@article{FreitasdaCruzPfahringerMartensenetal.2021,
  author    = {Freitas da Cruz, Harry and Pfahringer, Boris and Martensen, Tom and Schneider, Frederic and Meyer, Alexander and B{\"o}ttinger, Erwin and Schapranow, Matthieu-Patrick},
  title     = {Using interpretability approaches to update "black-box" clinical prediction models},
  series = {Artificial intelligence in medicine : AIM},
  volume    = {111},
  journal   = {Artificial intelligence in medicine : AIM},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0933-3657},
  doi       = {10.1016/j.artmed.2020.101982},
  pages     = {13},
  year      = {2021},
  abstract  = {Despite advances in machine learning-based clinical prediction models, only few of such models are actually deployed in clinical contexts. Among other reasons, this is due to a lack of validation studies. In this paper, we present and discuss the validation results of a machine learning model for the prediction of acute kidney injury in cardiac surgery patients initially developed on the MIMIC-III dataset when applied to an external cohort of an American research hospital. To help account for the performance differences observed, we utilized interpretability methods based on feature importance, which allowed experts to scrutinize model behavior both at the global and local level, making it possible to gain further insights into why it did not behave as expected on the validation cohort. The knowledge gleaned upon derivation can be potentially useful to assist model update during validation for more generalizable and simpler models. We argue that interpretability methods should be considered by practitioners as a further tool to help explain performance differences and inform model update in validation studies.},
  language  = {en}
}
@article{BorchertMockTomczaketal.2021,
  author    = {Borchert, Florian and Mock, Andreas and Tomczak, Aurelie and H{\"u}gel, Jonas and Alkarkoukly, Samer and Knurr, Alexander and Volckmar, Anna-Lena and Stenzinger, Albrecht and Schirmacher, Peter and Debus, J{\"u}rgen and J{\"a}ger, Dirk and Longerich, Thomas and Fr{\"o}hling, Stefan and Eils, Roland and Bougatf, Nina and Sax, Ulrich and Schapranow, Matthieu-Patrick},
  title     = {Correction to: Knowledge bases and software support for variant interpretation in precision oncology},
  series = {Briefings in bioinformatics},
  volume    = {22},
  journal   = {Briefings in bioinformatics},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1467-5463},
  doi       = {10.1093/bib/bbab246},
  pages     = {1},
  year      = {2021},
  language  = {en}
}
@article{BorchertMockTomczaketal.2021,
  author    = {Borchert, Florian and Mock, Andreas and Tomczak, Aurelie and H{\"u}gel, Jonas and Alkarkoukly, Samer and Knurr, Alexander and Volckmar, Anna-Lena and Stenzinger, Albrecht and Schirmacher, Peter and Debus, J{\"u}rgen and J{\"a}ger, Dirk and Longerich, Thomas and Fr{\"o}hling, Stefan and Eils, Roland and Bougatf, Nina and Sax, Ulrich and Schapranow, Matthieu-Patrick},
  title     = {Knowledge bases and software support for variant interpretation in precision oncology},
  series = {Briefings in bioinformatics},
  volume    = {22},
  journal   = {Briefings in bioinformatics},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1467-5463},
  doi       = {10.1093/bib/bbab134},
  pages     = {17},
  year      = {2021},
  abstract  = {Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.},
  language  = {en}
}
@article{KrausMathewStephenSchapranow2021,
  author    = {Kraus, Sara Milena and Mathew-Stephen, Mariet and Schapranow, Matthieu-Patrick},
  title     = {Eatomics},
  series = {Journal of proteome research},
  volume    = {20},
  journal   = {Journal of proteome research},
  number    = {1},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1535-3893},
  doi       = {10.1021/acs.jproteome.0c00398},
  pages     = {1070 -- 1078},
  year      = {2021},
  abstract  = {Quantitative proteomics data are becoming increasingly more available, and as a consequence are being analyzed and interpreted by a larger group of users. However, many of these users have less programming experience. Furthermore, experimental designs and setups are getting more complicated, especially when tissue biopsies are analyzed. Luckily, the proteomics community has already established some best practices on how to conduct quality control, differential abundance analysis and enrichment analysis. However, an easy-to-use application that wraps together all steps for the exploration and flexible analysis of quantitative proteomics data is not yet available. For Eatomics, we utilize the R Shiny framework to implement carefully chosen parts of established analysis workflows to (i) make them accessible in a user-friendly way, (ii) add a multitude of interactive exploration possibilities, and (iii) develop a unique experimental design setup module, which interactively translates a given research hypothesis into a differential abundance and enrichment analysis formula. In this, we aim to fulfill the needs of a growing group of inexperienced quantitative proteomics data analysts. Eatomics may be tested with demo data directly online via https://we.analyzegenomes.com/now/eatomics/or with the user's own data by installation from the Github repository at https://github.com/Millchmaedchen/Eatomics.},
  language  = {en}
}
@misc{EngelHornConradScholzetal.2020,
  author    = {Engel, Silke and Horn-Conrad, Antje and Scholz, Jana and Schapranow, Matthieu-Patrick and Zimmermann, Matthias and Kampe, Heike},
  title     = {Portal Wissen = Health},
  number    = {02/2020},
  organization    = {University of Potsdam, Press and Public Relations Department},
  issn      = {2198-9974},
  doi       = {10.25932/publishup-48145},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-481458},
  pages     = {58},
  year      = {2020},
  abstract  = {The Coronavirus pandemic has made it very clear how much health and well-being determine our lives. And that science led the way in this regard could not be ignored. At the University of Potsdam, too, many researchers deal with aspects of health maintenance, whether in nutritional sciences, sports and rehabilitation medicine, biochemistry, or psychology. Their research includes supporting chronically ill children and the professional handling of risks, as you can read in this issue of our magazine. With the establishment of our seventh faculty, the Faculty of Health Sciences, these and many new medical topics are getting more attention at the University of Potsdam. While in the beginning, the "Brandenburg Health Campus" funded by the federal state of Brandenburg was a virtual network of university and non-university research, it is now getting more points of intersection and, not only since COVID-19, a very practical use and plausible to everyone. The Faculty of Health Sciences, founded in 2018, is supported by three institutions: the University of Potsdam, the Brandenburg Technical University Cottbus-Senftenberg and the Brandenburg Medical School in Neuruppin. They pursue an interdisciplinary approach that holistically develops teaching, transfers new scientific findings from theory to practice and thus further improves overall medical care in Brandenburg. Their vision of being a central platform of research, teaching, and transfer combines socially relevant issues and existing expertise to align them with the needs of people in Brandenburg and use them to their benefit. This interdisciplinary structure has never been more important to advancing patient-oriented basic research and health care models. An innovative concept that can make Brandenburg a pioneer. In the meantime, the Faculty of Health Sciences has established 16 new professorships at the supporting universities, which are concerned with medicine and healthy aging, health services research, nursing and rehabilitation sciences, and telemedicine. Cardiology and physiology will play a central role as well. In general, the innovative faculty counts on strong interdisciplinary relationships, for example with nutritional sciences and the digital health department at the Digital Engineering Faculty. The role of digitization and well-prepared data in combating the Coronavirus pandemic can also be read about in this issue. As usual, the research magazine addresses the full range of research at the university: We introduce historian Dominik Geppert, who deals with the history of unified Germany after 1990 embedded in the tensions created by a context of national unification, European integration, and global networking. In a self-experiment, we explored together with a psycholinguist how to research word-finding disorders. Last but not least, we were able to take part in a trip to Namibia, where ecologists from Potsdam examine wildlife management in the threatened savannah. Let them take you where kudu and springbok live!},
  language  = {en}
}
@misc{EngelHornConradScholzetal.2020,
  author    = {Engel, Silke and Horn-Conrad, Antje and Scholz, Jana and Kampe, Heike and Schapranow, Matthieu-Patrick and Pchalek, Magda},
  title     = {Portal Wissen = Gesundheit},
  number    = {02/2020},
  organization    = {Universit{\"a}t Potsdam, Referat f{\"u}r Presse- und {\"O}ffentlichkeitsarbeit},
  issn      = {2194-4237},
  doi       = {10.25932/publishup-48144},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-481441},
  pages     = {98},
  year      = {2020},
  abstract  = {Wie stark Gesundheit und Wohlbefinden unser Leben bestimmen, hat uns die Corona-Pandemie eindringlich vor Augen gef{\"u}hrt. Und dass die Wissenschaft in diesem Kontext den Takt vorgibt, war nicht zu {\"u}berh{\"o}ren. Auch an der Universit{\"a}t Potsdam besch{\"a}ftigen sich zahlreich Forscherinnen und Forscher mit Fragen der Gesunderhaltung, ob in den Ern{\"a}hrungswissenschaften, der Sport- und Rehabilitationsmedizin, der Biochemie oder der Psychologie. Das Spektrum reicht von der Entwicklung antimikrobieller Polymere und eines Sensors f{\"u}r die Atemgasanalyse bis zur Unterst{\"u}tzung chronisch kranker Kinder und dem kompetenten Umgang mit Risiken, wie in dieser Ausgabe unseres Magazins zu lesen ist. Mit dem Aufbau unserer siebenten, einer Gesundheitswissenschaften Fakult{\"a}t r{\"u}cken solche und viele neue medizinische Themen an der Universit{\"a}t Potsdam st{\"a}rker in den Fokus. War der vom Land gef{\"o}rderte „Gesundheitscampus Brandenburg" am Anfang noch ein virtuelles Netzwerk von universit{\"a}rer und außeruniversit{\"a}rer Forschung, bekommt es nun mehr und mehr Knotenpunkte und nicht erst seit Corona einen ganz praktischen Nutzen - f{\"u}r jeden nachvollziehbar. Die 2018 gegr{\"u}ndete Fakult{\"a}t f{\"u}r Gesundheitswissenschaften wird von drei Einrichtungen getragen: der Universit{\"a}t Potsdam, der Brandenburgischen Technischen Universit{\"a}t Cottbus- Senftenberg und der Medizinischen Hochschule Brandenburg in Neuruppin. Gemeinsam verfolgen sie einen f{\"a}cher{\"u}bergreifenden Ansatz, der die Lehre ganzheitlich weiterentwickelt, neue wissenschaftliche Erkenntnisse von der Theorie in die Praxis bringt und damit insgesamt die medizinische Versorgung in Brandenburg weiter verbessert. Ihre Vision, zentrale Plattform in Forschung, Lehre und Transfer zu sein, b{\"u}ndelt gesellschaftlich relevante Fragen und vorhandene Expertisen, um sie am Bedarf der Menschen im Land auszurichten und f{\"u}r ihr Wohl einzusetzen. Nie war diese hochschul{\"u}bergreifende Struktur wichtiger, um patientenorientierte Grundlagenforschung und Modelle der Gesundheitsversorgung voranzutreiben. Ein wegweisendes Konzept, mit dem Brandenburg Vorreiter sein kann. Inzwischen hat die Fakult{\"a}t f{\"u}r Gesundheitswissenschaften 16 neue Professuren an den einzelnen Tr{\"a}gerhochschulen etabliert. Es geht um die Medizin und Gesundheit des Alterns, um Versorgungsforschung, Pflege- und Rehabilitationswissenschaften sowie Telemedizin. Auch die Kardiologie und Physiologie werden eine zentrale Rolle spielen. Generell setzt die innovative Fakult{\"a}t auf starke Querbeziehungen beispielsweise zu den Ern{\"a}hrungswissenschaften oder zum Fachgebiet Digital Health an der Digital Engineering Fakult{\"a}t. Welche Rolle die Digitalisierung und gut aufbereitete Daten bei der Bek{\"a}mpfung der Corona-Pandemie spielen, ist ganz aktuell auch in diesem Heft zu erfahren. Aber nat{\"u}rlich widmet sich das Forschungsmagazin wie stets der ganzen fachlichen Breite der Universit{\"a}t: So stellen wir den Historiker Dominik Geppert vor, der sich mit der Geschichte des vereinigten Deutschlands nach 1990 im Spannungsfeld von nationaler Einigung, europ{\"a}ischer Integration und globaler Vernetzung befasst. Im Selbstversuch haben wir mit einer Psycholinguistin erkundet, wie sich Wortfindungsst{\"o}rungen erforschen lassen. Ebenfalls einem Test unterzogen wir eine neuartige vegane Milch, die ein findiges Start-up aus Erbsen herstellt. Nicht zuletzt durften wir teilhaben an einer Reise nach Namibia, wo Potsdamer {\"O}kologen das Wildtiermanagement in der bedrohten Savanne untersuchen. Lassen Sie sich von ihnen dorthin mitnehmen, wo sich Kudu und Springbock Gute Nacht sagen!},
  language  = {de}
}
@phdthesis{Schapranow2012,
  author    = {Schapranow, Matthieu-Patrick},
  title     = {Real-time security extensions for EPCglobal networks},
  address   = {Potsdam},
  pages     = {XVII, 108, XXX S.},
  year      = {2012},
  language  = {en}
}
@inproceedings{KurbelNowakAzodietal.2015,
  author    = {Kurbel, Karl and Nowak, Dawid and Azodi, Amir and Jaeger, David and Meinel, Christoph and Cheng, Feng and Sapegin, Andrey and Gawron, Marian and Morelli, Frank and Stahl, Lukas and Kerl, Stefan and Janz, Mariska and Hadaya, Abdulmasih and Ivanov, Ivaylo and Wiese, Lena and Neves, Mariana and Schapranow, Matthieu-Patrick and F{\"a}hnrich, Cindy and Feinbube, Frank and Eberhardt, Felix and Hagen, Wieland and Plauth, Max and Herscheid, Lena and Polze, Andreas and Barkowsky, Matthias and Dinger, Henriette and Faber, Lukas and Montenegro, Felix and Czach{\´o}rski, Tadeusz and Nycz, Monika and Nycz, Tomasz and Baader, Galina and Besner, Veronika and Hecht, Sonja and Schermann, Michael and Krcmar, Helmut and Wiradarma, Timur Pratama and Hentschel, Christian and Sack, Harald and Abramowicz, Witold and Sokolowska, Wioletta and Hossa, Tymoteusz and Opalka, Jakub and Fabisz, Karol and Kubaczyk, Mateusz and Cmil, Milena and Meng, Tianhui and Dadashnia, Sharam and Niesen, Tim and Fettke, Peter and Loos, Peter and Perscheid, Cindy and Schwarz, Christian and Schmidt, Christopher and Scholz, Matthias and Bock, Nikolai and Piller, Gunther and B{\"o}hm, Klaus and Norkus, Oliver and Clark, Brian and Friedrich, Bj{\"o}rn and Izadpanah, Babak and Merkel, Florian and Schweer, Ilias and Zimak, Alexander and Sauer, J{\"u}rgen and Fabian, Benjamin and Tilch, Georg and M{\"u}ller, David and Pl{\"o}ger, Sabrina and Friedrich, Christoph M. and Engels, Christoph and Amirkhanyan, Aragats and van der Walt, Est{\´e}e and Eloff, J. H. P. and Scheuermann, Bernd and Weinknecht, Elisa},
  title     = {HPI Future SOC Lab},
  editor    = {Meinel, Christoph and Polze, Andreas and Oswald, Gerhard and Strotmann, Rolf and Seibold, Ulrich and Schulzki, Bernhard},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-102516},
  pages     = {iii, 154},
  year      = {2015},
  abstract  = {Das Future SOC Lab am HPI ist eine Kooperation des Hasso-Plattner-Instituts mit verschiedenen Industriepartnern. Seine Aufgabe ist die Erm{\"o}glichung und F{\"o}rderung des Austausches zwischen Forschungsgemeinschaft und Industrie. Am Lab wird interessierten Wissenschaftlern eine Infrastruktur von neuester Hard- und Software kostenfrei f{\"u}r Forschungszwecke zur Verf{\"u}gung gestellt. Dazu z{\"a}hlen teilweise noch nicht am Markt verf{\"u}gbare Technologien, die im normalen Hochschulbereich in der Regel nicht zu finanzieren w{\"a}ren, bspw. Server mit bis zu 64 Cores und 2 TB Hauptspeicher. Diese Angebote richten sich insbesondere an Wissenschaftler in den Gebieten Informatik und Wirtschaftsinformatik. Einige der Schwerpunkte sind Cloud Computing, Parallelisierung und In-Memory Technologien. In diesem Technischen Bericht werden die Ergebnisse der Forschungsprojekte des Jahres 2015 vorgestellt. Ausgew{\"a}hlte Projekte stellten ihre Ergebnisse am 15. April 2015 und 4. November 2015 im Rahmen der Future SOC Lab Tag Veranstaltungen vor.},
  language  = {en}
}