publications.html

---
title: Publications
description: Selected preprints and peer-reviewed publications from the group.
---
<div class="publication-content">
    <h3 id="2024">2024</h3>
    <ul class="publication-list">
            <li>SynCoTrain: A Dual Classifier PU-learning Framework for Synthesizability Prediction.
                <br /> Authors: Sasan Amariamir, Janine George, Philipp Benner.
                arXiv preprint (2024). arXiv:2411.12011 <br /><br /></li>
            <li>A neural network approach to learning solutions of a class of elliptic variational inequalities.
                <br /> Authors: Amal Alphonse, Michael Hintermüller, Alexander Kister, Chin Hang Lun, Clemens Sirotenko.
                arXiv preprint (2024). arXiv:2411.18565 <br /><br /></li>
            <li>Fiora: Local neighborhood-based prediction of compound mass spectra from single fragmentation events.
                <br /> Authors: Yannek Nowatzky, Francesco Russo, Jan Lisec, Alexander Kister, Knut Reinert, Thilo Muth, Philipp Benner.
                bioRxiv (2024). DOI: https://doi.org/10.1101/2024.04.22.590551 <br /><br /></li>
            <li>Machine learning-assisted equivalent circuit identification for dielectric spectroscopy of polymers.
                <br /> Authors: Bashar Albakri, Analice Turski Silva Diniz, Philipp Benner, Thilo Muth, Shinichi Nakajima, Marco Favaro, Alexander Kister.  
                Electrochimica Acta (2024). DOI: https://doi.org/10.1016/j.electacta.2024.144474 <br /><br /></li>
            <li>Natural hazards in a changing world: Methods for analyzing trends and non-linear changes.
                <br /> Authors: Kristin Vogel; Tobias Sieg; Georg Veh; Bernhard Fiedler; Thomas Moran; Madlen Peter; Erwin Rottler; Axel Bronstert.  
                Earth's Future (2024). DOI: https://doi.org/10.1029/2023EF003553 <br /><br /></li>
            <li>eCerto - versatile software for interlaboratory data evaluation and documentation during reference material production.
                <br /> Authors: Jan Lisec, Sebastian Recknagel, Carsten Prinz, Kristin Vogel, Matthias Koch, Roland Becker.  
                Analytical and Bioanalytical Chemistry (2024). DOI: https://doi.org/10.1007/s00216-023-05099-3 <br /><br /></li>
            <li>Machine learning methods for compound annotation in non-targeted mass spectrometry—A brief overview of fingerprinting, in silico fragmentation and de novo methods.
                <br /> Authors: Francesco F. Russo, Yannek Nowatzky, Carsten Jaeger, Maria K. Parr, Phillipp Benner, Thilo Muth, Jan Lisec.
                Rapid Communications in Mass Spectrometry (2024). DOI: https://doi.org/10.1002/rcm.9876 <br /><br /></li>
            <li>Robust Entropy Search for Safe Efficient Bayesian Optimization.
                <br /> Authors: Dorina Weichert, Alexander Kister, Patrick Link, Sebastian Houben, Gunar Ernis.
                arXiv preprint (2024). arXiv:2405.19059 <br /><br /></li>
    </ul>
</div>

<div class="publication-content">
    <h3 id="2023">2023</h3>
    <ul class="publication-list">
        <li>A foundation model for atomistic materials chemistry.
            <br /> Authors: Ilyes Batatia, Philipp Benner, Yuan Chiang, Alin M Elena, Dávid P Kovács, Janosh Riebesell, Xavier R Advincula, Mark Asta, William J Baldwin, Noam Bernstein, Arghya Bhowmik, Samuel M Blau, Vlad Cărare, James P Darby, Sandip De, Flaviano Della Pia, Volker L Deringer, Rokas Elijošius, Zakariya El-Machachi, Edvin Fako, Andrea C Ferrari, Annalena Genreith-Schriever, Janine George, Rhys EA Goodall, Clare P Grey, Shuang Han, Will Handley, Hendrik H Heenen, Kersti Hermansson, Christian Holm, Jad Jaafar, Stephan Hofmann, Konstantin S Jakob, Hyunwook Jung, Venkat Kapil, Aaron D Kaplan, Nima Karimitari, Namu Kroupa, Jolla Kullgren, Matthew C Kuner, Domantas Kuryla, Guoda Liepuoniute, Johannes T Margraf, Ioan-Bogdan Magdău, Angelos Michaelides, J Harry Moore, Aakash A Naik, Samuel P Niblett, Sam Walton Norwood, Niamh O'Neill, Christoph Ortner, Kristin A Persson, Karsten Reuter, Andrew S Rosen, Lars L Schaaf, Christoph Schran, Eric Sivonxay, Tamás K Stenczel, Viktor Svahn, Christopher Sutton, Cas van der Oord, Eszter Varga-Umbrich, Tejs Vegge, Martin Vondrák, Yangshuai Wang, William C Witt, Fabian Zills, Gábor Csányi.
            bioRxiv (2024). DOI: https://doi.org/10.48550/arXiv.2401.00096 <br /><br /></li>
        <li>A quantum-chemical bonding database for solid-state materials.
            <br />Authors: Aakash Ashok Naik, Christina Ertural, Nidal Dhamrait, Philipp Benner, Janine George. 
            Nature Scientific Data (2023). DOI: https://doi.org/10.1038/s41597-023-02477-5 <br /><br /></li>
        <li>Less extreme and earlier outbursts of ice-dammed lakes since 1900.
            <br />Authors: Georg Veh; Natalie Lützow; Jenny Tamm; Lisa V. Luna; Romain Hugonnet; Kristin Vogel; Marten Geertsema; John J. Clague; Oliver Korup. 
            Nature (2023). DOI: https://doi.org/10.1038/s41586-022-05642-9 <br /><br /></li>
        <li>Matbench Discovery -- A framework to evaluate machine learning crystal stability predictions.
            <br />Authors: Janosh Riebesell, Rhys E. A. Goodall, Philipp Benner, Yuan Chiang, Bowen Deng, Alpha A. Lee, Anubhav Jain, Kristin A. Persson. 
            arxiv (2023). DOI: https://doi.org/10.48550/arXiv.2308.14920 <br /><br /></li>
        <li>The Intersection Between Semantic Web and Materials Science.
            <br />Authors: Valdestilhas, Andre, Bernd Bayerlein, Benjamin Moreno Torres, Ghezal Ahmad Jan Zia, and Thilo Muth. 
            Advanced Intelligent Systems (2023). DOI: https://doi.org/10.1002/aisy.202300051<br /><br /></li>
        <li>NaturalMSEQueries—A Natural Way to Query Materials Science Engineering Data Experiments.
            <br />Authors: A. Valdestilhas, T. Hanke, S. Javadimasoudian, G. Zia, H. Feleemberg, T. Muth, 
            DOI: https://doi.org/10.5281/zenodo.7744532.(Paper accepted at ICWI 2023 - October).<br /></li>
    </ul>
</div>

<div class="publication-content">
    <h3 id="2022">2022</h3>
    <ul class="publication-list">
        <li>Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of
            phosphorylated and cross-linked peptides<br />Authors: Altenburg, T.; Giese, S.; Wang, S.; Muth, Thilo;
            Renard, B.Y.<br /><br /></li>
        <li>The BAM Data Store – an institutional RDM framework for Materials Science and Engineering<br />Authors:
            El-Athman, Rukeia<br /><br /></li>
        <li>Research Data Management of Structural Health Monitoring Projects and Subsequent Applications of Artificial
            Intelligence Methods<br />Authors: Simon, Patrick; Herrmann, Ralf; Schneider, Ronald; Hill, Falk; Baeßler,
            Matthias; El-Athman, Rukeia<br /><br /></li>
        <li>Research Data Management of Structural Health Monitoring Projects and Subsequent Applications of Artificial
            Intelligence Methods<br />Authors: Simon, Patrick; Herrmann, Ralf; Schneider, Ronald; Hille, Falk; Baeßler,
            Matthias; El-Athman, Rukeia<br /><br /></li>
        <li>MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One
            Hour<br />Authors: Tscheuschner, Georg; Kaiser, Melanie N.; Lisec, Jan; Beslic, D.; Muth, Thilo; Krüger, M.;
            Mages, H. W.; Dorner, B. G.; Knospe, J.; Schenk, J. A.; Sellrie, F.; Weller, Michael G.<br /><br /></li>
        <li>A Perspective on Digital Knowledge Representation in Materials Science and Engineering<br />Authors:
            Bayerlein, Bernd; Hanke, T.; Muth, Thilo; Riedel, Jens; Schilling, Markus; Schweizer, C.; Skrotzki, Birgit;
            Todor, A.; Moreno Torres, Benjami; Unger, Jörg F.; Völker, Christoph; Olbricht, Jürgen<br /><br /></li>
        <li>MALDI-TOF-MS-based identification of monoclonal murine anti-SARS-CoV-2 antibodies within one
            hour<br />Authors: Tscheuschner, Georg; Kaiser, Melanie N.; Lisec, Jan; Beslic, D.; Muth, Thilo; Krüger, M.;
            Mages, H.-W.; Dorner, B. G.; Knospe, J.; Schenk, J. A.; Sellrie, F.; Weller, Michael G.<br /><br /></li>
    </ul>
</div>

<div class="publication-content">
    <h3 id="2021">2021</h3>
    <ul class="publication-list">
        <li>3D printing of alginate dialdehyde-gelatin (ADA-GEL) hydrogels incorporating phytotherapeutic icariin loaded
            mesoporous SiO2-CaO nanoparticles for bone tissue engineering<br />Authors: Monavari, M.; Homaeigohar, S.;
            Fuentes-Chandía, M.; Nawaz, Q.; Monavari, Mehran; Venkatraman, A.; Boccaccini, A.<br /><br /></li>
        <li>Optimization of coupling and global collapse in diffusively coupled socio-ecological resource exploitation
            networks<br />Authors: Holstein, Tanja; Kurths, J; Wiedermann, M<br /><br /></li>
        <li>Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of
            metabolites, enzymes and proteins<br />Authors: Pech, S.; Rehberg, M.; Janke, R.; Benndorf, D.; Genzel, Y.;
            Muth, Thilo; Sickmann, A.; Rapp, E.; Reichl, U.<br /><br /></li>
        <li>Critical assessment of MetaProteome Investigation (CAMPI): A multi-laboratory comparison of established
            workflows<br />Authors: Van Den Bossche, T.; Kunath, B.; Schallert, K.; Schäpe, S.; Abraham, P. E.;
            Armengaud, J.; Arntzen, M. Ø.; Bassignani, A.; Benndorf, D.; Fuchs, S.; Giannone, R. J.; Griffin, T. J.;
            Hagen, L. H.; Halder, R.; Henry, C.; Hettich, R. L.; Heyer, R.; Jagtap, P.; Jehmlich, N.; Jensen, M.; Juste,
            C.; Kleiner, M.; Langella, O.; Lehmann, T.; Leith, E.; May, P.; Mesuere, B.; Miotello, G.; Peters, S. L.;
            Pible, O.; Queiros, P. T.; Reichl, U.; Renard, B. Y.; Schiebenhoefer, H.; Sczyrba, A.; Tanca, A.; Trappe,
            K.; Trezzi, J.-P.; Uzzau, S.; Verschaffelt, P.; von Bergen, M.; Wilmes, P.; Wolf, M.; Martens, L.; Muth,
            Thilo<br /><br /></li>
        <li>The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of
            microbiomes<br />Authors: Van Den Bossche, T.; Arntzen, M. O.; Becher, D.; Benndorf, D.; Eijsink, V. G. H.;
            Henry, C.; Jagtap, P. D.; Jehmlich, N.; Juste, C.; Kunath, B. J.; Mesuere, B.; Muth, Thilo; Pope, P. B.;
            Seifert, J.; Tanca, A.; Uzzau, S.; Wilmes, P.; Hettich, R. L.; Armengaud, J.<br /><br /></li>
        <li>Interconnecting data repositories: The Platform MaterialDigital (BMBF)<br />Authors: Skrotzki, Birgit; Muth,
            Thilo; Portella, Pedro Dolabella<br /><br /></li>
        <li>An environment for sustainable research software in Germany and beyond: current state, open challenges, and
            call for action<br />Authors: Anzt, H.; Bach, F.; Druskat, S.; Löffler, F.; Loewe, A.; Renard, B. Y.;
            Seemann, G.; Struck, A.; Achhammer, E.; Aggarwal, P.; Appel, F.; Bader, M.; Brusch, L.; Busse, C.;
            Chourdakis, G.; Dabrowski, P. W.; Ebert, P.; Flemisch, B.; Friedl, S.; Fritzsch, B.; Funk, M. D.; Gast, V.;
            Goth, F.; Grad, J.; Hegewald, J.; Hermann, S.; Hohmann, F.; Janosch, S.; Kutra, D.; Linxweiler, J.; Muth,
            Thilo; Peters-Kottig, W.; Rack, F.; Raters, F. H. C.; Rave, S.; Reina, G.; Reißig, M.; Ropinski, T.;
            Schaarschmidt, J.; Seibold, H.; Thiele, J. P.; Uekermann, B.; Unger, S.; Weeber, R.<br /><br /></li>
    </ul>
</div>

<div class="publication-content">
    <h3 id="2020">2020</h3>
    <ul class="publication-list">
        <li>Innovations- Plattform Material Digital<br />Authors: Bayerlein, Bernd; Weinberger, Katharina; Schilling,
            Markus<br /><br /></li>
        <li>TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra
            from Pathogenic Single-Organism Samples<br />Authors: Kuhring, M.; Doellinger, J.; Nitsche, A.; Muth, Thilo;
            Renard, B. Y.<br /><br /></li>
        <li>Die Digitalisierung der Materialwissenschaft und Werkstofftechnik - ein Überblick<br />Authors: Portella,
            Pedro Dolabella; Skrotzki, Birgit; Muth, Thilo<br /><br /></li>
        <li>Survey of metaproteomics software tools for functional microbiome analysis<br />Authors: Sajulga, R.;
            Easterly, C.; Riffle, M.; Mesuere, B.; Muth, Thilo; Mehta, S.; Kumar, P.; Johnson, J.; Gruening, B.;
            Schiebenhoefer, H.; Kolmeder, C.; Fuchs, S.; Nunn, B.; Rudney, J.; Griffin, T.; Jagtap, P.<br /><br /></li>
        <li>A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and
            Prophane<br />Authors: Schiebenhoefer, H.; Schallert, K.; Renard, B. Y.; Trappe, K.; Schmid, E.; Benndorf,
            D.; Riedel, K.; Muth, Thilo; Fuchs, S.<br /><br /></li>
        <li>Perspective on Proteomics for Virus Detection in Clinical Samples<br />Authors: Grossegesse, M.; Hartkopf,
            F.; Nitsche, A.; Schaade, L.; Doellinger, J.; Muth, Thilo<br /><br /></li>
        <li>Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data
            Analysis<br />Authors: Van den Bossche, T.; Verschaffelt, P.; Schallert, K.; Barsnes, H.; Dawyndt, P.;
            Benndorf, D.; Renard, B. Y.; Mesuere, B.; Martens, L.; Muth, Thilo<br /><br /></li>
    </ul>
</div>