Michael Hiller

Summary

Affiliation: University of Freiburg
Country: Germany

Publications

  1. doi request reprint Widespread and subtle: alternative splicing at short-distance tandem sites
    Michael Hiller
    Bioinformatics Group, Albert Ludwigs University Freiburg, 79110 Freiburg, Germany
    Trends Genet 24:246-55. 2008
  2. ncbi request reprint Efficient prediction of alternative splice forms using protein domain homology
    Michael Hiller
    Friedrich Schiller Universitaet Jena, Institute of Computer Science, Chair for Bioinformatics, Ernst Abbe Platz 1 4, D 07743 Jena, Germany
    In Silico Biol 4:195-208. 2004
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. pmc TassDB2 - A comprehensive database of subtle alternative splicing events
    Rileen Sinha
    Albert Ludwigs University Freiburg, Germany
    BMC Bioinformatics 11:216. 2010
  10. 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

Detail Information

Publications20

  1. doi request reprint Widespread and subtle: alternative splicing at short-distance tandem sites
    Michael Hiller
    Bioinformatics Group, Albert Ludwigs University Freiburg, 79110 Freiburg, Germany
    Trends Genet 24:246-55. 2008
    ..Stochastic splice site selection seems to play a major role in these processes. Here, we review recent progress in understanding functional and evolutionary aspects as well as the mechanism of splicing at short-distance tandem sites...
  2. ncbi request reprint Efficient prediction of alternative splice forms using protein domain homology
    Michael Hiller
    Friedrich Schiller Universitaet Jena, Institute of Computer Science, Chair for Bioinformatics, Ernst Abbe Platz 1 4, D 07743 Jena, Germany
    In Silico Biol 4:195-208. 2004
    ..To this end, we have developed an efficient polynomial-time algorithm, called ASFPred (Alternative Splice Form Prediction). This algorithm needs only a set of exons as input...
  3. 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/...
  4. 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...
  5. 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...
  6. 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...
  7. 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)...
  8. 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...
  9. 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...
  10. 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...
  11. pmc Non-EST based prediction of exon skipping and intron retention events using Pfam information
    Michael Hiller
    Institute of Computer Science, Friedrich Schiller University Jena, Chair for Bioinformatics, Ernst Abbe Platz 2, 07743 Jena, Germany
    Nucleic Acids Res 33:5611-21. 2005
    ..As Pfam domains are annotated in many other species, our strategy to predict exon skipping and intron retention events might be important for species with a lower number of ESTs...
  12. 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...
  13. 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...
  14. pmc Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function
    Michael Hiller
    Institute of Computer Science, Friedrich Schiller University Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Genome Biol 6:R58. 2005
    ..It is mainly carried out in two ways: by skipping exons that encode a certain protein feature and by introducing a frameshift that changes the downstream protein sequence. These mechanisms are widespread and well investigated...
  15. 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...
  16. pmc Pre-mRNA secondary structures influence exon recognition
    Michael Hiller
    Bioinformatics Group, Albert Ludwigs University Freiburg, Freiburg, Germany
    PLoS Genet 3:e204. 2007
    ..Our results explain the action of mutations that affect splicing and indicate that the structural context of splicing motifs is part of the mRNA splicing code...
  17. pmc Using RNA secondary structures to guide sequence motif finding towards single-stranded regions
    Michael Hiller
    Institute of Computer Science, Chair for Bioinformatics, Albert Ludwigs University Freiburg, Georges Koehler Allee 106, 79110 Freiburg, Germany
    Nucleic Acids Res 34:e117. 2006
    ..This algorithm can be used for finding the binding motif of single-stranded RNA-binding proteins in SELEX or other biological sequence data...
  18. pmc Alternative splicing at NAGNAG acceptors: simply noise or noise and more?
    Michael Hiller
    PLoS Genet 2:e207; author reply e208. 2006
  19. ncbi request reprint Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?
    Matthias Platzer
    Nat Biotechnol 24:1068-70. 2006
  20. pmc BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
    Swetlana Nikolajewa
    Department of Bioinformatics, Friedrich Schiller University Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Nucleic Acids Res 35:W688-93. 2007
    ..The BioBayesNet server is available at http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/...