Publications - Published papers

Please find below publications of our group. Currently, we list 508 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

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Publications of the bioinformatics group 2017

Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem

Prohaska, Sonja J and Berkemer, Sarah J and Gärtner, Fabian and Gatter, Thomas and Retzlaff, Nancy and Siederdissen, Christian Höner and Stadler, Peter F and others,
Journal of mathematical biology: 1--29
PREPRINT 18-044: [ Abstract ]
[ Publishers's page ]

Multidimensional segmentation of heterogeneous data

H. S. Saker, and P. F. Stadler, and A. M. Shahin,
2017 Fourth International Conference on Advances in Biomedical Engineering (ICABME)
PREPRINT 18-043: [ Abstract ]
[ Publishers's page ]

Design of Artificial Riboswitches as Biosensors

Sven Findeiß, and Maja Etzel, and Sebastian Will, and Mario Mörl, and Peter Stadler,
Sensors 17 (9): 1990
PREPRINT 18-042: [ Abstract ]
[ Publishers's page ]

Towards a consistent, quantitative evaluation of microRNA evolution

Yazbeck, Ali M and Tout, Kifah R and Stadler, Peter F and Hertel, Jana
Journal of Integrative Bioinformatics 14 (1)
PREPRINT 18-041: [ Abstract ]
[ Publishers's page ]

The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence.

Mages, Christina Fs and Wintsche, Axel and Bernhart, Stephan H. and Müller, Gerd A.
eLife 6
PREPRINT 18-027: [ Abstract ]
[ Publishers's page ]

DIEGO: Detection of Differential Alternative Splicing using Aitchison's Geometry.

Doose, Gero and Bernhart, Stephan H. and Wagener, Rabea and Hoffmann, Steve
Bioinformatics (Oxford, England)
PREPRINT 18-026: [ Abstract ]
[ Publishers's page ]

Algebraic Dynamic Programming on Trees

Berkemer, Sarah J and Siederdissen, Christian and Stadler, Peter F
Algorithms 10 (4): 135
PREPRINT 18-025:

Tractable RNA--ligand interaction kinetics

Kühnl, Felix and Stadler, Peter F. and Will, Sebastian
BMC Bioinformatics 18 (12): 424
PREPRINT 18-024: [ Abstract ]
[ Publishers's page ]

The Periodic System: A Mathematical Approach

Guillermo Restrepo,
Mendeleev to Oganesson: A Multidisciplinary Perspective on the Periodic Table
PREPRINT 18-023:

Una mirada a la estructura de semejanzas del sistema periódico de los elementos químicos

Restrepo, Guillermo
PREPRINT 18-021:

José Luis Villaveces, el humano detrás del sabio

Restrepo, Guillermo
PREPRINT 18-020:

Mendeleev to Oganesson: A Multidisciplinary Perspective on the Periodic Table

Eric Scerri, and Guillermo Restrepo,
Oxford University Press
PREPRINT 18-019:

iDotter - an interactive dot plot viewer

Daniel Gerighausen, and Alrik Hausdorf, and Sebastian Zaenker, and Dirk Zeckzer,
25th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision 2017
PREPRINT 18-018:

Partially Local Multi-Way Alignments

Retzlaff, Nancy and Stadler, Peter F.
PREPRINT 18-017: [ Abstract ]

Phylogenetics Beyond Biology

Retzlaff, Nancy and Stadler, Peter F.
Theory in Biosciences. 1-11 (2018)
PREPRINT 18-016: [ Abstract ]

Studying Language Evolution in the Age of Big Data

Bhattacharya, Tanmoy and Blasi, Damian and Croft, William and Cysouw, Michael and Hruschka, Daniel and Maddieson, Ian and Retzlaff, Nancy and Smith, Eric and Stadler, Peter F. and Starostin, George and M\
Journal of Language Evolution
PREPRINT 18-015: [ Abstract ]

A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma

Voigt, André and Nowick, Katja and Almaas, Eivind
PLOS Computational Biology 13 (9): 1-34
PREPRINT 18-012: [ Abstract ]
[ Publishers's page ]

Erratum to: Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens

Doublet, Vincent and Poeschl, Yvonne and Gogol-Döring, Andreas and Alaux, Cédric and Annoscia, Desiderato and Aurori, Christian and Barribeau, Seth M. and Bedoya-Reina, Oscar C. and Brown, Mark J. F. and Bull, James C. and Flenniken, Michelle L. and Galbraith, David A. and Genersch, Elke and Gisder, Sebastian and Grosse, Ivo and Holt, Holly L. and Hultmark, Dan and Lattorff, H. Michael G. and Le Conte, Yves and Manfredini, Fabio and McMahon, Dino P. and Moritz, Robin F. A. and Nazzi, Francesco and Ni\~no, Elina L. and Nowick, Katja and Rij, Ronald P. and Paxton, Robert J. and Grozinger, Christina M.
BMC Genomics 18 (1): 256
PREPRINT 18-011:
[ Publishers's page ]

Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens

Doublet, Vincent and Poeschl, Yvonne and Gogol-Döring, Andreas and Alaux, Cédric and Annoscia, Desiderato and Aurori, Christian and Barribeau, Seth M. and Bedoya-Reina, Oscar C. and Brown, Mark J. F. and Bull, James C. and Flenniken, Michelle L. and Galbraith, David A. and Genersch, Elke and Gisder, Sebastian and Grosse, Ivo and Holt, Holly L. and Hultmark, Dan and Lattorff, H. Michael G. and Le Conte, Yves and Manfredini, Fabio and McMahon, Dino P. and Moritz, Robin F. A. and Nazzi, Francesco and Ni\~no, Elina L. and Nowick, Katja and Rij, Ronald P. and Paxton, Robert J. and Grozinger, Christina M.
BMC Genomics 18 (1): 207
PREPRINT 18-010: [ Abstract ]
[ Publishers's page ]

wTO: an R package for computing weighted topological overlap and consensus networks with an integrated visualization tool

Morselli Gysi, D. and Voigt, A. and Fragoso, T.~d.~M. and Almaas, E. and Nowick, K.
ArXiv e-prints
PREPRINT 18-008:

Accurate Mapping of tRNA Reads

Hoffmann, A. and Fallmann, J. and Morl, M. and Stadler, P. F. and Amman, F.
Bioinformatics
PREPRINT 18-006:
[ Publishers's page ]

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Gruning, B. A. and Fallmann, J. and Yusuf, D. and Will, S. and Erxleben, A. and Eggenhofer, F. and Houwaart, T. and Batut, B. and Videm, P. and Bagnacani, A. and Wolfien, M. and Lott, S. C. and Hoogstrate, Y. and Hess, W. R. and Wolkenhauer, O. and Hoffmann, S. and Akalin, A. and Ohler, U. and Stadler, P. F. and Backofen, R.
Nucleic Acids Res.
PREPRINT 18-004:
[ Publishers's page ]

Recent advances in RNA folding

Fallmann, J. and Will, S. and Engelhardt, J. and Gruning, B. and Backofen, R. and Stadler, P. F.
J. Biotechnol. 261: 97--104
PREPRINT 18-003:

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

Backofen, R. and Engelhardt, J. and Erxleben, A. and Fallmann, J. and Gruning, B. and Ohler, U. and Rajewsky, N. and Stadler, P. F.
J. Biotechnol. 261: 76--84
PREPRINT 18-001:
[ Publishers's page ]

SMORE: Synteny Modulator of Repetitive Elements

Berkemer, Sarah J. and Hoffmann, Anne and Murray, Cameron R. A. and Stadler, Peter F.
Life 7 (4)
PREPRINT 17-015: [ Abstract ]
[ Publishers's page ]

Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1

Maria Beatriz Walter Costa, and Christian Höner zu Siederdissen, and Dan Tulpan, and Peter F. Stadler, and Katja Nowick,
Journal of Theoretical Biology 438 (Supplement C): 143 - 150
PREPRINT 17-014: [ Abstract ]  [ Supplement ]
[ Publishers's page ]

Detailed Secondary Structure Models of Invertebrate 7SK RNAs

Ali M. Yazbeck, Kifah R. Tout, Peter F. Stadler
RNA Biology 0 (0)
PREPRINT 17-013: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]

Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

Indrischek, Henrike and Prohaska, Sonja J and Gurevich, Vsevolod V and Gurevich, Eugenia V and Stadler, Peter F
BMC evolutionary biology 17: 163
PREPRINT 17-011:
[ Publishers's page ]

Ranking of 38 prokaryotes according to their uranium uptake capacity in aqueous solutions: An approach from order theory through the Hasse Diagram Technique

Quintero, Nancy Y and Bruggemann, Rainer and Restrepo, Guillermo
Toxicological \& Environmental Chemistry undefined: 1--28
PREPRINT 17-010:
[ Publishers's page ]

The Journal of Mathematical Chemistry: a bibliometric profile

Restrepo, Guillermo and Willett, Peter
Journal of Mathematical Chemistry undefined: 1--8
PREPRINT 17-009:
[ Publishers's page ]

Formal Concept Analysis Applications in Chemistry: From Radionuclides and Molecular Structure to Toxicity and Diagnosis

Quintero, Nancy Y and Restrepo, Guillermo
Partial Order Concepts in Applied Sciences: 207--217 (Springer)
PREPRINT 17-004:
[ Publishers's page ]

Evolution of Fungal U3 snoRNAs: Structural Variation and Introns

Sebastian Canzler, Peter F. Stadler, Jana Hertel
Non-Coding RNA 3.1 (2017): 3.
PREPRINT 16-018: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]