Publications

2022

[85]  Robledo-Ruiz D, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, Lieberman Aiden E, Osipova E, Hiller M, Morales HE, Magrath MJL, Clarke R, Sunnucks P, Pavlova A. Chromosome-length genome assembly and linkage map of a Critically Endangered Australian bird: the helmeted honeyeater. GigaScience, 11, 1-13, 2022
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[84] Blumer M, Brown T, Freitas MB, Destro AL, Oliveira JA, Morales A, Schell T, Greve C, Pippel M, Jebb D, Hecker N, Ahmed AW, Kirilenko BM, Foote M, Janke A, Lim BK, Hiller M #. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. Science Advances, 8 (12), eabm6494, 2022
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[83] Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M #. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Reports, 38(3):110280, 2022
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[82] A Ludwig A, Pippel M, Myers G, Hiller M #. DENTIST – using long reads to close assembly gaps at high accuracy. GigaScience, 11, giab100, 2022
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[81] Stefen C, Wagner F, Asztalos M, Giere P, Grobe P, Hiller M, Hofmann R, Jaehde M, Laechele U, Lehmann T, Ortmann S, Peters B, Ruf I, Schiffmann C, Thier N, Unterhitzenberger G, Vogt L, Rudolf M, Wehner P, Stuckas H. Phenotyping in the era of genomics: MaTrics a digital character matrix to document mammalian phenotypic traits coded numerically. Mammalian Biology, 102, 235–249, 2022

[80] Wagner F, Ruf I, Lehmann T, Hofmann R, Ortmann S, Schiffmann C, Hiller M, Stefen C, Stuckas H. Reconstruction of evolutionary changes in fat and toxin consumption reveals associations with gene losses in mammals: a case study for the lipase inhibitor PNLIPRP1 and the xenobiotic receptor NR1I3. Journal of Evolutionary Biology, 35, 225–239, 2022
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[79] Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini AD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Current Biology. 32, 1–15, 2022
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2021

[78] Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O’Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856):737-746. 2021
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[77] Springer MS #, Guerrero-Juarez CF, Huelsmann M, Collin MA, Danil K, McGowen MR, Oh JW, Ramos R, Hiller M #, Plikus MV #, Gatesy J #. Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos. Current Biology, 31 (10), 2124-2139.e3, 2021
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[76] Wang LF, Gamage AM, Chan WOY, Hiller M, Teeling EC. Decoding bat immunity: the need for a coordinated research approach. Nature Reviews Immunology, 21, 269–271, 2021
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[75] Muhandes L, Chapsa M, Pippel M, Behrendt R, Ge Y, Dahl A, Yi B, Dalpke A, Winkler S, Hiller M, Boutin S, Beissert S, Jessberger R, Fallon PG, Roers A. Low threshold for cutaneous allergen sensitization but no spontaneous dermatitis or atopy in filaggrin-deficient mice. Journal of Investigative Dermatology, 141(11), 2611-2619.e2, 2021

[74] Schneider C, Woehle C, Greve C, D’Haese CA, Wolf M, Hiller M, Janke A, Bálint M, Huettel B. Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola). GigaScience, 10 (5), giab035, 2021

[73] Roscito JG, Subramanian K, Naumann R, Sarov M, Shevchenko A, Bogdanova A, Kurth T, Foerster L, Kreysing M, Hiller M #. Recapitulating evolutionary divergence in a single cis-regulatory element is sufficient to cause expression changes of the lens gene Tdrd7. Mol Biol Evol, 38(2), 380–392, 2021
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2020

[72] Real FM, Haas SA, Franchini P, Xiong P, Simakov O, Kuhl H, Schöpflin R, Heller D, Moeinzadeh MH, Heinrich V, Krannich T, Bressin A, Hartmann MF, Wudy SA, Dechmann DKN, Hurtado A, Barrionuevo FJ, Schindler M, Harabula I, Osterwalder M, Hiller M, Wittler L, Visel A, Timmermann B, Meyer A, Vingron M, Jiménez R, Mundlos S, Lupiáñez DG. The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science, 370 (6513), 208-214, 2020

[71] Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, Winkler S, Jermiin LS, Skirmuntt EC, Katzourakis A, Burkitt-Gray L, Ray DA, Sullivan KAM, Roscito JG, Kirilenko BM, Dávalos LM, Corthals AP, Power ML, Jones G, Ransome RD, Dechmann D, Locatelli AG, Puechmaille SJ, Fedrigo O, Jarvis ED, Hiller M #, Vernes SC #, Myers EW #, Teeling EC #. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020
Link

[70] Sharma V, Hecker N, Walther F, Stuckas H, Hiller M #. Convergent losses of TLR5 suggest altered extracellular flagellin detection in four mammalian lineages. Mol Biol Evol, 37(7), 1847–1854, 2020
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[69] Rondelet A, Lin YC, Singh D, Porfetye AT, Thakur HC, Hecker A, Brinkert P, Schmidt N, Bendre S, Müller F, Mazul L, Widlund PO, Bange T, Hiller M, Vetter IR, Bird AW. Clathrin’s adaptor interaction sites are repurposed to stabilize microtubules during mitosis. Journal of Cell Biology, 219 (2): e201907083, 2020
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[68] Pippel M, Jebb D, Patzold F, Winkler S, Myers G, Hiller M #, Hundsdoerfer AK #. A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae). GigaScience, 9(1), giaa001, 2020
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[67] Hecker N, Hiller M #. A genome alignment of 120 mammals highlights ultraconserved element variability and placenta associated enhancers. GigaScience, 9(1), giz159, 2020
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2019

[66] Kirilenko B, Hagey LR, Barnes S, Falany CN, Hiller M #. Evolutionary analysis of bile acid-conjugating enzymes reveals a complex duplication and reciprocal loss history. Genome Biol Evol. 11(11), 3256–3268, 2019
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[65] Sharma V, Hiller M #. Losses of human disease-associated genes in placental mammals. NAR Genomics and Bioinformatics, 2(1), lqz012, 2019
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[64] Osipova E, Hecker N, Hiller M #. RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements. GigaScience, 8(11), giz132, 2019
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[63] Knöbel L, Breusing C, Bayer T, Sharma V, Hiller M, Melzner F, Stuckas H. Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus). Marine Genomics, 100700, 2019
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[62] Huelsmann M, Hecker N, Springer MS, Gatesy J, Sharma V, Hiller M #. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Adv, 5(9), eaaw6671, 2019
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[61] Hecker N, Lächele U, Stuckas H, Giere P, Hiller M. Convergent vomeronasal system reduction in mammals coincides with convergent losses of calcium signaling and odorant degrading genes. Molecular Ecology, 28(16), 3656-3668, 2019
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[60] Hecker N, Sharma V, Hiller M #. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019
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[59] Springer MS, Emerling CA, Gatesy J, Randall J, Collin MA, Hecker N, Hiller M, Delsuc F. Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales. BMC Evol Bio, 19:31, 2019
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2018

[58] Langer BE, Hiller M #. TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences. Nucleic Acids Res., 47(4) e19, 2018
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[57] Roscito JG, Sameith K, Pippel M, Francoijs KJ, Winkler S, Dahl A, Papoutsoglou G, Myers EW, Hiller M #. The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly. GigaScience, 7(12), giy141, 2018
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[56] Sharma V, Hiller M #. Loss of enzymes in the bile acid synthesis pathway explains differences in bile composition among mammals. Genome Biol Evol. 10(12), 3211-3217, 2018
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[55] Roscito JG, Sameith K, Parra G, Langer BE, Petzold A, Moebius C, Bickle M, Rodrigues MT, Hiller M #. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018
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[54] Langer BE, Roscito JG, Hiller M #. REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species. Mol Biol Evol, 35(12), 3027–3040, 2018
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[53] Jebb D, Hiller M #. Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains. Elife, 7, e38906, 2018
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[52] Lee JH, Lewis KM, Moural TW, Kirilenko B, Bogdanova B, Prange G, Koessl M, Huggenberger S, Kang C, Hiller M #. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Adv, 4(9), eaat9660, 2018
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[51] Sharma V, Lehmann T, Stuckas H, Funke L, Hiller M #. Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals. PLoS Biology, 16(6), e2005293, 2018
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[50] Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R. Freiburg RNA tools – a central online resource for RNA-focused research and teaching. Nucleic Acids Res., 46(W1), W25-W29, 2018
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[49] Kralovicova J, Sevcikova I, Stejskalova E, Obuca M, Hiller M, Stanek D, Vorechovsky I. PUF60-activated exons uncover altered 3’ splice-site selection by germline missense mutations in a single RRM. Nucleic Acids Res., 46(12), 6166-6187, 2018
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[48] Florio M, Heide M, Pinson A, Brandl H, Albert M, Winkler S, Wimberger P, Huttner WB #, Hiller M #. Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex. Elife, 7, e32332, 2018
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[47] Sharma V, Hecker N, Roscito JG, Foerster L, Langer BE, Hiller M #. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018
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[46] Nowoshilow S, Schloissnig S #, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M #, Tanaka EM #, Myers E. The axolotl genome and the evolution of key tissue formation regulators. Nature, 554(7690), 50-55, 2018
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[45] Grohme MA, Pippel M, Rozanski A, Young G, Winkler S, Brandl H, Henry I, Dahl A, Powell S, Hiller M, Schloissnig S, Myers E, Rink JC. The genome of Schmidtea mediterranea highlights the evolutionary plasticity of core mechanism. Nature, 554(7690), 56-61, 2018PDF  Link

2017

[44] Hecker N, Sharma V, Hiller M #. Transition to an aquatic habitat permitted the repeated loss of the pleiotropic KLK8 gene in mammals. Genome Biol Evol. 9(11), 3179–3188, 2017
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[43] Sharma V, Schwede P, Hiller M #. CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation. Bioinformatics, 33(24), 3985–3987, 2017
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[42] Sharma V, Hiller M #. 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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[41] Suarez H, Langer BE, Ladde P, Hiller M #. chainCleaner improves genome alignment specificity and sensitivity. Bioinformatics, 33(11), 1596-1603, 2017
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[40] Sameith K, Roscito JG, Hiller M #. Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly. Brief Bioinform., 18(1), 1-8, 2017
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2016

[39] Florio M, Namba T, Pääbo S, Hiller M, Huttner WB. A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification. Science Adv, 2(12), e1601941, 2016
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[38] Prudent X, Parra G, Schwede P, Roscito JG, Hiller M #. Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species’ phenotypic and genomic differences. Mol Biol Evol, 33(8), 2135-50, 2016
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[37] Sharma V, Elghafari A, Hiller M #. Coding Exon-Structure Aware Realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation. Nucleic Acids Res., 44(11), e103, 2016
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2015

[36] Reichwald K, Petzold A, Koch P, Downie BR, Hartmann N, Pietsch S, Baumgart M, Chalopin D, Felder M, Bens M, Sahm A, Szafranski K, Taudien S, Groth M, Arisi I, Weise A, Bhatt SS, Sharma V, Kraus JM, Schmid F, Priebe S, Liehr T, Görlach M, Than ME, Hiller M, Kestler HA, Volff JN, Schartl M, Cellerino A, Englert C, and Platzer M. Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish. Cell, 163(6), 1527-1538, 2015

[35] Aprea J, Lesche M, Massalini S, Prenninger S, Alexopoulou D, Dahl A, Hiller M #, Calegari F #. Identification and expression patterns of novel long non-coding RNAs in neural progenitors of the developing mammalian cortex. Neurogenesis, 2(1), e995524, DOI: 10.1080/23262133.2014.995524, 2015

2014

[34] Szafranski K, Fritsch C, Schumann F, Siebel L, Sinha R, Hampe J, Hiller M, Englert C, Huse K, Platzer M. Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons. Nucleic Acids Res., 42(14), 8895-904, 2014
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2013

[33] Aprea J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, Zocher S, Massalini S, Alexopoulou D, Lesche M, Dahl A, Groszer M, Hiller M, Calegari F. Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment. EMBO J, 32, 3130 – 3144, 2013
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[32] Hiller M #, Agarwal S, Notwell JH, Parikh R, Guturu H, Wenger AM, Bejerano G #. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. Nucleic Acids Res., 41(15):e151, 2013
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[31] Shen M, Bellaousov S, Hiller M, de La Grange P, Creamer TP, Malina O, Sperling R, Mathews DH, Stoilov P, Stamm S. Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure. Nucleic Acids Res., 41(6), 3819-32, 2013
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2012

[30] Hiller M #, Schaar BT, Bejerano G #. Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res, 40(22), 11463–11476, 2012
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[29] Hiller M #, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G #. A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Reports, 2(4), 817-823, 2012
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2011 and before

[28] Rose D, Hiller M, Schutt K, Hackermüller J, Backofen R, Stadler PF. Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinformatics, 27(14), 1894-1900, 2011
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[27] McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnol. 28(5):495-501, 2010.
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[26] Sinha R, Lenser T, Jahn N, Gausmann U, Friedel S, Szafranski K, Huse K, Rosenstiel P, Hampe J, Schuster S, Hiller M, Backofen R, Platzer M. TassDB2 – A comprehensive database of subtle alternative splicing events. BMC Bioinformatics 11(1), 216, 2010

[25] Zhang Z, Theler D, Kaminska KH, Hiller M, Grange PD, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH, Stamm S. The YTH domain is a novel RNA binding domain. J Biol Chem. 285(19), 14701-10, 2010
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[24] Hiller M #, Findeiss S, Lein S, Marz M, Nickel C, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res. 19(7), 1289-300, 2009

[23] Sinha R, Nikolajewa S, Szafranski K, Hiller M, Jahn N, Huse K, Platzer M, Backofen R. Accurate prediction of NAGNAG alternative splicing. Nucleic Acids Res. 37(11), 3569-79, 2009.
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[22] Heinrich B, Zhang Z, Raitskin O, Hiller M, Benderska N, Hartmann AM, Bracco L, Elliott D, Ben-Ari S, Soreq H, Sperling J, Sperling R, Stamm S. Heterogeneous nuclear ribonucleoprotein G regulates splice site selection by binding to CC(A/C)-rich regions in pre-mRNA. J Biol Chem. 284(21), 14303-15, 2009

[21] Sinha S, Hiller M, Pudimat R, Gausmann U, Platzer M, Backofen R. Improved identification of conserved cassette exons using Bayesian networks. BMC Bioinformatics, 9:477, 2008
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[20] Huse K, Taudien S, Groth M, Rosenstiel P, Szafranski K, Hiller M, Hampe J, Junker K, Schubert J, Schreiber S, Birkenmeier G, Krawczak M, Platzer M. 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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[19] Schindler S, Szafranski K, Hiller M, Ali GS, Palusa SG, Backofen R, Platzer M, Reddy ASN. Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics, 9:159, 2008

[18] Hiller M #, Platzer P. Widespread and subtle: alternative splicing at short-distance tandem sites. Trends Genet. 24(5), 249-58, 2008
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[17] Hiller M #, Szafranski K, Huse K, Backofen R, Platzer M. Selection against tandem splice sites affecting structured protein regions. BMC Evol Bio, 8:89, 2008
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[16] Hiller M #, Szafranski K, Sinha R, Huse K, Nikolajewa S, Rosenstiel P, Schreiber S, Backofen R, Platzer M. Assessing the fraction of short-distance tandem splice sites under purifying selection. RNA, 14(4), 616-29, 2008
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[15] Hiller M, Zhang Z, Backofen R, Stamm S. Pre-mRNA secondary structures influence exon recognition. PLoS Genet. 3(11), e204, 2007

[14] Szafranski K, Schindler S, Taudien S, Hiller M, Huse K, Jahn N, Schreiber S, Backofen R, Platzer M. Violating the splicing rules: TG dinucleotides function as alternative 3′ splice sites in U2-dependent introns. Genome Biol. 8(8), R154, 2007
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[13] Nikolajewa S, Pudimat R, Hiller M, Backofen R. BioBayesNet: a web server for feature extraction and Bayesian network modelling of biological sequence data. Nucleic Acids Res. 35(Web Server Issue), W688-93, 2007
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[12] Hiller M #, Nikolajewa S, Huse K, Szafranski K, Rosenstiel P, Schuster S, Backofen R, Platzer M. TassDB: a database of alternative tandem splice sites. Nucleic Acids Res. 35(Database issue), D188-92, 2007.

[11] Hiller M, Szafranski K, Backofen R, Platzer M. Alternative splicing at NAGNAG acceptors: Simply noise or noise and more? PLoS Genet. 2(11), e207, 2006.

[10] Hiller M, Pudimat R, Busch A, Backofen R. Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res. 34(17), e117, 2006.
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[9] Platzer M, Hiller M, Szafranski K, Jahn N, Hampe J, Schreiber S, Backofen R, Huse K. Sequencing errors or SNPs at splice-acceptor guanines in dbSNP? Nature Biotechnol. 24(9), 1068-70, 2006.
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[8] Hiller M, Huse K, Szafranski K, Rosenstiel P, Schreiber S, Backofen R, Platzer M. Phylogenetically widespread alternative splicing at unusual GYNGYN donors. Genome Biology, 7(7):R65, 2006.

[7] Hiller M, Huse K, Szafranski K, Jahn N, Hampe J, Schreiber S, Backofen R, Platzer M. 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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[6] Hiller M #, Huse K, Platzer M, Backofen R #. Non-EST based prediction of exon skipping and intron retention events using Pfam information. Nucleic Acids Res. 33(17), 5611-21, 2005.
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[5] Hiller M, Huse K, Platzer M, Backofen R. Creation and disruption of protein features by alternative splicing – a novel mechanism to modulate function. Genome Biology, 6(7):R58, 2005.

[4] Hiller M, Huse K, Szafranski K, Jahn N, Hampe J, Schreiber S, Backofen R, Platzer M. Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nature Genet. 36(12), 1255-7, 2004.

[3] Hiller M, Backofen R, Heymann S, Busch A, Glaesser TM, Freytag JC. Efficient prediction of alternative splice forms using protein domain homology. In Silico Biol. 4(2), 2004.

[2] Hamzaoui R, Saupe D, Hiller M. Distortion minimization with fast local search for fractal image compression. Journal of Visual Communication and Image Representation, 12, 450-468, 2001.

[1] Hamzaoui R, Saupe D, Hiller M. Fast code enhancement with local search for fractal image compression. In Proc. of IEEE International Conference on Image Processing, Vancouver, 2000.

 70. Ludwig A, Pippel M, Myers G, Hiller M. DENTIST—using long reads for closing assembly gaps at high accuracy, GigaScience, Volume 11, 2022
DOI


 69. Juliana G. Roscito, Kaushikaram Subramanian, Ronald Naumann, Mihail Sarov, Anna Shevchenko, Aliona Bogdanova, Thomas Kurth, Leo Foerster, Moritz Kreysing, Michael Hiller
Recapitulating evolutionary divergence in a single cis-regulatory element is sufficient to cause expression changes of the lens gene Tdrd7.
Mol Biol Evol, Art. No. doi: 10.1093/molbev/msaa212 (2020)
DOI 


 68. Joana Damas, Graham M Hughes, Kathleen C Keough, Corrie A Painter, Nicole S Persky, Marco Corbo, Michael Hiller, Klaus-Peter Koepfli, Andreas R Pfenning, Huabin Zhao, Diane P Genereux, Ross Swofford, Katherine S Pollard, Oliver A Ryder, Martin T Nweeia, Kerstin Lindblad-Toh, Emma Teeling, Elinor K Karlsson, Harris A Lewin
Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.
Proc Natl Acad Sci U.S.A., Art. No. doi: 10.1073/pnas.2010146117 (2020)
DOI 


 67. David Jebb, Zixia Huang, Martin Pippel, Graham M Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S Jermiin, Emilia C Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A Ray, Kevin F. Sullivan, Juliana G. Roscito, Bogdan Kirilenko, Liliana M Dávalos, Angelique P Corthals, Megan L Power, Gareth Jones, Roger D Ransome, Dina K N Dechmann, Andrea G Locatelli, Sébastien J Puechmaille, Olivier Fedrigo, Erich D Jarvis, Michael Hiller, Sonja Vernes, Eugene W Myers, Emma Teeling
Six reference-quality genomes reveal evolution of bat adaptations.
Nature, 583(7817) 578-584 (2020)
DOI 
 

 66. Virag Sharma, Nikolai Hecker, Felix Walther, Heiko Stuckas, Michael Hiller
Convergent Losses of TLR5 Suggest Altered Extracellular Flagellin Detection in Four Mammalian Lineages.
Mol Biol Evol, 37(7) 1847-1854 (2020)
DOI 
 

 65. Loreen Knöbel, Corinna Breusing, Till Bayer, Virag Sharma, Michael Hiller, Frank Melzner, Heiko Stuckas
Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus)
Mar Genomics, 51 Art. No. 100700 (2020)
DOI 
 

 64. Arnaud Rondelet, Yu-Chih Lin, Divya Singh, Arthur T Porfetye, Harish C Thakur, Andreas Hecker, Pia Brinkert, Nadine Schmidt, Shweta Bendre, Franziska Müller, Lisa Mazul, Per Widlund, Tanja Bange, Michael Hiller, Ingrid R Vetter, Alexander W. Bird
Clathrin’s adaptor interaction sites are repurposed to stabilize microtubules during mitosis.
J Cell Biol, 219(2) Art. No. e201907083 (2020)
DOI 
 

 63. Virag Sharma, Michael Hiller
Losses of human disease-associated genes in placental mammals
NAR Genomics and Bioinformatics, 2(1) Art. No. doi: 10.1093/nargab/lqz012 (2020)
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 62. Martin Pippel, David Jebb, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller, Anna K Hundsdoerfer
A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).
GigaScience, 9(1) Art. No. giaa001 (2020)
DOI 
 

 61 Nikolai Hecker, Michael Hiller
A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.
GigaScience, 9(1) Art. No. giz159 (2020)
DOI 
 

 60. Wagner F, Ruf I, Lehmann T, Hofmann R, Ortmann S, Schiffmann C, Hiller M, Stefen C, Stuckas H. Reconstruction of evolutionary changes in fat and toxin consumption reveals associations with gene losses in mammals: a case study for the lipase inhibitor PNLIPRP1 and the xenobiotic receptor NR1I3. Journal of Evolutionary Biology (2021)
DOI


59. Stefen C, Wagner F, Asztalos M, Giere P, Grobe P, Hiller M, Hofmann R, Jähde M, Lächele U, Lehmann T, Ortmann S, Peters B, Ruf I, Schiffmann C, Thier N, Unterhitzenberger G, Vogt L, Rudolf M, Wehner P, Stuckas H. Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits. Mammalian Biology (2021).
DOI


58. Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini AD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Current Biology. 32, 1–15, 2022

DOI


57. Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O’Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592(7856):737-746. 2021

DOI


56. Springer MS, Guerrero-Juarez CF, Huelsmann M, Collin MA, Danil K, McGowen MR, Won Oh J, Ramos R, Hiller M, Plikus MV, Gatesy J. Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos. Current Biology

https://www.sciencedirect.com/science/article/abs/pii/S0960982221003018
DOI 


55. Wang LF, Gamage AM, Chan WOY, Hiller M, Teeling EC. Decoding bat immunity: the need for a coordinated research approach. Nature Reviews Immunology. https://doi.org/10.1038/s41577-021-00523-0, 2021

DOI 

54. Ekaterina Osipova, Nikolai Hecker, Michael Hiller
RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements.
GigaScience, 8(11) Art. No. giz132 (2019)
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 53. Bogdan Kirilenko, Lee R Hagey, Stephen Barnes, Charles N Falany, Michael Hiller
Evolutionary Analysis of Bile Acid-Conjugating Enzymes Reveals a Complex Duplication and Reciprocal Loss History.
Genome Biol Evol, 11(11) 3256-3268 (2019)
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52. Juliana G. Roscito, Michael Hiller
Methods to Detect and Associate Divergence in Cis-Regulatory Elements to Phenotypic Divergence.
In: Evolution, Origin of Life, Concepts and Methods . (Eds.) Pierre Pontarotti,Cham,Springer International Publishing (2019),113-134 Ch. 6
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 51. Matthias Huelsmann, Nikolai Hecker, Mark S Springer, John Gatesy, Virag Sharma, Michael Hiller
Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations.
Sci Adv, 5(9) Art. No. eaaw6671 (2019)
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 50. Nikolai Hecker, Ulla Lächele, Heiko Stuckas, Peter Giere, Michael Hiller
Convergent vomeronasal system reduction in mammals coincides with convergent losses of calcium signalling and odorant-degrading genes.
Mol. Ecol., 28(16) 3656-3668 (2019)
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 49. Björn Langer, Michael Hiller
TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences.
Nucleic Acids Res, 47(4) Art. No. e19 (2019)
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 48. Nikolai Hecker, Virag Sharma, Michael Hiller
Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores.
Proc Natl Acad Sci U.S.A., 116(8) 3036-3041 (2019)
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 47. Mark S Springer, Christopher A Emerling, John Gatesy, Jason Randall, Matthew A Collin, Nikolai Hecker, Michael Hiller, Frédéric Delsuc
Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales.
BMC Evol Biol, 19(1) Art. No. 31 (2019)
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 46. Virag Sharma, Michael Hiller. Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene Annotation.
Methods Mol Biol, 1962 179-191 (2019)
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 45. Juliana G. Roscito, Katrin Sameith, Martin Pippel, Kees-Jan Francoijs, Sylke Winkler, Andreas Dahl, Georg Papoutsoglou, Gene Myers, Michael Hiller
The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.
GigaScience, 7(12) Art. No. giy141 (2018)
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 44. Björn Langer, Juliana G. Roscito, Michael Hiller
REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species.
Mol Biol Evol, 35(12) 3027-3040 (2018)
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 43. Virag Sharma, Michael Hiller
Loss of Enzymes in the Bile Acid Synthesis Pathway Explains Differences in Bile Composition among Mammals.
Genome Biol Evol, 10(12) 3211-3217 (2018)
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 42. Juliana G. Roscito, Katrin Sameith, Genis Parra, Bjoern Langer, Andreas Petzold, Claudia Moebius, Marc Bickle, Miguel Trefaut Rodrigues, Michael Hiller
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution.
Nat Commun, 9(1) Art. No. 4737 (2018)
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 41. David Jebb, Michael Hiller. Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains.
Elife, 7 Art. No. e38906 (2018)
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 40. Jun Hoe Lee, Kevin M Lewis, Timothy W Moural, Bogdan Kirilenko, Barbara Borgonovo, Gisa Prange, Manfred Koessl, Stefan Huggenberger, ChulHee Kang, Michael Hiller
Molecular parallelism in fast-twitch muscle proteins in echolocating mammals
Sci Adv, 4(9) Art. No. eaat9660 (2018)
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 39. Jana Královicová, Ivana Ševcíková, Eva Stejskalová, Mina Obuca, Michael Hiller, David R. Stanek, Igor Vorechovský
PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM.
Nucleic Acids Res, 46(12) 6166-6187 (2018)
DOI 

38. Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
Nucleic Acids Res, 46(W1) 25-29 (2018)
DOI 

 37. Virag Sharma, Thomas Lehmann, Heiko Stuckas, Liane Funke, Michael Hiller
Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals.
PLoS Biol, 16(6) Art. No. e2005293 (2018)
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 36. Virag Sharma, Nikolai Hecker, Juliana G. Roscito, Leo Foerster, Björn Langer, Michael Hiller
A genomics approach reveals insights into the importance of gene losses for mammalian adaptations.
Nat Commun, 9(1) Art. No. 1215 (2018)
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 35. Marta Florio, Michael Heide, Anneline Pinson, Holger Brandl, Mareike Albert, Sylke Winkler, Pauline Wimberger, Wieland B. Huttner, Michael Hiller
Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex.
Elife, 7 Art. No. e32332 (2018)
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 34. Markus Grohme, Siegfried Schloissnig, Andrei Rozanski, Martin Pippel, George Robert Young, Sylke Winkler, Holger Brandl, Ian Henry, Andreas Dahl, Sean Powell, Michael Hiller, Eugene Myers, Jochen Rink
The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms.
Nature, 554(7690) 56-61 (2018)
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 33. Sergej Nowoshilow, Siegfried Schloissnig, Jifeng Fei, Andreas Dahl, Andy W C Pang, Martin Pippel, Sylke Winkler, Alex R Hastie, George Young, Juliana G. Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller, Elly M. Tanaka, Eugene W Myers
The axolotl genome and the evolution of key tissue formation regulators.
Nature, 554(7690) 50-55 (2018)
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 32. Virag Sharma, Peter Schwede, Michael Hiller
CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation.
Bioinformatics, 33(24) 3985-3987 (2017)
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 31. Nikolai Hecker, Virag Sharma, Michael Hiller
Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals.
Genome Biol Evol, 9(11) 3179-3188 (2017)
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 30. Jun Hoe Lee, Michael Hiller
Genome-Wide Screens for Molecular Convergent Evolution in Mammals
In: Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts . (Eds.) Pierre Pontarotti,Cham,Springer International Publishing (2017),297-312
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 29. 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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 28. Hernando Suarez, Björn Langer, Pradnya Ladde, Michael Hiller
chainCleaner improves genome alignment specificity and sensitivity.
Bioinformatics, 33(11) 1596-1603 (2017)
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 27. Katrin Sameith, Juliana G. Roscito, Michael Hiller
Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly.
Brief Bioinform, 18(1) 1-8 (2017)
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 26. 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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 25. Xavier Prudent, Genis Parra, Peter Schwede, Juliana G. 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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 24. 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)

 23. 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)
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 22. 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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 21. 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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 20. 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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 19. Michael Hiller. Vom Phänotyp zum Genotyp : Forward Genomics – ein neuer Ansatz der vergleichenden Sequenzanalyse
Biologie in unserer Zeit, 43(1) 34-39 (2013)
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 18. 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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 17. 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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 16. 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)
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 15. 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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 14. 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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 13. 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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 12. 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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 11. 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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 1o. 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)


 9. 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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 8. 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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 7. 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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 6. 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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 5. 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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 4. 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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 3. 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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 2. 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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 1. 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)