Affiliation: Leibniz Institute for Age Research
- Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exonsKarol Szafranski
Fritz Lipmann Institute Institute for Age Research, Beutenbergstr 11, 07745 Jena, Germany
Nucleic Acids Res 42:8895-904. 2014..Together, the results indicate a physiological AS regulation mechanism that functions almost independently from the splice site context and sequence. ..
- Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungiAnke Burmester
Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Beutenbergstrasse 11a, Jena, 07745, Germany
Genome Biol 12:R7. 2011....
- Phylogenetically widespread alternative splicing at unusual GYNGYN donorsMichael Hiller
Institute of Computer Science, Albert Ludwigs University Freiburg, Georges Koehler Allee 106, 79110 Freiburg, Germany
Genome Biol 7:R65. 2006..Here, we focus on unusual donor sites with the motif GYNGYN (Y stands for C or T; N stands for A, C, G, or T)...
- Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencingStefan Taudien
Leibniz Institute for Age Research Fritz Lipmann Institute, Jena, Germany
BMC Genomics 12:243. 2011..g. by the 1000 Genomes Project is confined by an affordable sequence depth. Combining target enrichment with NGS may represent a feasible approach...
- Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencingStefan Taudien
Leibniz Institute for Age Research Fritz Lipmann Institute, Jena, Germany
BMC Genomics 11:252. 2010..Here, we demonstrate that amplicon sequencing of pooled individual PCR products by the 454 technology allows in-depth determination of MSV haplotypes and estimation of DEFB CNs in parallel...
- Comparative analysis of sequence features involved in the recognition of tandem splice sitesRalf Bortfeldt
Department of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz 2, D 07743 Jena, Germany
BMC Genomics 9:202. 2008....
- Selection against tandem splice sites affecting structured protein regionsMichael Hiller
Bioinformatics Group, Albert Ludwigs University Freiburg, Georges Koehler Allee 106, 79110 Freiburg, Germany
BMC Evol Biol 8:89. 2008..Here, we analyzed whether in-frame tandem sites leading to subtle mRNA insertions/deletions of 3, 6, or 9 nucleotides are under natural selection...
- TassDB2 - A comprehensive database of subtle alternative splicing eventsRileen Sinha
Albert Ludwigs University Freiburg, Germany
BMC Bioinformatics 11:216. 2010..Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species...
- tuple_plot: fast pairwise nucleotide sequence comparison with noise suppressionKarol Szafranski
Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute Beutenbergstr 11, 07745 Jena, Germany
Bioinformatics 22:1917-8. 2006..The proposed scoring scheme appreciably increases the signal-to-noise ratio and may help to improve other word-based sequence comparison approaches...
- Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent intronsKarol Szafranski
Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr, 07745 Jena, Germany
Genome Biol 8:R154. 2007..Intrigued by anecdotal evidence for functional non-AG 3' splice sites, we carried out a human genome-wide screen...
- High-resolution mapping of the 8p23.1 beta-defensin cluster reveals strictly concordant copy number variation of all genesMarco Groth
Genome Analysis, Leibniz Institute for Age Research Fritz Lipmann Institute, Jena, Germany
Hum Mutat 29:1247-54. 2008..On this basis, MLPA represents a reliable technique for medium- to high-throughput typing of 8p23.1 defensin CNV in association studies for diverse clinical phenotypes...
- Accurate prediction of NAGNAG alternative splicingRileen Sinha
Leibniz Institute for Age Research Fritz Lipmann Institute, Genome Analysis, Beutenbergstrasse 11, 07745 Jena, Germany
Nucleic Acids Res 37:3569-79. 2009..Our results suggest that the mechanism behind NAGNAG AS is simple, stochastic, and conserved among vertebrates and beyond...
- Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genesStefanie Schindler
Genome Analysis, Leibniz Institute for Age Research Fritz Lipmann Institute, Beutenbergstr 11, 07745 Jena, Germany
BMC Genomics 9:159. 2008..As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes...
- Genetic variants of the copy number polymorphic beta-defensin locus are associated with sporadic prostate cancerKlaus Huse
Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany
Tumour Biol 29:83-92. 2008..This structural variation considerably hampers genetic studies. In a new approach considering both sequence as well as copy number variations we aimed to compare the defensin locus at 8p23 in prostate cancer patients and controls...
- Comparison of methods for quantification of subtle splice variantsStefanie Schindler
Genome Analysis, Leibniz Institute for Age Research, Jena, Germany
Electrophoresis 30:3674-81. 2009..As proof of concept, we determine the splice ratios of variants differing by 3 and 12 nt in five human tissues. We demonstrate that CE-LIF is the most precise and also the most labor- and time-efficient method...
- Gene organization features in A/T-rich organismsKarol Szafranski
Department of Genome Analysis, Institute for Molecular Biotechnology Jena, Beutenbergstr 11, D 07745 Jena, Germany
J Mol Evol 60:90-8. 2005..Instead both the shift of the nucleotide usage in coding regions to A/T-rich codons and the longer intergenic regions make an equal contribution to the higher A/T content in this organism...
- FRAMA: from RNA-seq data to annotated mRNA assembliesMartin Bens
Leibniz Institute on Ageing Fritz Lipmann Institute, Beutenbergstr 11, 07745, Jena, Germany
BMC Genomics 17:54. 2016....
- High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging researchKathrin Reichwald
Leibniz Institute for Age Research Fritz Lipmann Institute, Beutenbergstr, 07745 Jena, Germany
Genome Biol 10:R16. 2009..Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research...
- DictyMOLD-a Dictyostelium discoideum genome browser databaseMarius Felder
IMB Jena, Department of Genome Analysis Beutenbergstrasse 11, 07745 Jena, Germany
Bioinformatics 21:696-7. 2005..discoideum chromosomes 1 and 2 sequences together with related annotations. To visualise maps, sequences and annotations and to provide access for the scientific community a perl-based browser was developed...
- Sequence and analysis of chromosome 2 of Dictyostelium discoideumGernot Glockner
IMB Jena, Department of Genome Analysis, Beutenbergstr 11, 07745 Jena, Germany
Nature 418:79-85. 2002..This analysis strengthens the view that the evolutionary position of D. discoideum is located before the branching of metazoa and fungi but after the divergence of the plant kingdom, placing it close to the base of metazoan evolution...
- Alternative splicing at NAGNAG acceptors: simply noise or noise and more?Michael Hiller
PLoS Genet 2:e207; author reply e208. 2006
- Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?Matthias Platzer
Nat Biotechnol 24:1068-70. 2006
- Assessing the fraction of short-distance tandem splice sites under purifying selectionMichael Hiller
Bioinformatics Group, Albert Ludwigs University Freiburg, 79110 Freiburg, Germany
RNA 14:616-29. 2008..We propose that stochastic splice site selection can be an advantageous mechanism that allows constant splice variant ratios in situations where a deviation in this ratio is deleterious...
- Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequenceStefan Taudien
Genomanalyse, Institut fur Molekulare Biotechnologie, Jena, Germany
BMC Genomics 5:92. 2004..1. This DEF locus, however, represents one of the regions in the euchromatic part of the final human genome sequence which contains segmental duplications, and recalcitrant gaps indicating high structural dynamics...
- Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicingMichael Hiller
Institute of Computer Science, Chair for Bioinformatics, Friedrich Schiller University Jena, Germany
Am J Hum Genet 78:291-302. 2006..Against the background of a general lack of methods for identifying splice-relevant SNPs, the presented approach is highly effective in the prediction of polymorphisms that are causal for variations in alternative splicing...
- TassDB: a database of alternative tandem splice sitesMichael Hiller
Institute of Computer Science, Chair for Bioinformatics, Albert Ludwigs University Freiburg, Georges Koehler Allee 106, 79110 Freiburg, Germany
Nucleic Acids Res 35:D188-92. 2007..This database should facilitate further experimental studies and large-scale bioinformatics analyses of tandem splice sites. The database is available at http://helios.informatik.uni-freiburg.de/TassDB/...
- The Dictyostelium genome encodes numerous RasGEFs with multiple biological rolesAndrew Wilkins
School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
Genome Biol 6:R68. 2005..They are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium...
- Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticityMichael Hiller
Institute of Computer Science, Friedrich Schiller University Jena, Chair for Bioinformatics, Ernst Abbe Platz 2, 07743 Jena, Germany
Nat Genet 36:1255-7. 2004..Because of their subtle effects on mRNA and protein structures, these splice acceptors are often overlooked or underestimated, but they may have a great impact on biology and disease...