2017

Virag Sharma, Peter Schwede, Michael Hiller
CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation.
Bioinformatics, Art. No. doi: 10.1093/bioinformatics/btx527 (2017)
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Virag Sharma, Michael Hiller
Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.
Nucleic Acids Res, 45(14) 8369-8377 (2017)
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Hernando Suarez, Bjorn Langer, Pradnya Ladde, Michael Hiller
chainCleaner improves genome alignment specificity and sensitivity.
Bioinformatics, 33(11) 1596-1603 (2017)
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Jun Hoe Lee
Detecting signaturesof convergent evolution genome-wide
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2017)
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Nikolai Hecker, Virag Sharma, Michael Hiller
Transition to an aquatic habitat permitted the repeated loss of the pleiotropic KLK8 gene in mammals
GBE, 1-1 (2017)
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Katrin Sameith, Juliana Roscito, Michael Hiller
Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly.
Brief. Bioinformatics, 18(1) 1-8 (2017)

2016

Marta Florio, Takashi Namba, Svante Pääbo, Michael Hiller, Wieland B. Huttner
A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification
Sci Adv, 2(12) Art. No. e1601941 (2016)
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Xavier Prudent, Genis Parra, Peter Schwede, Juliana Roscito, Michael Hiller
Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences.
Mol Biol Evol, 33(8) 2135-2150 (2016)
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Virag Sharma, Anas Elghafari, Michael Hiller
Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.
Nucleic Acids Res, 44(11) Art. No. e103 (2016)

2015

Kathrin Reichwald, Andreas Petzold, Philipp Koch, Bryan R Downie, Nils Hartmann, Stefan Pietsch, Mario Baumgart, Domitille Chalopin, Marius Felder, Martin Bens, Arne Sahm, Karol Szafranski, Stefan Taudien, Marco Groth, Ivan Arisi, Anja Weise, Samarth S Bhatt, Virag Sharma, Johann M Kraus, Florian Schmid, Steffen Priebe, Thomas Liehr, Matthias Görlach, Manuel E Than, Michael Hiller, Hans A Kestler, Jean-Nicolas Volff, Manfred Schartl, Alessandro Cellerino, Christoph Englert, Matthias Platzer
Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish.
Cell, 163(6) 1527-1538 (2015)
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Julieta Aprea, Mathias Lesche, Simone Massalini, Silvia Prenninger, Dimitra Alexopoulou, Andreas Dahl, Michael Hiller, Federico Calegari
Identification and expression patterns of novel long non-coding RNAs in neural progenitors of the developing mammalian cortex
Neurogenesis, 2(1) Art. No. e995524 (2015)

2014

Karol Szafranski, Claudia Fritsch, Frank Schumann, Lisa Siebel, Rileen Sinha, Jochen Hampe, Michael Hiller, Christoph Englert, Klaus Huse, Matthias Platzer
Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons.
Nucleic Acids Res, 42(14) 8895-8904 (2014)

2013

Julieta Aprea, Silvia Prenninger, Martina Dori, Tanay Ghosh, Laura Sebastian Monasor, Elke Wessendorf, Sara Zocher, Simone Massalini, Dimitra Alexopoulou, Mathias Lesche, Andreas Dahl, Matthias Groszer, Michael Hiller, Federico Calegari
Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment.
EMBO J, 32(24) 3145-3160 (2013)
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Michael Hiller, Saatvik Agarwal, James H Notwell, Ravi Parikh, Harendra Guturu, Aaron M Wenger, Gill Bejerano
Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.
Nucleic Acids Res, 41(15) Art. No. e151 (2013)
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Manli Shen, Stanislav Bellaousov, Michael Hiller, Pierre de la Grange, Trevor P Creamer, Orit Malina, Ruth Sperling, David H Mathews, Peter Stoilov, Stefan Stamm
Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure.
Nucleic Acids Res, 41(6) 3819-3832 (2013)
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Michael Hiller
Vom Phänotyp zum Genotyp : Forward Genomics - ein neuer Ansatz der vergleichenden Sequenzanalyse
Biologie in unserer Zeit, 43(1) 34-39 (2013)

2012

Michael Hiller, Bruce T Schaar, Gill Bejerano
Hundreds of conserved non-coding genomic regions are independently lost in mammals.
Nucleic Acids Res, 40(22) 11463-11476 (2012)
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Michael Hiller, Bruce T Schaar, Vahan B Indjeian, David M Kingsley, Lee R Hagey, Gill Bejerano
A "Forward Genomics" Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species.
Cell Rep, 2(4) 817-823 (2012)
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Michael Hiller
Analysis of pre-mRNA secondary structures and alternative splicing
In: Alternative pre-mRNA splicing : theory and protocols. (Eds.) Stefan Stamm, Chris Smith, Reinhard Lührmann,Weinheim,Wiley-Blackwell (2012),575-580

2011

Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F Stadler
Computational discovery of human coding and non-coding transcripts with conserved splice sites.
Bioinformatics, 27(14) 1894-1900 (2011)

2010

Zhaiyi Zhang, Dominik Theler, Katarzyna H Kaminska, Michael Hiller, Pierre de la Grange, Rainer Pudimat, Ilona Rafalska, Bettina Heinrich, Janusz M Bujnicki, Frédéric H-T Allain, Stefan Stamm
The YTH domain is a novel RNA binding domain.
J Biol Chem, 285(19) 14701-14710 (2010)
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Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano
GREAT improves functional interpretation of cis-regulatory regions.
Nat Biotechnol, 28(5) 495-501 (2010)
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Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer
TassDB2 - A comprehensive database of subtle alternative splicing events.
BMC Bioinformatics, 11 Art. No. 216 (2010)

2009

Michael Hiller, Sven Findeiss, Sandro Lein, Manja Marz, Claudia Nickel, Dominic Rose, Christine Schulz, Rolf Backofen, Sonja J Prohaska, Gunter Reuter, Peter F Stadler
Conserved introns reveal novel transcripts in Drosophila melanogaster.
Genome Res, 19(7) 1289-1300 (2009)
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Rileen Sinha, Swetlana Nikolajewa, Karol Szafranski, Michael Hiller, Niels Jahn, Klaus Huse, Matthias Platzer, Rolf Backofen
Accurate prediction of NAGNAG alternative splicing.
Nucleic Acids Res, 37(11) 3569-3579 (2009)
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Bettina Heinrich, Zhaiyi Zhang, Oleg Raitskin, Michael Hiller, Natalya Benderska, Annette M Hartmann, Laurent Bracco, David Elliott, Shani Ben-Ari, Hermona Soreq, Joseph Sperling, Ruth Sperling, Stefan Stamm
Heterogeneous nuclear ribonucleoprotein G regulates splice site selection by binding to CC(A/C)-rich regions in pre-mRNA.
J Biol Chem, 284(21) 14303-14315 (2009)

2008

Michael Hiller, Matthias Platzer
Widespread and subtle: alternative splicing at short-distance tandem sites.
Trends Genet, 24(5) 246-255 (2008)
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Michael Hiller, Karol Szafranski, Rileen Sinha, Klaus Huse, Swetlana Nikolajewa, Philip Rosenstiel, Stefan Schreiber, Rolf Backofen, Matthias Platzer
Assessing the fraction of short-distance tandem splice sites under purifying selection.
RNA, 14(4) 616-629 (2008)
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Michael Hiller, Karol Szafranski, Klaus Huse, Rolf Backofen, Matthias Platzer
Selection against tandem splice sites affecting structured protein regions.
BMC Evol Biol, 8 89-89 (2008)
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Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer, Rolf Backofen
Improved identification of conserved cassette exons using Bayesian networks.
BMC Bioinformatics, 9 477-477 (2008)
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Klaus Huse, Stefan Taudien, Marco Groth, Philip Rosenstiel, Karol Szafranski, Michael Hiller, Jochen Hampe, Kerstin Junker, Jorg Schubert, Stefan Schreiber, Gerd Birkenmeier, Michael Krawczak, Matthias Platzer
Genetic variants of the copy number polymorphic beta-defensin locus are associated with sporadic prostate cancer.
Tumour Biol, 29(2) 83-92 (2008)
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Stefanie Schindler, Karol Szafranski, Michael Hiller, Gul Shad Ali, Saiprasad G Palusa, Rolf Backofen, Matthias Platzer, Anireddy S N Reddy
Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes.
BMC Genomics, 9 159-159 (2008)

2007

Michael Hiller, Zhaiyi Zhang, Rolf Backofen, Stefan Stamm
Pre-mRNA secondary structures influence exon recognition.
PLoS Genet, 3(11) 204-204 (2007)
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Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data.
Nucleic Acids Res, 35(Web Server issue) 688-693 (2007)
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Karol Szafranski, Stefanie Schindler, Stefan Taudien, Michael Hiller, Klaus Huse, Niels Jahn, Stefan Schreiber, Rolf Backofen, Matthias Platzer
Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns.
Genome Biol, 8(8) 154-154 (2007)
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Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer
TassDB: a database of alternative tandem splice sites.
Nucleic Acids Res, 35(Database issue) 188-192 (2007)

2006

Michael Hiller, Karol Szafranski, Rolf Backofen, Matthias Platzer
Alternative splicing at NAGNAG acceptors: simply noise or noise and more?
PLoS Genet, 2(11) 207-208 (2006)
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Matthias Platzer, Michael Hiller, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Klaus Huse
Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?
Nat Biotechnol, 24(9) 1068-1070 (2006)
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Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Matthias Platzer
Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing.
Am J Hum Genet, 78(2) 291-302 (2006)
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Michael Hiller, Rainer Pudimat, Anke Busch, Rolf Backofen
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.
Nucleic Acids Res, 34(17) 117-117 (2006)
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Michael Hiller, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schreiber, Rolf Backofen, Matthias Platzer
Phylogenetically widespread alternative splicing at unusual GYNGYN donors.
Genome Biol, 7(7) 65-65 (2006)

2005

Michael Hiller, Klaus Huse, Matthias Platzer, Rolf Backofen
Non-EST based prediction of exon skipping and intron retention events using Pfam information.
Nucleic Acids Res, 33(17) 5611-5621 (2005)
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Michael Hiller, Klaus Huse, Matthias Platzer, Rolf Backofen
Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function.
Genome Biol, 6(7) 58-58 (2005)

2004

Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Matthias Platzer
Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity.
Nat Genet, 36(12) 1255-1257 (2004)
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Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Glaesser, Johann-Christoph Freytag
Efficient prediction of alternative splice forms using protein domain homology.
In Silico Biol, 4(2) 195-208 (2004)