Publications Alexander Stark | Scientific Papers Stark Lab

Chen, S., Loubiere, V., Hollingsworth, EW., Murakami, K., Mandlburger, N., Jacinto, SH., Dizehchi, A., Schreiber, J., Kvon, EZ., Stark, A. (2026)

Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.

Nat Genet. 58(9):2129-2133

Chen, S., Loubiere, V., Hollingsworth, EW., Jacinto, SH., Dizehchi, A., Schreiber, J., Kvon, EZ., Stark, A. (2025)

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo.

bioRxiv.

Pachano, T., Leng, H., Dugied, G., Tribble, T., Loubiere, V., Rauh, F., Lee, Y., Schleiffer, A., Young, V., Weller, B., Lyons, EA., Hass, MR., Kottayan, LC., Weirauch, MT., Fuxman Bass, JI., Newton, HJ., Ensminger, AW., Braun, PF., Schramek, D., Stark, A., Taipale, M. (2025)

Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways.

bioRxiv.

Nemčko, F., Stark, A. (2025)

A tighter grip on gene expression.

Science. 389(6755):31-32

Thomas, HF., Feng, S., Haslhofer, F., Huber, M., García Gallardo, M., Loubiere, V., Vanina, D., Pitasi, M., Stark, A., Buecker, C. (2025)

Enhancer cooperativity can compensate for loss of activity over large genomic distances.

Mol Cell. 85(2):362-375.e9

Hofbauer, L., Pleyer, LM., Reiter, F., Schleiffer, A., Vlasova, A., Serebreni, L., Huang, A., Stark, A. (2024)

A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression.

Mol Cell. 84(23):4503-4521.e14

Loubiere, V., de Almeida, BP., Pagani, M., Stark, A. (2024)

Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila.

Nat Commun. 15(1):8584

Nemčko, F., Himmelsbach, M., Loubiere, V., Yelagandula, R., Pagani, M., Fasching, N., Brennecke, J., Elling, U., Stark, A., Ameres, SL. (2024)

Proteome-scale tagging and functional screening in mammalian cells by ORFtag.

Nat Methods.

Frank, O., Balboa, DA., Novatchkova, M., Özkan, E., Strobl, MM., Yelagandula, R., Albanese, TG., Endler, L., Amman, F., Felsenstein, V., Gavrilovic, M., Acosta, M., Patocka, T., Vogt, A., Tamir, I., Klikovits, J., Zoufaly, A., Seitz, T., Födinger, M., Bergthaler, A., Indra, A., Schmid, D., Klimek, P., Stark, A., Allerberger, F., Benka, B., Reich, K., Cochella, L., Elling, U. (2024)

Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023.

Euro Surveill. 29(23)

de Almeida, BP., Schaub, C., Pagani, M., Secchia, S., Furlong, EEM., Stark, A. (2024)

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.

Nature. 626(7997):207-211

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

Chan, YC., Kienle, E., Oti, M., Di Liddo, A., Mendez-Lago, M., Aschauer, DF., Peter, M., Pagani, M., Arnold, C., Vonderheit, A., Schön, C., Kreuz, S., Stark, A., Rumpel, S. (2023)

An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo.

Sci Rep. 13(1):6745

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

Reiter, F., de Almeida, BP., Stark, A. (2023)

Enhancers display constrained sequence flexibility and context-specific modulation of motif function.

Genome Res.

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

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

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

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

Nemčko, F., Stark, A. (2022)

Proteome-scale identification of transcriptional activators in human cells.

Mol Cell. 82(3):497-499

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

Serebreni, L., Stark, A. (2021)

Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions.

Curr Opin Cell Biol. 70:58-66

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

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

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

Stark, A. (2013)

Regulatory Genomics - Decoding Drosophila Regulatory Sequences.

Biomed Tech (Berl). 58 Suppl 1

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

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., 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)

Catarino, RR., Stark, A. (2018)

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.

Genes Dev. 32(3-4):202-223

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

Gene Regulation: Activation through Space.

Curr Biol. 26(19):R895-R898

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

Reiter, F., Wienerroither, S., Stark, A. (2017)

Combinatorial function of transcription factors and cofactors.

Curr Opin Genet Dev. 43:73-81

Zabidi, MA., Stark, A. (2016)

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

Trends Genet. 32(12):801-814

Catarino, RR., Neumayr, C., Stark, A. (2017)

Promoting transcription over long distances.

Nat Genet. 49(7):972-973

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

Shlyueva, D., Meireles-Filho, AC., Pagani, M., Stark, A. (2016)

Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation.

PLoS One. 11(8):e0161997

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

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

Muerdter, F., Boryń, ŁM., Arnold, CD. (2015)

STARR-seq - principles and applications.

Genomics. 106(3):145-150

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

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

Coordinating the human looks.

Cell. 163(1):24-6

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

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

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

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

Muerdter, F., Stark, A. (2014)

Genomics: Hiding in plain sight.

Nature. 512(7515):374-5

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

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

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

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.

Nat Rev Genet. 15(4):272-86

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

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

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

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

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

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

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., 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

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

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

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

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

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

Developmental gene regulation in the era of genomics.

Dev Biol. 339(2):230-9

Stark, A. (2009)

Learning the transcriptional regulatory code.

Mol Syst Biol. 5:329

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

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

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

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

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

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

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

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

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

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

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

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

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

Reliable prediction of regulator targets using 12 Drosophila genomes.

Genome Res. 17(12):1919-31

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

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

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

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., 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

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

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

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

Genes Dev. 20(20):2769-72

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

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., Russell, RB., Cohen, SM. (2005)

Principles of microRNA-target recognition.

PLoS Biol. 3(3):e85

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

Identification of Drosophila MicroRNA targets.

PLoS Biol. 1(3):E60

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

Not miR-ly muscular: microRNAs and muscle development.

Genes Dev. 19(19):2261-4

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

Finding functional sites in structural genomics proteins.

Structure. 12(8):1405-12

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

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

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

Stark, A., Russell, RB. (2003)

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

Nucleic Acids Res. 31(13):3341-4

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

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

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

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