Items where Research Area is "Bioinformatics and Computational Biology" and Year is 2011

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Number of items: 30.

Journal Paper

  • RNA Accessibility in cubic time.
    Bernhart, Stephan H and Mückstein, Ulrike and Hofacker, Ivo L Algorithms for Molecular Biology, 6 (1). p. 3 ISSN 1748-7188 Biomed Central (2011)

  • Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
    Dinh, Huy Q. Nucleic Acids Res., 40. pp. 2454-2469 ISSN 1362-4962 (2011)

  • RNApredator: Fast accessibility-Based Prediction of sRNA targets
    Eggenhofer, Florian and Tafer, Hakim and Stadler, Peter F. and Hofacker, Ivo L. Nucleic Acids Research, 39 (S2). W149-W154 Oxford University Press (2011)

  • Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids.
    Findeiß, Sven and Engelhardt, Jan and Prohaska, Sonja J and Stadler, Peter F Biochemie, 93 (11). pp. 2019-2023 (2011)

  • Traces of post-transcriptional RNA modifications in deep sequencing data
    Findeiß, Sven and Langenberger, David and Stadler, Peter F and Hoffmann, Steve The Journal of Biological Chemistry, 392 (4). pp. 305-313 American Society for Biochemistry and Molecular Biology (2011)

  • Non-hereditary Maximum Parsimony trees.
    Fischer, Mareike Journal of mathematical biology, - (-). ISSN 1432-1416 (In Press) (2011)

  • From structure prediction to genomic screens for novel non-coding RNAs.
    Gorodkin, Jan and Hofacker, Ivo L PLoS computational biology, 7 (8). e1002100 ISSN 1553-7358 PLoS (2011)

  • AREsite: a database for the comprehensive investigation of AU-rich elements.
    Gruber, Andreas R and Fallmann, Jörg and Kratochvill, Franz and Kovarik, Pavel and Hofacker, Ivo L. Nucleic Acids Research, 39. D66-D69 Oxford University Press (2011)

  • Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering
    Hackl, Matthias and Jakobi, Tobias and Blom, Jochen and Doppmeier, Daniel and Brinkrolff, Karina and Sczepanowski, Rafael and Bernhart, Stephan and Höner zu Siederdissen, Christian and Hernandez-Bort, Juan and Wieser, Matthias and Kunert, Renate and Jeffs, Simon and Hofacker, Ivo L. and Goesmann, Alexander and Pühler, Alfred and Borth, Nicole and Grillari, Johannes Journal of Biotechnology, 153 (1-2). pp. 62-75 Elsevier (2011)

  • A Folding Algorithm for Extended RNA Secondary Structures
    Höner zu Siederdissen, Christian and Berhart, Stephan H. and Stadler, Peter F. and Hofacker, Ivo L. Bioinformatics, 27 ( ). i129-i136 Oxford University Press (2011)

  • Genetic Rearrangements Can Modify Chromatin Features at Epialleles
    Kakutani, Tetsuji and Foerster, Andrea M. and Dinh, Huy Q. and Sedman, Laura and Wohlrab, Bonnie and Mittelsten Scheid, Ortrun PLoS Genetics, 7 (10). e1002331 ISSN 1553-7404 (In Press) (2011)

  • Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination.
    Koestler, Tina and Ebersberger, Ingo Genome biology and evolution, 3 (-). pp. 186-94 ISSN 1759-6653 (2011)

  • Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation.
    Kratochvill, Franz and Machacek, Christian and Vogl, Claus and Ebner, Florian and Sedlyarov, Vitaly and Gruber, Andreas R and Hartweger, Hartweger and Vielnascher, Raimund and Karaghiosoff, Marina and Rülicke, Thomas and Müller, Mathias and Hofacker, Ivo L. and Lang, Roland and Kovarik, Pavel Molecular Systems Biology, 7 (560). Nature publishing group (2011)

  • Consequences of different null models on the tree shape bias of supertree methods.
    Kupczok, Anne Systematic biology, 60 (2). pp. 218-25 ISSN 1076-836X (2011)

  • Split-based computation of majority-rule supertrees.
    Kupczok, Anne BMC evolutionary biology, 11 (-). p. 205 ISSN 1471-2148 (2011)

  • Proteinortho: detection of (co-)orthologs in large-scale analysis.
    Lechner, Marcus and Findeiß, Sven and Steiner, Lydia and Marz, Manja and Stadler, Peter F and Prohaska, Sonja J BMC Bioinformatics, 12 (124). (2011)

  • ViennaRNA Package 2.0
    Lorenz, Ronny and Bernhart, Stephan H and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. Algorithms for Molecular Biology, 6 (1). p. 26 Biomed Central (2011)

  • Animal snoRNAs and scaRNAs with Exceptional Structures
    Marz, Manja and Gruber, Andreas R. and Höner zu Siederdissen, Christian and Amman, Fabian and Badelt, Stefan and Bartschat, Sebastian and Bernhart, Stephan H. and Beyer, Stephanie and Lorenz, Ronny and Tanzer, Andrea and Yusuf, Dilmurat and Tafer, Hakim and Hofacker, Ivo L. and Stadler, Peter F. RNA Biology, 8 (6). ISSN 1547-6286 Landes Bioscience (2011)

  • MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment.
    Nguyen, Minh Anh Thi and Klaere, Steffen and von Haeseler, Arndt Molecular biology and evolution, 28 (1). pp. 143-52 ISSN 1537-1719 (2011)

  • Phylogenomic analyses of malaria parasites and evolution of their exported proteins.
    Pick, Christian and Ebersberger, Ingo and Spielmann, Tobias and Bruchhaus, Iris and Burmester, Thorsten BMC evolutionary biology, 11 (-). p. 167 ISSN 1471-2148 (2011)

  • The performance of phylogenetic algorithms in estimating haplotype genealogies with migration.
    Salzburger, Walter and Ewing, Greg B and Von Haeseler, Arndt Molecular ecology, 20 (9). pp. 1952-63 ISSN 1365-294X (2011)

  • The plant heat stress transcription factor (Hsf) family: Structure, function and evolution
    Scharf, Klaus-Dieter and Berberich, Thomas and Ebersberger, Ingo and Nover, Lutz Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, - (-). ISSN 18749399 (In Press) (2011)

  • Genome-wide transcriptome analysis in the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.
    Schmidtke, Cornelius and Sven, Findeiß (co-first author) and Sharma, Cythia M and Kuhfuß, Juliane and Hoffmann, Steve and Vogel, Jörg and Stadler, Peter F and Bonas, Ulla Nucleic Acids Research. Oxford University Press (Submitted) (2011)

  • PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
    Seemann, Stefan E and Richter, Andreas S and Gesell, Tanja and Backofen, Rolf and Gorodkin, Jan Bioinformatics (Oxford, England), 27 (2). pp. 211-9 ISSN 1367-4811 (2011)

  • Fast Accessibility-Based Prediction of RNA-RNA Interactions
    Tafer, Hakim and Ammann, Fabian and Eggenhoffer, Florian and Stadler, Peter F. and Hofacker, Ivo L. Bioinformatics, 27 (14). pp. 1924-1940 Oxford University Press (2011)

  • ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods.
    Thi Nguyen, Minh Anh and Gesell, Tanja and von Haeseler, Arndt Molecular biology and evolution, - (-). ISSN 1537-1719 (In Press) (2011)

  • Random Tree-Puzzle leads to the Yule-Harding distribution.
    Vinh, Le Sy and Fuehrer, Andrea and von Haeseler, Arndt Molecular biology and evolution, 28 (2). pp. 873-7 ISSN 1537-1719 (2011)

  • RNAcode: robust prediction of protein coding regions in comparative genomics data
    Washietl, Stefan and Findeiß, Sven and Müller, Stephan and Kalkhof, Stefan and Bergen, Martin von and Hofacker, Ivo L. and Stadler, Peter F. and Goldman, Nick RNA , 17 (4). pp. 578-594 Cold Spring Harbor Laboratory Press (2011)

  • RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
    Washietl, Stefan and Findeiß, Sven and Müller, Stephan A and Kalkhof, Stefan and von Bergen, Martin and Hofacker, Ivo L. and Stadler, Peter F and Goldman, Nick RNA, 17 (4). pp. 578-594 (2011)

  • Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda
    von Reumont, B. M. and Jenner, R. A. and Wills, M. A. and Dell'Ampio, E. and Pass, G. and Ebersberger, I. and Meyer, B. and Koenemann, S. and Iliffe, T. M. and Stamatakis, A. and Niehuis, O. and Meusemann, K. and Misof, B. Molecular Biology and Evolution, - (-). ISSN 0737-4038 (In Press) (2011)

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