Publications

Daniel Wiegreffe, Lydia Müller, Jens Steuck, Dirk Zeckzer, and Peter F Stadler. The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments. BMC Res. Notes, (11)1:512, July 2018. [PUMA: ChIP-seq; Histone Peak-caller; Replicate analysis modifications;]

Damien Graux, Gezim Sejdiu, Hajira Jabeen, Jens Lehmann, Danning Sui, Dominik Muhs, and Johannes Pfeffer. Profiting from Kitties on Ethereum: Leveraging Blockchain RDF with SANSA. 14th International Conference on Semantic Systems, Poster & Demos, 2018. [PUMA: 2018 bde graux group_aksw jabeen lehmann sansa sejdiu] URL

Ronny Lorenz, and Peter F Stadler. RNA secondary structures with limited base pair span: Exact backtracking and an application. Genes (Basel), (12)1:14, MDPI AG, December 2020. [PUMA: RNA algorithm elements; hyper-stable prediction; scanning secondary structure]

Markus Kreuz, Dominik J Otto, Susanne Fuessel, Conny Blumert, Catharina Bertram, Sophie Bartsch, Dennis Loeffler, Sven-Holger Puppel, Michael Rade, Tilo Buschmann, Sabina Christ, Kati Erdmann, Maik Friedrich, Michael Froehner, Michael H Muders, Stephan Schreiber, Michael Specht, Marieta I Toma, Fabio Benigni, Massimo Freschi, Giorgio Gandaglia, Alberto Briganti, Gustavo B Baretton, Markus Loeffler, Jörg Hackermüller, Kristin Reiche, Manfred Wirth, and Friedemann Horn. ProstaTrend-A multivariable prognostic RNA expression score for aggressive prostate cancer. Eur. Urol., (78)3:452--459, Elsevier BV, September 2020. [PUMA: Biomarker; Molecular Next-generation Personalized Prostate Transcriptome cancer; diagnostic medicine; pathology; sequencing; testing;]

Sebastian Canzler, Peter F Stadler, and Jana Schor. The fungal snoRNAome. RNA, (24)3:342--360, March 2018. [PUMA: RNAs; conservation; evolution; fungi; nucleolar small snoRNA snoRNA; switch target target;]

Jens Przybilla, Peter Ahnert, Holger Bogatsch, Frank Bloos, Frank M Brunkhorst, SepNet Critical Care Trials Group, Progress Study Group, Michael Bauer, Markus Loeffler, Martin Witzenrath, Norbert Suttorp, and Markus Scholz. Markov state modelling of disease courses and mortality risks of patients with community-acquired pneumonia. J. Clin. Med., (9)2:393, MDPI AG, February 2020. [PUMA: Markov SOFA community-acquired continuous-time decision making; medical model model; pneumonia; prognosis; score; sepsis; stochastic]

Souhrid Mukherjee, Joy D Cogan, John H Newman, John A Phillips, 3rd, Rizwan Hamid, Undiagnosed Diseases Network, Jens Meiler, and John A Capra. Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. Am. J. Hum. Genet., (108)10:1946--1963, Elsevier BV, October 2021. [PUMA: Diseases Network; UDN; Undiagnosed clinical digenic disease disease; learning; machine oligogenic prediction; rare topic_lifescience]

Chiara Maria Lavinia Loeffler, Nadine T Gaisa, Hannah Sophie Muti, Marko van Treeck, Amelie Echle, Narmin Ghaffari Laleh, Christian Trautwein, Lara R Heij, Heike I Grabsch, Nadina Ortiz Bruechle, and Jakob Nikolas Kather. Predicting mutational status of driver and suppressor genes directly from histopathology with Deep Learning: A systematic study across 23 solid tumor types. Front. Genet., (12):806386, 2021. [PUMA: (AI); TCGA; artificail cancer deep genes; genetic intelligence learning; pathway pathway;]

A D Lokits, H Indrischek, J Meiler, H E Hamm, and P F Stadler. Tracing the evolution of the heterotrimeric G protein $\alpha$ subunit in Metazoa. BMC Evol. Biol., (18)1:51, April 2018. [PUMA: Evolution; G Genome Heterotrimeric Orthology; Paralog; Whole annotation; coupled duplication genome protein protein; receptors; topic_lifescience]

Stefan J Schunk, Marcus E Kleber, Winfried März, Shichao Pang, Stephen Zewinger, Sarah Triem, Philipp Ege, Matthias C Reichert, Marcin Krawczyk, Susanne N Weber, Isabella Jaumann, David Schmit, Tamim Sarakpi, Stefan Wagenpfeil, Rafael Kramann, Eric Boerwinkle, Christie M Ballantyne, Megan L Grove, Vinicius Tragante, Anna P Pilbrow, A Mark Richards, Vicky A Cameron, Robert N Doughty, Marie-Pierre Dubé, Jean-Claude Tardif, Yassamin Feroz-Zada, Maxine Sun, Chang Liu, Yi-An Ko, Arshed A Quyyumi, Jaana A Hartiala, W H Wilson Tang, Stanley L Hazen, Hooman Allayee, Caitrin W McDonough, Yan Gong, Rhonda M Cooper-DeHoff, Julie A Johnson, Markus Scholz, Andrej Teren, Ralph Burkhardt, Andreas Martinsson, J Gustav Smith, Lars Wallentin, Stefan K James, Niclas Eriksson, Harvey White, Claes Held, Dawn Waterworth, Stella Trompet, J Wouter Jukema, Ian Ford, David J Stott, Naveed Sattar, Sharon Cresci, John A Spertus, Hannah Campbell, Sascha Tierling, Jörn Walter, Emmanuel Ampofo, Barbara A Niemeyer, Peter Lipp, Heribert Schunkert, Michael Böhm, Wolfgang Koenig, Danilo Fliser, Ulrich Laufs, Thimoteus Speer, eQTLGen consortium, and BIOS consortium. Genetically determined NLRP3 inflammasome activation associates with systemic inflammation and cardiovascular mortality. Eur. Heart J., (42)18:1742--1756, Oxford University Press (OUP), May 2021. [PUMA: Cardiovascular Coronary Inflammasome; Inflammation; NLRP3 artery disease; diseases;]

Sebastian Rosch, Karl-Philipp Rommel, Markus Scholz, Holger Thiele, and Philipp Lurz. Transcriptomic research in heart failure with preserved ejection fraction: Current state and future perspectives. Card. Fail. Rev., (6):e24, Radcliffe Group Ltd, March 2020. [PUMA: Heart LIFE-Heart; RNA; blood cells; ejection expression; failure fraction; gene mononuclear peripheral preserved transcriptome with]

Veronika Scholz, Peter Winkler, Andreas Hornig, Maik Gude, and Angelos Filippatos. Structural damage identification of composite rotors based on fully connected neural networks and convolutional neural networks. Sensors (Basel), (21)6:2005, MDPI AG, March 2021. [PUMA: (SHM) composite composites; connected convolutional dense fully health learning; machine monitoring networks; neural rotors; structural]

Dirk Zeckzer, Alrik Hausdorf, Nicole Hinzmann, Lydia Müller, and Daniel Wiegreffe. Masakari: visualization supported statistical analysis of genome segmentations. BMC Bioinformatics, (21)1:437, Springer Science and Business Media LLC, October 2020. [PUMA: Cell ChIP-seq; Chromatin Histone development; modifications state;]

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: association brain; factors; genome-wide matter neuroimaging; risk study; topic_lifescience white]

John Anders, Hannes Petruschke, Nico Jehmlich, Sven-Bastiaan Haange, Martin von Bergen, and Peter F Stadler. A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. BMC Bioinformatics, (22)1:277, Springer Science and Business Media LLC, May 2021. [PUMA: Metaproteogenomics; Microbial Peptide-spectrum Small communitities; matches; proteins]

Jean Shin, Shaojie Ma, Edith Hofer, Yash Patel, Daniel E Vosberg, Steven Tilley, Gennady V Roshchupkin, André M M Sousa, Xueqiu Jian, Rebecca Gottesman, Thomas H Mosley, Myriam Fornage, Yasaman Saba, Lukas Pirpamer, Reinhold Schmidt, Helena Schmidt, Amaia Carrion-Castillo, Fabrice Crivello, Bernard Mazoyer, Joshua C Bis, Shuo Li, Qiong Yang, Michelle Luciano, Sherif Karama, Lindsay Lewis, Mark E Bastin, Mathew A Harris, Joanna M Wardlaw, Ian E Deary, Markus Scholz, Markus Loeffler, A Veronica Witte, Frauke Beyer, Arno Villringer, Nicola J Armstrong, Karen A Mather, David Ames, Jiyang Jiang, John B Kwok, Peter R Schofield, Anbupalam Thalamuthu, Julian N Trollor, Margaret J Wright, Henry Brodaty, Wei Wen, Perminder S Sachdev, Natalie Terzikhan, Tavia E Evans, Hieab H H H Adams, M Arfan Ikram, Stefan Frenzel, Sandra van der Auwera-Palitschka, Katharina Wittfeld, Robin Bülow, Hans Jörgen Grabe, Christophe Tzourio, Aniket Mishra, Sophie Maingault, Stephanie Debette, Nathan A Gillespie, Carol E Franz, William S Kremen, Linda Ding, Neda Jahanshad, ENIGMA Consortium, Nenad Sestan, Zdenka Pausova, Sudha Seshadri, Tomas Paus, and neuroCHARGE Working Group. Global and regional development of the human cerebral cortex: Molecular architecture and occupational aptitudes. Cereb. Cortex, (30)7:4121--4139, Oxford University Press (OUP), June 2020. [PUMA: aptitude area; association brain cortical development; genome-wide occupational study; surface thickness;]

Mathias Gorski, Bettina Jung, Yong Li, Pamela R Matias-Garcia, Matthias Wuttke, Stefan Coassin, Chris H L Thio, Marcus E Kleber, Thomas W Winkler, Veronika Wanner, Jin-Fang Chai, Audrey Y Chu, Massimiliano Cocca, Mary F Feitosa, Sahar Ghasemi, Anselm Hoppmann, Katrin Horn, Man Li, Teresa Nutile, Markus Scholz, Karsten B Sieber, Alexander Teumer, Adrienne Tin, Judy Wang, Bamidele O Tayo, Tarunveer S Ahluwalia, Peter Almgren, Stephan J L Bakker, Bernhard Banas, Nisha Bansal, Mary L Biggs, Eric Boerwinkle, Erwin P Bottinger, Hermann Brenner, Robert J Carroll, John Chalmers, Miao-Li Chee, Miao-Ling Chee, Ching-Yu Cheng, Josef Coresh, Martin H de Borst, Frauke Degenhardt, Kai-Uwe Eckardt, Karlhans Endlich, Andre Franke, Sandra Freitag-Wolf, Piyush Gampawar, Ron T Gansevoort, Mohsen Ghanbari, Christian Gieger, Pavel Hamet, Kevin Ho, Edith Hofer, Bernd Holleczek, Valencia Hui Xian Foo, Nina Hutri-Kähönen, Shih-Jen Hwang, M Arfan Ikram, Navya Shilpa Josyula, Mika Kähönen, Chiea-Chuen Khor, Wolfgang Koenig, Holly Kramer, Bernhard K Krämer, Brigitte Kühnel, Leslie A Lange, Terho Lehtimäki, Wolfgang Lieb, Lifelines Cohort Study, Regeneron Genetics Center, Ruth J F Loos, Mary Ann Lukas, Leo-Pekka Lyytikäinen, Christa Meisinger, Thomas Meitinger, Olle Melander, Yuri Milaneschi, Pashupati P Mishra, Nina Mononen, Josyf C Mychaleckyj, Girish N Nadkarni, Matthias Nauck, Kjell Nikus, Boting Ning, Ilja M Nolte, Michelle L O'Donoghue, Marju Orho-Melander, Sarah A Pendergrass, Brenda W J H Penninx, Michael H Preuss, Bruce M Psaty, Laura M Raffield, Olli T Raitakari, Rainer Rettig, Myriam Rheinberger, Kenneth M Rice, Alexander R Rosenkranz, Peter Rossing, Jerome I Rotter, Charumathi Sabanayagam, Helena Schmidt, Reinhold Schmidt, Ben Schöttker, Christina-Alexandra Schulz, Sanaz Sedaghat, Christian M Shaffer, Konstantin Strauch, Silke Szymczak, Kent D Taylor, Johanne Tremblay, Layal Chaker, Pim van der Harst, Peter J van der Most, Niek Verweij, Uwe Völker, Melanie Waldenberger, Lars Wallentin, Dawn M Waterworth, Harvey D White, James G Wilson, Tien-Yin Wong, Mark Woodward, Qiong Yang, Masayuki Yasuda, Laura M Yerges-Armstrong, Yan Zhang, Harold Snieder, Christoph Wanner, Carsten A Böger, Anna Köttgen, Florian Kronenberg, Cristian Pattaro, and Iris M Heid. Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline. Kidney Int., (99)4:926--939, Elsevier BV, April 2021. [PUMA: acute association decline disease; eGFRcrea end-stage genome-wide injury; kidney rapid study;]

Carl Beuchel, Susen Becker, Julia Dittrich, Holger Kirsten, Anke Toenjes, Michael Stumvoll, Markus Loeffler, Holger Thiele, Frank Beutner, Joachim Thiery, Uta Ceglarek, and Markus Scholz. Clinical and lifestyle related factors influencing whole blood metabolite levels - A comparative analysis of three large cohorts. Mol. Metab., (29):76--85, Elsevier BV, November 2019. [PUMA: Acylcarnitines; Amino Clinical Lifestyle Metabolomics; Network acids; analysis factors;]

Jan Gaebel, Hans-Georg Wu, Alexander Oeser, Mario A Cypko, Matthaeus Stoehr, Andreas Dietz, Thomas Neumuth, Stefan Franke, and Steffen Oeltze-Jafra. Modeling and processing up-to-dateness of patient information in probabilistic therapy decision support. Artif. Intell. Med., (104)101842:101842, Elsevier BV, April 2020. [PUMA: Arden Decision Head Medical Therapy and decision delay; logic model modules; neck oncology; support syntax; system;]

Lina Muhandes, Maria Chapsa, Martin Pippel, Rayk Behrendt, Yan Ge, Andreas Dahl, Buqing Yi, Alexander Dalpke, Sylke Winkler, Michael Hiller, Sebastien Boutin, Stefan Beissert, Rolf Jessberger, Padraic G Fallon, and Axel Roers. Low threshold for cutaneous allergen sensitization but no spontaneous dermatitis or atopy in FLG-deficient mice. J. Invest. Dermatol., (141)11:2611--2619.e2, Elsevier BV, November 2021. [PUMA: atopic barrier dermatitis; eczema; filaggrin; function; genetics mouse]