Alexander Stark

2014

• Yáñez-Cuna JO, Arnold CD, Stampfel G, Boryń ŁM, Gerlach D, Rath M, Stark A. (2014). Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Research. Epub ahead of print.
• Shlyueva D, Stelzer C, Gerlach D, Yáñez-Cuna JO, Rath M, Boryń ŁM, Arnold CD, Stark A. (2014). Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression and targeting of closed chromatin. Mol Cell. 54(1):180-192.
• Shlyueva D, Stampfel G, Stark A. (2014). Transcriptional enhancers: from properties to genome-wide predictions. Nature Reviews Genetics. 15:272-286.
• Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE. (2014). A conserved role for Snail as a potentiator of active transcription. Genes Dev. 28(2):167-81.
• Meireles-Filho AC, Bardet AF, Yáñez-Cuna JO, Stampfel G, Stark A. (2014). cis-Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock. Current Biology. 24(1):1-10.

2013

• Kazmar T, Kvon EZ, Stark A, Lampert CH. (2013). Drosophila Embryo Stage Annotation using Label Propagation. International Conference on Computer Vision (ICCV). Springer. 1089–1096.
• Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. (2013). Identification of transcription factor binding sites from ChIP-seq data at high-resolution. Bioinformatics. 29(21):2705-2713.
• Arnold CD, Gerlach D, Stelzer C, Boryń LM, Rath M, Stark A. (2013). Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 339(6123):1074-1077.
• Yáñez-Cuna JO*, Kvon EZ*, Stark A. (2013). Deciphering the transcriptional cis-regulatory code. Trends Genet. 29(1):11-22.

2012

• Hnisz D, Bardet AF, Nobile CJ, Petryshyn A, Glaser W, Schöck U, Stark A, Kuchler K. (2012). A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis. PLoS Genet. 8(12):e1003118.
• Yáñez-Cuna JO, Dinh HQ*, Kvon EZ*, Shlyueva D*, Stark A. (2012). Uncovering cis-regulatory sequence requirements for context specific transcription factor binding. Genome Res. 22(10):2018-2030.
• Kvon EZ*, Stampfel G*, Yáñez-Cuna JO, Dickson BJ, Stark A. (2012). HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev. 26(9):908-913.

2011

• Bardet AF, He Q, Zeitlinger J, Stark A. (2011). A computational pipeline for comparative ChIP-seq analyses. Nat Protoc. 7(1):45-61.
• 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. (2011). Forward and Reverse Genetics through Derivation of Haploid Mouse Embryonic Stem Cells. Cell Stem Cell. 9(6):563-74.
• 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. (2011). A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478(7370):476-82.
• Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B. (2011). Neural-specific elongation of 3' UTRs during Drosophila development. Proc Natl Acad Sci U S A. 108(38):15864-9.
• Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J. (2011). A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J. 30(19):3977-93.
• He Q*, Bardet AF*, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A^§ & Zeitlinger J^§. (2011). High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet. 43(5):414-20.

2010

• Karginov, FV., Cheloufi, S., Chong, MM., Stark, A., Smith, AD., Hannon, GJ. (2010). Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol Cell. 38(6):781-8 (abstract)
• 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)
• Schnorrer, F., Schönbauer, C., Langer, CC., Dietzl, G., Novatchkova, M., Schernhuber, K., Fellner, M., Azaryan, A., Radolf, M., Stark, A., Keleman, K., Dickson, BJ. (2010). Systematic genetic analysis of muscle morphogenesis and function in Drosophila. Nature. 464(7286):287-91 (abstract)
• Zeitlinger, J., Stark, A. (2010). Developmental gene regulation in the era of genomics. Dev Biol. 339(2):230-9 (abstract)
• Zheng, K., Xiol, J., Reuter, M., Eckardt, S., Leu, NA., McLaughlin, KJ., Stark, A., Sachidanandam, R., Pillai, RS., Wang, PJ. (2010). 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. 107(26):11841-6 (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)
• Stark, A., Lin, MF., Kheradpour, P., Pedersen, JS., Parts, L., Carlson, JW., Crosby, MA., Rasmussen, MD., Roy, S., Deoras, AN., Ruby, JG., Brennecke, J., Hodges, E., Hinrichs, AS., Caspi, A., Paten, B., Park, SW., Han, MV., Maeder, ML., Polansky, BJ., Robson, BE., Aerts, S., van Helden, J., Hassan, B., Gilbert, DG., Eastman, DA., Rice, M., Weir, M., Hahn, MW., Park, Y., Dewey, CN., Pachter, L., Kent, WJ., Haussler, D., Lai, EC., Bartel, DP., Hannon, GJ., Kaufman, TC., Eisen, MB., Clark, AG., Smith, D., Celniker, SE., Gelbart, WM., Kellis, M. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450(7167):219-32 (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

• Stark, A., Shkumatov, A., Russell, RB. (2004). Finding functional sites in structural genomics proteins. Structure. 12(8):1405-12 (abstract)

2003

• Aloy, P., Ceulemans, H., Stark, A., Russell, RB. (2003). The relationship between sequence and interaction divergence in proteins. J Mol Biol. 332(5):989-98 (abstract)
• Aloy, P., Stark, A., Hadley, C., Russell, RB. (2003). Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins. 53 Suppl 6:436-56 (abstract)
• Brennecke, J., Hipfner, DR., Stark, A., Russell, RB., Cohen, SM. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell. 113(1):25-36 (abstract)
• Lorentzen, E., Pohl, E., Zwart, P., Stark, A., Russell, RB., Knura, T., Hensel, R., Siebers, B. (2003). Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins. J Biol Chem. 278(47):47253-60 (abstract)
• Stark, A., Brennecke, J., Russell, RB., Cohen, SM. (2003). Identification of Drosophila MicroRNA targets. PLoS Biol. 1(3):E60 (abstract)
• Stark, A., Russell, RB. (2003). Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res. 31(13):3341-4 (abstract)
• Stark, A., Sunyaev, S., Russell, RB. (2003). A model for statistical significance of local similarities in structure. J Mol Biol. 326(5):1307-16 (abstract)

2002

• Métivier, R., Stark, A., Flouriot, G., Hübner, MR., Brand, H., Penot, G., Manu, D., Denger, S., Reid, G., Kos, M., Russell, RB., Kah, O., Pakdel, F., Gannon, F. (2002). A dynamic structural model for estrogen receptor-alpha activation by ligands, emphasizing the role of interactions between distant A and E domains. Mol Cell. 10(5):1019-32 (abstract)

2000

• Hatano, E., Bradham, CA., Stark, A., Iimuro, Y., Lemasters, JJ., Brenner, DA. (2000). The mitochondrial permeability transition augments Fas-induced apoptosis in mouse hepatocytes. J Biol Chem. 275(16):11814-23 (abstract)