Publications

Nico Eisenhauer, Karin Frank, Alexandra Weigelt, Bartosz Bartkowski, Rémy Beugnon, Katja Liebal, Miguel Mahecha, Martin Quaas, Djamil Al-Halbouni, Ana Bastos, Friedrich J. Bohn, Mariana Madruga de Brito, Joachim Denzler, Hannes Feilhauer, Rico Fischer, Immo Fritsche, Claudia Guimaraes-Steinicke, Martin Hänsel, Daniel B. M. Haun, Hartmut Herrmann, Andreas Huth, Heike Kalesse-Los, Michael Koetter, Nina Kolleck, Melanie Krause, Marlene Kretschmer, Pedro J. Leitão, Torsten Masson, Karin Mora, Birgit Müller, Jian Peng, Mira L. Pöhlker, Leonie Ratzke, Markus Reichstein, Solveig Richter, Nadja Rüger, Beatriz Sánchez-Parra, Maha Shadaydeh, Sebastian Sippel, Ina Tegen, Daniela Thrän, Josefine Umlauft, Manfred Wendisch, Kevin Wolf, Christian Wirth, Hannes Zacher, Sönke Zaehle, and Johannes Quaas. A belowground perspective on the nexus between biodiversity change, climate change, and human well-being. Journal of Sustainable Agriculture and Environment, (3)2:e212108, 2024. [PUMA: change, well-being, biodiversity topic_lifescience climate soil human] URL

Moritz Vinzent Seiler, Raphael Patrick Prager, Pascal Kerschke, and Heike Trautmann. A collection of deep learning-based feature-free approaches for characterizing single-objective continuous fitness landscapes. Proceedings of the Genetic and Evolutionary Computation Conference, ACM, New York, NY, USA, July 2022. [PUMA: topic_lifescience]

Mani Lokamani, Jeffrey Kelling, Robin Ohmann, Jörg Meyer, Tim Kühne, Gianaurelio Cuniberti, Jannic Wolf, Thomas Huhn, Peter Zahn, Francesca Moresco, and Sibylle Gemming. A combined experimental and theoretical study of 1,4-bis(phenylethynyl)-2,5-bis(ethoxy)benzene adsorption on Au(111). Surf. Sci., (712)121877:121877, Elsevier BV, October 2021. [PUMA: topic_lifescience]

Martin Pippel, David Jebb, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller, and Anna K Hundsdoerfer. A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae). Gigascience, (9)1Oxford University Press (OUP), January 2020. [PUMA: genome comparison hawkmoth-silk gene annotation; moth topic_lifescience reads; long assembly; PacBio]

Matti Wiegmann, Jan Heinrich Reimer, Maximilian Ernst, Martin Potthast, Matthias Hagen, and Benno Stein. A Mastodon Corpus to Evaluate Federated Microblog Search. In Sheikh Farzana, Maik Fröbe, Michael Granitzer, Gijs Hendriksen, Djoerd Hiemstra, Martin Potthast, and Saber Zerhoudi (Eds.), Proceedings of the First International Workshop on Open Web Search (WOWS 2024), (3689):37--49, CEUR Workshop Proceedings, March 2024. [PUMA: 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. J. Proteome Res., (20)8:4089--4100, American Chemical Society (ACS), August 2021. [PUMA: multitask convolutional prediction; memory transmembrane deep learning; neural networks; topology long short-term structure secondary topic_lifescience prediction]

Johannes Kiesel, Lars Meyer, Florian Kneist, Benno Stein, and Martin Potthast. An empirical comparison of web page segmentation algorithms. Lecture Notes in Computer Science, 62--74, Springer International Publishing, Cham, 2021. [PUMA: topic_lifescience]

Tom Kaune, Claudia Ruffert, Nico Hesselbarth, Marko Damm, Sebastian Krug, Julian Cardinal von Widdern, Emmanuelle Masson, Jian-Min Chen, Vinciane Rebours, Louis Buscail, Claude Férec, Robert Grützmann, Rene H M Te Morsche, Joost Ph Drenth, Giulia Martina Cavestro, Raffaella Alessia Zuppardo, Adrian Saftoiu, Ewa Malecka-Panas, Stanislaw Głuszek, Peter Bugert, Markus M Lerch, Matthias Sendler, Frank Ulrich Weiss, Wen-Bin Zou, Shun-Jiang Deng, Zhuan Liao, Markus Scholz, Holger Kirsten, Peter Hegyi, Heiko Witt, Patrick Michl, Heidi Griesmann, and Jonas Rosendahl. Analysis of GPRC6A variants in different pancreatitis etiologies. Pancreatology, (20)7:1262--1267, Elsevier BV, October 2020. [PUMA: G-Protein Calcium; Pancreatitis Inflammation; topic_lifescience coupled Genetics; receptor;]

Tuomo Lehtonen, Anna Rapberger, Markus Ulbricht, and Johannes P Wallner. Argumentation frameworks induced by assumption-based argumentation: Relating size and complexity. Proceedings of the Twentieth International Conference on Principles of Knowledge Representation and Reasoning, 440--450, International Joint Conferences on Artificial Intelligence Organization, California, September 2023. [PUMA: topic_lifescience]

Raphael Patrick Prager, Moritz Vinzent Seiler, Heike Trautmann, and Pascal Kerschke. Automated algorithm selection in single-objective continuous optimization: A comparative study of deep learning and landscape analysis methods. Lecture Notes in Computer Science, 3--17, Springer International Publishing, Cham, 2022. [PUMA: topic_lifescience]

Jeffrey Mendenhall, Benjamin P Brown, Sandeepkumar Kothiwale, and Jens Meiler. BCL::Conf: Improved open-source knowledge-based conformation sampling using the Crystallography Open Database. J. Chem. Inf. Model., (61)1:189--201, American Chemical Society (ACS), January 2021. [PUMA: topic_lifescience]

Eli Fritz McDonald, Taylor Jones, Lars Plate, Jens Meiler, and Alican Gulsevin. Benchmarking AlphaFold2 on peptide structure prediction. Structure, (31)1:111--119.e2, Elsevier BV, January 2023. [PUMA: bonds; benchmark; folding; peptides; AlphaFold2; disulfide protein topic_lifescience prediction pLDDT; structure]

David Georg Reichelt, Lars-Peter Meyer, and Stefan Kühne. Better a Microbenchmark on a Cluster than a User at the Office: Flink Cluster Benchmarking. In Udo Kelter (Eds.), Softwaretechnik-Trends Band 39, Heft 3, 52--54, Gesellschaft für Informatik e.V., Bonn, 2019. [PUMA: topic_lifescience]

Aarohi Srivastava, Abhinav Rastogi, Abhishek Rao, Abu Awal 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 Karakas, 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, Cameron Diao, Cameron Dour, Catherine Stinson, Cedrick Argueta, César Ferri Ram\'ırez, 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 Mosegu\'ı 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, 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 Mart\'ınez-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, 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 Berant, Jörg Frohberg, Jos Rozen, Jose Hernandez-Orallo, Joseph Boudeman, 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 Senel, Maarten Bosma, Maarten Sap, Maartje ter Hoeve, Maheen Farooqi, Manaal Faruqui, Mantas Mazeika, Marco Baturan, Marco Marelli, Marco Maru, Maria Jose Ram\'ırez 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 Swedrowski, Michele Bevilacqua, Michihiro Yasunaga, Mihir Kale, Mike Cain, Mimee Xu, Mirac Suzgun, Mo Tiwari, Mohit Bansal, Moin Aminnaseri, Mor Geva, Mozhdeh Gheini, T, Mukund Varma, Nanyun Peng, Nathan Chi, Nayeon Lee, Neta Gur-Ari Krakover, Nicholas Cameron, Nicholas Roberts, Nick Doiron, 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, Ramón Risco Delgado, 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, Timothy Telleen-Lawton, 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. arXiv, 2022. [PUMA: topic_lifescience]

Davide Sala, Peter W Hildebrand, and Jens Meiler. Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties. Front. Mol. Biosci., (10):1121962, February 2023. [PUMA: (G-protein-coupled receptors); protein GPCRs kinases; topic_lifescience prediction function; AlphaFold; structure]

Lars-Peter Meyer, Jan Frenzel, Eric Peukert, René Jäkel, and Stefan Kühne. Big Data Services. Service Engineering, 63--77, Springer Fachmedien Wiesbaden, Wiesbaden, 2018. [PUMA: topic_lifescience]

Praveen Vasudevan, Markus Wolfien, Heiko Lemcke, Cajetan Immanuel Lang, Anna Skorska, Ralf Gaebel, Anne-Marie Galow, Dirk Koczan, Tobias Lindner, Wendy Bergmann, Brigitte Mueller-Hilke, Brigitte Vollmar, Bernd Joachim Krause, Olaf Wolkenhauer, Gustav Steinhoff, and Robert David. CCR2 macrophage response determines the functional outcome following cardiomyocyte transplantation. Genome Med., (15)1:61, August 2023. [PUMA: Macrophages; learning; Myocardial topic_lifescience infarction; Immunocompromised; Cell therapy; Machine Single-cell]

Jacopo Urbani, Markus Krötzsch, and Thomas Eiter. Chasing Streams with Existential Rules. Proceedings of the 19th International Conference on Principles of Knowledge Representation and Reasoning, 415--419, August 2022. [PUMA: topic_lifescience] URL

Nicola J Armstrong, Karen A Mather, Muralidharan Sargurupremraj, Maria J Knol, Rainer Malik, Claudia L Satizabal, Lisa R Yanek, Wei Wen, Vilmundur G Gudnason, Nicole D Dueker, Lloyd T Elliott, Edith Hofer, Joshua Bis, Neda Jahanshad, Shuo Li, Mark A Logue, Michelle Luciano, Markus Scholz, Albert V Smith, Stella Trompet, Dina Vojinovic, Rui Xia, Fidel Alfaro-Almagro, David Ames, Najaf Amin, Philippe Amouyel, Alexa S Beiser, Henry Brodaty, Ian J Deary, Christine Fennema-Notestine, Piyush G Gampawar, Rebecca Gottesman, Ludovica Griffanti, Clifford R Jack, Jr, Mark Jenkinson, Jiyang Jiang, Brian G Kral, John B Kwok, Leonie Lampe, David C M Liewald, Pauline Maillard, Jonathan Marchini, Mark E Bastin, Bernard Mazoyer, Lukas Pirpamer, José Rafael Romero, Gennady V Roshchupkin, Peter R Schofield, Matthias L Schroeter, David J Stott, Anbupalam Thalamuthu, Julian Trollor, Christophe Tzourio, Jeroen van der Grond, Meike W Vernooij, Veronica A Witte, Margaret J Wright, Qiong Yang, Zoe Morris, Siggi Siggurdsson, Bruce Psaty, Arno Villringer, Helena Schmidt, Asta K Haberg, Cornelia M van Duijn, J Wouter Jukema, Martin Dichgans, Ralph L Sacco, Clinton B Wright, William S Kremen, Lewis C Becker, Paul M Thompson, Thomas H Mosley, Joanna M Wardlaw, M Arfan Ikram, Hieab H H Adams, Sudha Seshadri, Perminder S Sachdev, Stephen M Smith, Lenore Launer, William Longstreth, Charles DeCarli, Reinhold Schmidt, Myriam Fornage, Stephanie Debette, and Paul A Nyquist. Common genetic variation indicates separate causes for periventricular and deep white matter hyperintensities. Stroke, (51)7:2111--2121, Ovid Technologies (Wolters Kluwer Health), July 2020. [PUMA: genome-wide neuroimaging; white study; topic_lifescience association brain; risk factors; matter]