Publications Alexander Stark | Scientific Papers Stark Lab

Stark, A. (2013)

Regulatory Genomics - Decoding Drosophila Regulatory Sequences.

Biomed Tech (Berl). 58 Suppl 1

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

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

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

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

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

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

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

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

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

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

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

Stark, A. (2009)

Learning the transcriptional regulatory code.

Mol Syst Biol. 5:329

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

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

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

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

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

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

Kheradpour, P., Stark, A., Roy, S., Kellis, M. (2007)

Reliable prediction of regulator targets using 12 Drosophila genomes.

Genome Res. 17(12):1919-31

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

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

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

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

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

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

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

Cohen, SM., Brennecke, J., Stark, A. (2006)

Denoising feedback loops by thresholding--a new role for microRNAs.

Genes Dev. 20(20):2769-72

Brennecke, J., Stark, A., Cohen, SM. (2005)

Not miR-ly muscular: microRNAs and muscle development.

Genes Dev. 19(19):2261-4

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

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

Brennecke, J., Stark, A., Russell, RB., Cohen, SM. (2005)

Principles of microRNA-target recognition.

PLoS Biol. 3(3):e85

Publications

2013

2012

2010

2009

2008

2007

2006

2005

Cookie Settings