Publications

Yunchao (Lance) Liu, Yu Wang, Oanh Vu, Rocco Moretti, Bobby Bodenheimer, Jens Meiler, and Tyler Derr. Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery. Proceedings of the AAAI Conference on Artificial Intelligence, (37)12:14356–14364, Association for the Advancement of Artificial Intelligence (AAAI), June 2023. [PUMA: imported topic_lifescience] URL

D. Sala, F. Engelberger, H.S. Mchaourab, and J. Meiler. Modeling conformational states of proteins with AlphaFold. Current Opinion in Structural Biology, (81):102645, Elsevier BV, August 2023. [PUMA: imported topic_lifescience] URL

Eli Fritz McDonald, Kathryn E. Oliver, Jonathan P. Schlebach, Jens Meiler, and Lars Plate. Benchmarking AlphaMissense Pathogenicity Predictions Against Cystic Fibrosis Variants. Cold Spring Harbor Laboratory, October 2023. [PUMA: imported topic_lifescience] URL

Moritz Ertelt, Vikram Khipple Mulligan, Jack B. Maguire, Sergey Lyskov, Rocco Moretti, Torben Schiffner, Jens Meiler, and Clara T. Schoeder. Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. In Joanna Slusky (Eds.), PLOS Computational Biology, (20)3:e1011939, Public Library of Science (PLoS), March 2024. [PUMA: imported topic_lifescience] URL

Moritz Ertelt, Rocco Moretti, Jens Meiler, and Clara T. Schoeder. Self-supervised machine learning methods for protein design improve sampling, but not the identification of high-fitness variants. Cold Spring Harbor Laboratory, June 2024. [PUMA: imported topic_lifescience] URL

Alican Gulsevin, Bing Han, Jason C. Porta, Hassane S. Mchaourab, Jens Meiler, and Anne K. Kenworthy. Template-free prediction of a new monotopic membrane protein fold and oligomeric assembly by Alphafold2. Cold Spring Harbor Laboratory, July 2022. [PUMA: imported topic_lifescience] URL

Diego del Alamo, Davide Sala, Hassane S Mchaourab, and Jens Meiler. Sampling alternative conformational states of transporters and receptors with AlphaFold2. eLife, (11)eLife Sciences Publications, Ltd, March 2022. [PUMA: imported topic_lifescience] URL

Bian Li, Jeffrey Mendenhall, John A. Capra, and Jens Meiler. A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins. Journal of Proteome Research, (20)8:4089–4100, American Chemical Society (ACS), July 2021. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Jeffrey Mendenhall, and Jens Meiler. Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. Journal of Computer-Aided Molecular Design, (30)3:209–217, Springer Science and Business Media LLC, December 2015. [PUMA: imported topic_lifescience] URL

Michael Kuhn, Jens Meiler, and David Baker. Strand‐loop‐strand motifs: Prediction of hairpins and diverging turns in proteins. Proteins: Structure, Function, and Bioinformatics, (54)2:282–288, Wiley, December 2003. [PUMA: imported topic_lifescience] URL

Charles P. Kuntz, Hope Woods, Andrew G. McKee, Nathan B. Zelt, Jeffrey L. Mendenhall, Jens Meiler, and Jonathan P. Schlebach. Towards Generalizable Predictions for the Effects of Mutations on G-Protein Coupled Receptor Expression. Cold Spring Harbor Laboratory, December 2021. [PUMA: imported topic_lifescience] URL

Yunchao (Lance) Liu, Rocco Moretti, Yu Wang, Ha Dong, Bailu Yan, Bobby Bodenheimer, Tyler Derr, and Jens Meiler. Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors. Cold Spring Harbor Laboratory, April 2023. [PUMA: imported topic_lifescience] URL

Jens Meiler, Walter Maier, Martin Will, and Reinhard Meusinger. Using Neural Networks for 13C NMR Chemical Shift Prediction–Comparison with Traditional Methods. Journal of Magnetic Resonance, (157)2:242–252, Elsevier BV, August 2002. [PUMA: imported topic_lifescience] URL

Vladimir Golkov, Marcin J. Skwark, Atanas Mirchev, Georgi Dikov, Alexander R. Geanes, Jeffrey Mendenhall, Jens Meiler, and Daniel Cremers. 3D Deep Learning for Biological Function Prediction from Physical Fields. 2020 International Conference on 3D Vision (3DV), 928–937, IEEE, November 2020. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Sandeepkumar Kothiwale, Jens Meiler, and Edward W. Lowe. Computational Methods in Drug Discovery. In Eric L. Barker (Eds.), Pharmacological Reviews, (66)1:334–395, American Society for Pharmacology & Experimental Therapeutics (ASPET), December 2013. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Edward W. Lowe, Mariusz Butkiewicz, and Jens Meiler. BCL::EMAS — Enantioselective Molecular Asymmetry Descriptor for 3D-QSAR. Molecules, (17)8:9971–9989, MDPI AG, August 2012. [PUMA: imported topic_lifescience] URL

Alican Gulsevin, and Jens Meiler. Benchmarking Peptide Structure Prediction with AlphaFold2. Cold Spring Harbor Laboratory, February 2022. [PUMA: imported topic_lifescience] URL

Shan Jiang, Zhaoqian Su, Nathaniel Bloodworth, Yunchao Liu, Cristina Martina, David G. Harrison, and Jens Meiler. Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL

Benjamin P. Brown, Oanh Vu, Alexander R. Geanes, Sandeepkumar Kothiwale, Mariusz Butkiewicz, Edward W. Lowe, Ralf Mueller, Richard Pape, Jeffrey Mendenhall, and Jens Meiler. Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery. Frontiers in Pharmacology, (13)Frontiers Media SA, February 2022. [PUMA: imported topic_lifescience] URL

Sam DeLuca, and Jens Meiler. A Novel Method for Guiding Protein-Ligand Docking with QSAR-Derived Pharmacophore Maps. Biophysical Journal, (100)3:394a–395a, Elsevier BV, February 2011. [PUMA: imported topic_lifescience] URL

Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George, and Jens Meiler. Predicting the Functional Impact of KCNQ1 Variants with Artificial Neural Networks. Cold Spring Harbor Laboratory, December 2021. [PUMA: imported topic_lifescience] URL

Eli Fritz McDonald, Kathryn E. Oliver, Jonathan P. Schlebach, Jens Meiler, and Lars Plate. Benchmarking AlphaMissense pathogenicity predictions against cystic fibrosis variants. In Jeffrey L Brodsky (Eds.), PLOS ONE, (19)1:e0297560, Public Library of Science (PLoS), January 2024. [PUMA: imported topic_lifescience] URL

Marion F. S. Fischer, James E. Crowe, and Jens Meiler. Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. In Dina Schneidman (Eds.), PLOS Computational Biology, (18)12:e1010230, Public Library of Science (PLoS), December 2022. [PUMA: imported topic_lifescience] URL

Vladimir Golkov, Alexander Becker, Daniel T. Plop, Daniel Čuturilo, Neda Davoudi, Jeffrey Mendenhall, Rocco Moretti, Jens Meiler, and Daniel Cremers. Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions. arXiv, 2020. [PUMA: imported topic_lifescience] URL

Xiaohan Kuang, zhaoqian su, Yunchao Liu, Xiaobo Lin, Jesse Spencer Smith, Tyler Derr, Yinghao Wu, and Jens Meiler. SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL

Sandeepkumar Kothiwale, Corina Borza, Ambra Pozzi, and Jens Meiler. Quantitative Structure–Activity Relationship Modeling of Kinase Selectivity Profiles. Molecules, (22)9:1576, MDPI AG, September 2017. [PUMA: imported topic_lifescience] URL

Jens Meiler, and Martin Will. Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks. Journal of Chemical Information and Computer Sciences, (41)6:1535–1546, American Chemical Society (ACS), October 2001. [PUMA: imported topic_lifescience] URL

Alexandra M. Blee, Bian Li, Turner Pecen, Jens Meiler, Zachary D. Nagel, John A. Capra, and Walter J. Chazin. An Active Learning Framework Improves Tumor Variant Interpretation. Cancer Research, (82)15:2704–2715, American Association for Cancer Research (AACR), June 2022. [PUMA: imported topic_lifescience] URL

Louisa Gonzalez Somermeyer, Aubin Fleiss, Alexander S. Mishin, Nina G. Bozhanova, Anna A. Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V. Putintseva, Karen S. Sarkisyan, and Fyodor A. Kondrashov. Heterogeneity of the GFP fitness landscape and data-driven protein design. Cold Spring Harbor Laboratory, December 2021. [PUMA: imported topic_lifescience] URL

Jens Meiler, and David Baker. Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences, (100)21:12105–12110, Proceedings of the National Academy of Sciences, October 2003. [PUMA: imported topic_lifescience] URL

Alexander R. Geanes, Hykeyung P. Cho, Kellie D. Nance, Kevin M. McGowan, P. Jeffrey Conn, Carrie K. Jones, Jens Meiler, and Craig W. Lindsley. Ligand-based virtual screen for the discovery of novel M5 inhibitor chemotypes. Bioorganic & Medicinal Chemistry Letters, (26)18:4487–4491, Elsevier BV, September 2016. [PUMA: imported topic_lifescience] URL

Diego del Alamo, Davide Sala, Hassane S. Mchaourab, and Jens Meiler. Sampling the conformational landscapes of transporters and receptors with AlphaFold2. Cold Spring Harbor Laboratory, November 2021. [PUMA: imported topic_lifescience] URL

Christopher W. Moth, Jonathan H. Sheehan, Abdullah Al Mamun, R. Michael Sivley, Alican Gulsevin, David Rinker, John A. Capra, and Jens Meiler. VUStruct: a compute pipeline for high throughput and personalized structural biology. Cold Spring Harbor Laboratory, August 2024. [PUMA: imported topic_lifescience] URL

Caleb A. H. Jones, Benjamin P. Brown, Daniel C. Schultz, Julie Engers, Valerie M. Kramlinger, Jens Meiler, and Craig W. Lindsley. Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists. ACS Chemical Neuroscience, (15)12:2396–2407, American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL

Julia Koehler, Nils Woetzel, René Staritzbichler, Charles R. Sanders, and Jens Meiler. A unified hydrophobicity scale for multispan membrane proteins. Proteins: Structure, Function, and Bioinformatics, (76)1:13–29, Wiley, December 2008. [PUMA: imported topic_lifescience] URL

Oanh Vu, Jeffrey Mendenhall, Doaa Altarawy, and Jens Meiler. BCL::Mol2D—a robust atom environment descriptor for QSAR modeling and lead optimization. Journal of Computer-Aided Molecular Design, (33)5:477–486, Springer Science and Business Media LLC, April 2019. [PUMA: imported topic_lifescience] URL

Jens Meiler, Reinhard Meusinger, and Martin Will. Neural Network Prediction of 13C NMR Chemical Shifts of Substituted Benzenes. Monatshefte für Chemie / Chemical Monthly, (130)9:1089–1095, Springer Science and Business Media LLC, September 1999. [PUMA: imported topic_lifescience] URL

Jeffrey Mendenhall, and Jens Meiler. Improving quantitative structure–activity relationship models using Artificial Neural Networks trained with dropout. Journal of Computer-Aided Molecular Design, (30)2:177–189, Springer Science and Business Media LLC, February 2016. [PUMA: imported topic_lifescience] URL

Edward W. Lowe, Alysia Ferrebee, Alice L. Rodriguez, P. Jeffrey Conn, and Jens Meiler. 3D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulators. Bioorganic & Medicinal Chemistry Letters, (20)19:5922–5924, Elsevier BV, October 2010. [PUMA: imported topic_lifescience] URL

Louisa Gonzalez Somermeyer, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor A Kondrashov. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife, (11)eLife Sciences Publications, Ltd, May 2022. [PUMA: imported topic_lifescience] URL

Benjamin P. Brown, Jeffrey Mendenhall, Alexander R. Geanes, and Jens Meiler. General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. Journal of Chemical Information and Modeling, (61)2:603–620, American Chemical Society (ACS), January 2021. [PUMA: imported topic_lifescience] URL

Mariusz Butkiewicz, Ralf Mueller, Danilo Selic, Eric Dawson, and Jens Meiler. Application of machine learning approaches on quantitative structure activity relationships. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 255–262, IEEE, March 2009. [PUMA: imported topic_lifescience] URL

E. W. Lowe, M. Butkiewicz, N. Woetzel, and J. Meiler. GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 314–320, IEEE, May 2012. [PUMA: imported topic_lifescience] URL

Mariusz Butkiewicz, Edward W. Lowe, and Jens Meiler. Bcl∷ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimer’s Disease. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 329–334, IEEE, May 2012. [PUMA: imported topic_lifescience] URL

Joseph DeCorte, Benjamin Brown, and Jens Meiler. Interpretable deep-learning pKa prediction for small molecule drugs via atomic sensitivity analysis. American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL

J. Meiler, R. Meusinger, and M. Will. Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks. Journal of Chemical Information and Computer Sciences, (40)5:1169–1176, American Chemical Society (ACS), August 2000. [PUMA: imported topic_lifescience] URL

Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George, and Jens Meiler. Predicting the functional impact of KCNQ1 variants with artificial neural networks. In Joanna Slusky (Eds.), PLOS Computational Biology, (18)4:e1010038, Public Library of Science (PLoS), April 2022. [PUMA: imported topic_lifescience] URL

Annalen Bleckmann, and Jens Meiler. Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks. QSAR & Combinatorial Science, (22)7:722–728, Wiley, October 2003. [PUMA: imported topic_lifescience] URL

Laura M. Chamness, Charles P. Kuntz, Andrew G. McKee, Wesley D. Penn, Christopher M. Hemmerich, Douglas B. Rusch, Hope Woods, Dyotima, Jens Meiler, and Jonathan P. Schlebach. Divergent Pairwise Epistasis in the Context of Unstable Membrane Protein Variants. eLife Sciences Publications, Ltd, December 2023. [PUMA: imported topic_lifescience] URL

Alican Gulsevin, Bing Han, Jason C. Porta, Hassane S. Mchaourab, Jens Meiler, and Anne K. Kenworthy. Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2. Biophysical Journal, (122)11:2041–2052, Elsevier BV, June 2023. [PUMA: imported topic_lifescience] URL

Mariusz Butkiewicz, Edward Lowe, Ralf Mueller, Jeffrey Mendenhall, Pedro Teixeira, C. Weaver, and Jens Meiler. Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database. Molecules, (18)1:735–756, MDPI AG, January 2013. [PUMA: imported topic_lifescience] URL

Jens Meiler, and Matthias Köck. Novel methods of automated structure elucidation based on 13C NMR spectroscopy. Magnetic Resonance in Chemistry, (42)12:1042–1045, Wiley, October 2004. [PUMA: imported topic_lifescience] URL

Benjamin P. Brown, Richard A. Stein, Jens Meiler, and Hassane S. Mchaourab. Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations. Journal of Chemical Theory and Computation, (20)3:1434–1447, American Chemical Society (ACS), January 2024. [PUMA: imported topic_lifescience] URL

Davide Sala, Peter W. Hildebrand, and Jens Meiler. Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties. Frontiers in Molecular Biosciences, (10)Frontiers Media SA, February 2023. [PUMA: imported topic_lifescience] URL

Benjamin P. Brown, Richard A. Stein, Jens Meiler, and Hassane Mchaourab. Approximating conformational Boltzmann distributions with AlphaFold2 predictions. Cold Spring Harbor Laboratory, August 2023. [PUMA: imported topic_lifescience] URL

Julia Koehler, Ralf Mueller, and Jens Meiler. Improved prediction of trans-membrane spans in proteins using an artificial neural network. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 68–74, IEEE, March 2009. [PUMA: imported topic_lifescience] URL

Edward W. Lowe, Mariusz Butkiewicz, Matthew Spellings, Albert Omlor, and Jens Meiler. Comparative analysis of machine learning techniques for the prediction of logP. 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 1–6, IEEE, April 2011. [PUMA: imported topic_lifescience] URL

Ralf Mueller, Eric S. Dawson, Jens Meiler, Alice L. Rodriguez, Brian A. Chauder, Brittney S. Bates, Andrew S. Felts, Jeffrey P. Lamb, Usha N. Menon, Sataywan B. Jadhav, Alexander S. Kane, Carrie K. Jones, Karen J. Gregory, Colleen M. Niswender, P. Jeffrey Conn, Christopher M. Olsen, Danny G. Winder, Kyle A. Emmitte, and Craig W. Lindsley. Discovery of 2‐(2‐Benzoxazoyl amino)‐4‐Aryl‐5‐Cyanopyrimidine as Negative Allosteric Modulators (NAMs) of Metabotropic Glutamate Receptor 5 (mGlu5): From an Artificial Neural Network Virtual Screen to an In Vivo Tool Compound. ChemMedChem, (7)3:406–414, Wiley, January 2012. [PUMA: imported topic_lifescience] URL

Ali Al-Fatlawi, Nazia Afrin, Cigdem Ozen, Negin Malekian, and Michael Schroeder. NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction. Frontiers in Bioinformatics, (2)Frontiers Media SA, March 2022. [PUMA: topic_lifescience imported] URL

Sarah Naomi Bolz, and Michael Schroeder. Promiscuity in drug discovery on the verge of the structural revolution: recent advances and future chances. Expert Opinion on Drug Discovery, (18)9:973–985, Informa UK Limited, July 2023. [PUMA: topic_lifescience imported] URL

Negin Malekian, Amay A. Agrawal, Thomas U. Berendonk, Ali Al-Fatlawi, and Michael Schroeder. A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance. Scientific Reports, (12)1Springer Science and Business Media LLC, May 2022. [PUMA: topic_lifescience imported] URL

Negin Malekian, Srividhya Sainath, Ali Al-Fatlawi, and Michael Schroeder. Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance. Frontiers in Microbiology, (14)Frontiers Media SA, December 2023. [PUMA: topic_lifescience imported] URL

Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, Frank Noé, Simon Olsson, Lluís Raich, Robin Winter, Hatice Gokcan, Filipp Gusev, Evgeny M. Gutkin, Olexandr Isayev, Maria G. Kurnikova, Chamali H. Narangoda, Roman Zubatyuk, Ivan P. Bosko, Konstantin V. Furs, Anna D. Karpenko, Yury V. Kornoushenko, Mikita Shuldau, Artsemi Yushkevich, Mohammed B. Benabderrahmane, Patrick Bousquet‐Melou, Ronan Bureau, Beatrice Charton, Bertrand C. Cirou, Gérard Gil, William J. Allen, Suman Sirimulla, Stanley Watowich, Nick Antonopoulos, Nikolaos Epitropakis, Agamemnon Krasoulis, Vassilis Pitsikalis, Stavros Theodorakis, Igor Kozlovskii, Anton Maliutin, Alexander Medvedev, Petr Popov, Mark Zaretckii, Hamid Eghbal‐Zadeh, Christina Halmich, Sepp Hochreiter, Andreas Mayr, Peter Ruch, Michael Widrich, Francois Berenger, Ashutosh Kumar, Yoshihiro Yamanishi, Kam Y. J. Zhang, Emmanuel Bengio, Yoshua Bengio, Moksh J. Jain, Maksym Korablyov, Cheng‐Hao Liu, Gilles Marcou, Enrico Glaab, Kelly Barnsley, Suhasini M. Iyengar, Mary Jo Ondrechen, V. Joachim Haupt, Florian Kaiser, Michael Schroeder, Luisa Pugliese, Simone Albani, Christina Athanasiou, Andrea Beccari, Paolo Carloni, Giulia D’Arrigo, Eleonora Gianquinto, Jonas Goßen, Anton Hanke, Benjamin P. Joseph, Daria B. Kokh, Sandra Kovachka, Candida Manelfi, Goutam Mukherjee, Abraham Muñiz‐Chicharro, Francesco Musiani, Ariane Nunes‐Alves, Giulia Paiardi, Giulia Rossetti, S. Kashif Sadiq, Francesca Spyrakis, Carmine Talarico, Alexandros Tsengenes, Rebecca C. Wade, Conner Copeland, Jeremiah Gaiser, Daniel R. Olson, Amitava Roy, Vishwesh Venkatraman, Travis J. Wheeler, Haribabu Arthanari, Klara Blaschitz, Marco Cespugli, Vedat Durmaz, Konstantin Fackeldey, Patrick D. Fischer, Christoph Gorgulla, Christian Gruber, Karl Gruber, Michael Hetmann, Jamie E. Kinney, Krishna M. Padmanabha Das, Shreya Pandita, Amit Singh, Georg Steinkellner, Guilhem Tesseyre, Gerhard Wagner, Zi‐Fu Wang, Ryan J. Yust, Dmitry S. Druzhilovskiy, Dmitry A. Filimonov, Pavel V. Pogodin, Vladimir Poroikov, Anastassia V. Rudik, Leonid A. Stolbov, Alexander V. Veselovsky, Maria De Rosa, Giada De Simone, Maria R. Gulotta, Jessica Lombino, Nedra Mekni, Ugo Perricone, Arturo Casini, Amanda Embree, D. Benjamin Gordon, David Lei, Katelin Pratt, Christopher A. Voigt, Kuang‐Yu Chen, Yves Jacob, Tim Krischuns, Pierre Lafaye, Agnès Zettor, M. Luis Rodríguez, Kris M. White, Daren Fearon, Frank Von Delft, Martin A. Walsh, Dragos Horvath, Charles L. Brooks, Babak Falsafi, Bryan Ford, Adolfo García‐Sastre, Sang Yup Lee, Nadia Naffakh, Alexandre Varnek, Günter Klambauer, and Thomas M. Hermans. A community effort in SARS‐CoV‐2 drug discovery. Molecular Informatics, (43)1Wiley, November 2023. [PUMA: topic_lifescience imported] URL

Philipp Schake, Klevia Dishnica, Florian Kaiser, Christoph Leberecht, V. Joachim Haupt, and Michael Schroeder. An interaction-based drug discovery screen explains known SARS-CoV-2 inhibitors and predicts new compound scaffolds. Scientific Reports, (13)1Springer Science and Business Media LLC, June 2023. [PUMA: topic_lifescience imported] URL

Melissa F. Adasme, Sarah Naomi Bolz, Ali Al-Fatlawi, and Michael Schroeder. Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening. Journal of Cheminformatics, (14)1Springer Science and Business Media LLC, March 2022. [PUMA: topic_lifescience imported] URL

Kortney Melancon, Palina Pliushcheuskaya, Jens Meiler, and Georg Künze. Targeting ion channels with ultra-large library screening for hit discovery. Frontiers in Molecular Neuroscience, (16)Frontiers Media SA, January 2024. [PUMA: topic_lifescience imported] URL

Rodolfo A. Maniero, Cristiana Picco, Anja Hartmann, Felipe Engelberger, Antonella Gradogna, Joachim Scholz-Starke, Michael Melzer, Georg Künze, Armando Carpaneto, Nicolaus von Wirén, and Ricardo F. H. Giehl. Ferric reduction by a CYBDOM protein counteracts increased iron availability in root meristems induced by phosphorus deficiency. Nature Communications, (15)1Springer Science and Business Media LLC, January 2024. [PUMA: topic_lifescience imported] URL

Palina Pliushcheuskaya, Sandeep Kesh, Emma Kaufmann, Sophie Wucherpfennig, Frank Schwede, Georg Künze, and Vasilica Nache. Similar Binding Modes of cGMP Analogues Limit Selectivity in Modulating Retinal CNG Channels via the Cyclic Nucleotide-Binding Domain. ACS Chemical Neuroscience, (15)8:1652–1668, American Chemical Society (ACS), April 2024. [PUMA: topic_lifescience imported] URL

Abibe Useini, Inken Kaja Schwerin, Georg Künze, and Norbert Sträter. Structural Studies on the Binding Mode of Bisphenols to PPARγ. Biomolecules, (14)6:640, MDPI AG, May 2024. [PUMA: topic_lifescience imported] URL

Sheikh Mastura Farzana, Maik Fröbe, Michael Granitzer, Gijs Hendriksen, Djoerd Hiemstra, Martin Potthast, and Saber Zerhoudi. The First International Workshop on Open Web Search (WOWS). European Conference on Information Retrieval, 426--431, 2024. [PUMA: topic_language imported]

Michael Granitzer, Stefan Voigt, Noor Afshan Fathima, Martin Golasowski, Christian Guetl, Tobias Hecking, Gijs Hendriksen, Djoerd Hiemstra, Jan Martinovic, Jelena Mitrović, and others. Impact and development of an Open Web Index for open web search. Journal of the Association for Information Science and Technology, (75)5:512--520, Wiley Online Library, 2024. [PUMA: topic_language imported]

Nandan Thakur, Luiz Bonifacio, Maik Fröbe, Alexander Bondarenko, Ehsan Kamalloo, Martin Potthast, Matthias Hagen, and Jimmy Lin. Systematic Evaluation of Neural Retrieval Models on the Touché 2020 Argument Retrieval Subset of BEIR. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1420–1430, ACM, July 2024. [PUMA: topic_language imported] URL

Christine Bauer, Ben Carterette, Nicola Ferro, Norbert Fuhr, Joeran Beel, Timo Breuer, Charles LA Clarke, Anita Crescenzi, Gianluca Demartini, Giorgio Maria Di Nunzio, and others. Report on the Dagstuhl Seminar on Frontiers of Information Access Experimentation for Research and Education. ACM SIGIR Forum, (57)1:1--28, 2023. [PUMA: topic_language imported]

Maik Fröbe, Jan Heinrich Reimer, Sean MacAvaney, Niklas Deckers, Janek Bevendorff, Benno Stein, Matthias Hagen, and Martin Potthast. The Information Retrieval Experiment Platform (Extended Abstract). Lernen. Wissen. Daten. Analysen. -- LWDA 2023, 179--191, CEUR-WS.org, October 2023. [PUMA: topic_language imported] URL

Maik Fröbe, Jan Heinrich Reimer, Sean MacAvaney, Niklas Deckers, Simon Reich, Janek Bevendorff, Benno Stein, Matthias Hagen, and Martin Potthast. The Information Retrieval Experiment Platform (Extended Abstract). Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence, 8405–8410, International Joint Conferences on Artificial Intelligence Organization, August 2024. [PUMA: topic_language imported] URL

Maik Fröbe, Theresa Elstner, Harrisen Scells, and Martin Potthast. Prototyping Open Web Search Applications with TIRA: A Case Study in Research-oriented Teaching. In Andreas Wagner, Christian Guetl, Michael Granitzer, and Stefan Voigt (Eds.), 5th International Symposium on Open Search Technology (OSSYM 2023), International Open Search Symposium, October 2023. [PUMA: topic_language imported] URL

Maik Fröbe, Gijs Hendriksen, Arjen P de Vries, and Martin Potthast. Open Web Search at LongEval 2023: Reciprocal Rank Fusion on Automatically Generated Query Variants. Sl: CEUR, 2023. [PUMA: topic_language imported]

Johannes Kiesel, Cagrı Cöltekin, Maximilian Heinrich, Maik Fröbe, Milad Alshomary, Bertrand De Longueville, Tomaz Erjavec, Nicolas Handke, Matyás Kopp, Nikola Ljubesić, and others. Overview of Touché 2024: Argumentation Systems. 2024. [PUMA: topic_language imported]

Abinew Ali Ayele, Nikolay Babakov, Janek Bevendorff, Xavier Bonet Casals, Berta Chulvi, Daryna Dementieva, Ashaf Elnagar, Dayne Freitag, Maik Fröbe, Damir Korencić, and others. Overview of PAN 2024: Multi-author Writing Style Analysis, Multilingual Text Detoxification, Oppositional Thinking Analysis, and Generative AI Authorship Verification Condensed Lab Overview. International Conference of the Cross-Language Evaluation Forum for European Languages, 231--259, 2024. [PUMA: topic_language imported]

Maik Fröbe, Harrisen Scells, Theresa Elstner, Christopher Akiki, Lukas Gienapp, Jan Heinrich Reimer, Sean MacAvaney, Benno Stein, Matthias Hagen, and Martin Potthast. Resources for Combining Teaching and Research in Information Retrieval Coursework. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1115–1125, ACM, July 2024. [PUMA: topic_language imported] URL

Niklas Deckers, Maik Fröbe, Johannes Kiesel, Gianluca Pandolfo, Christopher Schröder, Benno Stein, and Martin Potthast. The infinite index: Information retrieval on generative text-to-image models. Proceedings of the 2023 conference on human information interaction and retrieval, 172--186, 2023. [PUMA: topic_language imported]

Lukas Gienapp, Harrisen Scells, Niklas Deckers, Janek Bevendorff, Shuai Wang, Johannes Kiesel, Shahbaz Syed, Maik Fröbe, Guido Zuccon, Benno Stein, Matthias Hagen, and Martin Potthast. Evaluating Generative Ad Hoc Information Retrieval. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1916–1929, ACM, July 2024. [PUMA: topic_language imported] URL

Magdalena Wolska, Matti Wiegmann, Christopher Schröder, Ole Borchardt, Benno Stein, and Martin Potthast. Trigger Warnings: Bootstrapping a Violence Detector for Fan Fiction. Findings of the Association for Computational Linguistics: EMNLP 2023, 569–576, Association for Computational Linguistics, 2023. [PUMA: topic_language imported] URL

Christopher Schröder, Lydia Müller, Andreas Niekler, and Martin Potthast. Small-Text: Active Learning for Text Classification in Python. In Danilo Croce, and Luca Soldaini (Eds.), Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations, 84--95, Association for Computational Linguistics, Dubrovnik, Croatia, May 2023. [PUMA: topic_language imported] URL

Shahbaz Syed, Khalid Al Khatib, and Martin Potthast. TL;DR Progress: Multi-faceted Literature Exploration in Text Summarization. In Nikolaos Aletras, and Orphee De Clercq (Eds.), Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations, 195--206, Association for Computational Linguistics, St. Julians, Malta, March 2024. [PUMA: topic_language imported] URL

Shahbaz Syed, Timon Ziegenbein, Philipp Heinisch, Henning Wachsmuth, and Martin Potthast. Frame-oriented Summarization of Argumentative Discussions. Proceedings of the 24th Meeting of the Special Interest Group on Discourse and Dialogue, 114–129, Association for Computational Linguistics, 2023. [PUMA: topic_language imported] URL

Matti Wiegmann, Magdalena Wolska, Benno Stein, and Martin Potthast. Introducing Computational Research on Trigger Warnings. In Katrin Weller, Pascal Siegers, Indira Sen, and Christina Dahn (Eds.), Conference on Harmful Online Communication (CHOC 2023), Gesis, Cologne, Germany, November 2023. [PUMA: topic_language imported]

Aarohi Srivastava, Abhinav Rastogi, Abhishek Rao, Abu Awal Md Shoeb, Abubakar Abid, Adam Fisch, Adam R. Brown, Adam Santoro, Aditya Gupta, Adrià Garriga-Alonso, Agnieszka Kluska, Aitor Lewkowycz, Akshat Agarwal, Alethea Power, Alex Ray, Alex Warstadt, Alexander W. Kocurek, Ali Safaya, Ali Tazarv, Alice Xiang, Alicia Parrish, Allen Nie, Aman Hussain, Amanda Askell, Amanda Dsouza, Ambrose Slone, Ameet Rahane, Anantharaman S. Iyer, Anders Andreassen, Andrea Madotto, Andrea Santilli, Andreas Stuhlmüller, Andrew Dai, Andrew La, Andrew Lampinen, Andy Zou, Angela Jiang, Angelica Chen, Anh Vuong, Animesh Gupta, Anna Gottardi, Antonio Norelli, Anu Venkatesh, Arash Gholamidavoodi, Arfa Tabassum, Arul Menezes, Arun Kirubarajan, Asher Mullokandov, Ashish Sabharwal, Austin Herrick, Avia Efrat, Aykut Erdem, Ayla Karakaş, B. Ryan Roberts, Bao Sheng Loe, Barret Zoph, Bartłomiej Bojanowski, Batuhan Özyurt, Behnam Hedayatnia, Behnam Neyshabur, Benjamin Inden, Benno Stein, Berk Ekmekci, Bill Yuchen Lin, Blake Howald, Bryan Orinion, Cameron Diao, Cameron Dour, Catherine Stinson, Cedrick Argueta, César Ferri Ramírez, Chandan Singh, Charles Rathkopf, Chenlin Meng, Chitta Baral, Chiyu Wu, Chris Callison-Burch, Chris Waites, Christian Voigt, Christopher D. Manning, Christopher Potts, Cindy Ramirez, Clara E. Rivera, Clemencia Siro, Colin Raffel, Courtney Ashcraft, Cristina Garbacea, Damien Sileo, Dan Garrette, Dan Hendrycks, Dan Kilman, Dan Roth, Daniel Freeman, Daniel Khashabi, Daniel Levy, Daniel Moseguí González, Danielle Perszyk, Danny Hernandez, Danqi Chen, Daphne Ippolito, Dar Gilboa, David Dohan, David Drakard, David Jurgens, Debajyoti Datta, Deep Ganguli, Denis Emelin, Denis Kleyko, Deniz Yuret, Derek Chen, Derek Tam, Dieuwke Hupkes, Diganta Misra, Dilyar Buzan, Dimitri Coelho Mollo, Diyi Yang, Dong-Ho Lee, Dylan Schrader, Ekaterina Shutova, Ekin Dogus Cubuk, Elad Segal, Eleanor Hagerman, Elizabeth Barnes, Elizabeth Donoway, Ellie Pavlick, Emanuele Rodola, Emma Lam, Eric Chu, Eric Tang, Erkut Erdem, Ernie Chang, Ethan A. Chi, Ethan Dyer, Ethan Jerzak, Ethan Kim, Eunice Engefu Manyasi, Evgenii Zheltonozhskii, Fanyue Xia, Fatemeh Siar, Fernando Martínez-Plumed, Francesca Happé, Francois Chollet, Frieda Rong, Gaurav Mishra, Genta Indra Winata, Gerard de Melo, Germán Kruszewski, Giambattista Parascandolo, Giorgio Mariani, Gloria Wang, Gonzalo Jaimovitch-López, Gregor Betz, Guy Gur-Ari, Hana Galijasevic, Hannah Kim, Hannah Rashkin, Hannaneh Hajishirzi, Harsh Mehta, Hayden Bogar, Henry Shevlin, Hinrich Schütze, Hiromu Yakura, Hongming Zhang, Hugh Mee Wong, Ian Ng, Isaac Noble, Jaap Jumelet, Jack Geissinger, Jackson Kernion, Jacob Hilton, Jaehoon Lee, Jaime Fernández Fisac, James B. Simon, James Koppel, James Zheng, James Zou, Jan Kocoń, Jana Thompson, Janelle Wingfield, Jared Kaplan, Jarema Radom, Jascha Sohl-Dickstein, Jason Phang, Jason Wei, Jason Yosinski, Jekaterina Novikova, Jelle Bosscher, Jennifer Marsh, Jeremy Kim, Jeroen Taal, Jesse Engel, Jesujoba Alabi, Jiacheng Xu, Jiaming Song, Jillian Tang, Joan Waweru, John Burden, John Miller, John U. Balis, Jonathan Batchelder, Jonathan Berant, Jörg Frohberg, Jos Rozen, Jose Hernandez-Orallo, Joseph Boudeman, Joseph Guerr, Joseph Jones, Joshua B. Tenenbaum, Joshua S. Rule, Joyce Chua, Kamil Kanclerz, Karen Livescu, Karl Krauth, Karthik Gopalakrishnan, Katerina Ignatyeva, Katja Markert, Kaustubh D. Dhole, Kevin Gimpel, Kevin Omondi, Kory Mathewson, Kristen Chiafullo, Ksenia Shkaruta, Kumar Shridhar, Kyle McDonell, Kyle Richardson, Laria Reynolds, Leo Gao, Li Zhang, Liam Dugan, Lianhui Qin, Lidia Contreras-Ochando, Louis-Philippe Morency, Luca Moschella, Lucas Lam, Lucy Noble, Ludwig Schmidt, Luheng He, Luis Oliveros Colón, Luke Metz, Lütfi Kerem Şenel, Maarten Bosma, Maarten Sap, Maartje ter Hoeve, Maheen Farooqi, Manaal Faruqui, Mantas Mazeika, Marco Baturan, Marco Marelli, Marco Maru, Maria Jose Ramírez Quintana, Marie Tolkiehn, Mario Giulianelli, Martha Lewis, Martin Potthast, Matthew L. Leavitt, Matthias Hagen, Mátyás Schubert, Medina Orduna Baitemirova, Melody Arnaud, Melvin McElrath, Michael A. Yee, Michael Cohen, Michael Gu, Michael Ivanitskiy, Michael Starritt, Michael Strube, Michał Swędrowski, Michele Bevilacqua, Michihiro Yasunaga, Mihir Kale, Mike Cain, Mimee Xu, Mirac Suzgun, Mitch Walker, Mo Tiwari, Mohit Bansal, Moin Aminnaseri, Mor Geva, Mozhdeh Gheini, Mukund Varma T, Nanyun Peng, Nathan A. Chi, Nayeon Lee, Neta Gur-Ari Krakover, Nicholas Cameron, Nicholas Roberts, Nick Doiron, Nicole Martinez, Nikita Nangia, Niklas Deckers, Niklas Muennighoff, Nitish Shirish Keskar, Niveditha S. Iyer, Noah Constant, Noah Fiedel, Nuan Wen, Oliver Zhang, Omar Agha, Omar Elbaghdadi, Omer Levy, Owain Evans, Pablo Antonio Moreno Casares, Parth Doshi, Pascale Fung, Paul Pu Liang, Paul Vicol, Pegah Alipoormolabashi, Peiyuan Liao, Percy Liang, Peter Chang, Peter Eckersley, Phu Mon Htut, Pinyu Hwang, Piotr Miłkowski, Piyush Patil, Pouya Pezeshkpour, Priti Oli, Qiaozhu Mei, Qing Lyu, Qinlang Chen, Rabin Banjade, Rachel Etta Rudolph, Raefer Gabriel, Rahel Habacker, Ramon Risco, Raphaël Millière, Rhythm Garg, Richard Barnes, Rif A. Saurous, Riku Arakawa, Robbe Raymaekers, Robert Frank, Rohan Sikand, Roman Novak, Roman Sitelew, Ronan LeBras, Rosanne Liu, Rowan Jacobs, Rui Zhang, Ruslan Salakhutdinov, Ryan Chi, Ryan Lee, Ryan Stovall, Ryan Teehan, Rylan Yang, Sahib Singh, Saif M. Mohammad, Sajant Anand, Sam Dillavou, Sam Shleifer, Sam Wiseman, Samuel Gruetter, Samuel R. Bowman, Samuel S. Schoenholz, Sanghyun Han, Sanjeev Kwatra, Sarah A. Rous, Sarik Ghazarian, Sayan Ghosh, Sean Casey, Sebastian Bischoff, Sebastian Gehrmann, Sebastian Schuster, Sepideh Sadeghi, Shadi Hamdan, Sharon Zhou, Shashank Srivastava, Sherry Shi, Shikhar Singh, Shima Asaadi, Shixiang Shane Gu, Shubh Pachchigar, Shubham Toshniwal, Shyam Upadhyay, Shyamolima, Debnath, Siamak Shakeri, Simon Thormeyer, Simone Melzi, Siva Reddy, Sneha Priscilla Makini, Soo-Hwan Lee, Spencer Torene, Sriharsha Hatwar, Stanislas Dehaene, Stefan Divic, Stefano Ermon, Stella Biderman, Stephanie Lin, Stephen Prasad, Steven T. Piantadosi, Stuart M. Shieber, Summer Misherghi, Svetlana Kiritchenko, Swaroop Mishra, Tal Linzen, Tal Schuster, Tao Li, Tao Yu, Tariq Ali, Tatsu Hashimoto, Te-Lin Wu, Théo Desbordes, Theodore Rothschild, Thomas Phan, Tianle Wang, Tiberius Nkinyili, Timo Schick, Timofei Kornev, Titus Tunduny, Tobias Gerstenberg, Trenton Chang, Trishala Neeraj, Tushar Khot, Tyler Shultz, Uri Shaham, Vedant Misra, Vera Demberg, Victoria Nyamai, Vikas Raunak, Vinay Ramasesh, Vinay Uday Prabhu, Vishakh Padmakumar, Vivek Srikumar, William Fedus, William Saunders, William Zhang, Wout Vossen, Xiang Ren, Xiaoyu Tong, Xinran Zhao, Xinyi Wu, Xudong Shen, Yadollah Yaghoobzadeh, Yair Lakretz, Yangqiu Song, Yasaman Bahri, Yejin Choi, Yichi Yang, Yiding Hao, Yifu Chen, Yonatan Belinkov, Yu Hou, Yufang Hou, Yuntao Bai, Zachary Seid, Zhuoye Zhao, Zijian Wang, Zijie J. Wang, Zirui Wang, and Ziyi Wu. Beyond the Imitation Game: Quantifying and extrapolating the capabilities of language models. 2023. [PUMA: topic_language imported] URL

Efstathios Stamatatos, Krzysztof Kredens, Piotr Pezik, Annina Heini, Janek Bevendorff, Benno Stein, and Martin Potthast. Overview of the Authorship Verification Task at PAN 2023. In Mohammad Aliannejadi, Guglielmo Faggioli, Nicola Ferro, and Michalis Vlachos (Eds.), Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023), (3497):2476--2491, September 2023. [PUMA: topic_language imported] URL

Eva Zangerle, Maximilian Mayerl, Martin Potthast, and Benno Stein. Overview of the Multi-Author Writing Style Analysis Task at PAN 2023.. CLEF (Working Notes), 2513--2522, 2023. [PUMA: topic_language imported]

Lukas Gienapp, Wolfgang Kircheis, Bjarne Sievers, Benno Stein, and Martin Potthast. A large dataset of scientific text reuse in Open-Access publications. Scientific Data, (10)1:58, Nature Publishing Group UK London, 2023. [PUMA: topic_language imported]

Aleksandra Piktus, Odunayo Ogundepo, Christopher Akiki, Akintunde Oladipo, Xinyu Zhang, Hailey Schoelkopf, Stella Biderman, Martin Potthast, and Jimmy Lin. GAIA Search: Hugging Face and Pyserini Interoperability for NLP Training Data Exploration. Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations), 588–598, Association for Computational Linguistics, 2023. [PUMA: topic_language imported] URL

Khalid Al Khatib, Michael Voelske, Anh Le, Shahbaz Syed, Martin Potthast, and Benno Stein. A New Dataset for Causality Identification in Argumentative Texts. Proceedings of the 24th Meeting of the Special Interest Group on Discourse and Dialogue, 349–354, Association for Computational Linguistics, 2023. [PUMA: topic_language imported] URL

Ines Zelch, Matthias Hagen, and Martin Potthast. Advertising in Generative Information Retrieval. Workshop on the Impact of Generative AI on Search and Search Engine Research, September 2023. [PUMA: topic_language imported]

Timon Ziegenbein, Shahbaz Syed, Felix Lange, Martin Potthast, and Henning Wachsmuth. Modeling Appropriate Language in Argumentation. Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), 4344–4363, Association for Computational Linguistics, 2023. [PUMA: topic_language imported] URL

Shuai Wang, Harrisen Scells, Martin Potthast, Bevan Koopman, and Guido Zuccon. Generating Natural Language Queries for More Effective Systematic Review Screening Prioritisation. 2023. [PUMA: topic_language imported] URL

Ines Zelch, Matthias Hagen, and Martin Potthast. Commercialized Generative AI: A Critical Study of the Feasibility and Ethics of Generating Native Advertising Using Large Language Models in Conversational Web Search. 2023. [PUMA: topic_language imported] URL

Matti Wiegmann, Magdalena Wolska, Martin Potthast, and Benno Stein. Overview of the Trigger Detection Task at PAN 2023.. CLEF (Working Notes), 2523--2536, 2023. [PUMA: topic_language imported]

Shahbaz Syed, Ahmad Hakimi, Khalid Al-Khatib, and Martin Potthast. Citance-Contextualized Summarization of Scientific Papers. In Houda Bouamor, Juan Pino, and Kalika Bali (Eds.), Findings of the Association for Computational Linguistics: EMNLP 2023, 8551--8568, Association for Computational Linguistics, Singapore, December 2023. [PUMA: topic_language imported] URL

Shahbaz Syed, Dominik Schwabe, Khalid Khatib, and Martin Potthast. Indicative Summarization of Long Discussions. Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing, 2752–2788, Association for Computational Linguistics, 2023. [PUMA: topic_language imported] URL