Publications

Eli Fritz McDonald, Hope Woods, Shannon T Smith, Minsoo Kim, Clara T Schoeder, Lars Plate, and Jens Meiler. Structural comparative modeling of multi-domain F508del CFTR. Biomolecules, (12)3:471, MDPI AG, March 2022. [PUMA: VX-809; chaperones; comparative computational cystic discovery disease; drug fibrosis; folding modeling; pharmacological protein structure-based topic_lifescience]

Jaana A Hartiala, Yi Han, Qiong Jia, James R Hilser, Pin Huang, Janet Gukasyan, William S Schwartzman, Zhiheng Cai, Subarna Biswas, David-Alexandre Trégouët, Nicholas L Smith, INVENT Consortium, CHARGE Consortium Hemostasis Working Group, GENIUS-CHD Consortium, Marcus Seldin, Calvin Pan, Margarete Mehrabian, Aldons J Lusis, Peter Bazeley, Yan V Sun, Chang Liu, Arshed A Quyyumi, Markus Scholz, Joachim Thiery, Graciela E Delgado, Marcus E Kleber, Winfried März, Laurence J Howe, Folkert W Asselbergs, Marion van Vugt, Georgios J Vlachojannis, Riyaz S Patel, Leo-Pekka Lyytikäinen, Mika Kähönen, Terho Lehtimäki, Tuomo V M Nieminen, Pekka Kuukasjärvi, Jari O Laurikka, Xuling Chang, Chew-Kiat Heng, Rong Jiang, William E Kraus, Elizabeth R Hauser, Jane F Ferguson, Muredach P Reilly, Kaoru Ito, Satoshi Koyama, Yoichiro Kamatani, Issei Komuro, Biobank Japan, Lindsey K Stolze, Casey E Romanoski, Mohammad Daud Khan, Adam W Turner, Clint L Miller, Redouane Aherrahrou, Mete Civelek, Lijiang Ma, Johan L M Björkegren, S Ram Kumar, W H Wilson Tang, Stanley L Hazen, and Hooman Allayee. Genome-wide analysis identifies novel susceptibility loci for myocardial infarction. Eur. Heart J., (42)9:919--933, Oxford University Press (OUP), March 2021. [PUMA: Genetic Genome-wide Meta-analysis; Myocardial SLC44A3 association factors; infarction; study; topic_lifescience]

Samuel Schmitz, Emily A Schmitz, James E Crowe, Jr, and Jens Meiler. The human antibody sequence space and structural design of the V, J regions, and CDRH3 with Rosetta. MAbs, (14)1:2068212, Informa UK Limited, January 2022. [PUMA: Human-likeness; HumanizationABBREVIATIONS antibody biostatistics; design; immunome repertoire; rosetta; topic_lifescience]

Saksham Phul, Georg Kuenze, Carlos G Vanoye, Charles R Sanders, Alfred L George, Jr, and Jens Meiler. Predicting the functional impact of KCNQ1 variants with artificial neural networks. PLoS Comput. Biol., (18)4:e1010038, Public Library of Science (PLoS), April 2022. [PUMA: topic_lifescience]

Justin Curry, Sayan Mukherjee, and Katharine Turner. How many directions determine a shape and other sufficiency results for two topological transforms. arXiv, 2018. [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]

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]

Theresa Elstner, Johannes Kiesel, Lars Meyer, Max Martius, Sebastian Schmidt, Benno Stein, and Martin Potthast. Visual Web Archive Quality Assessment. Linking Theory and Practice of Digital Libraries, 365--371, Springer International Publishing, Cham, 2022. [PUMA: topic_lifescience]

Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L Gedman, Lindsey J Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C Vernes, Tanya M Lama, Frank Grutzner, Wesley C Warren, Christopher N Balakrishnan, Dave Burt, Julia M George, Matthew T Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F Kautt, Paolo Franchini, H William Detrich, 3rd, Hannes Svardal, Maximilian Wagner, Gavin J P Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B Kingan, Richard Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E Green, Nicholas H Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E Dagnew, Dengfeng Guan, Sarah E London, David F Clayton, Claudio V Mello, Samantha R Friedrich, Peter V Lovell, Ekaterina Osipova, Farooq O Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S Harris, Kateryna D Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H S Kraus, Andrew J Crawford, M Thomas P Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A Ryder, David Haussler, Stephen J O'Brien, Jonas Korlach, Harris A Lewin, Kerstin Howe, Eugene W Myers, Richard Durbin, Adam M Phillippy, and Erich D Jarvis. Towards complete and error-free genome assemblies of all vertebrate species. Nature, (592)7856:737--746, Springer Science and Business Media LLC, April 2021. [PUMA: topic_lifescience]

Lucas Schneider, Eva Krieghoff-Henning, Sara Laiouar-Pedari, Sara Kuntz, Achim Hekler, Jakob N Kather, Timo Gaiser, Stefan Fröhling, and Titus J Brinker. Response to letter entitled: Re: Integration of deep learning-based image analysis and genomic data in cancer pathology: A systematic review. Eur. J. Cancer, (172):403--404, Elsevier BV, September 2022. [PUMA: topic_lifescience]

Shannon T Smith, Laura Shub, and Jens Meiler. PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking. PLoS One, (17)5:e0269072, Public Library of Science (PLoS), May 2022. [PUMA: topic_lifescience]

Moritz Seiler, Heike Trautmann, and Pascal Kerschke. Enhancing resilience of deep learning networks by means of transferable adversaries. 2020 International Joint Conference on Neural Networks (IJCNN), IEEE, July 2020. [PUMA: topic_lifescience]

Henry Kirveslahti, and Sayan Mukherjee. Representing fields without correspondences: The lifted Euler characteristic transform. arXiv, 2021. [PUMA: topic_lifescience]

Beatriz Guillen-Guio, Jose M Lorenzo-Salazar, Shwu-Fan Ma, Pei-Chi Hou, Tamara Hernandez-Beeftink, Almudena Corrales, M Isabel Garc\'ıa-Laorden, Jonathan Jou, Elena Espinosa, Arturo Muriel, David Dom\'ınguez, Leonardo Lorente, Mar\'ıa M Mart\'ın, Carlos Rodr\'ıguez-Gallego, Jordi Solé-Violán, Alfonso Ambrós, Demetrio Carriedo, Jesús Blanco, José M Añón, John P Reilly, Tiffanie K Jones, Caroline Ag Ittner, Rui Feng, Franziska Schöneweck, Michael Kiehntopf, Imre Noth, Markus Scholz, Frank M Brunkhorst, André Scherag, Nuala J Meyer, Jesús Villar, and Carlos Flores. Sepsis-associated acute respiratory distress syndrome in individuals of European ancestry: a genome-wide association study. Lancet Respir. Med., (8)3:258--266, Elsevier BV, March 2020. [PUMA: topic_lifescience]

Björn Böttcher, Martin Keller-Ressel, and René L Schilling. Distance multivariance: New dependence measures for random vectors. Ann. Stat., (47)5:2757--2789, Institute of Mathematical Statistics, October 2019. [PUMA: topic_lifescience]

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

Nacira Abbas, Kholoud Alghamdi, Mortaza Alinam, Francesca Alloatti, Glenda Amaral, Claudia d'Amato, Luigi Asprino, Martin Beno, Felix Bensmann, Russa Biswas, Ling Cai, Riley Capshaw, Valentina Anita Carriero, Irene Celino, Amine Dadoun, Stefano De Giorgis, Harm Delva, John Domingue, Michel Dumontier, Vincent Emonet, Marieke van Erp, Paola Espinoza Arias, Omaima Fallatah, Sebastián Ferrada, Marc Gallofré Ocaña, Michalis Georgiou, Genet Asefa Gesese, Frances Gillis-Webber, Francesca Giovannetti, Mar\`ıa Granados Buey, Ismail Harrando, Ivan Heibi, Vitor Horta, Laurine Huber, Federico Igne, Mohamad Yaser Jaradeh, Neha Keshan, Aneta Koleva, Bilal Koteich, Kabul Kurniawan, Mengya Liu, Chuangtao Ma, Lientje Maas, Martin Mansfield, Fabio Mariani, Eleonora Marzi, Sepideh Mesbah, Maheshkumar Mistry, Alba Catalina Morales Tirado, Anna Nguyen, Viet Bach Nguyen, Allard Oelen, Valentina Pasqual, Heiko Paulheim, Axel Polleres, Margherita Porena, Jan Portisch, Valentina Presutti, Kader Pustu-Iren, Ariam Rivas Mendez, Soheil Roshankish, Sebastian Rudolph, Harald Sack, Ahmad Sakor, Jaime Salas, Thomas Schleider, Meilin Shi, Gianmarco Spinaci, Chang Sun, Tabea Tietz, Molka Tounsi Dhouib, Alessandro Umbrico, Wouter van den Berg, and Weiqin Xu. Knowledge Graphs evolution and preservation -- A technical report from ISWS 2019. arXiv, 2020. [PUMA: topic_lifescience]

Susanne N Gröbner, ICGC PedBrain-Seq Project, Barbara C Worst, Joachim Weischenfeldt, Ivo Buchhalter, Kortine Kleinheinz, Vasilisa A Rudneva, Pascal D Johann, Gnana Prakash Balasubramanian, Maia Segura-Wang, Sebastian Brabetz, Sebastian Bender, Barbara Hutter, Dominik Sturm, Elke Pfaff, Daniel Hübschmann, Gideon Zipprich, Michael Heinold, Jürgen Eils, Christian Lawerenz, Serap Erkek, Sander Lambo, Sebastian Waszak, Claudia Blattmann, Arndt Borkhardt, Michaela Kuhlen, Angelika Eggert, Simone Fulda, Manfred Gessler, Jenny Wegert, Roland Kappler, Daniel Baumhoer, Stefan Burdach, Renate Kirschner-Schwabe, Udo Kontny, Andreas E Kulozik, Dietmar Lohmann, Simone Hettmer, Cornelia Eckert, Stefan Bielack, Michaela Nathrath, Charlotte Niemeyer, Günther H Richter, Johannes Schulte, Reiner Siebert, Frank Westermann, Jan J Molenaar, Gilles Vassal, Hendrik Witt, Birgit Burkhardt, Christian P Kratz, Olaf Witt, Cornelis M van Tilburg, Christof M Kramm, Gudrun Fleischhack, Uta Dirksen, Stefan Rutkowski, Michael Frühwald, Katja von Hoff, Stephan Wolf, Thomas Klingebiel, Ewa Koscielniak, Pablo Landgraf, Jan Koster, Adam C Resnick, Jinghui Zhang, Yanling Liu, Xin Zhou, Angela J Waanders, Danny A Zwijnenburg, Pichai Raman, Benedikt Brors, Ursula D Weber, Paul A Northcott, Kristian W Pajtler, Marcel Kool, Rosario M Piro, Jan O Korbel, Matthias Schlesner, Roland Eils, David T W Jones, Peter Lichter, Lukas Chavez, Marc Zapatka, Stefan M Pfister, and ICGC MMML-Seq Project. The landscape of genomic alterations across childhood cancers. Nature, (555)7696:321--327, Springer Science and Business Media LLC, March 2018. [PUMA: topic_lifescience]

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]