See dedicated STARR-seq and STAP-seq pages for detailed information, protocols, and plasmids

2026

• Tomas Pachano, He Leng, Guillaume Dugied, Travis Tribble, Vincent Loubiere, Yeojin Lee, Felix Rauh, Victor Manon, Kevin Yuan, Jocelyn Nurtanto, Alexander Schleiffer, Veronika Young, Benjamin Weller, Eleanor A. Lyons, Matthew R. Hass, Leah C. Kottyan, Matthew T. Weirauch, Juan I. Fuxman Bass, Hayley J. Newton, Alexander W. Ensminger, Pascal Falter-Braun, Jue Chen, Daniel Schramek, Alexander Stark & Mikko Taipale. Systematic discovery of pathogen effector functions across human pathogens and pathways. Cell, June 2026. Code | eORFeome dictionary

2023

• Bernardo P. de Almeida, Christoph Schaub, Michaela Pagani, Stefano Secchia, Eileen E. M. Furlong & Alexander Stark. Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo. Nature, December 2023. scATAC-Seq | Code

• Jacobs J, Pagani M, Wenzl C, Stark A. Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila. Science, July 2023. GEO | UCSC

• Serebreni L, Pleyer LM, Haberle V, Hendy O, Vlasova A, Loubiere V, Nemčko F, Bergauer K, Roitinger E, Mechtler K, Stark A. Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns. EMBO Journal, April 2023. GEO | ProteomeXchange PXD028090 | ProteomeXchange PXD028094

• Reiter F, de Almeida BP, Stark A. Enhancers display constrained sequence flexibility and context-specific modulation of motif function. Genome Research, March 2023. GEO | ZENODO | CODE

2022

• Klaus L, de Almeida BP, Vlasova A, Nemčko F, Schleiffer A, Bergauer K, Hofbauer L, Rath M, Stark A. Systematic identification and characterization of repressive domains in Drosophila transcription factors. EMBO Journal, December 2022. GEO | ZENODO | UCSC

• Jacobs J, Pagani M, Wenzl C, Stark A. Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila. bioRxiv, November 2022. UCSC

• Serebreni L, Pleyer LM, Haberle V, Hendy O, Vlasova A, Loubiere V, Nemčko F, Bergauer K, Roitinger E, Mechtler K, Stark A. Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns. bioRxiv, October 2022. GEO

• Hendy O, Serebreni L, Bergauer K, Muerdter F, Huber L, Nemčko F, Stark A. Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers. Molecular Cell, September 2022. GEO

• Neumayr C*, Haberle V*, Serebreni L, Karner K, Hendy O, Boija A, Henninger JE, Li CH, Stejskal K, Lin G, Bergauer K, Pagani M, Rath M, Mechtler K, Arnold CD, Stark A. Differential cofactor dependencies define distinct types of human enhancers. Nature, June 2022. GEO

• de Almeida BP, Reiter F, Pagani M, Stark A. DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. Nature Genetics, May 2022. GEO | CODE | DATA and MODEL | KIPOI

2021

• de Almeida BP, Reiter F, Pagani M, Stark A. DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers. bioRxiv. WEBINAR | TWITTER SUMMARY | CODE

2020

• Yelagandula R, Bykov A, Vogt A, Heinen R, Özkan E, Strobl MM, Baar J, Uzunova K, Hajdusits B, Kordic D, Suljic E, Kurtovic-Kozaric A, Izetbegovic S, Schaefer J, Hufnagl P, Zoufaly A, Seitz T, VCDI, Foedinger M, Allerberger F, Stark A, Cochella L^§ & Elling U^§. Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq. Nature Communications, 2021. CODE | DATA

2019

• Haberle V*, Arnold CD*, Pagani M, Rath M, Schernhuber K, Stark A. Transcriptional cofactors display specificity for distinct types of core promoters. Nature 2019, May 15. Pubmed 31092928 DATA: FLY S2 CELLS COF-STAP-seq | FLY OSC CELLS COF-STAP-seq | FLY Kc167 CELLS COF-STAP-seq | FLY S2 CELLS ENHANCER STAP-seq | HUMAN HCT116 CELLS COF-STAP-seq

2018

• Arnold CD*, Nemčko F*, Woodfin AR*, Wienerroither S*, Vlasova A*, Schleiffer A, Pagani M, Rath M, Stark A. A high-throughput method to identify trans-activation domains within transcription factor sequences. EMBO J. 2018 Jul 13. DATA

• 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 Feb 15(2). DATA | starr-seq.starklab.org

2017

• 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

• Arnold CD*, Zabidi MA*, Pagani M, Rath M, Schernhuber K, Kazmar T, Stark A. Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. Nature Biotechnology, 2017 Feb;35(2):136-144. Pubmed 28024147. DATA | PLASMIDS

2016

• Shlyueva D, Meireles-Filho ACA, Pagani M, Stark A. Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation. PLoS ONE, 2016. Aug 30;11(8):e0161997. Pubmed 27575958. DATA

2015

• Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A. Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature, 2015. Dec 03;528(7580):147-51. For DATA see factors.starklab.org | PLASMIDS

• 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 26;518(7540):556-9. Pubmed 25517091. DATA | PLASMIDS

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

• Kvon EZ, Kazmar T, Stampfel G*, Yáñez-Cuna JO*, Pagani M, Schernhuber K, Dickson BJ, Stark A. Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature, 2014. Aug 7;512(7512):91-5. Pubmed 24896182. 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

• 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

• Meireles-Filho ACA, Bardet AF, Yáñez-Cuna JO, Stampfel G, Stark A. cis-Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock. Current Biology. 2014 DATA

2013

• Bardet AF*, Steinmann J*, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high-resolution. Bioinformatics. 2013 Aug;29(21):2705-2713. Pubmed 23980024. DATA

• 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

2012

• Yáñez-Cuna JO, Dinh HQ*, Kvon EZ*, Shlyueva D*, Stark A. Uncovering cis-regulatory sequence requirements for context specific transcription factor binding. Genome Res. 2012 Oct;22(10):2018-2030. Pubmed 22534400. DATA

• Kvon EZ*, Stampfel G*, Yáñez-Cuna JO, Dickson BJ, Stark A. HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev. 2012 May 1;26(9):908-913. [Epub 2012 Apr 12]. Pubmed 22499593. DATA

2011

• Bardet AF, He Q, Zeitlinger J, Stark A. A computational pipeline for comparative ChIP-seq analyses. Nat Protoc. 2011 Dec 15;7(1):45-61. DATA

• Elling U, Taubenschmid J, Wirnsberger G, O’Malley R, Demers S, Vanhaelen Q, Shukalyuk A, Schmauss G, Schramek D, Schnuetgen F, von Melchner H, Ecker J, Stanford WS, Zuber J, Stark A, Penninger JM. Forward and reverse mouse genetics through derivation of haploid embryonic stem cells. Cell Stem Cell. 2011 Dec 2;9(6):563-74. DATA

• He Q*, Bardet AF*, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet. 2011 May;43(5):414-20. Epub 2011 Apr 10. DATA

* equal contribution