Casas-Vila N*, Bluhm A*, Sayols S*, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY and Butter F (2017). The developmental proteome of Drosophila melanogaster. Genome Res, doi: 10.1101/gr.213694.116 [Epub ahead of print]

Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F and Neugebauer KM (2017). Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome Res, doi: 10.1101/gr.215954.116 [Epub ahead of print]

Kappei D*, Scheibe M*, Paszkowski-Rogacz M, Bluhm A, Gossmann T, Dejung M, Herlyn H, Buchholz F#, Mann M# and Butter F# (2017). Phylointeractomics reconstructs functional evolution of protein binding. Nat Commun, 8, 14334

Jahn A*, Rane G*, Paszkowski-Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño-Vallejo JA, Kumar AP, Buchholz F#, Butter F# and Kappei D# (2017) ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator. EMBO Rep, e201744095

Lebedeva S, de Jesus Domingues AM, Butter F, Ketting RF (2017). Characterization of a genetic loss-of-function of Fus in zebrafish. RNA Biol, 14, 29-35

Bluhm A, Casas-Vila N, Scheibe M and Butter F (2016). Reader interactome of epigenetic histone marks in birds. Proteomics, 16, 427-436

Cicova Z, Dejung M, Skalicky T, Eisenhuth N, Hanselmann S, Morriswood B, Figueiredo LM, Butter F# and Janzen CJ# (2016). Two flagellar BAR domain proteins in Trypanosoma brucei with stage-specific regulation. Sci Rep, 6, 35826 (#indicates joint correspondence)

Dejung M, Subota I, Brucerius F, Dindar G, Freiwald A, Engstler M, Boshart M, Butter F# and Janzen CJ# (2016). Quantitative proteomics uncovers novel factors involved in developmental differentiation of Trypanosoma brucei. PLoS Pathog, 12, e1005439 (#indicates joint correspondence)

Klassen R, Ciftci A, Funk J, Bruch A, Butter F and Schaffrath R (2016). tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast. Nucleic Acids Res, 44, 10946-10959

Casas-Vila N, Scheibe M, Freiwald A, Kappei D and Butter F (2015). Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeats. BMC Genomics, 16, 965

Roovers EF, Rosenkranz D, Mahdipour M, Han CT, He N, Chuva de Sousa Lopes SM, van der Westerlaken LAJ, Zischler H, Butter F, Roelen BAJ and Ketting RF (2015). Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Reports, 10, 2069-82

Ericson M, Janes MA, Butter F, Mann M, Ullu E and Tschudi C (2014). On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei. BMC Biol, 12, 14

Hornburg D, Drepper C, Butter F, Meissner F, Sendtner M and Mann M (2014). Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics. Mol Cell Proteomics, mcp.M113.037291

Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF and Neugebauer KM (2014). Global identification of coilin binding partners reveals hundreds of small non-coding RNAs that traffic through Cajal bodies. Mol Cell, 56, 389-399

Sharma NL, Massie CE, Butter F, Mann M, Bon H, Ramos-Montoya A, Menon S, Stark R, Lamb AD, Scott HE, Warren AY, Neal DE and Mills IG (2014). The ETS family member GABPα modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer. Nucleic Acids Res, 42, 6256-6269

Butter F, Bucerius F, Michel M, Cicova Z, Mann M and Janzen CJ (2013). Comparative proteomics of two life cycle stages of stable isotope-labeled Trypanosoma brucei reveals novel components of the parasite's host adaptation machinery. Mol Cell Proteomics, 12, 172-179

Kappei D*, Butter F*, Benda C, Scheibe M, Draškovič I, Stevense M, Novo CL, Basquin C, Araki M, Araki K, Krastev DB, Kittler R, Jessberger R, Londoño-Vallejo JA, Mann M and Buchholz F (2013). HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment.  EMBO J, 32,1681-1701 (*indicates joint contribution)

Klass DM, Scheibe M, Butter F, Hogan GJ, Mann M and Brown PO (2013). Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. Genome Res, 23, 1028-1038

Powers NR, Eicher JD, Butter F, Kong Y, Miller LL, Ring SM, Mann M and Gruen JR (2013). Alleles of a Polymorphic ETV6 Binding Site in DCDC2 Confer Risk of Reading and Language Impairment. Am J Hum Genet, 93, 19-28

Scheibe M, Arnoult N, Kappei D, Buchholz F, Decottignies A, Butter F* and Mann M* (2013). Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators. Genome Res, 23, 2149-2157 (*co-corresponding authors)

Viturawong T Meissner F, Butter F# and Mann M# (2013) A DNA-centric protein-interaction map of ultra-conserved elements reveals major contribution of  transcription factor binding hubs to conservation. Cell Rep, 5, 531–545 (#indicates joint correspondence)

Butter F, Davison L, Viturawong T, Scheibe M, Vermeulen M, Todd JA and Mann M (2012). Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding. PLoS Genetics, 8, e1002982

Gregory AP, Dendrou CA, Attfield KE, Haghikia A, Xifara DK, Butter F, Poschmann G, Kaur G, Lambert L, Leach OA, Prömel S, Punwani D, Felce JH, Davis SJ, Gold R, Nielsen FC, Siegel RM, Mann M, Bell JI, McVean G and Fugger L (2012). TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis. Nature, 488, 508-511

Scheibe M, Butter F, Hafner M, Tuschl T and Mann M (2012). Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. Nucleic Acids Res, 40, 9897-9902

Butter F, Kappei D, Buchholz F, Vermeulen M and Mann M (2010). A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth. EMBO Reports, 11, 305-311

Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG and Mann M (2010). Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell, 142, 967-980

Butter F, Scheibe M, Mörl M and Mann M (2009). Unbiased RNA-protein interaction screen by quantitative proteomics. Proc Natl Acad Sci U S A, 106, 10626-10631

Mittler G, Butter F and Mann M (2009). A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res, 19, 284-293

Just A, Butter F, Trenkmann M, Heitkam T, Mörl M and Betat H (2008). A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme. Nucleic Acids Res, 36, 5212-5220