Curriculum Vitae

Name:	Kristian Mikael Rother
Date of Birth:	11.4.1977 in Berlin
Nationality:	Finnish/German

Academic Degrees and Positions

from	to	position	location
10/2009	now	DAAD Fellowship	Biological Faculty, UAM Poznan, Poland
10/2006	09/2009	Marie Curie Fellowship in the 6th EU RTN "DNA Enzymes"	Lab of Dr. habil. Janusz Bujnicki, International Institute of Molecular Cell Biology Warszawa
07/2002	05/2006	Graduate student - thesis: Efficient use of a Protein Structure Annotation Database	Protein Structure Theory Group, Prof. Dr. Cornelius Frömmel, Charité Berlin
10/1996	03/2002	Diploma of Biochemistry - thesis: Packing Density and Packing Defects in Protein Structures	Freie Universität Berlin;
08/2001	02/2002	Web administrator	Neuroinformatics Group, Institute of Biology, Humboldt Universität Berlin.
05/2000	08/2001	Student coworker	Protein Structure Theory Group, Prof. Dr. Cornelius Frömmel, Charité Berlin

Languages

language	level
German	native
Finnish	native
English	experienced
Polish	fluent
Latin	9 years in school

Computer Skills

Python (advanced)

Adobe Flex, Java, Delphi, Fortran, PHP, ANSI C (basic)

certified IBM DB2 User

PostGreSQL, SQLite

Django, TurboGears, Zope

UML

Test-Driven-Development

Bioinformatics Skills

RNA 3D structure modeling	RNA 3D structure prediction
3D Structure analysis	Structure visualisation
Database design	Database integration
Protein sequence analysis	Homology modeling
Contributing to bioinformatics libraries	Annotation of metabolic maps

Other practical Skills

Didactic methodology and techniques

Project organization and management

Time management

Kanban

SCRUM

Personal Interests

Chess/go/board games

Ballroom dancing

Calligraphy and painting

Teaching

course	location	duration	date
Advanced Python for bioinformatics students	Adam Mickiewicz University Poznan	two-week course	2007-2010
Presentation training	IIMCB Warsaw/UAM Poznan	2h seminar	2007-2009
Structural biology of nucleic acids	IMIM, Spain	10h course	2009
Introduction to Python	IIMCB Warsaw	one-day seminar	2008
Bioinformatics Applications in Python	Adam Mickiewicz University Poznan	15h seminar	2008
Applied bioinformatics	Freie Universität Berlin	6 ECTS points	2003, 2005 and 2006
Homology modeling of aa-tRNA-synthetases for bioinformatics students	Freie Universität Berlin	two-week course	2005
Chemistry for medical students	Charité Berlin	weekly seminar	2005 (2x), and 2006
Chemistry for medical students	Charité Berlin	5-day lab course	2005 (2x), and 2006
Biochemistry for medical students	Charité Berlin	weekly seminar	2004
Molecular modeling for biologists	Humboldt Universität Berlin	two-week block course	2001-2004 (2x)

References

Scientific papers

Musielak M, Rother K, Puton T, Bujnicki JM. ModeRNA builds RNA 3D Models from Template Structures. ERCIM News (in press).

Rother K, Musielak M, Pleus A, Upmeier zu Belzen A, Multi-Stage Learning Aids applied to hands-on software training. Briefings in Bioinformatics (in press).

Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhutter HG (2010) IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities. Biophys J 98: 2478-2486.

Bauer R, Rother K, Moor P, Bujnicki JM, Preissner R. Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors. Algorithms 2009, 2(2), 692-709.

Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak J, Bujnicki JM, Grosjean H, Rother K. MODOMICS: A database of RNA modification pathways. 2008 update. Nucleic Acids Res. 2009 Jan;37(Database issue):D118-21. Epub 2008 Oct 14.

Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R. Voronoia: Analyzing packing in protein structures. Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5. Epub 2008 Oct 23.

Bauer RA, Rother K, Bujnicki JM, Preissner R. Suffix techniques as a rapid method for RNA substructure search. Genome Informatics, Vol. 20 (2008), pp. 183-198.

Smit S, Rother K, Heringa J, Knight R (2008). From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal, RNA. 2008 Mar;14(3):410-6.

Hodis E, Schreiber G, Rother K, Sussman JL. eMovie: a storyboard-based tool for making molecular movies. Trends Biochem Sci. 2007 May;32(5):199-204. Epub 2007 Apr 19.

Zbilut JP, Chua GH, Krishnan A, Bossa C, Rother K, Webber CL Jr, Giuliani A. A topologically related singularity suggests a maximum preferred size for protein domains. Proteins. 2007 Feb 15;66(3):621-9.

Günther S, Hempel D, Dunkel M, Rother K, Preissner R.SuperHapten: a comprehensive database for small immunogenic compounds. Nucleic Acids Res. 2007 Jan;35(Database issue):D906-10. Epub 2006 Nov 7.

Günther S, Rother K, Frömmel C. Molecular flexibility in protein-DNA-interactions. Biosystems 2006.Aug;85(2):126-36. Epub Feb 20.

Rother K, Dunkel M, Michalsky E, Trissl S, Goede A, Leser U, Preißner R. A structural keystone for drug design. Journal of Integrative Bioinformatics. 2006 Jan 19; 0019. Online Journal.

Rother K, Michalsky E, Leser U. How well are protein structures annotated in secondary databases? Proteins. 2005 Sep 1; 60(4):571-576.

Trissl S, Rother K, Müller H, Steinke T, Koch I, Preißner R, Frömmel C, Leser U. Columba: an integrated database of proteins, structures, and annotations. BMC Bioinformatics 2005, Mar 31;6(81).

Hildebrandt P, Rother K, Preißner R, Goede A, Frömmel C. Packing density and packing defects in helical membrane proteins. Biophys J 2005, 88;1970-1977.

Rother K, Müller H, Trissl S, Koch I, Steinke T, Preißner R, Frömmel C, Leser, U. Columba: Multidimensional data integration of protein annotations. DILS conference on databases in life sciences 2004, 2994, 156-171.

Rother K, Preißner R, Goede A, Frömmel C. Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics. 2003 Nov 1;19(16):2112-2121.

Preißner R, Goede A, Rother K, Osterkamp F, Koert U, Frömmel C. Matching organic libraries with protein-substructures. J Comput Aided Mol Des. 2001 Sep;15(9):811-817.

Gille C, Goede A, Preißner R, Rother K, Frömmel C. Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits. J Mol Biol. 2000 Jun 16;299(4):1147-1154.

Book Contributions

Czerwoniec A, Kasprzak JM, Kaminska KH, Rother K, Bujnicki JM. Folds and functions of domains in RNA modification enzymes. In „DNA and RNA Enzymes“ edited by Henri Grosjean. Landes Bioscience 2009. ISBN-13/EAN: 9781587063299.

Rother K, Czerwoniec A, Bujnicki JM, Grosjean H. Chemical Structures, classification of modified nucleosides in RNA and the MODOMICS database concerning the corresponding RNA modification enzymes. In „DNA and RNA Enzymes“ edited by Henri Grosjean. Landes Bioscience 2009. ISBN-13/EAN: 9781587063299.

Rother K, Papaj G, Bujnicki JM. Databases of DNA Modifications. In „DNA and RNA Enzymes“ edited by Henri Grosjean. Landes Bioscience 2009. ISBN-13/EAN: 9781587063299.

Rother K. Zwanzig Zeichen. In „Ein Entscheidender Teil fehlt“ edited by Käthe Wenzel, Lisa Glauer and Tatjana Fell . Mensch & Buch Verlag Berlin, 208 pages.

Knapp W, Wenzel K, Frömmel C, Schnalke T (Ed.): The Missing Link. Art meets Biomedicine. Public understanding of art and sciences. Berlin 2005. ISBN 3-89462-133.

Exhibitions

Oscillations, Budapest (2009).

Visual Reflections on Science, ISMB/ECCB 2009, Stockholm (2009). Awarded 1st prize.

Proteinkalligraphie. Institute of Biochemistry, FU Berlin (2006).

Missing Link - Art Meets Biomedicine, The Rubelle & Norman Schafler Gallery, Brooklyn, N.Y. (2006).

arts & science in vitro - Der seltsame Tanz der sozialen Amöbe. Institute of Biochemistry, Charité Berlin (2006).

The Missing Link – Communication in Science and Arts. BMM Charité (2005).

Kristian Rother (8/2009)