Publications - Published papers

Please find below publications of our group. Currently, we list 500 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 2016

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.

Jühling, Frank and Kretzmer, Helene and Bernhart, Stephan H. and Otto, Christian and Stadler, Peter F. and Hoffmann, Steve
Genome research 26 (2): 256--262
PREPRINT 18-031: [ Abstract ]
[ Publishers's page ]

Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma.

Okosun, Jessica and Wolfson, Rachel L. and Wang, Jun and Araf, Shamzah and Wilkins, Lucy and Castellano, Brian M. and Escudero-Ibarz, Leire and Al Seraihi, Ahad Fahad and Richter, Julia and Bernhart, Stephan H. and Efeyan, Alejo and Iqbal, Sameena and Matthews, Janet and Clear, Andrew and Guerra-Assun\cc\~ao, José Afonso and Bödör, Csaba and Quentmeier, Hilmar and Mansbridge, Christopher and Johnson, Peter and Davies, Andrew and Strefford, Jonathan C. and Packham, Graham and Barrans, Sharon and Jack, Andrew and Du, Ming-Qing and Calaminici, Maria and Lister, T. Andrew and Auer, Rebecca and Montoto, Silvia and Gribben, John G. and Siebert, Reiner and Chelala, Claude and Zoncu, Roberto and Sabatini, David M. and Fitzgibbon, Jude
Nature genetics 48 (2): 183--188
PREPRINT 18-030: [ Abstract ]
[ Publishers's page ]

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis.

Hezaveh, Kebria and Kloetgen, Andreas and Bernhart, Stephan H. and Mahapatra, Kunal Das and Lenze, Dido and Richter, Julia and Haake, Andrea and Bergmann, Anke K. and Brors, Benedikt and Burkhardt, Birgit and Claviez, Alexander and Drexler, Hans G. and Eils, Roland and Haas, Siegfried and Hoffmann, Steve and Karsch, Dennis and Klapper, Wolfram and Kleinheinz, Kortine and Korbel, Jan and Kretzmer, Helene and Kreuz, Markus and Küppers, Ralf and Lawerenz, Chris and Leich, Ellen and Loeffler, Markus and Mantovani-Loeffler, Luisa and L\'opez, Cristina and McHardy, Alice C. and Möller, Peter and Rohde, Marius and Rosenstiel, Philip and Rosenwald, Andreas and Schilhabel, Markus and Schlesner, Matthias and Scholz, Ingrid and Stadler, Peter F. and Stilgenbauer, Stephan and Sungalee, Stéphanie and Szczepanowski, Monika and Trümper, Lorenz and Weniger, Marc A. and Siebert, Reiner and Borkhardt, Arndt and Hummel, Michael and Hoell, Jessica I. and ICGC MMML-Seq Project,
Haematologica 101 (11): 1380--1389
PREPRINT 18-029: [ Abstract ]
[ Publishers's page ]

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer.

Bernhart, Stephan H. and Kretzmer, Helene and Holdt, Lesca M. and Jühling, Frank and Ammerpohl, Ole and Bergmann, Anke K. and Northoff, Bernd H. and Doose, Gero and Siebert, Reiner and Stadler, Peter F. and Hoffmann, Steve
Scientific reports 6: 37393
PREPRINT 18-028: [ Abstract ]
[ Publishers's page ]

Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution

Sedlyarov, Vitaly and Fallmann, Jörg and Ebner, Florian and Huemer, Jakob and Sneezum, Lucy and Ivin, Masa and Kreiner, Kristina and Tanzer, Andrea and Vogl, Claus and Hofacker, Ivo and Kovarik, Pavel
Molecular Systems Biology 12 (5)
PREPRINT 18-007:
[ Publishers's page ]

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Hölzer, Martin and Krähling, Verena and Amman, Fabian and Barth, Emanuel and Bernhart, Stephan H. and Carmelo, Victor A. O. and Collatz, Maximilian and Doose, Gero and Eggenhofer, Florian and Ewald, Jan and Fallmann, Jörg and Feldhahn, Lasse M. and Fricke, Markus and Gebauer, Juliane and Gruber, Andreas J. and Hufsky, Franziska and Indrischek, Henrike and Kanton, Sabina and Linde, Jörg and Mostajo, Nelly and Ochsenreiter, Roman and Riege, Konstantin and Rivarola-Duarte, Lorena and Sahyoun, Abdullah H. and Saunders, Sita J. and Seemann, Stefan E. and Tanzer, Andrea and Vogel, Bertram and Wehner, Stefanie and Wolfinger, Michael T. and Backofen, Rolf and Gorodkin, Jan and Grosse, Ivo and Hofacker, Ivo and Hoffmann, Steve and Kaleta, Christoph and Stadler, Peter F. and Becker, Stephan and Marz, Manja
Scientific Reports 6 (1)
PREPRINT 18-005:
[ Publishers's page ]

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements

Fallmann, Jörg and Sedlyarov, Vitaly and Tanzer, Andrea and Kovarik, Pavel and Hofacker, Ivo L.
Nucleic Acids Research 44 (D1): D90--D95
PREPRINT 18-002:
[ Publishers's page ]

Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies

Velandia-Huerto, Cristian A. and Berkemer, Sarah J. and Hoffmann, Anne and Retzlaff, Nancy and Romero Marroqu\'in, Liliana C. and Hernández-Rosales, Maribel and Stadler, Peter F. and Berm\'udez-Santana, Clara I.
BMC Genomics 17 (1): 617
PREPRINT 17-016: [ Abstract ]
[ Publishers's page ]

A Bibliometric Profile of MATCH Communications in Mathematical and in Computer Chemistry

Restrepo, Guillermo and Willett, Peter
MATCH Communications in Mathematical and in Computer Chemistry undefined: undefined
PREPRINT 17-008:
[ Publishers's page ]

Lemont B. Kier: Art, Science and Green Cheese.

Restrepo, Guillermo
Current computer-aided drug design 12: 314
PREPRINT 17-007:
[ Publishers's page ]

Assessing greenness of chemical reactions and synthesis plans through posetic landscapes

Restrepo, Guillermo and Stadler, Peter F
ACS Sustainable Chemistry \& Engineering 4: 2191--2199
PREPRINT 17-006:
[ Publishers's page ]

How frequently do clusters occur in hierarchical clustering analysis? A graph theoretical approach to studying ties in proximity

Leal, Wilmer and Llanos, Eugenio J and Restrepo, Guillermo and Suárez, Carlos F and Patarroyo, Manuel Elkin
Journal of cheminformatics 8: 4
PREPRINT 17-005:
[ Publishers's page ]

A consensus network of gene regulatory factors in the human frontal lobe

Berto, Stefano and Perdomo-Sabogal, Alvaro and Gerighausen, Daniel and Qin, Jing and Nowick, Katja
Frontiers in genetics 2016; 7: 31.
PREPRINT 16-020: [ Abstract ]
[ Publishers's page ]

Analyzing Histone Modifications in iPS Cells Using Tiled Binned 3D Scatter Plots

Dirk Zeckzer, and Daniel Gerighausen, and Lydia Müller,
International Symposium on Big Data Visual Analytics 2016
PREPRINT 16-019:

Sound--meaning association biases evidenced across thousands of languages

Blasi, Damián E and Wichmann, S\oren and Hammarström, Harald and Stadler, Peter F and Christiansen, Morten H
Proceedings of the National Academy of Sciences undefined: 201605782
PREPRINT 16-017:   [ PDF ]
[ Publishers's page ]

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and-steering

Müller, Lydia and Gerighausen, Daniel and Farman, Mariam and Zeckzer, Dirk
BMC Bioinformatics 17: 377
PREPRINT 16-016: [ Abstract ]
[ Publishers's page ]

Spectral classes of regular, random, and empirical graphs

Gu, Jiao and Jost, Jürgen and Liu, Shiping and Stadler, Peter F
Linear Algebra and its Applications 489: 30--49
PREPRINT 16-013:
[ Publishers's page ]

The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies

Indrischek, Henrike and Wieseke, Nicolas and Stadler, Peter F and Prohaska, Sonja J
Algorithms for Molecular Biology 11: 1
PREPRINT 16-002: [ Abstract ]
[ Publishers's page ]

Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.

Righetti, Francesco and Nuss, Aaron M. and Twittenhoff, Christian and Beele, Sascha and Urban, Kristina and Will, Sebastian and Bernhart, Stephan H. and Stadler, Peter F. and Dersch, Petra and Narberhaus, Franz
Proceedings of the National Academy of Sciences of the United States of America 113 (26): 7237--7242
PREPRINT 16-001: [ Abstract ]  [ Supplement ]
[ Publishers's page ]

An updated human snoRNAome

Hadi Jorjani,*, Stephanie Kehr,*, Dominik J. Jedlinski, Rafal Gumienny, Jana Hertel, Peter F. Stadler, Mihaela Zavolan, Andreas R. Gruber
Nucl. Acids Res. (20 June 2016) 44 (11): 5068-5082.
PREPRINT 15-065: [ Abstract ]  [ Supplement ]
[ Publishers's page ]

U6 snRNA Intron Insertion Occurred Multiple Times During Fungi Evolution

Sebastian Canzler, Jana Hertel, Peter F. Stadler
RNA biology 13.2 (2016): 119-127
PREPRINT 15-046: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]