Publications

M Siemann, A Alvarado-Marin, M Pietzsch, and C Syldatk. A D-specific hydantoin amidohydrolase: properties of the metalloenzyme purified from Arthrobacter crystallopoietes. JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, (6)3:387-397, ELSEVIER SCIENCE BV, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS, March 1999. [PUMA: dihydropyrimidinase; myown urease; purification; hydantoin; protein amino acid} amidase; {hydantoinase; cyclic] URL

C. Kreutz, M.M. Bartolome Rodriguez, T. Maiwald, M. Seidl, H.E. Blum, L. Mohr, and J. Timmer. An error model for protein quantification. Bioinformatics, (23)20:2747--2753, Oxford University Press (OUP), September 2007. [PUMA: error protein model] URL

E. A. Oprzeska-Zingrebe, and J. Smiatek. Aqueous ionic liquids in comparison with standard co-solutes - Differences and common principles in their interaction with protein and DNA structures. Biophysical Reviews, (10)3:809-824, June 2018. [PUMA: sfb716 visus:smiatejs protein vis(us) chemistry dna simulation sfb716-c8 physical] URL

Tobias Kulschewski, and Jürgen Pleiss. Binding of solvent molecules to a protein surface in binary mixtures follows a competitive Langmuir model. Langmuir, (32):8960-8968, 2016. [PUMA: sfb716-c1 sfb716 dynamics molecular protein vis(us) chemistry simulation visus:pleissjn physical] URL

Ingo Amm, Mona Kawan, and Dieter H. Wolf. Characterization of protein quality control components via dual reporter-containing misfolded cytosolic model substrates. ANALYTICAL BIOCHEMISTRY, (515):14-21, ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA, December 2016. [PUMA: dehydrogenase} Cytosolic degradation; protein proteins; control; {Misfolded Luciferase; Chaperones; Proteasomal beta-isopropylmalate quality]

Tamara Bobic, and Roman Klinger. Committee-based Selection of Weakly Labeled Instances for Learning Relation Extraction. Research in Computing Science, (70):187-197, 2013. [PUMA: weak myown labeling distant protein supervision relation recognition] URL

Christian U. Stehle, Wasim Abuillana, Bruno Gompf, and Martin Dressel. Far-infrared spectroscopy on free-standing protein films under defined temperature and hydration control. The Journal of Chemical Physics, (136)7:075102, February 2012. [PUMA: films free-standing protein]

VL Katanaev, AS Spirin, M Reuss, and M Siemann. Formation of bacteriophage MS2 infectious units in a cell-free translation system. FEBS LETTERS, (397)2-3:143-148, ELSEVIER SCIENCE BV, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS, November 1996. [PUMA: myown protein proteinsynthesis]

Tamara Bobic, Roman Klinger, Philippe Thomas, and Martin Hofmann-Apitius. Improving Distantly Supervised Extraction of Drug-Drug and Protein-Protein Interactions. Proceedings of the Joint Workshop on Unsupervised and Semi-Supervised Learning in NLP, 35-43, Association for Computational Linguistics, Avignon, France, April 2012. [PUMA: nlp drug myown protein ddi ppi interaction bionlp] URL

Marc Benjamin Hahn, Tihomir Solomun, Robert Wellhausen, Sabrina Hermann, Harald Seitz, Susann Meyer, Hans-Jörg Kunte, Johannes Zeman, Frank Uhlig, Jens Smiatek, and Heinz Sturm. Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA. Journal of Physical Chemistry B, (119)49:15212--15220, 2015. [PUMA: sfb716 molecular chemistry simulation sfb716-c8 dynamics visus:smiatejs 2015 protein vis(us) dna physical]

Michael Krone, Martin Falk, S. Rehm, Jürgen Pleiss, and Thomas Ertl. Interactive exploration of protein cavities. Comput. Graph. Forum, (30):673-682, 2011. [PUMA: sfb716-d4 visus:kroneml sfb716 visus:ertlts protein vis(us) simulation] URL

Michael Krone, Guido Reina, Christoph Schulz, Tobias Kulschewski, Jürgen Pleiss, and Thomas Ertl. Interactive extraction and tracking of biomolecular surface features. Comput. Graph. Forum, (32):331-340, 2013. [PUMA: sfb716-d4 visus:kroneml sfb716 visus:ertlts protein vis(us) simulation] URL

Philippe Thomas, Illés Solt, Roman Klinger, and Ulf Leser. Learning Protein Protein Interaction Extraction using Distant Supervision. Proceedings of Workshop on Robust Unsupervised and Semisupervised Methods in Natural Language Processing, 25-32, Hissar, Bulgaria, September 2011. [PUMA: myown distant protein supervision ppi] URL

S Arnold, M Siemann-Herzberg, J Schmid, and M Reuss. Model-based inference of gene expression dynamics from sequence information. In Nielsen, J (Eds.), BIOTECHNOLOGY FOR THE FUTURE, (100):89-179, SPRINGER-VERLAG BERLIN, HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY, 2005. [PUMA: transcription; simulation; myown modeling mRNA {dynamic degradation} protein and biosynthesis; translation;] URL

Ingo Amm, and Dieter H. Wolf. Molecular mass as a determinant for nuclear San1-dependent targeting of misfolded cytosolic proteins to proteasomal degradation. FEBS LETTERS, (590)12:1765-1775, WILEY-BLACKWELL, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA, June 2016. [PUMA: ubiquitin cytosolic San1; ligase; protein proteins; control; {Misfolded nucleus; Ubr1} quality]

Larry Smith, Lorraine K. Tanabe, Rie Johnson nee Ando, Cheng-Ju Juo, I-Fang Chung, Chun-Nan Hsu, Yu-Shi Lin, Roman Klinger, Christoph M. Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu, Barry Haddow, Craig A. Struble, Richard J. Povinelli, Andreas Vlachos, William A. Baumgartner Jr., Lawrence Hunter, Bob Carpenter, Richard Tzong-Han Tsai, Hong jie Dai, Feng Liu, Yifei Chen, Chengjie Sun, Sophia Katrenko, Pieter Adriaans, Christian Blaschke, Rafel Torres Perez, Mariana Neves, Preslav Nakov, Anna Divoli, Manuel Mana, Jacinto Mata-Vazquez, and W. John Wilbur. Overview of BioCreative II Gene Mention Recognition. Genome Biology, (9)Suppl 2:S2.2-S2.18, September 2008. [PUMA: shared myown task gene protein competition ner bionlp] URL

Jürgen Pleiss. Protein design in metabolic engineering and synthetic biology. Curr.Opin.Biotech., (22):1-7, 2011. [PUMA: sfb716 dynamics molecular protein vis(us) chemistry simulation visus:pleissjn 2011 physical] URL

B. Gompf, A. Matei, N. Drichko, M. Dressel, F. Bös, and J. Pleiss. Protein dynamics in the THz-range. IRMMW 2004/THz 2004: 739, 2004. [PUMA: dynamics protein]

Helmut Bertagnolli, and Wolfgang. Kaim. The dinuclear CuA center in cytochrome c oxidase and N2O reductase. A metal-metal bond in biology?. Angewandte Chemie, International Edition in English, (34)7:771--773, 1995. [PUMA: dinuclear center protein copper review]