics Data for Feature Selection and Classification Lecture Notes in Computer Science, A. Holzinger, P. Kieseberg, A. Tjoa, E. Weippl (Eds.), Vol.11713, Machine Learning and Knowledge extraction, 2019 BibTeX
DOI
Borong Shao, Maria Bjaanaes, Aslaug Helland, Christof Schütte, Tim Conrad EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma PLOS ONE, 14(1), 2019 BibTeX
DOI
Wei Zhang, Stefan Klus, Tim Conrad, Christof Schütte Learning chemical reaction networks from trajectory data SIAM Journal on Applied Dynamical Systems (SIADS), 18(4), pp. 2000-2046, 2019 BibTeX
arXiv
DOI

2018

Maren Alchikh, Tim Conrad, Christian Hoppe, Xiaolin Ma, Eeva K. Broberg, P. Penttinen, J. Reiche, Barbara Biere, Brunhilde Schweiger, Barbara Rath 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) BibTeX
DOI
F. Kork, Claudia Spies, Tim Conrad, B. Weiss, T. Roenneberg, K.-D. Wernecke, Felix Balzer Associations of postoperative mortality with the time of day, week and year Anaesthesia, 2018 (accepted for publication) BibTeX
F. Kork, Tim Conrad, B. Weiss, T. Roenneberg, K.-D. Wernecke, Felix Balzer Associations of postoperative mortality with the time of day, week and year Anaesthesia, 73(6), pp. 711-718, 2018 BibTeX
Xiaolin Ma, Tim Conrad, Maren Alchikh, J. Reiche, Brunhilde Schweiger, Barbara Rath 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) BibTeX
DOI
Patrick Obermeier, A. Heim, Barbara Biere, E. Hage, Maren Alchikh, Tim Conrad, Brunhilde Schweiger, Barbara Rath 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) BibTeX
Forough Marzban, Tim Conrad, Pouria Marban, Sahar Sodoudi 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 BibTeX
DOI
Victor Mireles, Tim Conrad Reusable building blocks in biological systems Journal of the Royal Society Interface, 15(149), pp. 1-10, 2018 (accepted for publication) BibTeX
DOI

2017

Fahrnaz Jayrannejad, Tim Conrad Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining Springer Lecture Notes in Artificial Intelligence, p. studi, 2017 (accepted for publication) BibTeX
Fahrnaz Jayrannejad, Tim Conrad Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining Springer Lecture Notes in Artificial Intelligence, 2017 (in press) BibTeX
L. Seeber, Tim Conrad, Christian Hoppe, Patrick Obermeier, X. Chen, K. Karsch, S. Muehlhans, Franziska Tief, Sindy Boettcher, S. Diedrich, Brunhilde Schweiger, Barbara Rath 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) BibTeX
DOI
Borong Shao, Carlo Vittorio Cannistraci, Tim Conrad 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 BibTeX
DOI
Shao Borong, Carlo Cannistraci, Tim Conrad 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) BibTeX
DOI
Barbara Rath, Tim Conrad, Puja Myles, Maren Alchikh, Xiaolin Ma, Christian Hoppe, Franziska Tief, Xi Chen, Patrick Obermeier, Bron Kisler, Brunhilde Schweiger 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 BibTeX
DOI
Tim Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Alexander Benedikt Leichtle, Jan Vybiral, Gitta Kytyniok, Christof Schütte 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 BibTeX
DOI
Tim Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Jan Vybiral, Gitta Kutyniok, Christof Schütte 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 BibTeX
DOI

2016

Tim Conrad, Xintian You Acfs: accurate circRNA identification and quantification from NGS data Nature Scientific Reports, Vol.6, 2016 BibTeX
DOI
Franziska Tief, Christian Hoppe, L. Seeber, Patrick Obermeier, X. Chen, K. Karsch, S. Muehlhans, E. Adamou, Tim Conrad, Brunhilde Schweiger, T. Adam, Barbara Rath 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 BibTeX
DOI
Victor Mireles, Tim Conrad Decomposing biological systems into reusable modules reveals characteristic module size distributions 2016 (under review) BibTeX
Patrick Obermeier, S. Muehlhans, Christian Hoppe, K. Karsch, Franziska Tief, L. Seeber, X. Chen, Tim Conrad, Sindy Boettcher, S. Diedrich, Barbara Rath Enabling Precision Medicine With Digital Case Classification at the Point-of-Care EBioMedicine, Vol.4, pp. 191-196, 2016 BibTeX
DOI
Borong Shao, Tim Conrad 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 BibTeX
DOI
Iliusi Vega, Christof Schütte, Tim Conrad Finding metastable states in real-world time series with recurrence networks Physica A: Statistical Mechanics and its Applications, Vol.445, pp. 1-17, 2016 BibTeX
DOI
Christian Hoppe, Patrick Obermeier, S. Mehlhans, Maren Alchikh, L. Seeber, Franziska Tief, K. Karsch, X. Chen, Sindy Boettcher, S. Diedrich, Tim Conrad 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 BibTeX
DOI

2015

Tim Conrad, Leonie Wallmeyer, Mona Rams, Stefan Börno, Bernd Timmermann, Sarah Hedtrich Analyzing the Influence of Filaggrin on Other Skin Associated Genes in a Filaggrin Deficient Skin Model Using the Core Network Approach Technical Report, 2015 BibTeX
Tim Conrad, Borong Shao 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 BibTeX
DOI
Tim Conrad, K. Karsch, Patrick Obermeier, L. Seeber, X. Chen, Franziska Tief, S. Muehlhans, Christian Hoppe, Sindy Boettcher, S. Diedrich, Barbara Rath Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children The Pediatric Infectious Disease Journal, 34(10), 2015 BibTeX
Tim Conrad, Victor Mireles Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrics Procedia Computer Science, Vol.51, pp. 2967-2971, 2015 BibTeX
DOI
Tim Conrad, Matthias Lenga Non-convex regularization for supervised learning Technical Report, 2015 PDF
BibTeX

2014

Marco Sarich, Natasa Djurdjevac Conrad, Sharon Bruckner, Tim Conrad, Christof Schütte Modularity revisited: A novel dynamics-based concept for decomposing complex networks Journal of Computational Dynamics, 1(1), pp. 191-212, 2014 PDF
BibTeX
DOI
Iliusi Vega, Christof Schütte, Tim Conrad SAIMeR: Self-adapted method for the identification of metastable states in real-world time series ZIB-Report 14-16 PDF
BibTeX
URN
Christof Schütte, Tim Conrad 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 BibTeX

2013

Pooja Gupta, Norbert Reinsch, Andreas Spötter, Tim Conrad, Kaspar Bienefeld 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 BibTeX
DOI
Tim Conrad, Sharon Bruckner, Bastian Kayser Finding Modules in Networks with Non-modular Regions Lecture Notes in Computer Science (Proceedings of SEA 2013), Vol.7933, pp. 188-199, 2013 BibTeX
DOI
Tim Conrad, Alexander Benedikt Leichtle, Uta Ceglarek, P. Weinert, C.T. Nakas, Jean-Marc Nuoffer, Julia Kase, Helmut Witzigmann, Joachim Thiery, Georg Martin Fiedler Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma Metabolomics, 9(3), pp. 677-687, 2013 BibTeX
DOI
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 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 BibTeX

2012

Tim Conrad, Christof Schütte, Stephan Aiche, Knut Reinert, Diana Hildebrand, Hartmut Schlüter Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs PLoS ONE, 7(7), 2012 BibTeX
DOI
Natasa Djurdjevac Conrad, Stefanie Bruckner, Tim Conrad, Christof Schütte Random Walks on Complex Modular Networks Journal of Numerical Analysis, Industrial and Applied Mathematics, 6(1-2), pp. 29-50, 2012 BibTeX
Tim Conrad, Alexander Benedikt Leichtle, Jean-Marc Nuoffer, Uta Ceglarek, Julia Kase, Helmut Witzigmann, Joachim Thiery, Georg Martin Fiedler Serum amino acid profiles and their alterations in colorectal cancer Metabolomics, 2012 BibTeX
DOI
Pooja Gupta, Tim Conrad, Andreas Spötter, Norbert Reinsch, Kaspar Bienefeld Simulating a base population in honey bee for molecular genetic studies Genetics Selection Evolution, 2012 BibTeX
DOI

2004

Tim Conrad Metabolic Pathways Doctoral thesis, Monash University Melbourne, unknown (Advisor), 2004 BibTeX
Tim Conrad New Appraches for Visualizing and Analyzing Metabolic Pathways Proceedings of the Second Australian Undergraduate Students? Computing Conference, 2004 BibTeX
  • Research
    • Solutions for Individualized Medicine
    • Molecular and Biological Processes
    • Materials and Optical Processes
    • Combinatorics and MINLP
    • MSO for Multiscale Systems
    • Robust Solutions under Uncertainty
    • Digital Humanities
    • Efficient Infrastructure and Logistics
    • Large-Scale Data Management, Curation & Analysis
    • Highly Parallel Computing
    • Scalable and Fault-Tolerant Algorithms
    • Publications
    • Books
    • Features
  • Institute
    • Research Campus MODAL
    • Intel oneAPI CoE
    • Joint Lab Optics
    • Oracle Center of Excellence
    • Organization
    • Organizational Chart
    • Committees and Regulations
    • Spin-Offs
    • Konrad Zuse
    • Hall of Fame
  • Research Services
    • NHR Center at ZIB
    • Supercomputing
    • Data Archive
    • KOBV
    • BRAIN
    • Software
    • Room Reservation
    • Library
  • Members
  • Training & Outreach
    • Graduate Students
    • Scholarships
    • Lectures
    • Trainee Openings
    • Schools
    • Press
    • Public Events
    • Guided Tours
    • Alumni
    • Topics for theses
  • Contact