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Alexander Stark

The regulation of gene expression in response to developmental or environmental stimuli is a crucial mechanism in all organisms. We are fascinated by the question how transcription is regulated at the level of enhancer and core-promoter DNA elements, and the transcription factor and cofactor proteins that mediate transcription activation. We use genome-wide functional assays, bioinformatics, and mass-spectrometry; and develop highly-controllable reporter assays that provide direct functional readouts. Our goal is to understand transcription and – ultimately – how transcriptional networks define cellular and developmental programs.



Jacobs, J., Pagani, M., Wenzl, C., Stark, A. (2023)

Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila.

Science. 381(6654):198-204
Klaus, L., de Almeida, BP., Vlasova, A., Nemčko, F., Schleiffer, A., Bergauer, K., Hofbauer, L., Rath, M., Stark, A. (2023)

Systematic identification and characterization of repressive domains in Drosophila transcription factors.

EMBO J. 42(3):e112100
Serebreni, L., Pleyer, LM., Haberle, V., Hendy, O., Vlasova, A., Loubiere, V., Nemčko, F., Bergauer, K., Roitinger, E., Mechtler, K., Stark, A. (2023)

Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns.

EMBO J. :e113519


de Almeida, BP., Reiter, F., Pagani, M., Stark, A. (2022)

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.

Nat Genet. 54(5):613-624
Hendy, O., Serebreni, L., Bergauer, K., Muerdter, F., Huber, L., Nemčko, F., Stark, A. (2022)

Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers.

Mol Cell. 82(19):3598-3612.e7
Nemčko, F., Stark, A. (2022)

Proteome-scale identification of transcriptional activators in human cells.

Mol Cell. 82(3):497-499
Neumayr, C., Haberle, V., Serebreni, L., Karner, K., Hendy, O., Boija, A., Henninger, JE., Li, CH., Stejskal, K., Lin, G., Bergauer, K., Pagani, M., Rath, M., Mechtler, K., Arnold, CD., Stark, A. (2022)

Differential cofactor dependencies define distinct types of human enhancers.

Nature. 606(7913):406-413


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. (2021)

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.

Nat Commun. 12(1):6078
Yelagandula, R., Bykov, A., Vogt, A., Heinen, R., Özkan, E., Strobl, MM., Baar, JC., Uzunova, K., Hajdusits, B., Kordic, D., Suljic, E., Kurtovic-Kozaric, A., Izetbegovic, S., Schaeffer, J., Hufnagl, P., Zoufaly, A., Seitz, T., Födinger, M., Allerberger, F., Stark, A., Cochella, L., Elling, U. (2021)

Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq.

Nat Commun. 12(1):3132


Haberle, V., Arnold, CD., Pagani, M., Rath, M., Schernhuber, K., Stark, A. (2019)

Transcriptional cofactors display specificity for distinct types of core promoters.

Nature. 570(7759):122-126
Neumayr, C., Pagani, M., Stark, A., Arnold, CD. (2019)

STARR-seq and UMI-STARR-seq: Assessing Enhancer Activities for Genome-Wide-, High-, and Low-Complexity Candidate Libraries.

Curr Protoc Mol Biol. 128(1):e105


Arnold, CD., Nemčko, F., Woodfin, AR., Wienerroither, S., Vlasova, A., Schleiffer, A., Pagani, M., Rath, M., Stark, A. (2018)

A high-throughput method to identify trans-activation domains within transcription factor sequences.

EMBO J. 37(16)
Haberle, V., Stark, A. (2018)

Eukaryotic core promoters and the functional basis of transcription initiation.

Nat Rev Mol Cell Biol. 19(10):621-637
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. (2018)

Resolving systematic errors in widely used enhancer activity assays in human cells.

Nat Methods. 15(2):141-149


Arnold, CD., Zabidi, MA., Pagani, M., Rath, M., Schernhuber, K., Kazmar, T., Stark, A. (2017)

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution.

Nat Biotechnol. 35(2):136-144
Catarino, RR., Neumayr, C., Stark, A. (2017)

Promoting transcription over long distances.

Nat Genet. 49(7):972-973
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. (2017)

A reversible haploid mouse embryonic stem cell biobank resource for functional genomics.

Nature. 550(7674):114-118
Franz, A., Shlyueva, D., Brunner, E., Stark, A., Basler, K. (2017)

Probing the canonicity of the Wnt/Wingless signaling pathway.

PLoS Genet. 13(4):e1006700
Reiter, F., Wienerroither, S., Stark, A. (2017)

Combinatorial function of transcription factors and cofactors.

Curr Opin Genet Dev. 43:73-81


Muerdter, F., Stark, A. (2016)

Gene Regulation: Activation through Space.

Curr Biol. 26(19):R895-R898
Rickels, R., Hu, D., Collings, CK., Woodfin, AR., Piunti, A., Mohan, M., Herz, HM., Kvon, E., Shilatifard, A. (2016)

An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS.

Mol Cell. 63(2):318-328
Stepien, BK., Oppitz, C., Gerlach, D., Dag, U., Novatchkova, M., Krüttner, S., Stark, A., Keleman, K. (2016)

RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2.

Proc Natl Acad Sci U S A. 113(45):E7030-E7038
Zabidi, MA., Stark, A. (2016)

Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.

Trends Genet. 32(12):801-814


Haberle, V., Stark, A. (2015)

Coordinating the human looks.

Cell. 163(1):24-6
Muerdter, F., Boryń, ŁM., Arnold, CD. (2015)

STARR-seq - principles and applications.

Genomics. 106(3):145-150
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. (2015)

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.

Nature. 525(7570):543-547
Spletter, ML., Barz, C., Yeroslaviz, A., Schönbauer, C., Ferreira, IR., Sarov, M., Gerlach, D., Stark, A., Habermann, BH., Schnorrer, F. (2015)

The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle.

EMBO Rep. 16(2):178-91
Stampfel, G., Kazmar, T., Frank, O., Wienerroither, S., Reiter, F., Stark, A. (2015)

Transcriptional regulators form diverse groups with context-dependent regulatory functions.

Nature. 528(7580):147-51
Zabidi, MA., Arnold, CD., Schernhuber, K., Pagani, M., Rath, M., Frank, O., Stark, A. (2015)

Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

Nature. 518(7540):556-9


Arnold, CD., Gerlach, D., Spies, D., Matts, JA., Sytnikova, YA., Pagani, M., Lau, NC., Stark, A. (2014)

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution.

Nat Genet. 46(7):685-92
Kvon, EZ., Kazmar, T., Stampfel, G., Yáñez-Cuna, JO., Pagani, M., Schernhuber, K., Dickson, BJ., Stark, A. (2014)

Genome-scale functional characterization of Drosophila developmental enhancers in vivo.

Nature. 512(7512):91-5
Meireles-Filho, ACA., Bardet, AF., Yáñez-Cuna, JO., Stampfel, G., Stark, A. (2014)

cis-regulatory requirements for tissue-specific programs of the circadian clock.

Curr Biol. 24(1):1-10
Muerdter, F., Stark, A. (2014)

Genomics: Hiding in plain sight.

Nature. 512(7515):374-5
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
Shlyueva, D., Stampfel, G., Stark, A. (2014)

Transcriptional enhancers: from properties to genome-wide predictions.

Nat Rev Genet. 15(4):272-86
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
Yáñez-Cuna, JO., Arnold, CD., Stampfel, G., Boryń, LM., Gerlach, D., Rath, M., Stark, A. (2014)

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.

Genome Res. 24(7):1147-56


Arnold, CD., Gerlach, D., Stelzer, C., Boryń, ŁM., Rath, M., Stark, A. (2013)

Genome-wide quantitative enhancer activity maps identified by STARR-seq.

Science. 339(6123):1074-7
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):2705-13
Kazmar, T., Kvon EZ., Stark, A., Lampert, CH.. (2013)

Drosophila Embryo Stage Annotation using Label Propagation

International Conference on Computer Vision (ICCV). Springer. Dec:1089–1096
Stark, A. (2013)

Regulatory Genomics - Decoding Drosophila Regulatory Sequences.

Biomed Tech (Berl). 58 Suppl 1
Yáñez-Cuna, JO., Kvon, EZ., Stark, A. (2013)

Deciphering the transcriptional cis-regulatory code.

Trends Genet. 29(1):11-22


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
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):908-13
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):2018-30


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
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
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
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., Baldwin, J., Bloom, T., Chin, CW., Heiman, D., Nicol, R., Nusbaum, C., Young, S., Wilkinson, J., Worley, KC., Kovar, CL., Muzny, DM., Gibbs, RA., 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., 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


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
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
Zeitlinger, J., Stark, A. (2010)

Developmental gene regulation in the era of genomics.

Dev Biol. 339(2):230-9
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


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
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
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
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
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
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
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
Stark, A. (2009)

Learning the transcriptional regulatory code.

Mol Syst Biol. 5:329


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
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
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
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
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
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


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
Clark, AG., Eisen, MB., Smith, DR., Bergman, CM., Oliver, B., Markow, TA., Kaufman, TC., Kellis, M., Gelbart, W., Iyer, VN., Pollard, DA., Sackton, TB., Larracuente, AM., Singh, ND., Abad, JP., Abt, DN., Adryan, B., Aguade, M., Akashi, H., Anderson, WW., Aquadro, CF., Ardell, DH., Arguello, R., Artieri, CG., Barbash, DA., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, SA., Bradley, RK., Brand, AD., Brent, MR., Brooks, AN., Brown, RH., Butlin, RK., Caggese, C., Calvi, BR., Bernardo de Carvalho, A., Caspi, A., Castrezana, S., Celniker, SE., Chang, JL., Chapple, C., Chatterji, S., Chinwalla, A., Civetta, A., Clifton, SW., Comeron, JM., Costello, JC., Coyne, JA., Daub, J., David, RG., Delcher, AL., Delehaunty, K., Do, CB., Ebling, H., Edwards, K., Eickbush, T., Evans, JD., Filipski, A., Findeiss, S., Freyhult, E., Fulton, L., Fulton, R., Garcia, AC., Gardiner, A., Garfield, DA., Garvin, BE., Gibson, G., Gilbert, D., Gnerre, S., Godfrey, J., Good, R., Gotea, V., Gravely, B., Greenberg, AJ., Griffiths-Jones, S., Gross, S., Guigo, R., Gustafson, EA., Haerty, W., Hahn, MW., Halligan, DL., Halpern, AL., Halter, GM., Han, MV., Heger, A., Hillier, L., Hinrichs, AS., Holmes, I., Hoskins, RA., Hubisz, MJ., Hultmark, D., Huntley, MA., Jaffe, DB., Jagadeeshan, S., Jeck, WR., Johnson, J., Jones, CD., Jordan, WC., Karpen, GH., Kataoka, E., Keightley, PD., Kheradpour, P., Kirkness, EF., Koerich, LB., Kristiansen, K., Kudrna, D., Kulathinal, RJ., Kumar, S., Kwok, R., Lander, E., Langley, CH., Lapoint, R., Lazzaro, BP., Lee, SJ., Levesque, L., Li, R., Lin, CF., Lin, MF., Lindblad-Toh, K., Llopart, A., Long, M., Low, L., Lozovsky, E., Lu, J., Luo, M., Machado, CA., Makalowski, W., Marzo, M., Matsuda, M., Matzkin, L., McAllister, B., McBride, CS., McKernan, B., McKernan, K., Mendez-Lago, M., Minx, P., Mollenhauer, MU., Montooth, K., Mount, SM., Mu, X., Myers, E., Negre, B., Newfeld, S., Nielsen, R., Noor, MA., O'Grady, P., Pachter, L., Papaceit, M., Parisi, MJ., Parisi, M., Parts, L., Pedersen, JS., Pesole, G., Phillippy, AM., Ponting, CP., Pop, M., Porcelli, D., Powell, JR., Prohaska, S., Pruitt, K., Puig, M., Quesneville, H., Ram, KR., Rand, D., Rasmussen, MD., Reed, LK., Reenan, R., Reily, A., Remington, KA., Rieger, TT., Ritchie, MG., Robin, C., Rogers, YH., Rohde, C., Rozas, J., Rubenfield, MJ., Ruiz, A., Russo, S., Salzberg, SL., Sanchez-Gracia, A., Saranga, DJ., Sato, H., Schaeffer, SW., Schatz, MC., Schlenke, T., Schwartz, R., Segarra, C., Singh, RS., Sirot, L., Sirota, M., Sisneros, NB., Smith, CD., Smith, TF., Spieth, J., Stage, DE., Stark, A., Stephan, W., Strausberg, RL., Strempel, S., Sturgill, D., Sutton, G., Sutton, GG., Tao, W., Teichmann, S., Tobari, YN., Tomimura, Y., Tsolas, JM., Valente, VL., Venter, E., Venter, JC., Vicario, S., Vieira, FG., Vilella, AJ., Villasante, A., Walenz, B., Wang, J., Wasserman, M., Watts, T., Wilson, D., Wilson, RK., Wing, RA., Wolfner, MF., Wong, A., Wong, GK., Wu, CI., Wu, G., Yamamoto, D., Yang, HP., Yang, SP., Yorke, JA., Yoshida, K., Zdobnov, E., Zhang, P., Zhang, Y., Zimin, AV., Baldwin, J., Abdouelleil, A., Abdulkadir, J., Abebe, A., Abera, B., Abreu, J., Acer, SC., Aftuck, L., Alexander, A., An, P., Anderson, E., Anderson, S., Arachi, H., Azer, M., Bachantsang, P., Barry, A., Bayul, T., Berlin, A., Bessette, D., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Bourzgui, I., Brown, A., Cahill, P., Channer, S., Cheshatsang, Y., Chuda, L., Citroen, M., Collymore, A., Cooke, P., Costello, M., D'Aco, K., Daza, R., De Haan, G., DeGray, S., DeMaso, C., Dhargay, N., Dooley, K., Dooley, E., Doricent, M., Dorje, P., Dorjee, K., Dupes, A., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Fisher, S., Foley, CD., Franke, A., Friedrich, D., Gadbois, L., Gearin, G., Gearin, CR., Giannoukos, G., Goode, T., Graham, J., Grandbois, E., Grewal, S., Gyaltsen, K., Hafez, N., Hagos, B., Hall, J., Henson, C., Hollinger, A., Honan, T., Huard, MD., Hughes, L., Hurhula, B., Husby, ME., Kamat, A., Kanga, B., Kashin, S., Khazanovich, D., Kisner, P., Lance, K., Lara, M., Lee, W., Lennon, N., Letendre, F., LeVine, R., Lipovsky, A., Liu, X., Liu, J., Liu, S., Lokyitsang, T., Lokyitsang, Y., Lubonja, R., Lui, A., MacDonald, P., Magnisalis, V., Maru, K., Matthews, C., McCusker, W., McDonough, S., Mehta, T., Meldrim, J., Meneus, L., Mihai, O., Mihalev, A., Mihova, T., Mittelman, R., Mlenga, V., Montmayeur, A., Mulrain, L., Navidi, A., Naylor, J., Negash, T., Nguyen, T., Nguyen, N., Nicol, R., Norbu, C., Norbu, N., Novod, N., O'Neill, B., Osman, S., Markiewicz, E., Oyono, OL., Patti, C., Phunkhang, P., Pierre, F., Priest, M., Raghuraman, S., Rege, F., Reyes, R., Rise, C., Rogov, P., Ross, K., Ryan, E., Settipalli, S., Shea, T., Sherpa, N., Shi, L., Shih, D., Sparrow, T., Spaulding, J., Stalker, J., Stange-Thomann, N., Stavropoulos, S., Stone, C., Strader, C., Tesfaye, S., Thomson, T., Thoulutsang, Y., Thoulutsang, D., Topham, K., Topping, I., Tsamla, T., Vassiliev, H., Vo, A., Wangchuk, T., Wangdi, T., Weiand, M., Wilkinson, J., Wilson, A., Yadav, S., Young, G., Yu, Q., Zembek, L., Zhong, D., Zimmer, A., Zwirko, Z., Jaffe, DB., Alvarez, P., Brockman, W., Butler, J., Chin, C., Gnerre, S., Grabherr, M., Kleber, M., Mauceli, E., MacCallum, I. (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
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
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
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
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
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


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
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


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

Not miR-ly muscular: microRNAs and muscle development.

Genes Dev. 19(19):2261-4
Brennecke, J., Stark, A., Russell, RB., Cohen, SM. (2005)

Principles of microRNA-target recognition.

PLoS Biol. 3(3):e85
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
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


Stark, A., Shkumatov, A., Russell, RB. (2004)

Finding functional sites in structural genomics proteins.

Structure. 12(8):1405-12


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
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
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
Stark, A., Brennecke, J., Russell, RB., Cohen, SM. (2003)

Identification of Drosophila MicroRNA targets.

PLoS Biol. 1(3):E60
Stark, A., Russell, RB. (2003)

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

Nucleic Acids Res. 31(13):3341-4
Stark, A., Sunyaev, S., Russell, RB. (2003)

A model for statistical significance of local similarities in structure.

J Mol Biol. 326(5):1307-16


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


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