Peter F Stadler

Summary

Affiliation: University of Leipzig
Country: Germany

Publications

  1. pmc Evolution of the let-7 microRNA family
    Jana Hertel
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    RNA Biol 9:231-41. 2012
  2. pmc Armless mitochondrial tRNAs in Enoplea (Nematoda)
    Frank Jühling
    Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
    RNA Biol 9:1161-6. 2012
  3. pmc ViennaRNA Package 2.0
    Ronny Lorenz
    Institute for Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstraße 17 3, A 1090 Vienna, Austria
    Algorithms Mol Biol 6:26. 2011
  4. ncbi request reprint Evolution of the vertebrate ParaHox clusters
    Sonja J Prohaska
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D 04107 Leipzig, Germany
    J Exp Zool B Mol Dev Evol 306:481-7. 2006
  5. pmc Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)
    Karen E Chambers
    Department of Genetics, Rutgers University, Piscataway, NJ, USA
    Theory Biosci 128:109-20. 2009
  6. pmc "Genes"
    Sonja J Prohaska
    Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
    Theory Biosci 127:215-21. 2008
  7. pmc Defining genes: a computational framework
    Peter F Stadler
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
    Theory Biosci 128:165-70. 2009
  8. pmc Bcheck: a wrapper tool for detecting RNase P RNA genes
    Dilmurat Yusuf
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    BMC Genomics 11:432. 2010
  9. pmc Detection of RNA structures in porcine EST data and related mammals
    Stefan E Seemann
    Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK 1870 Frederiksberg, Denmark
    BMC Genomics 8:316. 2007
  10. pmc Comparative promoter region analysis powered by CORG
    Christoph Dieterich
    Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    BMC Genomics 6:24. 2005

Detail Information

Publications86

  1. pmc Evolution of the let-7 microRNA family
    Jana Hertel
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    RNA Biol 9:231-41. 2012
    ..The foundation of a second let-7 locus in the common ancestor of vertebrates and urochordates predates the vertebrate-specific genome duplications, which then caused a rapid expansion of the let-7 family...
  2. pmc Armless mitochondrial tRNAs in Enoplea (Nematoda)
    Frank Jühling
    Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
    RNA Biol 9:1161-6. 2012
    ....
  3. pmc ViennaRNA Package 2.0
    Ronny Lorenz
    Institute for Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstraße 17 3, A 1090 Vienna, Austria
    Algorithms Mol Biol 6:26. 2011
    ..abstract:..
  4. ncbi request reprint Evolution of the vertebrate ParaHox clusters
    Sonja J Prohaska
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D 04107 Leipzig, Germany
    J Exp Zool B Mol Dev Evol 306:481-7. 2006
    ....
  5. pmc Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)
    Karen E Chambers
    Department of Genetics, Rutgers University, Piscataway, NJ, USA
    Theory Biosci 128:109-20. 2009
    ..The data are consistent with-but do not conclusively prove-that Osteoglossomorpha shares the FSGD...
  6. pmc "Genes"
    Sonja J Prohaska
    Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
    Theory Biosci 127:215-21. 2008
    ....
  7. pmc Defining genes: a computational framework
    Peter F Stadler
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
    Theory Biosci 128:165-70. 2009
    ..The definition seeks to satisfy the practical requirements imposed by annotation, capture logical aspects of regulation, and encompass the evolutionary property of homology...
  8. pmc Bcheck: a wrapper tool for detecting RNase P RNA genes
    Dilmurat Yusuf
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    BMC Genomics 11:432. 2010
    ..The core of Bcheck is a library of subfamily specific descriptor models and covariance models...
  9. pmc Detection of RNA structures in porcine EST data and related mammals
    Stefan E Seemann
    Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK 1870 Frederiksberg, Denmark
    BMC Genomics 8:316. 2007
    ..To investigate this further, we examined the large data set in the Sino-Danish PigEST resource http://pigest.ku.dk which also contains expression information distributed on 97 non-normalized cDNA libraries...
  10. pmc Comparative promoter region analysis powered by CORG
    Christoph Dieterich
    Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    BMC Genomics 6:24. 2005
    ..To support promoter analysis, we present CORG http://corg.molgen.mpg.de, a framework for studying upstream regions including untranslated exons (5' UTR)...
  11. pmc Proteinortho: detection of (co-)orthologs in large-scale analysis
    Marcus Lechner
    RNA Bioinformatics Group, Department of Pharmaceutical Chemistry, Philipps University Marburg, Germany
    BMC Bioinformatics 12:124. 2011
    ..The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases...
  12. pmc G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
    Mario Fasold
    Interdisciplinary Centre for Bioinformatics, University Leipzig, Germany
    BMC Bioinformatics 11:207. 2010
    ..Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis...
  13. pmc Fast local fragment chaining using sum-of-pair gap costs
    Christian Otto
    Bioinformatics Group, Dept, of Computer Science, University of Leipzig, Germany
    Algorithms Mol Biol 6:4. 2011
    ..abstract:..
  14. pmc Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees
    Christian Arnold
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Algorithms Mol Biol 5:25. 2010
    ....
  15. pmc The expansion of the metazoan microRNA repertoire
    Jana Hertel
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Genomics 7:25. 2006
    ..This allows us to reliably identify microRNA clusters that are derived from a common transcript...
  16. pmc Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum
    Claudia S Copeland
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Genomics 10:464. 2009
    ..The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available...
  17. ncbi request reprint Duplicated RNA genes in teleost fish genomes
    Dominic Rose
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    J Bioinform Comput Biol 6:1157-75. 2008
    ....
  18. doi request reprint Evolution of vault RNAs
    Peter F Stadler
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    Mol Biol Evol 26:1975-91. 2009
    ..In teleosts, expression of several paralogous vtRNA genes, most but not all located at the syntenically conserved protocadherin locus, was verified by reverse transcriptase-polymerase chain reaction...
  19. ncbi request reprint Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata
    Marleen Perseke
    Institute of Biology II Zoologie, Molekulare Evolution und Systematik der Tiere, University of Leipzig, Leipzig, Germany
    Mol Phylogenet Evol 56:201-11. 2010
    ..The variability in gene order and UAS regions in ophiuroid genomes suggest dominating rearrangement mechanisms by duplication events...
  20. ncbi request reprint NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences
    Dominic Rose
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Genomics 92:65-74. 2008
    ..The software is available under the GNU Public License at http://www.bioinf.uni-leipzig.de/Software/NcDNAlign/...
  21. ncbi request reprint Evolution of mitochondrial gene orders in echinoderms
    Marleen Perseke
    Institute of Biology II Zoologie, Molekulare Evolution und Systematik der Tiere, University of Leipzig, Talstrasse 33, D 04103 Leipzig, Germany
    Mol Phylogenet Evol 47:855-64. 2008
    ..Only two of these rearrangements are inversions, while we identify three tandem-duplication-random-loss events and three transpositions...
  22. pmc Non-coding RNA annotation of the genome of Trichoplax adhaerens
    Jana Hertel
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D 04107 Leipzig, Germany
    Nucleic Acids Res 37:1602-15. 2009
    ..We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome...
  23. doi request reprint Reconstruction of pedigrees in clonal plant populations
    Markus Riester
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Theor Popul Biol 78:109-17. 2010
    ..Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals...
  24. doi request reprint A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny
    Matthias Bernt
    Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D 04109 Leipzig, Germany Electronic address
    Mol Phylogenet Evol 69:352-64. 2013
    ..g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches...
  25. pmc SynBlast: assisting the analysis of conserved synteny information
    Jörg Lehmann
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Bioinformatics 9:351. 2008
    ..This situation can be improved in many cases by including conserved synteny information...
  26. pmc Conserved introns reveal novel transcripts in Drosophila melanogaster
    Michael Hiller
    Bioinformatics Group, Albert Ludwigs University Freiburg, 79110 Freiburg, Germany
    Genome Res 19:1289-300. 2009
    ..As conserved introns indicate both purifying selection on the exon-intron structure and conserved expression of the transcript in related species, the novel mlncRNAs are good candidates for functional transcripts...
  27. doi request reprint Computational discovery of human coding and non-coding transcripts with conserved splice sites
    Dominic Rose
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
    Bioinformatics 27:1894-900. 2011
    ..Most lncRNAs are under lower sequence constraints than protein-coding genes and lack conserved secondary structures, making it hard to predict them computationally...
  28. pmc Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
    Sebastian Will
    Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany
    PLoS Comput Biol 3:e65. 2007
    ....
  29. pmc RNAalifold: improved consensus structure prediction for RNA alignments
    Stephan H Bernhart
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    BMC Bioinformatics 9:474. 2008
    ..In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach...
  30. pmc Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements
    Frank Jühling
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16 18, D 04107 Leipzig, Germany
    Nucleic Acids Res 40:2833-45. 2012
    ..Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders...
  31. pmc Genomic organization of eukaryotic tRNAs
    Clara Bermudez-Santana
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Genomics 11:270. 2010
    ..We therefore set out to survey the genomic arrangement of tRNA genes and pseudogenes in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities...
  32. ncbi request reprint RNAs everywhere: genome-wide annotation of structured RNAs
    Rolf Backofen
    Bioinformatics Group, Department of Computer Science, University of Freiburg, D 79110 Freiburg, Germany
    J Exp Zool B Mol Dev Evol 308:1-25. 2007
    ..A series of exploratory studies are used to provide non-trivial examples for the discussion of some of the difficulties...
  33. ncbi request reprint Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data
    Jana Hertel
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Bioinformatics 22:e197-202. 2006
    ..The software was applied to recent genome-wide RNAz surveys of mammals, urochordates, and nematodes...
  34. doi request reprint Folding kinetics of large RNAs
    Michael Geis
    Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
    J Mol Biol 379:160-73. 2008
    ..The software is available as part of the ViennaRNA Package...
  35. pmc Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication
    Jörg Lehmann
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
    BMC Evol Biol 10:156. 2010
    ..A recent gain of such introns is difficult to prove. However, introns verified as novel are needed to evaluate contemporary processes of intron gain...
  36. ncbi request reprint Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history
    Manja Marz
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    J Bioinform Comput Biol 8:1-17. 2010
    ..Supplementary Table is available at http://www.worldscinet.com/jbcb/...
  37. pmc tRNAdb 2009: compilation of tRNA sequences and tRNA genes
    Frank Jühling
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Nucleic Acids Res 37:D159-62. 2009
    ....
  38. ncbi request reprint PCR survey of Xenoturbella bocki Hox genes
    Guido Fritzsch
    Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse Leipzig, Germany
    J Exp Zool B Mol Dev Evol 310:278-84. 2008
    ..We furthermore report on a re-evaluation of the available published evidence of Hox genes in other basal deuterostomes...
  39. ncbi request reprint CREx: inferring genomic rearrangements based on common intervals
    Matthias Bernt
    Parallel Computing and Complex Systems Group, University of Leipzig, Fraunhofer Institute IZI, Leipzig, Germany
    Bioinformatics 23:2957-8. 2007
    ..It supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based on common intervals, which reflect genes that appear consecutively in several of the input gene orders...
  40. pmc Computational RNomics of drosophilids
    Dominic Rose
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, Leipzig, Germany
    BMC Genomics 8:406. 2007
    ..This class of loci includes the majority of the known small ncRNAs as well as structured RNA motifs in mRNAs. We report here on a genome-wide survey using RNAz...
  41. doi request reprint Evolution of 7SK RNA and its protein partners in metazoa
    Manja Marz
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    Mol Biol Evol 26:2821-30. 2009
    ..Furthermore, we derive an improved secondary structure model of 7SK RNA, which shows that the structure is quite well-conserved across animal phyla despite the extreme divergence at sequence level...
  42. ncbi request reprint TSSAR: TSS annotation regime for dRNA-seq data
    Fabian Amman
    Bioinformatics Group, Department of Computer Science and the Interdisciplinary Center for Bioinformatic, University of Leipzig, Härtelstraße 16 18, 04107 Leipzig, Germany
    BMC Bioinformatics 15:89. 2014
    ..Hitherto, dRNA-seq data were analyzed by visualizing the sequencing reads mapped to the reference genome and manually annotating reliable positions. This is very labor intensive and, due to the subjectivity, biased...
  43. ncbi request reprint Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny
    Guido Fritzsch
    Interdisciplinary Center for Bioinformatics, University of Leipzig, Hartelstr 16 18, D 04107 Leipzig, Germany
    J Theor Biol 240:511-20. 2006
    ..We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts...
  44. pmc deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns
    David Langenberger
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universitat Leipzig, Philipp Rosenthal Strasse 27, D 04107 Leipzig, Germany
    Bioinformatics 28:17-24. 2012
    ..The miR-miR* pattern from microRNA precursors is the best-known, but by no means singular, example...
  45. ncbi request reprint The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis
    Marleen Perseke
    Institut fur Zoologie, Molekulare Evolution und Systematik der Tiere Universität Leipzig, Talstr 33, 04103, Leipzig, Germany
    Theory Biosci 126:35-42. 2007
    ..in Nature 444:85-88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata)...
  46. ncbi request reprint U7 snRNAs: a computational survey
    Manja Marz
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D 04107, Germany
    Genomics Proteomics Bioinformatics 5:187-95. 2007
    ..These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database...
  47. doi request reprint PLEXY: efficient target prediction for box C/D snoRNAs
    Stephanie Kehr
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    Bioinformatics 27:279-80. 2011
    ..While a fast and efficient target predictor for box H/ACA snoRNAs is available, no comparable tool exists for box C/D snoRNAs, even though they bind to their targets in a much less complex manner...
  48. ncbi request reprint snoStrip: a snoRNA annotation pipeline
    Sebastian Bartschat
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Bioinformatics 30:115-6. 2014
    ....
  49. ncbi request reprint Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae
    Kristin Missal
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    J Exp Zool B Mol Dev Evol 306:379-92. 2006
    ..Only a small fraction of these belongs to the known RNA classes, including tRNAs, snoRNAs, snRNAs, or microRNAs. A relatively small class of ncRNA candidates is associated with previously observed RNA-specific upstream elements...
  50. doi request reprint Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences
    Matthias Bernt
    Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D 04109 Leipzig, Germany Electronic address
    Mol Phylogenet Evol 69:320-7. 2013
    ....
  51. doi request reprint Near intron pairs and the metazoan tree
    Jörg Lehmann
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16 18, 04107 Leipzig, Germany
    Mol Phylogenet Evol 66:811-23. 2013
    ....
  52. doi request reprint Fast and sensitive mapping of bisulfite-treated sequencing data
    Christian Otto
    Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Department of Computer Science, University Leipzig, 04107 Leipzig, Germany
    Bioinformatics 28:1698-704. 2012
    ..As a consequence, currently available read mapping software often fails to achieve high sensitivity and in many cases requires unrealistic computational resources to cope with large real-life datasets...
  53. ncbi request reprint Evidence for human microRNA-offset RNAs in small RNA sequencing data
    David Langenberger
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    Bioinformatics 25:2298-301. 2009
    ....
  54. doi request reprint Evolution of spliceosomal snRNA genes in metazoan animals
    Manuela Marz
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
    J Mol Evol 67:594-607. 2008
    ..An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation...
  55. doi request reprint Innovation in gene regulation: the case of chromatin computation
    Sonja J Prohaska
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    J Theor Biol 265:27-44. 2010
    ....
  56. doi request reprint Fast accessibility-based prediction of RNA-RNA interactions
    Hakim Tafer
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D 04107 Leipzig, Germany
    Bioinformatics 27:1934-40. 2011
    ..Alternative methods neglecting intramolecular structures are fast enough for genome-wide applications, but are too inaccurate to be of much practical use...
  57. doi request reprint Traces of post-transcriptional RNA modifications in deep sequencing data
    Sven Findeiss
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelsrtrasse 16 18, Leipzig, Germany
    Biol Chem 392:305-13. 2011
    ..Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation...
  58. ncbi request reprint Customized strategies for discovering distant ncRNA homologs
    Axel Mosig
    Chair of Bioinformatics, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Brief Funct Genomic Proteomic 8:451-60. 2009
    ..We focus here, in particular, on strategies that can be successful in the 'twilight zone' where generic approaches from blast to infernal to start to fail...
  59. pmc Fast mapping of short sequences with mismatches, insertions and deletions using index structures
    Steve Hoffmann
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
    PLoS Comput Biol 5:e1000502. 2009
    ..Our approach is implemented in the software segemehl available at http://www.bioinf.uni-leipzig.de/Software/segemehl/...
  60. doi request reprint Genetic aspects of mitochondrial genome evolution
    Matthias Bernt
    Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D 04109 Leipzig, Germany Electronic address
    Mol Phylogenet Evol 69:328-38. 2013
    ..Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review...
  61. pmc The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
    Marleen Perseke
    Molecular Evolution and Animal Systematics, University of Leipzig, Talstr 33, 04103 Leipzig, Germany
    BMC Evol Biol 11:134. 2011
    ..Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch Rhabdopleura compacta to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution...
  62. pmc The common ancestral core of vertebrate and fungal telomerase RNAs
    Xiaodong Qi
    Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
    Nucleic Acids Res 41:450-62. 2013
    ..Overall, this study reveals the common ancestral cores of vertebrate and fungal TERs, and provides insights into the molecular evolution of fungal TER structure and function...
  63. ncbi request reprint A novel family of plasmid-transferred anti-sense ncRNAs
    Sven Findeiss
    BioinformaticsGroup, Department of Computer Science, and InterdisciplinaryCenter for Bioinformatics, University of Leipzig, Leipzig, Germany
    RNA Biol 7:120-4. 2010
    ..The secondary structure of PtaRNA1, furthermore, is very similar to that of the FinP anti-sense RNA found on F-like plasmids in Escherichia coli...
  64. ncbi request reprint Comparative analysis of eukaryotic U3 snoRNA
    Manja Marz
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    RNA Biol 6:503-7. 2009
    ..Many fungal U3 genes, in addition, contain introns. U3 promoters are snRNA-like but show substantial variations even between related species...
  65. ncbi request reprint Visualization of barrier tree sequences
    Christian Heine
    Image and Signal Processing Group, Department of Computer Science, University of Leipzig
    IEEE Trans Vis Comput Graph 12:781-8. 2006
    ..Since it is very general, we give a detailed description of each phase: constructing a supergraph for the trees, layout of that supergraph using a modified DoT algorithm, and presentation techniques for the final animation...
  66. ncbi request reprint Evolution of microRNAs located within Hox gene clusters
    Andrea Tanzer
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Kreuzstrasse 7b, D 04103 Leipzig, Germany
    J Exp Zool B Mol Dev Evol 304:75-85. 2005
    ..Here we describe their evolution in detail. We show that the micro RNAs closely follow the patterns of protein evolution in the Hox clusters, which is characterized by cluster duplications followed by differential gene loss...
  67. doi request reprint Biological evidence for the world's smallest tRNAs
    Sandra Wende
    University of Leipzig, Institute for Biochemistry, Leipzig, Germany
    Biochimie 100:151-8. 2014
    ..It opens new possibilities towards exploration/assessment of minimal structural motifs defining a functional tRNA and their evolution. ..
  68. doi request reprint Matching of Soulmates: coevolution of snoRNAs and their targets
    Stephanie Kehr
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    Mol Biol Evol 31:455-67. 2014
    ..Because of the high overall entropy of snoRNA sequences, such relationships are hard to detect by means of sequence homology search methods alone. ..
  69. pmc Progressive multiple sequence alignments from triplets
    Matthias Kruspe
    Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    BMC Bioinformatics 8:254. 2007
    ..Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors...
  70. pmc HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis
    Steve Hoffmann
    Department of Bioinformatics, Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
    Am J Hum Genet 83:219-27. 2008
    ..In summary, we identified genetic factors determining the immunogenicity of IFN-beta, a protein-based disease-modifying agent for the treatment of MS...
  71. ncbi request reprint Non-coding RNAs in Ciona intestinalis
    Kristin Missal
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
    Bioinformatics 21:ii77-8. 2005
    ..Extending these comparative studies beyond vertebrates is difficult, however, since most ncRNAs evolve quickly at the sequence level while conserving their characteristic secondarystructures...
  72. doi request reprint RNA interactions
    Manja Marz
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    Adv Exp Med Biol 722:20-38. 2011
    ..Conservation of both sequence and structure thus this can give indications of the functioning of the diversity of ncRNAs...
  73. pmc Widespread purifying selection on RNA structure in mammals
    Martin A Smith
    RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology and Center for Integrative Bioinformatics Vienna CIBIV, Max F Perutz Laboratories MFPL, University of Vienna, Medical University of Vienna, Dr Bohr Gasse 9, A 1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D 04103 Leipzig, Germany, Center for non coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent s Clinical School, University of New South Wales, London
    Nucleic Acids Res 41:8220-36. 2013
    ..This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes. ..
  74. pmc De novo design of a synthetic riboswitch that regulates transcription termination
    Manja Wachsmuth
    Institute for Biochemistry, University of Leipzig, Bruderstr 34, 04103 Leipzig, Germany
    Nucleic Acids Res 41:2541-51. 2013
    ....
  75. ncbi request reprint "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity
    Irma Lozada-Chávez
    Computational EvoDevo Group, University of Leipzig, Härtelstrasse 16 18, 04107, Leipzig, Germany
    Orig Life Evol Biosph 41:587-607. 2011
    ....
  76. pmc Multiple sequence alignments of partially coding nucleic acid sequences
    Roman R Stocsits
    Interdisciplinary Centre for Bioinformatics, University of Leipzig, Haertelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Bioinformatics 6:160. 2005
    ..On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes...
  77. pmc DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments
    Mario Fasold
    Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Department of Computer Science, University Leipzig, Germany
    Nucleic Acids Res 39:W112-7. 2011
    ..It provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates. The DARIO web site can be accessed at http://dario.bioinf.uni-leipzig.de/...
  78. doi request reprint Near intron positions are reliable phylogenetic markers: an application to holometabolous insects
    Veiko Krauss
    Department of Genetics, Institute of Biology II, University of Leipzig, Leipzig, Germany
    Mol Biol Evol 25:821-30. 2008
    ....
  79. doi request reprint A topological approach to chemical organizations
    Gil Benkö
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
    Artif Life 15:71-88. 2009
    ..This abstract representation in turn suggests the exploration of the chemical meaning of well-established topological concepts. As an example, we consider connectedness in some detail...
  80. pmc FRANz: reconstruction of wild multi-generation pedigrees
    Markus Riester
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    Bioinformatics 25:2134-9. 2009
    ..The accuracy of the algorithm is demonstrated for simulated data as well as an empirical dataset with known pedigree. The parentage inference is robust even in the presence of genotyping errors...
  81. doi request reprint In silico evolution of early metabolism
    Alexander Ullrich
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
    Artif Life 17:87-108. 2011
    ..In later and more complex stages, enzyme recruitment supersedes forward evolution, keeping a core set of pathways from the early phase...
  82. ncbi request reprint Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer
    Dennis Löffler
    Institute of Clinical Immunology and Transfusion Medicine, Medical Faculty, University of Leipzig, Leipzig, Germany
    Blood 110:1330-3. 2007
    ..Ectopically raising miR-21 expression in myeloma cells in the absence of IL-6 significantly reduced their apoptosis levels. These data provide strong evidence that miR-21 induction contributes to the oncogenic potential of Stat3...
  83. ncbi request reprint Visualization of graph products
    Stefan Jänicke
    Institute for Computer Science, University of Leipzig, Germany
    IEEE Trans Vis Comput Graph 16:1082-9. 2010
    ..We also present how our method is integrated as a new component into the TopoLayout framework. Our implementation is used for further research of graph products in a biological context...
  84. doi request reprint The use and abuse of -omes
    Sonja J Prohaska
    Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    Methods Mol Biol 719:173-96. 2011
    ..Here, we focus on the dark corners of Omics research, where the problems, limitations, conceptual difficulties, and lack of knowledge are hidden...
  85. pmc Molecular evolution of the non-coding eosinophil granule ontogeny transcript
    Dominic Rose
    Bioinformatics Group, Department of Computer Science, University of Freiburg Freiburg, Germany
    Front Genet 2:69. 2011
    ..The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element...
  86. ncbi request reprint Exclusion of repetitive DNA elements from gnathostome Hox clusters
    Claudia Fried
    Bioinformatics Group, Department of Computer Science, University of Leipzig Kreuzstrabetae 7b, D 04103 Leipzig, Germany
    J Exp Zool B Mol Dev Evol 302:165-73. 2004
    ..This invasion appears to be correlated with relaxed constraints associated with gene loss after cluster duplications...