2017
2016
2015
2014
2013
2012
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