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.INTERVIEW

• Henry Thomas, Songjie Feng, Marie Huber, Vincent Loubiere, Daria Vanina, Mattia Pitasi, Alexander Stark, Christa Buecker. Enhancer cooperativity can compensate for loss of activity over large genomic distances. bioRxiv, December 2023.

• Vincent Loubiere, Bernardo P. de Almeida, Michaela Pagani, Alexander Stark. Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila. bioRxiv, October 2023.

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

• Ya-Chien Chan, Eike Kienle, Martin Oti, Antonella Di Liddo, Maria Mendez-Lago, Dominik F. Aschauer, Manuel Peter, Michaela Pagani, Cosmas Arnold, Andreas Vonderheit, Christian Schön, Sebastian Kreuz, Alexander Stark & Simon Rumpel. An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo. Scientific Reports, April 2023.

• 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. INTERVIEW

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

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. INTERVIEW

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

• 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.

• 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.

• Reiter F*, de Almeida BP*, Stark A. Enhancers display constrained sequence flexibility and context-specific modulation of motif function. bioRxiv, September 2022.

• Klaus L, de Almeida BP, Vlasova A, Nemčko F, Schleiffer A, Bergauer K, Rath M, Stark A. Identification and characterization of repressive domains in Drosophila transcription factors. bioRxiv, August 2022.

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

• 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. WEBINAR | TWITTER UPDATES | INTERVIEW

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 | HAIKU

• Appel LM*, Franke V*, Bruno M*, Grishkovskaya I*, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications, October 2021.

• 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.

• Serebreni L, Stark A. Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions. Current Opinion in Cell Biology June 2021, 70:58-66

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, VCDI, Allerberger F, Stark A, Cochella L^§ & Elling U^§. SARSeq, a robust and highly multiplexed NGS assay for parallel detection of SARS-CoV2 and other respiratory infections. medRxiv, 2020.

• Kellner MJ*^§, Ross JJ*, Schnabl J*, Dekens MPS, Heinen R, Tanner NA, Fritsche-Polanz R, Traugott M, Seitz T, Zoufaly A, Födinger M, Wenisch C, Zuber J, Vienna Covid-19 Diagnostics Initiative (VCDI), Pauli A^§, Brennecke J^§. A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing. bioRxiv

• Appel LM*, Franke V*, Bruno M*, Grishkovskaya I*, Kasiliauskaite A, Schoeberl UE, Puchinger MG, Kostrhon S, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC. bioRxiv, 2020.

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.

• 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

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

• Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation Nat Rev Mol Cell Biol. 2018 Jun 26

• Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev. 2018 Feb 1;32(3-4):202-223

• 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 ** 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

• Elling U, Wimmer RA, Leibbrandt A, Burkard T, Michlits G, Leopoldi A, Micheler T, Abdeen D, Zhuk S, Aspalter IM, Handl C, Liebergesell J, Hubmann M, Husa AM, Kinzer M, Schuller N, Wetzel E, van de Loo N, Martinez JAZ, Estoppey D, Riedl R, Yang F, Fu B, Dechat T, Ivics Z, Agu CA, Bell O, Blaas D, Gerhardt H, Hoepfner D, Stark A, Penninger JM. A reversible haploid mouse embryonic stem cell biobank resource for functional genomics. Nature. 2017 Oct 5;550(7674):114-118 Pubmed 28953874

• Catarino RR, Neumayr C, Stark A. Promoting transcription over long distances. Nature Genetics, 2017 Jun 28;49(7):972-973. Pubmed [28656981] (http://www.ncbi.nlm.nih.gov/pubmed/28656981).

• 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] (http://www.ncbi.nlm.nih.gov/pubmed/28369070).

• Reiter F*, Wienerroither S*, Stark A. Combinatorial function of transcription factors and cofactors. Current Opinion in Genetics & Development, 2017 Jan 19;43:73-81. Pubmed [28110180] (http://www.ncbi.nlm.nih.gov/pubmed/28110180).

• 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. Featured in: ** Core promoters across the genome. Nature Biotechnology, 2017 Feb 8;35(2):123-124. ** Genomics: A functional assay for promoters. Nature Methods Highlights. 2017 Feb;14(2):109.

2016

• Zabidi MA, Stark A. Regulatory Enhancer Core-Promoter Communication via Transcription Factors and Cofactors. Trends in Genetics, 2016. Dec;32(12):801-814. Pubmed 27816209.

• Muerdter F, Stark A. Gene Regulation: Activation through Space. Current Biology, 2016. Oct 10;26(19):R895-R898. Pubmed [27728794] (http://www.ncbi.nlm.nih.gov/pubmed/27728794).

• 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] (http://www.ncbi.nlm.nih.gov/pubmed/27575958).

• Rickels R, Hu D, Collings CK, Woodfin AR, Piunti A, Mohan M, Herz HM, Kvon E, Shilatifard A. An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS. Molecular Cell, 2016. Jul 21;63(2):318-28. Pubmed [27447986] (http://www.ncbi.nlm.nih.gov/pubmed/27447986).

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. Pubmed 26550828. Featured in: ** Landscape and mechanisms of transcription factor cooperativity. Nature Reviews Genetics (2015).

• Chirn G, Rahman R, Sytnikova S, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLoS Genetics, 2015. Nov 20;11(11). Pubmed [26588211] (http://www.ncbi.nlm.nih.gov/pubmed/26588211).

• Haberle V, Stark A. Coordinating the Human Looks. Cell, 2015. Sep 24;163(1):24-26. Pubmed [26406365] (http://www.ncbi.nlm.nih.gov/pubmed/26406365).

• 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] (http://www.ncbi.nlm.nih.gov/pubmed/26367798).

• Spletter ML, Barz C, Yeroslaviz A, Schönbauer C, Ferreira IRS, Sarov M, Gerlach D, Stark A, Habermann B, Schnorrer F. The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle. EMBO reports, 2015. Feb;16(2)178-91. Pubmed [25532219] (http://www.ncbi.nlm.nih.gov/pubmed/25532219).

• Muerdter F^§*, Boryń ŁM, Arnold CD^§*. STARR-seq — Principles and applications. Genomics 2015. In print. Pubmed 26072434.

• 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. 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.

• Shlyueva D, Meireles-Filho AC, 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. BioRxiv pre-print doi:10.1101/012609.

2014

• Muerdter F, Stark A. Genomics: Hiding in plain sight. Nature 2014. Aug;512(7515):374-5. Pubmed 25164742.

• 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.

• 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. Featured in: ** Gene expression: An atlas of fruit fly enhancer activity. Nature Methods 11 (2014).

• 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. 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.

• Shlyueva D*, Stampfel G*, Stark A. Transcriptional enhancers: from properties to genome-wide predictions. Nature Reviews Genetics, 2014. Apr;15(4):272-86. Pubmed 24614317.

• Rembold M*, Ciglar L*, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE. A conserved role for Snail as a potentiator of active transcription. Genes Dev. 2014 Jan;28(2):167-81. Pubmed 24402316.

• Meireles-Filho AC, Bardet AF, Yáñez-Cuna JO, Stampfel G, Stark A. cis-Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock. Current Biology. 2014 Jan;24(1):1-10. Pubmed 24332542. Featured in: ** Circadian Clocks: The Tissue Is the Issue. Current Biology 24 (2014). ** Dissecting Circadian Circuits in the Head and Body. Biotechniques (2014).

2013

• Kazmar T, Kvon EZ, Stark A, Lampert CH. Drosophila Embryo Stage Annotation using Label Propagation. International Conference on Computer Vision (ICCV). Springer. 2013 Dec;1089–1096. PDF

• 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.

• 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. 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).

• Yáñez-Cuna JO*, Kvon, EZ*, Stark, A. Deciphering the transcriptional cis-regulatory code. Trends Genet. 2013 Jan;29(1):11-22. [Epub 2012 Oct 23]. Pubmed 23102583.

2012

• Hnisz D, Bardet AF, Nobile CJ, Petryshyn A, Glaser W, Sch&ocuml;ck U, Stark A, Kuchler K. A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis. PLoS Genet. 2012 Dec;8(12):e1003118. [Epub 2012 Dec 6]. Pubmed 23236295.

• 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.

• 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. Featured in a Perspective by Farley and Levine: ** HOT DNAs: a novel class of developmental enhancers

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. Pubmed 22179591.

• Elling U, Taubenschmid J, Wirnsberger G, O’Malley R, Demers SP, Vanhaelen Q, Shukalyuk AI, Schmauss G, Schramek D, Schnuetgen F, von Melchner H, Ecker JR, Stanford WL, Zuber J, Stark A, Penninger JM. Forward and Reverse Genetics through Derivation of Haploid Mouse Embryonic Stem Cells. Cell Stem Cell. 2011 Dec 2;9(6):563-74. Pubmed 22136931.

• Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Whye Chin C, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. Pubmed 21993624.

• Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B. Neural-specific elongation of 3’ UTRs during Drosophila development. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15864-9. Epub 2011 Sep 6. Pubmed 21896737.

• Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J. A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J. 2011 Aug 23;30(19):3977-93. Pubmed 21863019.

• 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. PubMed 21478888.

2010

• Karginov FV, Cheloufi S, Chong MM, Stark A, Smith AD, Hannon GJ. Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol Cell. 2010 Jun 25;38(6):781-8. PubMed 20620951.

• Zheng K, Xiol J, Reuter M, Eckardt S, Leu NA, McLaughlin KJ, Stark A, Sachidanandam R, Pillai RS, Wang PJ. Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway. Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11841-6. Epub 2010 Jun 1. PubMed 20534472.

• Schnorrer F, Schönbauer C, Langer CC, Dietzl G, Novatchkova M, Schernhuber K, Fellner M, Azaryan A, Radolf M, Stark A, Keleman K, Dickson BJ. Systematic genetic analysis of muscle morphogenesis and function in Drosophila. Nature. 2010 Mar 11;464(7286):287-91. PubMed 20220848.

• Shoji M, Tanaka T, Hosokawa M, Reuter M, Stark A, Kato Y, Kondoh G, Okawa K, Chujo T, Suzuki T, Hata K, Martin SL, Noce T, Kuramochi-Miyagawa S, Nakano T, Sasaki H, Pillai RS, Nakatsuji N, Chuma S. The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Dev Cell. 2009 Dec;17(6):775-87. PubMed 20059948.

• Zeitlinger J, Stark A. Developmental gene regulation in the era of genomics. Dev Biol. 2010 Mar 15;339(2):230-9. Epub 2010 Jan 4. Review. PubMed 20045679.

• Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Marshall Graves JA, Woods GM, Hannon GJ, Papenfuss AT. The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science. 2010 Jan 1;327(5961):84-7. PubMed 20044575.

2009

• Stark A. Learning the transcriptional regulatory code. Mol Syst Biol. 2009;5:329. Epub 2009 Nov 17. PubMed 19920814.

• Meireles-Filho AC, Stark A. Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr Opin Genet Dev. 2009 Dec;19(6):565-70. Epub 2009 Nov 11. Review. PubMed 19913403.

• Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS. Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat Struct Mol Biol. 2009 Jun;16(6):639-46. Epub 2009 May 24. PubMed 19465913.

• Malone CD, Brennecke J, Dus M, Stark A, McCombie WR, Sachidanandam R, Hannon GJ. Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell. 2009 May 1;137(3):522-35. Epub 2009 Apr 23. PubMed 19395010.

• Petsalaki E, Stark A, García-Urdiales E, Russell RB. Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput Biol. 2009 Mar;5(3):e1000335. Epub 2009 Mar 27. PubMed 19325869.

• Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009 May 7;459(7243):108-12. Epub 2009 Mar 18. PubMed 19295514.

• Shkumatava A, Stark A, Sive H, Bartel DP. Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Dev. 2009 Feb 15;23(4):466-81. PubMed 19240133.

2008

• Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 2008 Nov 28;322(5906):1387-92. PubMed 19039138.

• Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83. Erratum in: Nature. 2008 Sep 11;455(7210):256. Nefedov, Mikhail; de Jong, Pieter J. PubMed 18464734.

• Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ, Brennecke J. An endogenous small interfering RNA pathway in Drosophila. Nature. 2008 Jun 5;453(7196):798-802. Epub 2008 May 7. PubMed 18463631.

• Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grützner F, Stark A, Hannon GJ. Conservation of small RNA pathways in platypus. Genome Res. 2008 Jun;18(6):995-1004. Epub 2008 May 7. PubMed 18463306.

• Bushati N, Stark A, Brennecke J, Cohen SM. Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr Biol. 2008 Apr 8;18(7):501-6. PubMed 18394895.

• Stark A, Bushati N, Jan CH, Kheradpour P, Hodges E, Brennecke J, Bartel DP, Cohen SM, Kellis M. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 2008 Jan 1;22(1):8-13. PubMed 18172160.

Before 2008

See here: Member page Alexander Stark

* equal contribution ^§ shared corresponding author