2024

2023

[98]  Sadanandan KR, Ko MC, Low GW, Gahr M, Edwards SV, Hiller M, Sackton TB, Rheindt FE, Sin SYW, Baldwin MW. Convergence in hearing-related genes between echolocating birds and mammals. PNAS, 120(43):e2307340120, 2023
Link

[97]  Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, Armstrong J, Zweig AS, Kuhn RM, Kirilenko BM, Hiller M, Haussler D, Kent WJ, Haeussler M.  GenArk: towards a million UCSC genome browsers. Genome Biol. 24(1):217. 2023
Link

[96]  Hundsdoerfer AK, Schell T, Patzold F, Wright CJ, Yoshido A, Marec F, Daneck H, Winkler S, Greve C, Podsiadlowski L, Hiller M, Pippel M. High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae). BMC Genomics, 24(1):443, 2023
Link

[95]  Shatilovich A, Gade VR, Pippel M, Hoffmeyer TT, Tchesunov AV, Stevens L, Winkler S, Hughes GM, Traikov S, Hiller M, Rivkina E, Schiffer PH, Myers EW, Kurzchalia TV. A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva. PLoS Genet. 19(7):e1010798, 2023
Link

[94]  Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium, Hiller M #. Integrating gene annotation with orthology inference at scale. Science, 380(6643), eabn3107, 2023
Link to full text

[93]  Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR; Zoonomia Consortium§; Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. Science, 380(6643), eabn3943, 2023
Link

[92]  Wolf M, Zapf K, Gupta DK, Hiller M, Árnason U, Janke A. The genome of the pygmy right whale illuminates the evolution of rorquals. BMC Biol. 21(1), 79, 2023
Link

[91]   Déjosez M, Marin A, Hughes GM, Morales AE, Godoy-Parejo C, Gray J, Qin Y, Singh AA, Xu H, Juste J, Ibáñez C, White KM, Rosales R, Francoeur NJ, Sebra RP, Alcock D, Volkert TL, Puechmaille SJ, Pastusiak A, Frost SDW, Hiller M, Young RA, Teeling EC, García-Sastre A, Zwaka TP. Bat pluripotent stem cells reveal unusual entanglement between host and viruses. Cell, 186, 1–18, 2023
Link

[90]    Osipova E, Barsacchi R, Brown T, Sadanandan K, Gaede AH, Monte A, Jarrells J, Moebius C, Pippel M, Altshuler DL, Winkler S, Bickle M, Baldwin MW, Hiller M #. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science, 379(6628), 185-190, 2023
Link to full text   pdf

2022

[89]  Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. BMC Biology, 20(1):245m 2022
Link

[88]    Vernes SC, Devanna P, Hörpel SG, van Tussenbroek IA, Firzlaff U, Hagoort P, Hiller M, Hoeksema N, Hughes GM, Lavrichenko K, Mengede J, Morales AE, Wiesmann M. The pale spear‐nosed bat: A neuromolecular and transgenic model for vocal learning. Annals of the New York Academy of Sciences, doi: 10.1111/nyas.14884, 2022
Link

[87]    Indrischek H, Hammer J, Machate A, Hecker N, Kirilenko BM, Roscito JG, Hans S, Norden C, Brand M #, Hiller M #.  Vision-related convergent gene losses reveal SERPINE3’s unknown role in the eye. Elife, 11:e77999, 2022
Link

[86]    Doronina L, Hughes GM, Moreno-Santillan D, Lawless C, Lonergan T, Ryan L, Jebb D, Kirilenko BM, Korstian JM, Dávalos LM, Vernes SC, Myers EW, Teeling EC, Hiller M, Jermiin LS, Schmitz J, Springer MS, Ray DA. Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone. Genes 13(5), 2022
Link

[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
Link

[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
Link

[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
Link

[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
Link

[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
Link

[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
Link

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
Link

[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
Link

[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
Link

[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
Link

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
Link

[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
Link

[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
Link

[67] Hecker N, Hiller M #. A genome alignment of 120 mammals highlights ultraconserved element variability and placenta associated enhancers. GigaScience, 9(1), giz159, 2020
Link

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
PDF  Link

[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
PDF  Link

[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
Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
Link

[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
Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[41] Suarez H, Langer BE, Ladde P, Hiller M #. chainCleaner improves genome alignment specificity and sensitivity. Bioinformatics, 33(11), 1596-1603, 2017
PDF  Link

[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
PDF  Link

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
PDF  Link

[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
PDF  Link

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
PDF  Link

[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
PDF  Link

[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
PDF  Link

[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
PDF  Link

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
PDF  Link

[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.
PDF  Link

[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
PDF  Link

[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.
PDF  Link

[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
PDF  Link

[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
PDF Link

[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.