Research Topics
Genomes and Genes | Peter F StadlerSummaryAffiliation: University of Leipzig Country: Germany Publications
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Detail Information
Publications
ViennaRNA Package 2.0Ronny 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:..
Evolution of the vertebrate ParaHox clustersSonja 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....- Defining genes: a computational frameworkPeter 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... - 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... - "Genes"Sonja J Prohaska
Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
Theory Biosci 127:215-21. 2008.... - Bcheck: a wrapper tool for detecting RNase P RNA genesDilmurat 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... - Detection of RNA structures in porcine EST data and related mammalsStefan 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... - Comparative promoter region analysis powered by CORGChristoph 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)... - Proteinortho: detection of (co-)orthologs in large-scale analysisMarcus 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... - G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibrationMario 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... - Fast local fragment chaining using sum-of-pair gap costsChristian Otto
Bioinformatics Group, Dept, of Computer Science, University of Leipzig, Germany
Algorithms Mol Biol 6:4. 2011..abstract:.. - Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary treesChristian 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.... - Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicumClaudia 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... - Duplicated RNA genes in teleost fish genomesDominic Rose
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
J Bioinform Comput Biol 6:1157-75. 2008.... 
Evolution of vault RNAsPeter 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...- Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of EchinodermataMarleen 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... - The expansion of the metazoan microRNA repertoireJana 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... - Evolution of mitochondrial gene orders in echinodermsMarleen 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... - NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequencesDominic 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/... - Non-coding RNA annotation of the genome of Trichoplax adhaerensJana 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... - Reconstruction of pedigrees in clonal plant populationsMarkus 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... - SynBlast: assisting the analysis of conserved synteny informationJörg Lehmann
Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
BMC Bioinformatics 9:351. 2008..SOFTWARE: The SynBlast package written in Perl is available under the GNU General Public License at http://www.bioinf.uni-leipzig.de/Software/SynBlast/... - Inferring noncoding RNA families and classes by means of genome-scale structure-based clusteringSebastian Will
Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany
PLoS Comput Biol 3:e65. 2007.... - Conserved introns reveal novel transcripts in Drosophila melanogasterMichael 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... - RNAalifold: improved consensus structure prediction for RNA alignmentsStephan 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... - Computational discovery of human coding and non-coding transcripts with conserved splice sitesDominic 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... - Evolution of the let-7 microRNA familyJana 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... - Genomic organization of eukaryotic tRNAsClara 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... - Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary historyManja 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/... - Folding kinetics of large RNAsMichael 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... - Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplicationJörg 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... - Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics dataJana 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..AVAILABILITY: The program RNAmicro is available as source code and can be downloaded from http://www.bioinf.uni-leipzig/Software/RNAmicro... - RNAs everywhere: genome-wide annotation of structured RNAsRolf 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... - CREx: inferring genomic rearrangements based on common intervalsMatthias Bernt
Parallel Computing and Complex Systems Group, University of Leipzig, Fraunhofer Institute IZI, Leipzig, Germany
Bioinformatics 23:2957-8. 2007..CREx is based on common intervals, which reflect genes that appear consecutively in several of the input gene orders. AVAILABILITY: CREx is freely available at http://pacosy.informatik.uni-leipzig.de/crex.. - Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangementsFrank 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... - Evolution of 7SK RNA and its protein partners in metazoaManja 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... - Computational RNomics of drosophilidsDominic 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... - Alignments of mitochondrial genome arrangements: applications to metazoan phylogenyGuido 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... - deepBlockAlign: a tool for aligning RNA-seq profiles of read block patternsDavid 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... - The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysisMarleen 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)... - U7 snRNAs: a computational surveyManja 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... - Evolution of spliceosomal snRNA genes in metazoan animalsManuela 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... - Evidence for human microRNA-offset RNAs in small RNA sequencing dataDavid Langenberger
Department of Computer Science, University of Leipzig, Leipzig, Germany
Bioinformatics 25:2298-301. 2009.... - Customized strategies for discovering distant ncRNA homologsAxel 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... - Fast mapping of short sequences with mismatches, insertions and deletions using index structuresSteve 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/... - Traces of post-transcriptional RNA modifications in deep sequencing dataSven 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... - Fast accessibility-based prediction of RNA-RNA interactionsHakim 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... - Innovation in gene regulation: the case of chromatin computationSonja 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.... - The common ancestral core of vertebrate and fungal telomerase RNAsXiaodong 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... - The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of AmbulacrariaMarleen 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... - tRNAdb 2009: compilation of tRNA sequences and tRNA genesFrank 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.... - PCR survey of Xenoturbella bocki Hox genesGuido 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... - A novel family of plasmid-transferred anti-sense ncRNAsSven 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... - Comparative analysis of eukaryotic U3 snoRNAManja 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... - Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsaeKristin 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... - Visualization of barrier tree sequencesChristian 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... - PLEXY: efficient target prediction for box C/D snoRNAsStephanie 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... - Non-coding RNAs in Ciona intestinalisKristin 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... - Progressive multiple sequence alignments from tripletsMatthias 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... - RNA interactionsManja 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... - HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosisSteve 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... - 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.... - "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexityIrma Lozada-Chávez
Computational EvoDevo Group, University of Leipzig, Härtelstrasse 16 18, 04107, Leipzig, Germany
Orig Life Evol Biosph 41:587-607. 2011.... - Evolution of microRNAs located within Hox gene clustersAndrea 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... - Multiple sequence alignments of partially coding nucleic acid sequencesRoman 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... - FRANz: reconstruction of wild multi-generation pedigreesMarkus 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 parentage inference is robust even in the presence of genotyping errors. AVAILABILITY: The C source code of FRANz can be obtained under the GPL from http://www.bioinf.uni-leipzig.de/Software/FRANz/... - A topological approach to chemical organizationsGil 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... - DARIO: a ncRNA detection and analysis tool for next-generation sequencing experimentsMario 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/... - Near intron positions are reliable phylogenetic markers: an application to holometabolous insectsVeiko Krauss
Department of Genetics, Institute of Biology II, University of Leipzig, Leipzig, Germany
Mol Biol Evol 25:821-30. 2008.... - Fast and sensitive mapping of bisulfite-treated sequencing dataChristian 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... - Visualization of graph productsStefan 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... - Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancerDennis 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... - The use and abuse of -omesSonja 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... - In silico evolution of early metabolismAlexander 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... - Molecular evolution of the non-coding eosinophil granule ontogeny transcriptDominic 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... - Exclusion of repetitive DNA elements from gnathostome Hox clustersClaudia 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...