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Andreas Dräger
Dräger at the International Conference on Systems Biology (ICSB) in Okinawa 2019
Born (1980-09-20) 20 September 1980 (age 43)
Wippra, East Germany
Alma mater
Known for Mathematical modelling of infectious disease, JSBML
Scientific career
Fields
Institutions
Thesis Computational Modeling of Biochemical Networks (2011)
Doctoral advisor Andreas Zell
Other academic advisors
Website uni-tuebingen.de/en/127116

Andreas Dräger (German: [anˈdʁeːas ˈdʁɛːɡɐ]; born 20 September 1980) is a German bioinformatician who leads the research group for Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens at the University of Tübingen.

Education

In high school, Dräger was fascinated by computer science and recent advancements in genetics and biotechnology in the late 1990s. When he learned about a new degree program that allowed combining those technologies, he was immediately inspired. So, Dräger studied bioinformatics at the Martin Luther University of Halle-Wittenberg in Halle (Saale) from 2000 to 2006. He worked as an intern for genome sequencing at the Max Planck Institute for Molecular Genetics, Berlin. He prepared his thesis about heavy-metal-resistant bacteria at the microbiology department of the University of Illinois at Chicago. Dräger earned his doctorate at the Center for Bioinformatics in Tübingen (ZBIT), focusing on the dynamic simulation of metabolic networks in a virtual liver. During this time, he worked as a visiting research student for software engineering at Keio University in Yokohama in 2010. After returning from Japan, the Faculty of Science of the University of Tübingen honored his thesis with the 2011 dissertation award. [a]

Career

In early 2011, Dräger received funding for an independent research project as a postdoctoral junior group leader. In 2013, he undertook another two-year postdoc program as a Marie-Curie research scholar in La Jolla. He worked in the Systems Biology Research Group at the UCSD (the University of California, San Diego). Dräger returned to Tübingen in 2015, where he founded an independent research group at the university. In 2018 he was appointed as junior professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens within Tübingen's newly established interfaculty Institute for Bioinformatics and Medical Informatics (IBMI). His research group belongs to the German National Center for Infection Research (DZIF) and Tübingen's Cluster of Excellence, "Controlling Microbes to Fight Infections" (CMFI).

Research

Andreas Dräger's research focuses on mathematical models of the metabolic mechanisms behind antibiotic resistance. The central aspect of his research group is the human microbiome living within the airways from the nasal cavities to the lung. Dräger aims to identify new ways to combat life-threatening bacterial [1] [2] and viral infections. [3] [4] Hospital-acquired infections of the respiratory tract have the highest priority of the effort because this often involves germs with multi-resistance against antibiotic treatment. Particularly harmful bacteria in this habitat include Pseudomonas aeruginosa [5] [2] and Staphylococcus aureus. [1] Another research area involves risk groups, such as cystic fibrosis patients. Applying metabolic network modeling for this endeavor requires a comprehensive understanding of the underlying processes of mutual interactions between pathogens, commensal bacteria, and their host. [6] [7]

This work also requires developing specialized software to create, analyze, and share computer models in systems biology in general. For this reason, the group is also actively involved in several standardization efforts in systems biology [8] that are part of the initiatives by the Computational Modeling in Biology Network of international researchers. Dräger sees improved interoperability and reuse of the developed computer models according to the principles of FAIR data (findable, accessible, interoperable, and reusable) as a prerequisite for the reliable implementation of computer simulation in biology. [9] To this end, Dräger and his group develop scientific open-source software, such as JSBML or SBSCL. [10] In 2015, the scientific community elected him as an editor for developing the systems biology file format SBML and in 2018 as an editor for the graphical modeling language SBGN. [11] In 2016, Dräger was one of the founders of the annual community meeting with a special interest in systems modeling ( SysMod) [12] within the International Society of Computational Biology (ISCB), where he served as the de facto chairman from 2018 until he stepped down in 2022. [13]

During the COVID-19 pandemic, Dräger's work regarding computational modeling of SARS-CoV-2 within human cells [14] [15] raised international interest [b] [c] [d] [e] [f] [g] [h] because it predicted potentially exploitable targets for drug development. One of those is the human enzyme guanylate kinase. Dräger's ongoing work on this topic focuses on pandemic preparedness. [16]

Commitment and Volunteering

For over three years, he offered a course in bioinformatics and systems biology for high school students at the "Otto-Hahn" high school in Nagold, including mentorship in the Youth Researches competition. [i]

External links

Appearances in news and public media (selection)

  1. ^ "Zentrale Promotionsfeier der Universität Tübingen" [Central graduation ceremony of the University of Tübingen]. Newsletter Uni Tübingen aktuell Nr. 4/2011: Termine und Veranstaltungen (in German). University of Tübingen. 2011-07-16.
  2. ^ Wittig, Frank (2021-03-18). "Wo bleiben die Medikamente?" [Where are the drugs?]. odysso – Wissen im SWR (in German). SWR Fernsehen.
  3. ^ Augustin, Birgit (2021-02-03). "Corona: Wie wirksam sind neue Medikamente gegen das Virus?" [Corona: How effective are new drugs against the virus?]. Visite (in German). Norddeutscher Rundfunk.
  4. ^ Petrunova, Tsvetelina (2021-01-17). "Ексклузивно: Първа стъпка към откриването лекарство срещу COVID-19" [Exclusive: First step towards discovering a drug against COVID-19]. Тази неделя (in Bulgarian). bTV (Bulgaria).
  5. ^ Beremliyski, Nikolay (2021-01-17). "СЛАБОТО МЯСТО НА COVID-19: Близо ли сме до победата над заразата?" [THE COVID-19 WEAKNESS POINT: Are we close to beating the plague?]. неделята (in Bulgarian). Nova (Bulgarian TV channel).
  6. ^ "Ученые РФ и ФРГ нашли способы уничтожать COVID-19" [Scientists from Russia and Germany have found ways to destroy COVID-19]. Смотрим (in Russian). Russia-24. 2021-11-01.
  7. ^ Hannemann, Cornelia (2021-01-10). "Entdeckung könnte Weg zu Corona-Medikament ebnen" [Discovery could pave way to Corona drug]. Wissen (in German). n-tv.
  8. ^ Priese, Anna (2021-01-09). "Neuer Ansatz für Corona-Therapie an Tübinger Uni" [New approach for corona therapy at Tübingen University]. SWR Aktuell (in German). SWR Fernsehen.
  9. ^ "Mit Stolz präsentieren sie erste Ergebnisse" [They proudly present their first results]. Schwarzwälder Bote (in German). Schwarzwälder Bote Mediengesellschaft mbH. 2021-07-21.

References

  1. ^ a b Renz, Alina; Dräger, Andreas (2021). "Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus". npj Systems Biology and Applications. 7 (1): 30. doi: 10.1038/s41540-021-00188-4. PMC  8241996. PMID  34188046. S2CID  233598683.
  2. ^ a b Payne, Dawson D.; Renz, Alina; Dunphy, Laura J.; Lewis, Taylor; Dräger, Andreas; Papin, Jason A. (2021). "An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism" (PDF). npj Systems Biology and Applications. 7 (1): 37. doi: 10.1038/s41540-021-00198-2. PMC  8501023. PMID  34625561. S2CID  232224404.
  3. ^ Bernardes, Joana P.; Mishra, Neha; Tran, Florian; Bahmer, Thomas; Best, Lena; Blase, Johanna I.; Bordoni, Dora; Franzenburg, Jeanette; Geisen, Ulf; Josephs-Spaulding, Jonathan; Köhler, Philipp; Künstner, Axel; Rosati, Elisa; Aschenbrenner, Anna C.; Bacher, Petra; Baran, Nathan; Boysen, Teide; Brandt, Burkhard; Bruse, Niklas; Dörr, Jonathan; Dräger, Andreas; Elke, Gunnar; Ellinghaus, David; Fischer, Julia; Forster, Michael; Franke, Andre; Franzenburg, Sören; Frey, Norbert; Friedrichs, Anette; Fuß, Janina; Glück, Andreas; Hamm, Jacob; Hinrichsen, Finn; Hoeppner, Marc P.; Imm, Simon; Juenker, Ralf; Kaiser, Sina; Kan, Ying H.; Knoll, Rainer; Lange, Christoph; Laue, Georg; Lier, Clemes; Lindner, Matthias; Marinos, Georgios; Markewitz, Robert; Nattermann, Jacob; Noth, Rainer; Pickkers, Peter; Rabe, Klaus F.; Renz, Alina; Roecken, Christoph; Rupp, Jan; Schaffarzyk, Annika; Scheffold, Alexander; Schulte-Schrepping, Jonas; Schunck, Domagoj; Skowasch, Dirk; Ulas, Thomas; Wandinger, Klaus-Peter; Wittig, Michael; Zimmermann, Johannes; Busch, Hauke; Hoyer, Bimba F.; Kaleta, Christoph; Heyckendorf, Jan; Kox, Matthijs; Rybniker, Jan; Schreiber, Stefan; Schultze, Joachim; Rosenstiel, Philip; Banovich, Nicholas E.; Desai, Tushar; Eickelberg, Oliver; Haniffa, Muzlifa; Horvath, Peter; Kropski, Jonathan A.; Lafyatis, Robert; Lundeberg, Joakim; Meyer, Kerstin; Nawijn, Martijn C.; Nikolic, Marko; Ordovas Montanes, Jose; Pe'er, Dana; Tata, Purushothama Rao; Rawlins, Emma; Regev, Aviv; Reyfman, Paul; Samakovlis, Christos; Schultze, Joachim; Shalek, Alex; Shepherd, Douglas; Spence, Jason; Teichmann, Sarah; Theis, Fabian; Tsankov, Alexander; van den Berge, Maarten; von Papen, Michael; Whitsett, Jeffrey; Zaragosi, Laure Emmanuelle; Angelov, Angel; Bals, Robert; Bartholomäus, Alexander; Becker, Anke; Bezdan, Daniela; Bonifacio, Ezio; Bork, Peer; Clavel, Thomas; Colme-Tatche, Maria; Diefenbach, Andreas; Dilthey, Alexander; Fischer, Nicole; Förstner, Konrad; Frick, Julia Stefanie; Gagneur, Julien; Goesmann, Alexander; Hain, Torsten; Hummel, Michael; Janssen, Stefan; Kalinowski, Jörn; Kallies, René; Kehr, Birte; Keller, Andreas; Kim-Hellmuth, Sarah; Klein, Christoph; Kohlbacher, Oliver; Korbel, Jan O.; Kurth, Ingo; Landthaler, Markus; Li, Yang; Ludwig, Kerstin; Makarewicz, Oliwia; Marz, Manja; McHardy, Alice; Mertes, Christian; Nöthen, Markus; Nürnberg, Peter; Ohler, Uwe; Ossowski, Stephan; Overmann, Jörg; Peter, Silke; Pfeffer, Klaus; Poetsch, Anna R.; Pühler, Alfred; Rajewsky, Niklaus; Ralser, Markus; Rieß, Olaf; Ripke, Stephan; Nunes da Rocha, Ulisses; Saliba, Antoine Emmanuel; Sander, Leif Erik; Sawitzki, Birgit; Schiffer, Philipp; Schulte, Eva Christina; Sczyrba, Alexander; Stegle, Oliver; Stoye, Jens; Vehreschild, Janne; Vogel, Jörg; Kleist, Max von; Walker, Andreas; Walter, Jörn; Wieczorek, Dagmar; Ziebuhr, John (2020). "Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories". Immunity. 53 (6): 1296–1314.e9. doi: 10.1016/j.immuni.2020.11.017. ISSN  1074-7613. PMC  7689306. PMID  33296687. S2CID  227163641.
  4. ^ Ostaszewski, Marek; et al. (2021). "COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms". Molecular Systems Biology. 17 (10): e10387. doi: 10.15252/msb.202110387. PMC  8524328. PMID  34664389. S2CID  239027089.
  5. ^ Dahal, Sanjeev; Renz, Alina; Dräger, Andreas; Yang, Laurence (2023). "Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation" (PDF). Communications Biology. 6 (1): 165. doi: 10.1038/s42003-023-04540-8. PMC  9918512. PMID  36765199. S2CID  256702200.
  6. ^ Renz, Alina; Widerspick, Lina; Dräger, Andreas (2021). "First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies". Metabolites. 11 (4): 232. doi: 10.3390/metabo11040232. PMC  8069353. PMID  33918864. S2CID  233395707.
  7. ^ Brunk, Elizabeth; Sahoo, Swagatika; Zielinski, Daniel C.; Altunkaya, Ali; Dräger, Andreas; Mih, Nathan; Gatto, Francesco; Nilsson, Avlant; Preciat Gonzalez, German Andres; Aurich, Maike Kathrin; Prlić, Andreas; Sastry, Anand; Danielsdóttir, Anna D.; Heinken, Almut; Noronha, Alberto; Rose, Peter W.; Burley, Stephen K.; Fleming, Ronan M. T.; Nielsen, Jens; Thiele, Ines; Palsson, Bernhard O. (2018). "Recon3D enables a three-dimensional view of gene variation in human metabolism". Nature Biotechnology. 36 (3): 272–281. doi: 10.1038/nbt.4072. PMC  5840010. PMID  29457794. S2CID  210902494.
  8. ^ Dräger, Andreas; Waltemath, Dagmar (2021). "Overview: Standards for Modeling in Systems Medicine". Systems Medicine. pp. 345–353. doi: 10.1016/B978-0-12-816077-0.00001-7. ISBN  978-0-12-816078-7. S2CID  224975951.
  9. ^ Dräger, Andreas (2014). "Improving collaboration by standardization efforts in systems biology". Frontiers in Bioengineering and Biotechnology. 2 (61): 61. doi: 10.3389/fbioe.2014.00061. PMC  4259112. PMID  25538939. S2CID  16722945.
  10. ^ Panchiwala, Hemil; Shah, Shalin; Planatscher, Hannes; Zakharchuk, Mykola; König, Matthias; Dräger, Andreas (2022). "The Systems Biology Simulation Core Library". Bioinformatics. 38 (3): 864–865. doi: 10.1093/bioinformatics/btab669. PMC  8756180. PMID  34554191. S2CID  230546045.
  11. ^ Touré, Vasundra; Dräger, Andreas; Luna, Augustin; Dogrusoz, Ugur; Rougny, Adrien (2021). "The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine". Systems Medicine. pp. 372–381. doi: 10.1016/B978-0-12-801238-3.11515-6. ISBN  978-0-12-816078-7. S2CID  213385953.
  12. ^ Dräger, Andreas; Helikar, Tomáš; Barberis, Matteo; Birtwistle, Marc; Calzone, Laurence; Chaouiya, Claudine; Hasenauer, Jan; Karr, Jonathan R.; Niarakis, Anna; Rodríguez Martínez, María; Saez-Rodriguez, Julio; Thakar, Juilee (2021). "SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems" (PDF). Bioinformatics. 37 (21): 3702–3706. doi: 10.1093/bioinformatics/btab229. PMC  8570808. PMID  34179955. S2CID  234620344.
  13. ^ Niarakis, Anna; Thakar, Juilee; Barberis, Matteo; Rodríguez Martínez, María; Helikar, Tomáš; Birtwistle, Marc; Chaouiya, Claudine; Calzone, Laurence; Dräger, Andreas (2022). "Computational modelling in health and disease. Highlights of the 6th annual SysMod meeting" (PDF). Bioinformatics. 38 (21): 4990–4993. doi: 10.1093/bioinformatics/btac609.
  14. ^ Renz, Alina; Widerspick, Lina; Dräger, Andreas (2020). "FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2" (PDF). Bioinformatics. 36 (Suppl 2): i813–i821. doi: 10.1093/bioinformatics/btaa813. PMC  7773487. PMID  33381848. S2CID  229929774.
  15. ^ Renz, Alina; Widerspick, Lina; Dräger, Andreas (2021). "Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target". Genes. 12 (6): 796. doi: 10.3390/genes12060796. PMC  8225150. PMID  34073716. S2CID  235300463.
  16. ^ Leonidou, Nantia; Renz, Alina; Mostolizadeh, Reihaneh; Dräger, Andreas (2023). "New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells". PLOS Computational Biology. 19 (3): e1010903. doi: 10.1371/journal.pcbi.1010903. PMC  10035753. PMID  36952396. S2CID  257715107.
Retrieved from " https://en.wikipedia.org/?title=Andreas_Dräger&oldid=1192190018"
From Wikipedia, the free encyclopedia
Andreas Dräger
Dräger at the International Conference on Systems Biology (ICSB) in Okinawa 2019
Born (1980-09-20) 20 September 1980 (age 43)
Wippra, East Germany
Alma mater
Known for Mathematical modelling of infectious disease, JSBML
Scientific career
Fields
Institutions
Thesis Computational Modeling of Biochemical Networks (2011)
Doctoral advisor Andreas Zell
Other academic advisors
Website uni-tuebingen.de/en/127116

Andreas Dräger (German: [anˈdʁeːas ˈdʁɛːɡɐ]; born 20 September 1980) is a German bioinformatician who leads the research group for Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens at the University of Tübingen.

Education

In high school, Dräger was fascinated by computer science and recent advancements in genetics and biotechnology in the late 1990s. When he learned about a new degree program that allowed combining those technologies, he was immediately inspired. So, Dräger studied bioinformatics at the Martin Luther University of Halle-Wittenberg in Halle (Saale) from 2000 to 2006. He worked as an intern for genome sequencing at the Max Planck Institute for Molecular Genetics, Berlin. He prepared his thesis about heavy-metal-resistant bacteria at the microbiology department of the University of Illinois at Chicago. Dräger earned his doctorate at the Center for Bioinformatics in Tübingen (ZBIT), focusing on the dynamic simulation of metabolic networks in a virtual liver. During this time, he worked as a visiting research student for software engineering at Keio University in Yokohama in 2010. After returning from Japan, the Faculty of Science of the University of Tübingen honored his thesis with the 2011 dissertation award. [a]

Career

In early 2011, Dräger received funding for an independent research project as a postdoctoral junior group leader. In 2013, he undertook another two-year postdoc program as a Marie-Curie research scholar in La Jolla. He worked in the Systems Biology Research Group at the UCSD (the University of California, San Diego). Dräger returned to Tübingen in 2015, where he founded an independent research group at the university. In 2018 he was appointed as junior professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens within Tübingen's newly established interfaculty Institute for Bioinformatics and Medical Informatics (IBMI). His research group belongs to the German National Center for Infection Research (DZIF) and Tübingen's Cluster of Excellence, "Controlling Microbes to Fight Infections" (CMFI).

Research

Andreas Dräger's research focuses on mathematical models of the metabolic mechanisms behind antibiotic resistance. The central aspect of his research group is the human microbiome living within the airways from the nasal cavities to the lung. Dräger aims to identify new ways to combat life-threatening bacterial [1] [2] and viral infections. [3] [4] Hospital-acquired infections of the respiratory tract have the highest priority of the effort because this often involves germs with multi-resistance against antibiotic treatment. Particularly harmful bacteria in this habitat include Pseudomonas aeruginosa [5] [2] and Staphylococcus aureus. [1] Another research area involves risk groups, such as cystic fibrosis patients. Applying metabolic network modeling for this endeavor requires a comprehensive understanding of the underlying processes of mutual interactions between pathogens, commensal bacteria, and their host. [6] [7]

This work also requires developing specialized software to create, analyze, and share computer models in systems biology in general. For this reason, the group is also actively involved in several standardization efforts in systems biology [8] that are part of the initiatives by the Computational Modeling in Biology Network of international researchers. Dräger sees improved interoperability and reuse of the developed computer models according to the principles of FAIR data (findable, accessible, interoperable, and reusable) as a prerequisite for the reliable implementation of computer simulation in biology. [9] To this end, Dräger and his group develop scientific open-source software, such as JSBML or SBSCL. [10] In 2015, the scientific community elected him as an editor for developing the systems biology file format SBML and in 2018 as an editor for the graphical modeling language SBGN. [11] In 2016, Dräger was one of the founders of the annual community meeting with a special interest in systems modeling ( SysMod) [12] within the International Society of Computational Biology (ISCB), where he served as the de facto chairman from 2018 until he stepped down in 2022. [13]

During the COVID-19 pandemic, Dräger's work regarding computational modeling of SARS-CoV-2 within human cells [14] [15] raised international interest [b] [c] [d] [e] [f] [g] [h] because it predicted potentially exploitable targets for drug development. One of those is the human enzyme guanylate kinase. Dräger's ongoing work on this topic focuses on pandemic preparedness. [16]

Commitment and Volunteering

For over three years, he offered a course in bioinformatics and systems biology for high school students at the "Otto-Hahn" high school in Nagold, including mentorship in the Youth Researches competition. [i]

External links

Appearances in news and public media (selection)

  1. ^ "Zentrale Promotionsfeier der Universität Tübingen" [Central graduation ceremony of the University of Tübingen]. Newsletter Uni Tübingen aktuell Nr. 4/2011: Termine und Veranstaltungen (in German). University of Tübingen. 2011-07-16.
  2. ^ Wittig, Frank (2021-03-18). "Wo bleiben die Medikamente?" [Where are the drugs?]. odysso – Wissen im SWR (in German). SWR Fernsehen.
  3. ^ Augustin, Birgit (2021-02-03). "Corona: Wie wirksam sind neue Medikamente gegen das Virus?" [Corona: How effective are new drugs against the virus?]. Visite (in German). Norddeutscher Rundfunk.
  4. ^ Petrunova, Tsvetelina (2021-01-17). "Ексклузивно: Първа стъпка към откриването лекарство срещу COVID-19" [Exclusive: First step towards discovering a drug against COVID-19]. Тази неделя (in Bulgarian). bTV (Bulgaria).
  5. ^ Beremliyski, Nikolay (2021-01-17). "СЛАБОТО МЯСТО НА COVID-19: Близо ли сме до победата над заразата?" [THE COVID-19 WEAKNESS POINT: Are we close to beating the plague?]. неделята (in Bulgarian). Nova (Bulgarian TV channel).
  6. ^ "Ученые РФ и ФРГ нашли способы уничтожать COVID-19" [Scientists from Russia and Germany have found ways to destroy COVID-19]. Смотрим (in Russian). Russia-24. 2021-11-01.
  7. ^ Hannemann, Cornelia (2021-01-10). "Entdeckung könnte Weg zu Corona-Medikament ebnen" [Discovery could pave way to Corona drug]. Wissen (in German). n-tv.
  8. ^ Priese, Anna (2021-01-09). "Neuer Ansatz für Corona-Therapie an Tübinger Uni" [New approach for corona therapy at Tübingen University]. SWR Aktuell (in German). SWR Fernsehen.
  9. ^ "Mit Stolz präsentieren sie erste Ergebnisse" [They proudly present their first results]. Schwarzwälder Bote (in German). Schwarzwälder Bote Mediengesellschaft mbH. 2021-07-21.

References

  1. ^ a b Renz, Alina; Dräger, Andreas (2021). "Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus". npj Systems Biology and Applications. 7 (1): 30. doi: 10.1038/s41540-021-00188-4. PMC  8241996. PMID  34188046. S2CID  233598683.
  2. ^ a b Payne, Dawson D.; Renz, Alina; Dunphy, Laura J.; Lewis, Taylor; Dräger, Andreas; Papin, Jason A. (2021). "An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism" (PDF). npj Systems Biology and Applications. 7 (1): 37. doi: 10.1038/s41540-021-00198-2. PMC  8501023. PMID  34625561. S2CID  232224404.
  3. ^ Bernardes, Joana P.; Mishra, Neha; Tran, Florian; Bahmer, Thomas; Best, Lena; Blase, Johanna I.; Bordoni, Dora; Franzenburg, Jeanette; Geisen, Ulf; Josephs-Spaulding, Jonathan; Köhler, Philipp; Künstner, Axel; Rosati, Elisa; Aschenbrenner, Anna C.; Bacher, Petra; Baran, Nathan; Boysen, Teide; Brandt, Burkhard; Bruse, Niklas; Dörr, Jonathan; Dräger, Andreas; Elke, Gunnar; Ellinghaus, David; Fischer, Julia; Forster, Michael; Franke, Andre; Franzenburg, Sören; Frey, Norbert; Friedrichs, Anette; Fuß, Janina; Glück, Andreas; Hamm, Jacob; Hinrichsen, Finn; Hoeppner, Marc P.; Imm, Simon; Juenker, Ralf; Kaiser, Sina; Kan, Ying H.; Knoll, Rainer; Lange, Christoph; Laue, Georg; Lier, Clemes; Lindner, Matthias; Marinos, Georgios; Markewitz, Robert; Nattermann, Jacob; Noth, Rainer; Pickkers, Peter; Rabe, Klaus F.; Renz, Alina; Roecken, Christoph; Rupp, Jan; Schaffarzyk, Annika; Scheffold, Alexander; Schulte-Schrepping, Jonas; Schunck, Domagoj; Skowasch, Dirk; Ulas, Thomas; Wandinger, Klaus-Peter; Wittig, Michael; Zimmermann, Johannes; Busch, Hauke; Hoyer, Bimba F.; Kaleta, Christoph; Heyckendorf, Jan; Kox, Matthijs; Rybniker, Jan; Schreiber, Stefan; Schultze, Joachim; Rosenstiel, Philip; Banovich, Nicholas E.; Desai, Tushar; Eickelberg, Oliver; Haniffa, Muzlifa; Horvath, Peter; Kropski, Jonathan A.; Lafyatis, Robert; Lundeberg, Joakim; Meyer, Kerstin; Nawijn, Martijn C.; Nikolic, Marko; Ordovas Montanes, Jose; Pe'er, Dana; Tata, Purushothama Rao; Rawlins, Emma; Regev, Aviv; Reyfman, Paul; Samakovlis, Christos; Schultze, Joachim; Shalek, Alex; Shepherd, Douglas; Spence, Jason; Teichmann, Sarah; Theis, Fabian; Tsankov, Alexander; van den Berge, Maarten; von Papen, Michael; Whitsett, Jeffrey; Zaragosi, Laure Emmanuelle; Angelov, Angel; Bals, Robert; Bartholomäus, Alexander; Becker, Anke; Bezdan, Daniela; Bonifacio, Ezio; Bork, Peer; Clavel, Thomas; Colme-Tatche, Maria; Diefenbach, Andreas; Dilthey, Alexander; Fischer, Nicole; Förstner, Konrad; Frick, Julia Stefanie; Gagneur, Julien; Goesmann, Alexander; Hain, Torsten; Hummel, Michael; Janssen, Stefan; Kalinowski, Jörn; Kallies, René; Kehr, Birte; Keller, Andreas; Kim-Hellmuth, Sarah; Klein, Christoph; Kohlbacher, Oliver; Korbel, Jan O.; Kurth, Ingo; Landthaler, Markus; Li, Yang; Ludwig, Kerstin; Makarewicz, Oliwia; Marz, Manja; McHardy, Alice; Mertes, Christian; Nöthen, Markus; Nürnberg, Peter; Ohler, Uwe; Ossowski, Stephan; Overmann, Jörg; Peter, Silke; Pfeffer, Klaus; Poetsch, Anna R.; Pühler, Alfred; Rajewsky, Niklaus; Ralser, Markus; Rieß, Olaf; Ripke, Stephan; Nunes da Rocha, Ulisses; Saliba, Antoine Emmanuel; Sander, Leif Erik; Sawitzki, Birgit; Schiffer, Philipp; Schulte, Eva Christina; Sczyrba, Alexander; Stegle, Oliver; Stoye, Jens; Vehreschild, Janne; Vogel, Jörg; Kleist, Max von; Walker, Andreas; Walter, Jörn; Wieczorek, Dagmar; Ziebuhr, John (2020). "Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories". Immunity. 53 (6): 1296–1314.e9. doi: 10.1016/j.immuni.2020.11.017. ISSN  1074-7613. PMC  7689306. PMID  33296687. S2CID  227163641.
  4. ^ Ostaszewski, Marek; et al. (2021). "COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms". Molecular Systems Biology. 17 (10): e10387. doi: 10.15252/msb.202110387. PMC  8524328. PMID  34664389. S2CID  239027089.
  5. ^ Dahal, Sanjeev; Renz, Alina; Dräger, Andreas; Yang, Laurence (2023). "Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation" (PDF). Communications Biology. 6 (1): 165. doi: 10.1038/s42003-023-04540-8. PMC  9918512. PMID  36765199. S2CID  256702200.
  6. ^ Renz, Alina; Widerspick, Lina; Dräger, Andreas (2021). "First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies". Metabolites. 11 (4): 232. doi: 10.3390/metabo11040232. PMC  8069353. PMID  33918864. S2CID  233395707.
  7. ^ Brunk, Elizabeth; Sahoo, Swagatika; Zielinski, Daniel C.; Altunkaya, Ali; Dräger, Andreas; Mih, Nathan; Gatto, Francesco; Nilsson, Avlant; Preciat Gonzalez, German Andres; Aurich, Maike Kathrin; Prlić, Andreas; Sastry, Anand; Danielsdóttir, Anna D.; Heinken, Almut; Noronha, Alberto; Rose, Peter W.; Burley, Stephen K.; Fleming, Ronan M. T.; Nielsen, Jens; Thiele, Ines; Palsson, Bernhard O. (2018). "Recon3D enables a three-dimensional view of gene variation in human metabolism". Nature Biotechnology. 36 (3): 272–281. doi: 10.1038/nbt.4072. PMC  5840010. PMID  29457794. S2CID  210902494.
  8. ^ Dräger, Andreas; Waltemath, Dagmar (2021). "Overview: Standards for Modeling in Systems Medicine". Systems Medicine. pp. 345–353. doi: 10.1016/B978-0-12-816077-0.00001-7. ISBN  978-0-12-816078-7. S2CID  224975951.
  9. ^ Dräger, Andreas (2014). "Improving collaboration by standardization efforts in systems biology". Frontiers in Bioengineering and Biotechnology. 2 (61): 61. doi: 10.3389/fbioe.2014.00061. PMC  4259112. PMID  25538939. S2CID  16722945.
  10. ^ Panchiwala, Hemil; Shah, Shalin; Planatscher, Hannes; Zakharchuk, Mykola; König, Matthias; Dräger, Andreas (2022). "The Systems Biology Simulation Core Library". Bioinformatics. 38 (3): 864–865. doi: 10.1093/bioinformatics/btab669. PMC  8756180. PMID  34554191. S2CID  230546045.
  11. ^ Touré, Vasundra; Dräger, Andreas; Luna, Augustin; Dogrusoz, Ugur; Rougny, Adrien (2021). "The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine". Systems Medicine. pp. 372–381. doi: 10.1016/B978-0-12-801238-3.11515-6. ISBN  978-0-12-816078-7. S2CID  213385953.
  12. ^ Dräger, Andreas; Helikar, Tomáš; Barberis, Matteo; Birtwistle, Marc; Calzone, Laurence; Chaouiya, Claudine; Hasenauer, Jan; Karr, Jonathan R.; Niarakis, Anna; Rodríguez Martínez, María; Saez-Rodriguez, Julio; Thakar, Juilee (2021). "SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems" (PDF). Bioinformatics. 37 (21): 3702–3706. doi: 10.1093/bioinformatics/btab229. PMC  8570808. PMID  34179955. S2CID  234620344.
  13. ^ Niarakis, Anna; Thakar, Juilee; Barberis, Matteo; Rodríguez Martínez, María; Helikar, Tomáš; Birtwistle, Marc; Chaouiya, Claudine; Calzone, Laurence; Dräger, Andreas (2022). "Computational modelling in health and disease. Highlights of the 6th annual SysMod meeting" (PDF). Bioinformatics. 38 (21): 4990–4993. doi: 10.1093/bioinformatics/btac609.
  14. ^ Renz, Alina; Widerspick, Lina; Dräger, Andreas (2020). "FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2" (PDF). Bioinformatics. 36 (Suppl 2): i813–i821. doi: 10.1093/bioinformatics/btaa813. PMC  7773487. PMID  33381848. S2CID  229929774.
  15. ^ Renz, Alina; Widerspick, Lina; Dräger, Andreas (2021). "Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target". Genes. 12 (6): 796. doi: 10.3390/genes12060796. PMC  8225150. PMID  34073716. S2CID  235300463.
  16. ^ Leonidou, Nantia; Renz, Alina; Mostolizadeh, Reihaneh; Dräger, Andreas (2023). "New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells". PLOS Computational Biology. 19 (3): e1010903. doi: 10.1371/journal.pcbi.1010903. PMC  10035753. PMID  36952396. S2CID  257715107.
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