2010
 
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. (2010). The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science. 327(5961):84-7 (abstract)
 
Zeitlinger, J., Stark, A. (2010). Developmental gene regulation in the era of genomics. Dev Biol. 339(2):230-239 (abstract)
 
2009
 
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. (2009). Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 459(7243):108-12 (abstract)
 
Malone, CD., Brennecke, J., Dus, M., Stark, A., McCombie, WR., Sachidanandam, R., Hannon, GJ. (2009). Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell. 137(3):522-35 (abstract)
 
Meireles-Filho, AC., Stark, A. (2009). Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr Opin Genet Dev. 19(6):565-70 (abstract)
 
Petsalaki, E., Stark, A., García-Urdiales, E., Russell, RB. (2009). Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput Biol. 5(3):e1000335 (abstract)
 
Reuter, M., Chuma, S., Tanaka, T., Franz, T., Stark, A., Pillai, RS. (2009). Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat Struct Mol Biol. 16(6):639-46 (abstract)
 
Shkumatava, A., Stark, A., Sive, H., Bartel, DP. (2009). Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Dev. 23(4):466-81 (abstract)
 
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. (2009). The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Dev Cell. 17(6):775-87 (abstract)
 
Stark, A. (2009). Learning the transcriptional regulatory code. Mol Syst Biol. 5:329 (abstract)
 
2008
 
Brennecke, J., Malone, CD., Aravin, AA., Sachidanandam, R., Stark, A., Hannon, GJ. (2008). An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 322(5906):1387-92 (abstract)
 
Bushati, N., Stark, A., Brennecke, J., Cohen, SM. (2008). Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr Biol. 18(7):501-6 (abstract)
 
Czech, B., Malone, CD., Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, JA., Sachidanandam, R., Hannon, GJ., Brennecke, J. (2008). An endogenous small interfering RNA pathway in Drosophila. Nature. 453(7196):798-802 (abstract)
 
Murchison, EP., Kheradpour, P., Sachidanandam, R., Smith, C., Hodges, E., Xuan, Z., Kellis, M., Grützner, F., Stark, A., Hannon, GJ. (2008). Conservation of small RNA pathways in platypus. Genome Res. 18(6):995-1004 (abstract)
 
Stark, A., Bushati, N., Jan, CH., Kheradpour, P., Hodges, E., Brennecke, J., Bartel, DP., Cohen, SM., Kellis, M. (2008). A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22(1):8-13 (abstract)
 
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. (2008). Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453(7192):175-83 (abstract)
 
2007
 
Brennecke, J., Aravin, AA., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., Hannon, GJ. (2007). Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 128(6):1089-103 (abstract)
 
Drosophila 12 Genomes Consortium. (2007). Evolution of Genes and Genomes on the Drosophila Phylogeny. Nature. 450(7167):203-18
 
Kheradpour, P., Stark, A., Roy, S., Kellis, M. (2007). Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res. 17(12):1919-31 (abstract)
 
Ruby, JG., Stark, A., Johnston, WK., Kellis, M., Bartel, DP., Lai, EC. (2007). Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17(12):1850-64 (abstract)
 
Stark, A., Kheradpour, P., Parts, L., Brennecke, J., Hodges, E., Hannon, GJ., Kellis, M. (2007). Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17(12):1865-79 (abstract)
 
Zeitlinger, J., Stark, A., Kellis, M., Hong, JW., Nechaev, S., Adelman, K., Levine, M., Young, RA. (2007). RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet. 39(12):1512-6 (abstract)
 
Zeitlinger, J., Zinzen, RP., Stark, A., Kellis, M., Zhang, H., Young, RA., Levine, M. (2007). Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev. 21(4):385-90 (abstract)
 
2006
 
Behm-Ansmant, I., Rehwinkel, J., Doerks, T., Stark, A., Bork, P., Izaurralde, E. (2006). mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 20(14):1885-98 (abstract)
 
Cohen, SM., Brennecke, J., Stark, A. (2006). Denoising feedback loops by thresholding--a new role for microRNAs. Genes Dev. 20(20):2769-72 (abstract)
 
Rehwinkel, J., Natalin, P., Stark, A., Brennecke, J., Cohen, SM., Izaurralde, E. (2006). Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol Cell Biol. 26(8):2965-75 (abstract)
 
2005
 
Brennecke, J., Stark, A., Cohen, SM. (2005). Not miR-ly muscular: microRNAs and muscle development. Genes Dev. 19(19):2261-4 (abstract)
 
Brennecke, J., Stark, A., Russell, RB., Cohen, SM. (2005). Principles of microRNA-target recognition. PLoS Biol. 3(3):e85 (abstract)
 
Neduva, V., Linding, R., Su-Angrand, I., Stark, A., de Masi, F., Gibson, TJ., Lewis, J., Serrano, L., Russell, RB. (2005). Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol. 3(12):e405 (abstract)
 
Stark, A., Brennecke, J., Bushati, N., Russell, RB., Cohen, SM. (2005). Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3\'UTR evolution. Cell. 123(6):1133-46 (abstract)
 

2004:

A. Stark, A. Shkumatov, R.B. Russell; Finding Functional Sites in Structural Genomics Proteins. Structure, 12(8), 1405-1412, 2004.

2003:

P. Aloy, A. Stark, C. Hadley, R.B. Russell; Predictions without templates: New folds, secondary structure and contacts in CASP5.  PROTEINS: Struct. Funct. Genet., 53, 436-456, 2003 (CASP5 special issue).

P. Aloy, H. Ceulemans, A. Stark, R.B. Russell; The relationship between sequence and interaction divergence in proteins.  J. Mol. Biol., 332, 989-998, 2003.

A. Stark*, J. Brennecke*, R.B. Russell, S. M Cohen; Identification of Drosophila miRNA Targets. PLoS Biology, 1(3), E60, 2003.

E. Lorentzen, E. Pohl, P. Zwart, A. Stark, R.B. Russell, T. Knura, R. Hensel, B. Sievers; Crystal structure of an Archaeal Class I Aldolase and the Evolution of (betaalpha)8 Barrel Proteins. J. Biol. Chem., 278(47), 47253-47260, 2003.

J. Brennecke, D.R. Hipfner, A. Stark, R.B. Russell, S.M. Cohen; Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the pro-apoptotic gene hid in Drosophila. Cell, 113, 25-36 , 2003.

A. Stark, R.B. Russell; Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res., 31(13), 3341-3344, 2003.

A. Stark, S. Sunyaev, R.B. Russell; A Model for Statistical Significance of Local Similarities in Structure. J. Mol. Biol., 326, 1307-1316, 2003.

Pre 2003:

R. Metivier, A. Stark, G. Flouriot, M.R. Huebner, H. Brand, G. Penot, D. Manu, S. Denger, G. Reid, M. Kos, R.B. Russell, O. Kah, F. Pakdel, F. Gannon; A Dynamic Structural Model for Estrogen Receptor-alpha Activation by Ligands, Emphasizing the Role of Interactions between Distant A and E Domains. Molecular Cell, 10, 1019-1032, 2002.

E. Hatano,  C.A. Bradham, A. Stark, Y. Iimuro, J.J. Lemasters, D.A. Brenner; The mitochondrial permeability transition augments Fas-induced apoptosis in mouse hepatocytes. J Biol Chem, 21;275(16):11814-23, 2000.

* denotes equal contribution; # denotes co-corresponding author
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