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, transcriptome, proteome and metabolome. Following the central dogma of molecular biology and its extensions these levels are highly interconnected and depend on each other. Within the MedLab, one of four labs of the Research Campus MODAL at ZIB, we will develop new mathematical methods that allow (1) identification of multivariate disease signatures that describe changes in multiple data-sources and (2) development of multi-level models that embeds these findings into the actual biological context. Both parts combined will eventually lead to a thorough understanding of the modeled process and open up the opportunity to use the respective model for diagnostic purposes for individuals, thus allowing high-throughput classification of biological samples. These techniques can then be adjusted to an individual by using its -omics data and thus allows to derive information about the individual's state, for example, as a diagnostic tool for a certain disease that is captured by the data and the model. All algorithms will be implemented using state-of-the art software frameworks that can copy with the very large data volumes.
Publikationen
2023 |
|||
Sydney Paltra, Tim Conrad | Effectiveness of Paxlovid - A Review | Frontiers in Public Health, 2023 (revision under review) |
BibTeX
|
Mingze Bai, Jingwen Deng, Chengxin Dai, Julianus Pfeuffer, Yasset Perez-Riverol | LFQ-based peptide and protein intensity downstream analysis | 2023 (published) |
BibTeX
DOI |
Christopher Secker, Konstantin Fackeldey, Marcus Weber, Sourav Ray, Christoph Gorgulla, Christof Schütte | Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists | 2023 (under review) |
BibTeX
|
Eftychia E. Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer, Timo Sachsenberg, Omkar Mohite, Matin Nuhamunanda, Oliver Kohlbacher, Tilmann Weber | UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysis | Journal of Cheminformatics, 15(52), 2023 (in press) |
BibTeX
DOI |
Kateryna Melnyk, Kuba Weimann, Tim Conrad | Understanding microbiome dynamics via interpretable graph representation learning | Scientific Reports, Vol.13, p. 2058, 2023 |
BibTeX
DOI |
Lisa Bautz | Unsupervised Shape Correspondence Estimation for Anatomical Shapes | Master's thesis, Technische Universität Berlin, Stefan Zachow, Tamaz Amiranashvili (Advisors), 2023 |
PDF
BibTeX |
2022 |
|||
Mona Rams, Tim Conrad | Dictionary learning allows model-free pseudotime estimation of transcriptomics data | BMC Genomics, Vol.23, 2022 |
BibTeX
DOI |
Sahar Iravani | Interpretable Deep Learning Approaches for Biomarker Detection from High-Dimensional Biomedical Data | Doctoral thesis, Freie Universität Berlin, Tim Conrad (Advisor), 2022 |
BibTeX
|
David Lüdke, Tamaz Amiranashvili, Felix Ambellan, Ivan Ezhov, Bjoern Menze, Stefan Zachow | Landmark-free Statistical Shape Modeling via Neural Flow Deformations | Medical Image Computing and Computer Assisted Intervention - MICCAI 2022, Vol.13432, Lecture Notes in Computer Science, 2022 |
BibTeX
DOI arXiv |
Tamaz Amiranashvili, David Lüdke, Hongwei Li, Bjoern Menze, Stefan Zachow | Learning Shape Reconstruction from Sparse Measurements with Neural Implicit Functions | Medical Imaging with Deep Learning, 2022 |
PDF
BibTeX |
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 |
David Lüdke | Neural flow-based deformations for statistical shape modelling | Master's thesis, Johann Wolfgang Goethe-Universität Frankfurt, Tamaz Amiranashvili, Stefan Zachow (Advisors), 2022 |
BibTeX
|
Mona Milena Rams | New approaches for unsupervised transcriptomic data analysis based on Dictionary learning | Doctoral thesis, Freie Universität Berlin, Tim Conrad (Advisor), 2022 |
BibTeX
|
Felix Peppert, Max von Kleist, Christof Schütte, Vikram Sunkara | On the Sufficient Condition for Solving the Gap-Filling Problem Using Deep Convolutional Neural Networks | IEEE Transactions on Neural Networks and Learning Systems, 33(11), pp. 6194-6205, 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 |
Saeed Mohammadzadeh, Vítor H. Nascimento, Rodrigo C. de Lamare, Noushin Hajarolasvadi | Robust Beamforming Based on Complex-Valued Convolutional Neural Networks for Sensor Arrays | IEEE Signal Processing Letters, Vol.29, pp. 2018-2021, 2022 |
BibTeX
DOI |
Noushin Hajarolasvadi, Vikram Sunkara, Sagar Khavnekar, Florian Beck, Robert Brandt, Daniel Baum | Volumetric macromolecule identification in cryo-electron tomograms using capsule networks | BMC Bioinformatics, 23(360), 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 |
Alexey Shestakov | A Deep Learning Method for Automated Detection of Meniscal Tears in Meniscal Sub-Regions in 3D MRI Data | Master's thesis, Freie Universität Berlin, Tack Alexander, Zachow Stefan (Advisors), 2021 |
BibTeX
|
Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M. Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexovy, Björn Grüning, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Van Den Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W. Deutsch, Juan Antonio Vizcaíno, Mingze Bai, Timo Sachsenberg, Lev I. Levitsky, Yasset Perez-Riverol | A proteomics sample metadata representation for multiomics integration and big data analysis | Nature Communications, 12(5854), 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 |
Jianning Li, Pedro Pimentel, Angelika Szengel, Moritz Ehlke, Hans Lamecker, Stefan Zachow, Laura Estacio, Christian Doenitz, Heiko Ramm, Haochen Shi, Xiaojun Chen, Franco Matzkin, Virginia Newcombe, Enzo Ferrante, Yuan Jin, David G. Ellis, Michele R. Aizenberg, Oldrich Kodym, Michal Spanel, Adam Herout, James G. Mainprize, Zachary Fishman, Michael R. Hardisty, Amirhossein Bayat, Suprosanna Shit, Bomin Wang, Zhi Liu, Matthias Eder, Antonio Pepe, Christina Gsaxner, Victor Alves, Ulrike Zefferer, Cord von Campe, Karin Pistracher, Ute Schäfer, Dieter Schmalstieg, Bjoern H. Menze, Ben Glocker, Jan Egger | AutoImplant 2020 - First MICCAI Challenge on Automatic Cranial Implant Design | IEEE Transactions on Medical Imaging, 40(9), pp. 2329-2342, 2021 |
BibTeX
DOI |
Patrick Gelss, Stefan Klus, Ingmar Schuster, Christof Schütte | Feature space approximation for kernel-based supervised learning | Knowledge-Based Sytems, Vol.221, 2021 |
BibTeX
DOI |
Husen M. Umer, Yafeng Zhu, Julianus Pfeuffer, Timo Sachsenberg, Janne Lehtiö, Rui Branca, Yasset Perez-Riverol | Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides | Bioinformatics, pp. 1470-1472, 2021 |
BibTeX
|
Jan Krause | Investigation of Options to Handle 3D MRI Data via Convolutional Neural Networks Application in Knee Osteoarthritits Classification | Master's thesis, Otto-von-Guericke-Universität Magdeburg, Alexander Tack, Stefan Zachow (Advisors), 2021 |
BibTeX
|
Dev Punjabi | Orientation-invariant Dense Correspondence using Graph Convolutional Neural Networks | Master's thesis, Universität Potsdam, Martin Grewe, Tamaz Amiranashvili, Zachow Stefan (Advisors), 2021 |
BibTeX
|
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 |
Alexander Tack, Felix Ambellan, Stefan Zachow | Towards novel osteoarthritis biomarkers: Multi-criteria evaluation of 46,996 segmented knee MRI data from the Osteoarthritis Initiative | PLOS One, 16(10), 2021 |
BibTeX
DOI |
K. Weimann, Tim Conrad | Transfer Learning for ECG Classification | Scientific Reports, Vol.11, 2021 |
BibTeX
DOI |
Laura Estacio, Moritz Ehlke, Alexander Tack, Eveling Castro-Gutierrez, Hans Lamecker, Rensso Mora, Stefan Zachow | Unsupervised Detection of Disturbances in 2D Radiographs | 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), pp. 367-370, 2021 |
BibTeX
DOI |
Anjany Sekuboyina, Malek E. Husseini, Amirhossein Bayat, Maximilian Löffler, Hans Liebl, Hongwei Li, Giles Tetteh, Jan Kukačka, Christian Payer, Darko Štern, Martin Urschler, Maodong Chen, Dalong Cheng, Nikolas Lessmann, Yujin Hu, Tianfu Wang, Dong Yang, Daguang Xu, Felix Ambellan, Tamaz Amiranashvili, Moritz Ehlke, Hans Lamecker, Sebastian Lehnert, Marilia Lirio, Nicolás Pérez de Olaguer, Heiko Ramm, Manish Sahu, Alexander Tack, Stefan Zachow, Tao Jiang, Xinjun Ma, Christoph Angerman, Xin Wang, Kevin Brown, Alexandre Kirszenberg, Élodie Puybareau, Di Chen, Yiwei Bai, Brandon H. Rapazzo, Timyoas Yeah, Amber Zhang, Shangliang Xu, Feng Hou, Zhiqiang He, Chan Zeng, Zheng Xiangshang, Xu Liming, Tucker J. Netherton, Raymond P. Mumme, Laurence E. Court, Zixun Huang, Chenhang He, Li-Wen Wang, Sai Ho Ling, Lê Duy Huynh, Nicolas Boutry, Roman Jakubicek, Jiri Chmelik, Supriti Mulay, Mohanasankar Sivaprakasam, Johannes C. Paetzold, Suprosanna Shit, Ivan Ezhov, Benedikt Wiestler, Ben Glocker, Alexander Valentinitsch, Markus Rempfler, Björn H. Menze, Jan S. Kirschke | VerSe: A Vertebrae labelling and segmentation benchmark for multi-detector CT images | Medical Image Analysis, Vol.73, 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
|
Pedro Pimentel, Angelika Szengel, Moritz Ehlke, Hans Lamecker, Stefan Zachow, Laura Estacio, Christian Doenitz, Heiko Ramm | Automated Virtual Reconstruction of Large Skull Defects using Statistical Shape Models and Generative Adversarial Networks | Towards the Automatization of Cranial Implant Design in Cranioplasty, Vol.12439, pp. 16-27, 2020 |
BibTeX
DOI |
Júlia Chaumel, Merlind Schotte, Joseph J. Bizzarro, Paul Zaslansky, Peter Fratzl, Daniel Baum, Mason N. Dean | Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage | Bone, Vol.134, p. 115264, 2020 (preprint available as ) |
BibTeX
DOI |
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 |
Stefan Klus, Feliks Nüske, Sebastian Peitz, Jan-Hendrik Niemann, Cecilia Clementi, Christof Schütte | Data-driven approximation of the Koopman generator: Model reduction, system identification, and control | Physica D: Nonlinear Phenomena, Vol.406, 2020 (epub ahead of print) |
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 |
Sourav Ray, Vikram Sunkara, Christof Schütte, Marcus Weber | How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs | Molecular Simulation, 46(18), pp. 1443-1452, 2020 (preprint available as ) |
BibTeX
DOI |
Merlind Schotte, Júlia Chaumel, Mason N. Dean, Daniel Baum | Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae | MethodsX, Vol.7, p. 100905, 2020 (preprint available as ) |
BibTeX
DOI |
Norbert Lindow, Florian Brünig, Vincent J. Dercksen, Gunar Fabig, Robert Kiewisz, Stefanie Redemann, Thomas Müller-Reichert, Steffen Prohaska, Daniel Baum | Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography | bioRxiv, 2020 |
BibTeX
DOI |
Mattes Mollenhauer, Ingmar Schuster, Stefan Klus, Christof Schütte | Singular Value Decomposition of Operators on Reproducing Kernel Hilbert Spaces | Advances om Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on his 60th birthday, Vol.304, pp. 109-131, Oliver Junge, O. Schütze, Gary Froyland, S. Ober-Blobaum, K. Padberg-Gehle (Eds.), Springer International, 2020, ISBN: 978-3-030-51264-4 |
BibTeX
DOI |
Anjany Sekuboyina, Amirhossein Bayat, Malek E. Husseini, Maximilian Löffler, Hongwei Li, Giles Tetteh, Jan Kukačka, Christian Payer, Darko Štern, Martin Urschler, Maodong Chen, Dalong Cheng, Nikolas Lessmann, Yujin Hu, Tianfu Wang, Dong Yang, Daguang Xu, Felix Ambellan, Tamaz Amiranashvili, Moritz Ehlke, Hans Lamecker, Sebastian Lehnert, Marilia Lirio, Nicolás Pérez de Olaguer, Heiko Ramm, Manish Sahu, Alexander Tack, Stefan Zachow, Tao Jiang, Xinjun Ma, Christoph Angerman, Xin Wang, Qingyue Wei, Kevin Brown, Matthias Wolf, Alexandre Kirszenberg, Élodie Puybareau, Alexander Valentinitsch, Markus Rempfler, Björn H. Menze, Jan S. Kirschke | VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images | arXiv, 2020 |
PDF
BibTeX arXiv |
2019 |
|||
Alexander Tack, Stefan Zachow | Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative | IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), pp. 40-43, 2019 (preprint available as ) |
BibTeX
DOI |
Pooja Gupta, Sarah Peter, Markus Jung, Astrid Lewin, Georg Hemmrich-Stanisak, Andre Franke, Max von Kleist, Christof Schütte, Ralf Einspanier, Soroush Sharbati, Jennifer zur Bruegge | Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections | Scientific Reports in Nature, Vol.9, 2019 |
BibTeX
DOI |
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
|
Felix Ambellan, Alexander Tack, Moritz Ehlke, Stefan Zachow | Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative | Medical Image Analysis, 52(2), pp. 109-118, 2019 (preprint available as ZIB-Report 19-06) |
PDF (ZIB-Report)
BibTeX DOI |
Felix Ambellan, Alexander Tack, Moritz Ehlke, Stefan Zachow | Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative (Supplementary Material) | Medical Image Analysis, 52(2), pp. 109-118, 2019 (OAI-ZIB dataset) |
BibTeX
DOI |
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 |
Thomas Hildebrandt, Jan Joris Bruening, Hans Lamecker, Stefan Zachow, Werner Heppt, Nora Schmidt, Leonid Goubergrits | Digital Analysis of Nasal Airflow Facilitating Decision Support in Rhinosurgery | Facial Plastic Surgery, 35(1), pp. 1-8, 2019 |
BibTeX
DOI |
Tobias Haase, Vikram Sunkara, Benjamin Kohl, Carola Meier, Patricia Bußmann, Jessica Becker, Michal Jagielski, Max von Kleist, Wolfgang Ertel | Discerning the spatio-temporal disease patterns of surgically induced OA mouse models | PLOS One, 14(4), 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 | Ergodic SDEs on submanifolds and related numerical sampling schemes | ESAIM: Mathematical Modelling and Numerical Analysis, 2019 |
BibTeX
arXiv |
Steffen Oeltze-Jaffra, Monique Meuschke, Mathias Neugebauer, Sylvia Saalfeld, Kai Lawonn, Gabor Janiga, Hans-Christian Hege, Stefan Zachow, Bernhard Preim | Generation and Visual Exploration of Medical Flow Data: Survey, Research Trends, and Future Challenges | Computer Graphics Forum, 38(1), pp. 87-125, 2019 |
BibTeX
DOI |
Carsten Hartmann, Christof Schütte, Wei Zhang | Jarzynski's equality, fluctuation theorems, and variance reduction: Mathematical analysis and numerical algorithms | Journal of Statistical Physics, 175(6), pp. 1214-1261, 2019 |
BibTeX
arXiv 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 |
Patrick Gelß, Stefan Klus, Jens Eisert, Christof Schütte | Multidimensional Approximation of Nonlinear Dynamical Systems | Journal of Computational and Nonlinear Dynamics, 14(6), 2019 |
BibTeX
DOI |
Tony Lelièvre, Wei Zhang | Pathwise estimates for effective dynamics: the case of nonlinear vectorial reaction coordinates | Multiscale Modeling and Simulation, pp. 1019-1051, 2019 |
BibTeX
arXiv DOI |
Felix Ambellan, Hans Lamecker, Christoph von Tycowicz, Stefan Zachow | Statistical Shape Models - Understanding and Mastering Variation in Anatomy | Biomedical Visualisation, Paul M. Rea (Ed.), Springer Nature Switzerland AG, 1, pp. 67-84, 2019, ISBN: 978-3-030-19384-3, ISBN: 978-3-030-19385-0 (preprint available as ZIB-Report 19-13) |
PDF (ZIB-Report)
BibTeX DOI |
Thomas Hildebrandt, Jan Joris Bruening, Nora Laura Schmidt, Hans Lamecker, Werner Heppt, Stefan Zachow, Leonid Goubergrits | The Healthy Nasal Cavity - Characteristics of Morphology and Related Airflow Based on a Statistical Shape Model Viewed from a Surgeon’s Perspective | Facial Plastic Surgery, 35(1), pp. 9-13, 2019 |
BibTeX
DOI |
2018 |
|||
Péter Koltai, Christof Schütte | A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics | SIAM J. Multiscale Model. Simul., 16(4), pp. 1455-1485, 2018 (preprint available as ) |
BibTeX
DOI |
Christoph von Tycowicz, Felix Ambellan, Anirban Mukhopadhyay, Stefan Zachow | An Efficient Riemannian Statistical Shape Model using Differential Coordinates | Medical Image Analysis, 43(1), pp. 1-9, 2018 (preprint available as ) |
BibTeX
DOI |
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
|
Felix Ambellan, Alexander Tack, Moritz Ehlke, Stefan Zachow | Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative | Medical Imaging with Deep Learning, 2018 |
PDF
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 |
Mohsen Akbari Shandiz, Paul Boulos, Stefan Sævarsson, Heiko Ramm, Chun Kit Fu, Stephen Miller, Stefan Zachow, Carolyn Anglin | Changes in Knee Shape and Geometry Resulting from Total Knee Arthroplasty | Journal of Engineering in Medicine, 232(1), pp. 67-79, 2018 |
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
|
Stefan Klus, Feliks Nüske, Peter Koltai, Hao Wu, Ioannis Kevrekidis, Christof Schütte, Frank Noé | Data-driven model reduction and transfer operator approximation | Journal of Nonlinear Science, 28(3), pp. 985-1010, 2018 |
BibTeX
DOI |
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 |
Alexander Tack, Anirban Mukhopadhyay, Stefan Zachow | Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative | Osteoarthritis and Cartilage, 26(5), pp. 680-688, 2018 (preprint available as ) |
BibTeX
DOI |
Manuel Dibak, Mauricio J. del Razo, David de Sancho, Christof Schütte, Frank Noé | MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations | Journal of Chemical Physics, 148(21), 2018 |
BibTeX
DOI |
Manuel Dibak, Mauricio J. del Razo, David De Sancho, Christof Schütte, Frank Noé | MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations | Journal of Chemical Physics, 148(214107), 2018 |
BibTeX
DOI |
Peter Koltai, Hao Wu, Frank Noé, Christof Schütte | Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics | Computation, 6(1), 2018 |
PDF
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 |
Max von Kleist, Christof Schütte, Wei Zhang | Statistical analysis of the first passage path ensemble of jump processes | Journal of Statistical Physics, Vol.170, pp. 809-843, 2018 |
BibTeX
DOI |
G. Hettich, R. A. Schierjott, C. Schilling, A. Maas, Heiko Ramm, Matthias Bindernagel, Hans Lamecker, T. M. Grupp | Validation of a Statistical Shape Model for Acetabular Bone Defect Analysis | ISTA 2018 London Abstract Book, 2018 (accepted for publication) |
BibTeX
|
2017 |
|||
Manish Sahu, Anirban Mukhopadhyay, Angelika Szengel, Stefan Zachow | Addressing multi-label imbalance problem of Surgical Tool Detection using CNN | International Journal of Computer Assisted Radiology and Surgery, 12(6), pp. 1013-1020, 2017 |
PDF
BibTeX DOI |
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
|
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 |
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 |
Stefanie Winkelmann, Christof Schütte | Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems | The Journal of Chemical Physics, 147(11), pp. 114115-1-114115-18, 2017 (preprint available as ) |
PDF
BibTeX DOI |
Pooja Gupta, Annika Gramatke, Ralf Einspanier, Christof Schütte, Max von Kleist, Jutta Sharbati | In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements | Toxicology in Vitro, Vol.41, pp. 179-188, 2017 (preprint available as ZIB-Report 17-08) |
PDF (ZIB-Report)
BibTeX |
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 |
Andreas Benn, Christian Hiepen, Marc Osterland, Christof Schütte, An Zwijsen, Petra Knaus | Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence | FASEB Journal, 31(11), pp. 4720-4733, 2017 |
BibTeX
DOI |
Florian Bernard, Luis Salamanca, Johan Thunberg, Alexander Tack, Dennis Jentsch, Hans Lamecker, Stefan Zachow, Frank Hertel, Jorge Goncalves, Peter Gemmar | Shape-aware Surface Reconstruction from Sparse 3D Point-Clouds | Medical Image Analysis, Vol.38, pp. 77-89, 2017 |
PDF
BibTeX DOI |
Rudolf Huttary, Leonid Goubergrits, Christof Schütte, Stefan Bernhard | Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling | Computers in Biology and Medicine, Vol.87, pp. 104-123, 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 |
David Wilson, Carolyn Anglin, Felix Ambellan, Carl Martin Grewe, Alexander Tack, Hans Lamecker, Michael Dunbar, Stefan Zachow | Validation of three-dimensional models of the distal femur created from surgical navigation point cloud data for intraoperative and postoperative analysis of total knee arthroplasty | International Journal of Computer Assisted Radiology and Surgery, 12(12), pp. 2097-2105, 2017 |
PDF
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 |
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 |
Natasa Djurdjevac Conrad, Marcus Weber, Christof Schütte | Finding dominant structures of nonreversible Markov processes | Multiscale Modeling and Simulation, 14(4), pp. 1319-1340, 2016 (preprint available as ) |
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 |
Anirban Mukhopadhyay, Arun Kumar, Suchendra Bhandarkar | Joint Geometric Graph Embedding for Partial Shape Matching in Images | IEEE Winter Conference on Applications of Computer Vision, pp. 1-9, IEEE, IEEE Winter Conference on Applications of Computer Vision (WACV), 2016 |
BibTeX
|
Peter Koltai, Giovanni Ciccotti, Christof Schütte | On Markov state models for non-equilibrium molecular dynamics | The Journal of Chemical Physics, 145(174103), 2016 (preprint available as ZIB-Report 16-11) |
PDF (ZIB-Report)
BibTeX DOI |
Stefan Klus, Peter Koltai, Christof Schütte | On the numerical approximation of the Perron-Frobenius and Koopman operator | Journal of Computational Dynamics, 3(1), pp. 51-77, 2016 |
BibTeX
DOI |
Anirban Mukhopadhyay, Oscar Morillo, Stefan Zachow, Hans Lamecker | Robust and Accurate Appearance Models Based on Joint Dictionary Learning Data from the Osteoarthritis Initiative | Lecture Notes in Computer Science, Patch-Based Techniques in Medical Imaging. Patch-MI 2016, pp. 25-33, Vol.9993, 2016 |
BibTeX
DOI |
Patrick Gelß, Sebastian Matera, Christof Schütte | Solving the master equation without kinetic Monte Carlo: Tensor train approximations for a CO oxidation model | Journal of Computational Physics, Vol.314, pp. 489-502, 2016 |
BibTeX
DOI |
Hans Lamecker, Stefan Zachow | Statistical Shape Modeling of Musculoskeletal Structures and Its Applications | Computational Radiology for Orthopaedic Interventions, Springer, pp. 1-23, 2016, ISBN: 978-3-319-23481-6 |
BibTeX
DOI |
Stefanie Winkelmann, Christof Schütte | The Spatiotemporal Master Equation: Approximation of Reaction-Diffusion Dynamics via Markov State Modeling | Journal of Chemical Physics, 145(21), 2016 (preprint available as ) |
PDF
BibTeX DOI |
Anirban Mukhopadhyay | Total Variation Random Forest: Fully automatic MRI segmentation in congenital heart disease | RAMBO 2016, HVSMR 2016: Reconstruction, Segmentation, and Analysis of Medical Images, pp. 165-171, Vol.LNCS 10129, 2016 |
BibTeX
DOI |
Stefan Klus, Christof Schütte | Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator | Journal of Computational Dynamics, 3(2), pp. 139-161, 2016 |
BibTeX
DOI |
2015 |
|||
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 |
Anirban Mukhopadhyay, Ilkay Oksuz, Marco Bevilacqua, Rohan Dharmakumar, Sotirios Tsaftaris | Data-Driven Feature Learning for Myocardial Segmentation of CP-BOLD MRI | Functional Imaging and Modeling of the Heart, pp. 189-197, Vol.9126, Lecture Notes in Computer Science, 2015 |
BibTeX
DOI |
Ilkay Oksuz, Anirban Mukhopadhyay, Marco Bevilacqua, Rohan Dharmakumar, Sotirios Tsaftaris | Dictionary Learning Based Image Descriptor for Myocardial Registration of CP-BOLD MR | Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015, pp. 205-213, Vol.9350, Lecture Notes in Computer Science, 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
|
Raheem Gul, Christof Schütte, Stefan Bernhard | Mathematical modeling and sensitivity analysis of arterial anastomosis in arm arteries | ZIB-Report 15-22 |
PDF
BibTeX URN |
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 |
Natasa Djurdjevac Conrad, Ralf Banisch, Christof Schütte | Modularity of Directed Networks: Cycle Decomposition Approach | Journal of Computational Dynamics 2 (2015) pp. 1-24, 2015 (preprint available as ) |
BibTeX
DOI |
Sulav Duwal, Stefanie Winkelmann, Christof Schütte, Max von Kleist | Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings | PloS Computational Biology, 11(4), 2015 |
BibTeX
DOI |
Ralf Banisch, Natasa Djurdjevac Conrad, Christof Schütte | Reactive flows and unproductive cycles for random walks on complex networks | The European Physical Journal Special Topics, vol. 224, iss. 12 (2015) pp. 2369-2387, 2015 (preprint available as ZIB-Report 15-19) |
PDF (ZIB-Report)
BibTeX DOI |
Marc Osterland, Andreas Benn, Steffen Prohaska, Christof Schütte | Single Cell Tracking in Phase-Contrast Microscopy | EMBL Symposium 2015 - Seeing is Believing - Imaging the Processes of Life, 2015 |
BibTeX
|
Ivan Kryven, Susanna Röblitz, Christof Schütte | Solution of the chemical master equation by radial basis functions approximation with interface tracking | BMC Systems Biology, 9(67), pp. 1-12, 2015 |
PDF
BibTeX DOI |
Anirban Mukhopadhyay, Ilkay Oksuz, Marco Bevilacqua, Rohan Dharmakumar, Sotirios Tsaftaris | Unsupervised myocardial segmentation for cardiac MRI | Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015, pp. 12-20, Vol.LNCS 9351, 2015 |
BibTeX
DOI |
2014 |
|||
Han Wang, Christof Schütte | Building Markov State Models for Periodically Driven Non-Equilibrium Systems | ZIB-Report 14-46 |
PDF
BibTeX URN |
Stefanie Winkelmann, Christof Schütte, Max von Kleist | Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1 | Communications in Mathematical Sciences, 12(5), pp. 859-877, 2014 (preprint available as ) |
BibTeX
DOI |
Pooja Gupta, Carola Krause, Paul Rikeit, Susanna Röblitz, Petra Knaus, Christof Schütte | Modeling of the BMP mediated co-regulation of the Smad and Non-Smad pathways in the context of cell density | 10th International BMP conference, 2014, Berlin, Germany, 2014 |
BibTeX
|
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 |
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 |
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 | New Appraches for Visualizing and Analyzing Metabolic Pathways | Proceedings of the Second Australian Undergraduate Students? Computing Conference, 2004 |
BibTeX
|