Professor Ferenc Mueller

Image of Ferenc Mueller

Institute of Cancer and Genomic Sciences
Professor in Developmental Genetics

Contact details

Institute of Cancer and Genomic Sciences
College of Medical and Dental Sciences
University of Birmingham
B15 2TT

Ferenc’s group studies transcription regulation in vertebrate embryo development. Their research focuses on the DNA sequence codes, which define promoter-enhancer interactions. They apply comparative/functional genomic analysis of cis-regulatory elements and develop high throughput approaches to study transcriptional regulators in the zebrafish embryo model system. They study the epigenetic mechanisms, which regulate genome activation and use epigenomics tools to characterize early development. They exploit the advantages of zebrafish in search for non-coding mutations causing human disease and study the in vivo roles of orthologs of human genes that have been associated with disease causing mutations. His group currently consists of 6 post docs and 3 PhD Students. Their research is funded by programmes of EU Horizon 2020, BBSRC, MRC, Human Frontier Science program and a Wellcome Trust Investigator award.


  • PhD, Hungarian Academy of Sciences PhD programme, 1997
  • MSc (equivalent 5 year degree), University of Gödöllö, Hungary, Biotechnology, 1993


Ferenc Mueller joined the University of Birmingham in 2007 as a Senior Lecturer. He became a Reader in 2010 before being awarded his Chair in 2014. Previous to this he was research group leader at the institute of Toxicology and Genetics, Forschungszentrum Karlsruhe (currently Karlsruhe Institute of Technology) in Germany (2001- 2007). He was postdoctoral fellow (EMBO and FRM fellowships) at the IGBMC Strasbourg, France (1997-2001) and research fellow at the University of Southampton, UK (1995-1997).


  • Director of Postgraduate Research, Institute of Cancer and Genomic Sciences
  • MSc Genomic Medicine - Introduction module joint coordinator
  • BMedSc
    • Molecular Biology, 2nd year, lecturing
    • Genes to Therapy, 3rd year course, course coordinator

Postgraduate supervision

Ferenc is interested in supervising doctoral research students in the following areas:

  • Transcription regulation in embryo development
  • Enhancer promoter interactions in transcription regulation
  • Imaging of transcription, single cell technologies in detecting gene activity
  • Epigenetic signals transcription regulation in embryo development
  • High throughout screening with zebrafish embryos
  • In vivo modelling of the genetic basis of human disease in zebrafish

Current PhD students: Ledean Cooper, Fabio D'Orazio, Rhiannon Hurst.

If you are interested in studying any of these subject areas please contact Ferenc on the contact details above, or for any general doctoral research enquiries, please email: or call +44 (0)121 414 5005.

For a full list of available Doctoral Research opportunities, please visit our Doctoral Research programme listings.


1. Transcription regulation in development

The Mueller group investigates transcriptional regulation processes that regulate protein coding and non-coding gene activities during and after the transition from a pluripotent cell mass of the blastula into a highly complex, differentiated vertebrate embryo. They combine comparative genomics and in vivo functional analysis of gene expression regulation exploiting the capabilities offered by the zebrafish model system. They have developed new techniques for high throughput in vivo analysis of cis-regulatory modules (CRMs) aiding in the identification of a large number of transcriptional enhancer elements in developmental genes. Their research contributed to the understanding of the complexity of core promoter regulation by the functional characterisation of members of the TATA binding protein family and core promoter sequence determinants. They established novel in vivo assays of studying general transcription factors in the complexity of the embryo using embryo manipulation tools and modern genomics techniques (RNA, CAGE and ChIP sequencing). Recently they extended their analysis to genome wide characterization of epigenetic features in gametes and embryos to dissect the contribution of chromatin mediated regulation of development. Lab members working on the topic: Dr Yavor Hadzhiev, Dr Nan Li, Dr Joseph Wragg and Dr Joseph Grice, Dr Xiaoquan Li. Positions are available.

2. Zebrafish as a vertebrate model for human genetics / disease

 i) Non-coding mutations in disease
CRMs and other non-coding functional elements of developmental regulator genes are mutated in numerous congenital disorders. The aberration of gene expression regulation can also lead to multifactorial diseases. The identification of non-coding functional elements will greatly enhance efforts in mapping non-coding mutations responsible for congenital and multifactorial disorders.  With collaborators (U. Liebel, M. Reischl at KIT, Karlsruhe) they automated imaging and screened tens of thousands of transgenic zebrafish embryos for cis-regulatory elements. To complement the technology development they apply bioinformatics (comparative genomics) and epigenomic prediction of cis-regulatory modules (ATAC, CAGE and ChIP-seq). They work in international collaborations such as ZENCODE-ITN and DANIO-CODE. Ultimately, this work will aid in their effort to develop the transparent and fast developing fish embryo as a high throughput transgenic sensor for efficient screening of functionally conserved cis-regulatory elements relevant in human diseases. Lab members working on the topic: Dr Yavor Hadzhiev, Dr Nan Li.Mr Fabio D’Orazio, Ms Ledean Cooper.

ii) Zebrafish models for genetic disorders
The Mueller group utilises their functional genomic experience with the fish model and collaborate with clinical and non-clinical investigators in their search for the in vivo function of disease causing genes. They have been studying the biological function of genes with newly discovered disease causing mutations and demonstrated essential organogenesis functions for genes causing familial syndromes such as ARC and Warburg Micro syndromes (collaborations with E. Maher, P. Gissen, N. Krone).

iii)  Tools for phenotype detection in drug screening
Based on their experience with high throughput screening of zebrafish embryos, the Mueller group together with A. Sik (Institute of Clinical Sciences) and J Fossey (Chemistry) exploit automated imaging and develop novel methods for physiological phenotype detection to screen for drug effects in zebrafish embryos. Lab members: Rhiannon Hurst.

Other activities

Ferenc is an Executive Board Member of the Birmingham Centre for Genome Biology.


Andersson R, Gebhard C, Miguel -Escalada I,  Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Fantom Consortium, Forrest AR, Carninci P, Rehli M and Sandelin A (2014) An atlas of active enhancers across human cell types and tissues. Nature 507(7493):455-61

Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki A-M, van IJcken W, Armant O, Ferg M, Strähle U, Carninci P, Müller F* and Lenhard B (2014) Two independent transcription initiation codes overlap on vertebrate core promoters. Nature 207(7492):381-5
*co-corresponding author

Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, Sanges R, Stupka E, Balciuniene J, Marsh EK, Balciunas D and Müller F (2014) Targeted transgene integration overcomes variability of position effects in zebrafish. Development 141(3):715-24

Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki A-M S, Sheng Y, Abdelhamid RA, Anand S, Gehrig J, Akalin A, Kockx CEM, van der Sloot AAJ, van IJcken WFJ, Armant O, Rastegar S, Watson C, Strähle U, Stupka E, Carninci P, Lenhard B and Müller F (2013) Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Research 23(11):1938-50

Pasquali L, Gaulton KJ, Rodríguez-Seguí S, Mularoni L, Miquel-Escalada I, Akerman I, Tena JJ, Morán I, Gomez-Marin C, van de Bunt M, Ponsa-Cobas J, Castro N, Nammo T, Cebola I, García-Hurtado J, Maestro MA, Pattou F, Piemonti L, Berney T, Gloyn AL, Ravassard P, Skarmeta JL, Müller F, McCarthy M and Ferrer J (2014) Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nature Genetics 46(2):136-43

Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Ostrup O, Winata C, Mathavan S, Müller F, Aleström P and Collas P (2011) Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Dev Cell 21(6):993-1004

Cullinane AR, Straatman-Iwanowska A, Zaucker A, Wakabayashi Y, Bruce CK, Luo G, Rahman F, Gürakan F, Utine E, Ozkan TB, Denecke J, Vukovic J, Di Rocco M, Mandel H, Cangul H, Matthews RP, Thomas SG, Rappoport JZ, Arias IM, Wolburg H, Knisely AS, Kelly DA, Müller F, Maher ER and Gissen P (2010) Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. Nat Genet 42(4):303-12

Gehrig J, Reischl M, Kalmar E, Ferg M, Hadzhiev Y, Zaucker A, Song C, Schindler S, Liebel U and Müller F (2009) Automated high throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nature Methods 6(12):911-6