Large-Scale Modeling of the Extracellular Matrix on Hybrid Supercomputers Using Highly Parallel Stencil Computations.

Alexander Schug Julian Herold Paul Brinkmeier Markus Götz Alexander Schug Achim Streit Large-Scale Modeling of the Extracellular Matrix on Hybrid Supercomputers Using Highly Parallel Stencil Computations. 1-14 2025 ISC https://ieeexplore.ieee.org/document/11017726 conf/supercomputer/2025 db/conf/supercomputer/isc2025.html#HeroldBGSS25

Fabrizio Pucci Mehari B. Zerihun Marianne Rooman Alexander Schug pycofitness - Evaluating the fitness landscape of RNA and protein sequences. 2024 February 40 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btae074 db/journals/bioinformatics/bioinformatics40.html#PucciZRS24

Julian Herold Eric Behle Jakob Rosenbauer Jacopo Ferruzzi Alexander Schug Development of a scoring function for comparing simulated and experimental tumor spheroids. 2023 March 19 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1010471 db/journals/ploscb/ploscb19.html#HeroldBRFS23

Oskar Taubert Marie Weiel Daniel Coquelin Anis Farshian Charlotte Debus Alexander Schug Achim Streit Markus Götz Massively Parallel Genetic Optimization Through Asynchronous Propagation of Populations. 106-124 2023 ISC https://doi.org/10.1007/978-3-031-32041-5_6 conf/supercomputer/2023 db/conf/supercomputer/isc2023.html#TaubertWCFDSSG23

Oskar Taubert Marie Weiel Daniel Coquelin Anis Farshian Charlotte Debus Alexander Schug Achim Streit Markus Götz Massively Parallel Genetic Optimization through Asynchronous Propagation of Populations. 2023 abs/2301.08713 CoRR https://doi.org/10.48550/arXiv.2301.08713 db/journals/corr/corr2301.html#abs-2301-08713

Arthur Voronin Alexander Schug pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics. 3325 2021 6 J. Open Source Softw. 68 https://doi.org/10.21105/joss.03325 https://www.wikidata.org/entity/Q113227654 db/journals/jossw/jossw6.html#VoroninS21

Marie Weiel Markus Götz André Klein Daniel Coquelin Ralf Floca Alexander Schug Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions. 727-734 2021 3 Nat. Mach. Intell. 8 https://doi.org/10.1038/s42256-021-00366-3 db/journals/natmi/natmi3.html#WeielGKCFS21

Ines Reinartz Mona Sarter Julia Otten Henning Höfig Martina Pohl Alexander Schug Andreas M. Stadler Jörg Fitter Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations. 4144 2021 21 Sensors 12 https://doi.org/10.3390/s21124144 db/journals/sensors/sensors21.html#ReinartzSOHPSSF21

Stefan Kesselheim Andreas Herten Kai Krajsek Jan Ebert Jenia Jitsev Mehdi Cherti Michael Langguth Bing Gong Scarlet Stadtler Amirpasha Mozaffari Gabriele Cavallaro Rocco Sedona Alexander Schug Alexandre Strube Roshni Kamath Martin G. Schultz Morris Riedel Thomas Lippert JUWELS Booster - A Supercomputer for Large-Scale AI Research. 453-468 2021 ISC Workshops https://doi.org/10.1007/978-3-030-90539-2_31 conf/supercomputer/2021w db/conf/supercomputer/isc2021w.html#KesselheimHKEJC21

Stefan Kesselheim Andreas Herten Kai Krajsek Jan Ebert Jenia Jitsev Mehdi Cherti Michael Langguth Bing Gong Scarlet Stadtler Amirpasha Mozaffari Gabriele Cavallaro Rocco Sedona Alexander Schug Alexandre Strube Roshni Kamath Martin G. Schultz Morris Riedel Thomas Lippert JUWELS Booster - A Supercomputer for Large-Scale AI Research. 2021 abs/2108.11976 CoRR https://arxiv.org/abs/2108.11976 db/journals/corr/corr2108.html#abs-2108-11976

Mehari B. Zerihun Fabrizio Pucci Emanuel K. Peter Alexander Schug pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences. 2264-2265 2020 36 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btz892 https://www.wikidata.org/entity/Q91505340 db/journals/bioinformatics/bioinformatics36.html#ZerihunPPS20

Marco Berghoff Jakob Rosenbauer Felix Hoffmann Alexander Schug Cells in Silico - introducing a high-performance framework for large-scale tissue modeling. 436 2020 21 BMC Bioinform. 1 https://doi.org/10.1186/s12859-020-03728-7 https://www.wikidata.org/entity/Q100461711 db/journals/bmcbi/bmcbi21.html#BerghoffRHS20

Jakob Rosenbauer Chengting Zhang Benjamin Mattes Ines Reinartz Kyle Wedgwood Simone Schindler Claude Sinner Steffen Scholpp Alexander Schug Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis. 2020 16 PLoS Comput. Biol. 6 https://doi.org/10.1371/journal.pcbi.1007417 https://www.wikidata.org/entity/Q96648764 db/journals/ploscb/ploscb16.html#RosenbauerZMRWS20

Oskar Taubert Markus Götz Alexander Schug Achim Streit Loss Scheduling for Class-Imbalanced Image Segmentation Problems. 426-431 2020 ICMLA https://doi.org/10.1109/ICMLA51294.2020.00073 conf/icmla/2020 db/conf/icmla/icmla2020.html#TaubertGSS20

Oskar Taubert Ines Reinartz Henning Meyerhenke Alexander Schug diSTruct v1.0: generating biomolecular structures from distance constraints. 5337-5338 2019 35 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btz578 https://www.wikidata.org/entity/Q92069672 db/journals/bioinformatics/bioinformatics35.html#TaubertRMS19

Semih Turk Alexander Schug Reinhard Viga Andreas Jupe Holger Vogt Optimization of the dielectric layer for electrowetting on dielectric. 50-59 2019 67 Integr. https://doi.org/10.1016/j.vlsi.2019.03.004 db/journals/integration/integration67.html#TurkSVJV19

Marie Weiel Ines Reinartz Alexander Schug Rapid interpretation of small-angle X-ray scattering data. 2019 15 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1006900 https://www.wikidata.org/entity/Q64063412 db/journals/ploscb/ploscb15.html#WeielRS19

Michael Wegner Oskar Taubert Alexander Schug Henning Meyerhenke Maxent-Stress Optimization of 3D Biomolecular Models. 70:1-70:15 2017 ESA https://doi.org/10.4230/LIPIcs.ESA.2017.70 conf/esa/2017 db/conf/esa/esa2017.html#WegnerTSM17

Michael Wegner Oskar Taubert Alexander Schug Henning Meyerhenke Maxent-Stress Optimization of 3D Biomolecular Models. 2017 abs/1706.06805 CoRR http://arxiv.org/abs/1706.06805 db/journals/corr/corr1706.html#WegnerTSM17

Benjamin Lutz Claude Sinner Stefan Bozic Ivan Kondov Alexander Schug Native structure-based modeling and simulation of biomolecular systems per mouse click. 292 2014 15 BMC Bioinform. https://doi.org/10.1186/1471-2105-15-292 https://www.wikidata.org/entity/Q30586906 db/journals/bmcbi/bmcbi15.html#LutzSBKS14

Stefan Bozic Jens Krüger 0002 Claude Sinner Benjamin Lutz Alexander Schug Ivan Kondov Integration of eSBMTools into the MoSGrid Portal Using the gUSE Technology. 85-90 2014 IWSG https://doi.org/10.1109/IWSG.2014.21 https://doi.ieeecomputersociety.org/10.1109/IWSG.2014.21 conf/iwsg/2014 db/conf/iwsg/iwsg2014.html#Bozic0SLSK14

Benjamin Lutz Claude Sinner Geertje Heuermann Abhinav Verma Alexander Schug eSBMTools 1.0: enhanced native structure-based modeling tools. 2795-2796 2013 29 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btt478 https://www.wikidata.org/entity/Q42617522 db/journals/bioinformatics/bioinformatics29.html#LutzSHVS13

Abhinav Verma Srinivasa M. Gopal Alexander Schug Jung S. Oh Konstantin V. Klenin Kyu H. Lee Wolfgang Wenzel Massively Parallel All Atom Protein Folding in a Single Day. 527-534 2007 PARCO conf/parco/2007 db/conf/parco/parco2007.html#VermaGSOKLW07 Thomas Herges Alexander Schug Wolfgang Wenzel Protein Structure Prediction with Stochastic Optimization Methods: Folding and Misfolding the Villin Headpiece. 454-464 https://doi.org/10.1007/978-3-540-24767-8_47 2004 conf/iccsa/2004-3 ICCSA (3) db/conf/iccsa/iccsa2004-3.html#HergesSW04 Eric Behle Marco Berghoff Stefan Bozic Paul Brinkmeier Gabriele Cavallaro Mehdi Cherti Daniel Coquelin Charlotte Debus Jan Ebert Anis Farshian Jacopo Ferruzzi Jörg Fitter Ralf Floca Bing Gong Srinivasa M. Gopal Markus Götz Thomas Herges Julian Herold Andreas Herten Geertje Heuermann Felix Hoffmann Henning Höfig Jenia Jitsev Andreas Jupe Roshni Kamath Stefan Kesselheim André Klein Konstantin V. Klenin Ivan Kondov Kai Krajsek Jens Krüger 0002 Michael Langguth Kyu H. Lee Thomas Lippert Benjamin Lutz Benjamin Mattes Henning Meyerhenke Amirpasha Mozaffari Jung S. Oh Julia Otten Emanuel K. Peter Martina Pohl Fabrizio Pucci Ines Reinartz Morris Riedel Marianne Rooman Jakob Rosenbauer Mona Sarter Simone Schindler Steffen Scholpp Martin G. Schultz Rocco Sedona Claude Sinner Andreas M. Stadler Scarlet Stadtler Achim Streit Alexandre Strube Oskar Taubert Semih Turk Abhinav Verma Reinhard Viga Holger Vogt Arthur Voronin Kyle Wedgwood Michael Wegner Marie Weiel Wolfgang Wenzel Mehari B. Zerihun Chengting Zhang