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Identification and functional characterization of mammalian enhancers and transcriptional co-factors during cellular signaling and cell fate transitions


DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers

Author(s): Bernardo P. de Almeida, Franziska Reiter, Michaela Pagani, Alexander Stark
Published in: bioRxiv, 2021
Publisher: bioRxiv
DOI: 10.1101/2021.10.05.463203

STARR-seq and UMI-STARR-seq: Assessing Enhancer Activities for Genome-Wide-, High-, and Low-Complexity Candidate Libraries.

Author(s): Christoph Neumayr; Michaela Pagani; Alexander Stark; Alexander Stark; Cosmas D. Arnold
Published in: Current Protocols in Molecular Biology, Issue 2, 2019, ISSN 1934-3647
Publisher: John Wiley and Sons Inc
DOI: 10.1002/cpmb.105

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

Author(s): Cosmas D Arnold, Muhammad A Zabidi, Michaela Pagani, Martina Rath, Katharina Schernhuber, Tomáš Kazmar, Alexander Stark
Published in: Nature Biotechnology, Issue 35/2, 2017, Page(s) 136-144, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/nbt.3739

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

Author(s): Rui R. Catarino, Alexander Stark
Published in: Genes & Development, Issue 32/3-4, 2018, Page(s) 202-223, ISSN 0890-9369
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.310367.117

Probing the canonicity of the Wnt/Wingless signaling pathway

Author(s): Alexandra Franz, Daria Shlyueva, Erich Brunner, Alexander Stark, Konrad Basler
Published in: PLOS Genetics, Issue 13/4, 2017, Page(s) e1006700, ISSN 1553-7404
Publisher: PLOS Genetics
DOI: 10.1371/journal.pgen.1006700

Resolving systematic errors in widely used enhancer activity assays in human cells

Author(s): Felix Muerdter, Łukasz M Boryń, Ashley R Woodfin, Christoph Neumayr, Martina Rath, Muhammad A Zabidi, Michaela Pagani, Vanja Haberle, Tomáš Kazmar, Rui R Catarino, Katharina Schernhuber, Cosmas D Arnold, Alexander Stark
Published in: Nature Methods, Issue 15/2, 2018, Page(s) 141-149, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/nmeth.4534

A high‐throughput method to identify trans‐activation domains within transcription factor sequences

Author(s): Cosmas D Arnold, Filip Nemčko, Ashley R Woodfin, Sebastian Wienerroither, Anna Vlasova, Alexander Schleiffer, Michaela Pagani, Martina Rath, Alexander Stark
Published in: The EMBO Journal, Issue 37/16, 2018, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.201798896

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