Karol Szafranski

Summary

Affiliation: Leibniz Institute for Age Research
Country: Germany

Publications

  1. pmc Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
    Anke 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
  2. pmc Phylogenetically widespread alternative splicing at unusual GYNGYN donors
    Michael Hiller
    Institute of Computer Science, Albert Ludwigs University Freiburg, Georges Koehler Allee 106, 79110 Freiburg, Germany
    Genome Biol 7:R65. 2006
  3. pmc Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing
    Stefan Taudien
    Leibniz Institute for Age Research Fritz Lipmann Institute, Jena, Germany
    BMC Genomics 12:243. 2011
  4. pmc Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing
    Stefan Taudien
    Leibniz Institute for Age Research Fritz Lipmann Institute, Jena, Germany
    BMC Genomics 11:252. 2010
  5. pmc Comparative analysis of sequence features involved in the recognition of tandem splice sites
    Ralf Bortfeldt
    Department of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz 2, D 07743 Jena, Germany
    BMC Genomics 9:202. 2008
  6. pmc Selection against tandem splice sites affecting structured protein regions
    Michael Hiller
    Bioinformatics Group, Albert Ludwigs University Freiburg, Georges Koehler Allee 106, 79110 Freiburg, Germany
    BMC Evol Biol 8:89. 2008
  7. pmc TassDB2 - A comprehensive database of subtle alternative splicing events
    Rileen Sinha
    Albert Ludwigs University Freiburg, Germany
    BMC Bioinformatics 11:216. 2010
  8. ncbi request reprint tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression
    Karol Szafranski
    Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute Beutenbergstr 11, 07745 Jena, Germany
    Bioinformatics 22:1917-8. 2006
  9. pmc Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns
    Karol Szafranski
    Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr, 07745 Jena, Germany
    Genome Biol 8:R154. 2007
  10. doi request reprint High-resolution mapping of the 8p23.1 beta-defensin cluster reveals strictly concordant copy number variation of all genes
    Marco Groth
    Genome Analysis, Leibniz Institute for Age Research Fritz Lipmann Institute, Jena, Germany
    Hum Mutat 29:1247-54. 2008

Collaborators

Detail Information

Publications26

  1. pmc Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
    Anke 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
    ....
  2. pmc Phylogenetically widespread alternative splicing at unusual GYNGYN donors
    Michael 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)...
  3. pmc Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing
    Stefan 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...
  4. pmc Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing
    Stefan 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...
  5. pmc Comparative analysis of sequence features involved in the recognition of tandem splice sites
    Ralf Bortfeldt
    Department of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz 2, D 07743 Jena, Germany
    BMC Genomics 9:202. 2008
    ....
  6. pmc Selection against tandem splice sites affecting structured protein regions
    Michael 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...
  7. pmc TassDB2 - A comprehensive database of subtle alternative splicing events
    Rileen 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...
  8. ncbi request reprint tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression
    Karol 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...
  9. pmc Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns
    Karol 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...
  10. doi request reprint High-resolution mapping of the 8p23.1 beta-defensin cluster reveals strictly concordant copy number variation of all genes
    Marco 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...
  11. pmc Accurate prediction of NAGNAG alternative splicing
    Rileen 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...
  12. pmc Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes
    Stefanie 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...
  13. doi request reprint Comparison of methods for quantification of subtle splice variants
    Stefanie 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...
  14. doi request reprint Genetic variants of the copy number polymorphic beta-defensin locus are associated with sporadic prostate cancer
    Klaus 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...
  15. pmc High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research
    Kathrin 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...
  16. ncbi request reprint DictyMOLD-a Dictyostelium discoideum genome browser database
    Marius 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...
  17. ncbi request reprint Sequence and analysis of chromosome 2 of Dictyostelium discoideum
    Gernot 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...
  18. pmc Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
    Stefan 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...
  19. ncbi request reprint Gene organization features in A/T-rich organisms
    Karol 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...
  20. pmc Assessing the fraction of short-distance tandem splice sites under purifying selection
    Michael 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...
  21. pmc Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing
    Michael 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...
  22. ncbi request reprint Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?
    Matthias Platzer
    Nat Biotechnol 24:1068-70. 2006
  23. pmc Alternative splicing at NAGNAG acceptors: simply noise or noise and more?
    Michael Hiller
    PLoS Genet 2:e207; author reply e208. 2006
  24. pmc TassDB: a database of alternative tandem splice sites
    Michael 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/...
  25. ncbi request reprint Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
    Michael 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...
  26. pmc The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles
    Andrew 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...