Stark Lab | STARR-seq | Home

STARR-seq publications from others and us (please let us know about your paper!)

2019

• Neumayr C, Pagani M, Stark A, Arnold CD STARR-seq and UMI-STARR-seq: Assessing enhancer activities for genome-wide, high-, and low- complexity candidate libraries. Current Protocols in Molecular Biology, 128, e105.

2018

• Klein JC, Keith A, Agarwal V, Durham T, Shendure J. Functional characterization of enhancer evolution in the primate lineage. Genome Biol. 2018 Jul 25;19(1):99 Pubmed 30045748
  [by the J.Shendure lab ( University of Washington)].

• Zhang P, Xia JH, Zhu J, Gao P, Tian YJ, … , Cerhan JR, Wang LD, Wei GH, Wang L. High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing. Nat Commun. 2018 May 22;9(1):2022 Pubmed 29789573
  [by the L.Wang lab (Department of Pathology, MCW Cancer Center, Medical College of Wisconsin)].

• Muerdter F*, Boryń ŁM*, Woodfin AR**, Neumayr C**, Rath M, Zabidi MA, Pagani M, Haberle V, Kazmar T, Catarino RR, Schernhuber K, Arnold CD, Stark A. Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterization. Nature Methods, 2018 February 15(2):141-149.
  DATA
  ** This manuscript resolves ORI-initiation and type-I-interferon response for enhancer-activity assays in human cells and publishes a novel genome-wide STARR-seq protocol.

2017

• Liu Y, Yu S, Dhiman VK, Brunetti T, Eckart H, White KP. Functional assessment of human enhancer activities using whole-genome STARR-sequencing. Genome Biol., 2017 Nov 20;18(1):219 Pubmed 29151363
  [by the K.White lab (University of Chicago)]

• Liu S, Liu Y, Zhang Q, Wu J, Liang J, Yu S, Wei GH, White KP, Wang X. Systematic identification of regulatory variants associated with cancer risk. Genome Biol. 2017 Oct 23;18(1):194 Pubmed 29061142
  [by the State Key Laboratory of Molecular Developmental Biology (Peking Union Medical College, Beijing)]

• Barakat TS, Halbritter F, Zhang M, Rendeiro AF, Bock C, Chambers I. Functional dissection of the enhancer repertoire in human embryonic stem cells. bioRxiv 2017 July 4.

• Lea AJ, Vockley CM, Johnston RA, Del Carpio CA, Barreiro LB, Reddy TE, Tung J. Genome-wide quantification of the effects of DNA methylation on human gene regulation. bioRxiv, 2017 June 7.
  [by the J. Tung lab (Duke University)]

• Franz A*, Shlyueva D*, Brunner E, Stark A, Basler K. Probing the canonicity of the Wnt/wingless signaling pathway. PLoS Genetics, 2017 Apr 3;13(4):e1006700. Pubmed 28369070.
  DATA

2016

• Vockley CM, D’Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. Cell, 2016. Aug 25;166(5):1269-81. Pubmed 27565349
  [by the T. Reddy lab (Duke University)]

• Verfaillie A, Svetlichnyy D, Imrichova H, Davie K, Fiers M, Atak ZK, Hulselmans G, Christiaens V, Aerts S. Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic. Genome Research, 2016. Jul;26(7):882-95. Pubmed 27197205
  [by the S. Aerts lab (University of Leuven)]

2015

• Rathert P, Roth M, Neumann T, Muerdter F, Roe JS, Muhar M, Deswal S, Cerny-Reiterer S, Peter B, Jude J, Hoffmann T, Boryń ŁM, Axelsson E, Schweifer N, Tontsch-Grunt U, Dow LE, Gianni D, Pearson M, Valent P, Stark A, Kraut N, Vakoc CR, Zuber J. Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature, 2015. Sep 24;525(7570)543-47. Pubmed 26367798.
  [with the J. Zuber lab (IMP)]

• Muerdter F^§*, Boryń ŁM, Arnold CD^§*. STARR-seq — Principles and applications. Genomics 2015. Sep;106(3):145-50. Pubmed 26072434.

• Vockley CM, Guo C, Majoros WH, Nodzenski M, Scholtens DM, Hayes MG, Lowe WL Jr, Reddy TE. Massively parallel quantification of the regulatory effects of non-coding genetic variation in a human cohort. Genome Research, 2015. Aug;25(8):1206-14. Pubmed 26084464
  [by the T. Reddy lab (Duke University)]

• Vanhille L, Griffon A, Maqbool MA, Zacarias-Cabeza J, Dao LT, Fernandez N, Ballester B, Andrau JC, Spicuglia S. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Nature Communications 2015. 2015 Apr 15;6:6905. Pubmed 25872643
  [by the S. Spicuglia lab (TAGC/Inserm)]

• Zabidi MA*, Arnold CD*, Schernhuber K, Pagani M, Rath M, Frank O, Stark A. Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation. Nature, 2015 Feb;518(7540):556-9. Pubmed 25517091.
  DATA
  Featured in:
  ** Enhancers: holding out for the right promoter. Current biology, 2015. Mar;25(7)R290-3.
  ** Enhancer Trafficking: Free Throws and Three-Pointers. Developmental Cell, 2015. Jan;32(2)135-37.

2014

• Arnold CD*, Gerlach D*, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet. 2014. Jul;46(7):685-92. Pubmed 24908250.
  DATA

• Yáñez-Cuna JO, Arnold CD, Stampfel G, Boryń ŁM, Gerlach D, Rath M, Stark A. Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Research, 2014. Jul;24(7):1147-56. Pubmed 24714811.
  DATA
  Featured in:
  ** Dinucleotide repeats form an enhancer signature. Nature Reviews Genetics 15 (2014).
  ** Predicting enhancers by their sequence. Nature Methods 11, 606-607 (2014).

• Shlyueva D, Stelzer C, Gerlach D, Yáñez-Cuna JO, Rath M, Boryń ŁM, Arnold CD, Stark A. Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression and targeting of closed chromatin. Molecular Cell, Apr 10;54(1):180-92. Pubmed 24685159.
  DATA

2013

• Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 2013 Mar 1;339(6123):1074-1077. Pubmed 23328393.
  DATA | PLASMIDS
  Featured in:
  ** Gene regulation: Enhancing the hunt for enhancers. Nature Reviews Genetics 14, 151 (2013).
  ** STARR-seq enterprise. Nature Structural & Molecular Biology 20, 308 (2013).
  ** Genome-wide enhancer maps. Nature Methods 10, 193 (2013).
  ** Enhancer-Suche mit Hilfe von STARR-seq. Laborjournal 03 (2013).
  ** Research Highlights. Nature Biotechnology 31, 212 (2013).