Publications

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

Sonja J Prohaska, Sarah J Berkemer, Fabian Gärtner, Thomas Gatter, Nancy Retzlaff, Students of the Graphs and Biological Networks Lab 2017, Christian Höner Zu Siederdissen, und Peter F Stadler. Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem. J. Math. Biol., (77)2:313--341, August 2018. [PUMA: Evolution Hamiltonian Kalmanson Non-homologous Phylogenetic Unequal clusters; combinatorics; crossing gene metrics; of over path problems; recombination;]

V Janett Olzog, Christiane Gärtner, Peter F Stadler, Jörg Fallmann, und Christina E Weinberg. cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3' cyclic phosphates and 5' hydroxyl ends. RNA Biol., (18)sup2:818--831, Informa UK Limited, November 2021. [PUMA: (RppH); 5ʹ-3ʹ KQ; RNA RtcB T4 Xrn1; exonuclease ligase ligase; next-generation pyrophosphohydrolase sequencing truncated]

Katja Hoffmann, Katja Cazemier, Christoph Baldow, Silvio Schuster, Yuri Kheifetz, Sibylle Schirm, Matthias Horn, Thomas Ernst, Constanze Volgmann, Christian Thiede, Andreas Hochhaus, Martin Bornhäuser, Meinolf Suttorp, Markus Scholz, Ingmar Glauche, Markus Loeffler, und Ingo Roeder. Integration of mathematical model predictions into routine workflows to support clinical decision making in haematology. BMC Med. Inform. Decis. Mak., (20)1:28, Februar 2020. [PUMA: Clinical Computer Data Haematology; Individual Mathematical Model-based Routine Support decision-making; management; modelling; optimization; planning; simulation; system therapy treatment workflow;]

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

Damien Graux, Gezim Sejdiu, Hajira Jabeen, Jens Lehmann, Danning Sui, Dominik Muhs, und 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, und Peter F Stadler. RNA secondary structures with limited base pair span: Exact backtracking and an application. Genes (Basel), (12)1:14, MDPI AG, Dezember 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, und 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, und Jana Schor. The fungal snoRNAome. RNA, (24)3:342--360, März 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, und 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, Februar 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, und 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, Oktober 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, und 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, und 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, und 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), Mai 2021. [PUMA: Cardiovascular Coronary Inflammasome; Inflammation; NLRP3 artery disease; diseases;]

Sebastian Rosch, Karl-Philipp Rommel, Markus Scholz, Holger Thiele, und Philipp Lurz. Transcriptomic research in heart failure with preserved ejection fraction: Current state and future perspectives. Card. Fail. Rev., (6):e24, Radcliffe Group Ltd, März 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, und 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, März 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, und Daniel Wiegreffe. Masakari: visualization supported statistical analysis of genome segmentations. BMC Bioinformatics, (21)1:437, Springer Science and Business Media LLC, Oktober 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, und 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), Juli 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, und 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, Mai 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), Juni 2020. [PUMA: aptitude area; association brain cortical development; genome-wide occupational study; surface thickness;]