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Items: 31

1.

Conserved phosphorylation hotspots in eukaryotic protein domain families.

Strumillo MJ, Oplová M, Viéitez C, Ochoa D, Shahraz M, Busby BP, Sopko R, Studer RA, Perrimon N, Panse VG, Beltrao P.

Nat Commun. 2019 Apr 29;10(1):1977. doi: 10.1038/s41467-019-09952-x.

2.

iProteinDB: An Integrative Database of Drosophila Post-translational Modifications.

Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N.

G3 (Bethesda). 2019 Jan 9;9(1):1-11. doi: 10.1534/g3.118.200637.

3.

Engineering potent long-acting variants of the Wnt inhibitor DKK2.

Sopko R, Mugford JW, Lehmann A, Shapiro RI, Rushe M, Kulkarni A, Worrall J, Amatucci J, Wen D, Pederson NE, Minesinger BK, Arndt JW, Pepinsky B.

Protein Eng Des Sel. 2017 May 1;30(5):359-372. doi: 10.1093/protein/gzx007.

4.

An Integrative Analysis of the InR/PI3K/Akt Network Identifies the Dynamic Response to Insulin Signaling.

Vinayagam A, Kulkarni MM, Sopko R, Sun X, Hu Y, Nand A, Villalta C, Moghimi A, Yang X, Mohr SE, Hong P, Asara JM, Perrimon N.

Cell Rep. 2016 Sep 13;16(11):3062-3074. doi: 10.1016/j.celrep.2016.08.029.

5.

The Atg1-Tor pathway regulates yolk catabolism in Drosophila embryos.

Kuhn H, Sopko R, Coughlin M, Perrimon N, Mitchison T.

Development. 2015 Nov 15;142(22):3869-78. doi: 10.1242/dev.125419. Epub 2015 Sep 22.

6.

Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi.

Housden BE, Valvezan AJ, Kelley C, Sopko R, Hu Y, Roesel C, Lin S, Buckner M, Tao R, Yilmazel B, Mohr SE, Manning BD, Perrimon N.

Sci Signal. 2015 Sep 8;8(393):rs9. doi: 10.1126/scisignal.aab3729.

7.

The Transgenic RNAi Project at Harvard Medical School: Resources and Validation.

Perkins LA, Holderbaum L, Tao R, Hu Y, Sopko R, McCall K, Yang-Zhou D, Flockhart I, Binari R, Shim HS, Miller A, Housden A, Foos M, Randkelv S, Kelley C, Namgyal P, Villalta C, Liu LP, Jiang X, Huan-Huan Q, Wang X, Fujiyama A, Toyoda A, Ayers K, Blum A, Czech B, Neumuller R, Yan D, Cavallaro A, Hibbard K, Hall D, Cooley L, Hannon GJ, Lehmann R, Parks A, Mohr SE, Ueda R, Kondo S, Ni JQ, Perrimon N.

Genetics. 2015 Nov;201(3):843-52. doi: 10.1534/genetics.115.180208. Epub 2015 Aug 28.

8.

Fat1 interacts with Fat4 to regulate neural tube closure, neural progenitor proliferation and apical constriction during mouse brain development.

Badouel C, Zander MA, Liscio N, Bagherie-Lachidan M, Sopko R, Coyaud E, Raught B, Miller FD, McNeill H.

Development. 2015 Aug 15;142(16):2781-91. doi: 10.1242/dev.123539. Epub 2015 Jul 24.

9.

A systems-level interrogation identifies regulators of Drosophila blood cell number and survival.

Sopko R, Lin YB, Makhijani K, Alexander B, Perrimon N, Brückner K.

PLoS Genet. 2015 Mar 6;11(3):e1005056. doi: 10.1371/journal.pgen.1005056. eCollection 2015 Mar.

10.

Combining genetic perturbations and proteomics to examine kinase-phosphatase networks in Drosophila embryos.

Sopko R, Foos M, Vinayagam A, Zhai B, Binari R, Hu Y, Randklev S, Perkins LA, Gygi SP, Perrimon N.

Dev Cell. 2014 Oct 13;31(1):114-27. doi: 10.1016/j.devcel.2014.07.027. Epub 2014 Oct 2.

11.

Does Baseline Heart Rate Variability Reflect Stable Positive Emotionality?

Silvia PJ, Jackson BA, Sopko RS.

Pers Individ Dif. 2014 Nov 1;70:183-187.

12.

FlyPrimerBank: an online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents.

Hu Y, Sopko R, Foos M, Kelley C, Flockhart I, Ammeux N, Wang X, Perkins L, Perrimon N, Mohr SE.

G3 (Bethesda). 2013 Sep 4;3(9):1607-16. doi: 10.1534/g3.113.007021.

13.

Receptor tyrosine kinases in Drosophila development.

Sopko R, Perrimon N.

Cold Spring Harb Perspect Biol. 2013 Jun 1;5(6). pii: a009050. doi: 10.1101/cshperspect.a009050. Review.

14.

Protein complex-based analysis framework for high-throughput data sets.

Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr SE, Perrimon N.

Sci Signal. 2013 Feb 26;6(264):rs5. doi: 10.1126/scisignal.2003629.

15.

The Hippo pathway regulates Wnt/beta-catenin signaling.

Varelas X, Miller BW, Sopko R, Song S, Gregorieff A, Fellouse FA, Sakuma R, Pawson T, Hunziker W, McNeill H, Wrana JL, Attisano L.

Dev Cell. 2010 Apr 20;18(4):579-91. doi: 10.1016/j.devcel.2010.03.007.

16.

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.

Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE.

Sci Signal. 2010 Feb 16;3(109):ra12. doi: 10.1126/scisignal.2000482.

17.

Dual regulation by pairs of cyclin-dependent protein kinases and histone deacetylases controls G1 transcription in budding yeast.

Huang D, Kaluarachchi S, van Dyk D, Friesen H, Sopko R, Ye W, Bastajian N, Moffat J, Sassi H, Costanzo M, Andrews BJ.

PLoS Biol. 2009 Sep;7(9):e1000188. doi: 10.1371/journal.pbio.1000188. Epub 2009 Sep 8.

18.

The skinny on Fat: an enormous cadherin that regulates cell adhesion, tissue growth, and planar cell polarity.

Sopko R, McNeill H.

Curr Opin Cell Biol. 2009 Oct;21(5):717-23. doi: 10.1016/j.ceb.2009.07.001. Epub 2009 Aug 11. Review.

PMID:
19679459
19.

Phosphorylation of the tumor suppressor fat is regulated by its ligand Dachsous and the kinase discs overgrown.

Sopko R, Silva E, Clayton L, Gardano L, Barrios-Rodiles M, Wrana J, Varelas X, Arbouzova NI, Shaw S, Saburi S, Matakatsu H, Blair S, McNeill H.

Curr Biol. 2009 Jul 14;19(13):1112-7. doi: 10.1016/j.cub.2009.05.049. Epub 2009 Jun 18.

20.

Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets.

Sopko R, Andrews BJ.

Mol Biosyst. 2008 Sep;4(9):920-33. doi: 10.1039/b801724g. Epub 2008 Jul 17. Review.

PMID:
18704230
21.

Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint.

Ghavidel A, Kislinger T, Pogoutse O, Sopko R, Jurisica I, Emili A.

Cell. 2007 Nov 30;131(5):915-26.

22.

Activation of the Cdc42p GTPase by cyclin-dependent protein kinases in budding yeast.

Sopko R, Huang D, Smith JC, Figeys D, Andrews BJ.

EMBO J. 2007 Oct 31;26(21):4487-500. Epub 2007 Sep 13.

23.

Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.

Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, Porter J, Chua G, Sopko R, Brost RL, Ho CH, Wang J, Ketela T, Brenner C, Brill JA, Fernandez GE, Lorenz TC, Payne GS, Ishihara S, Ohya Y, Andrews B, Hughes TR, Frey BJ, Graham TR, Andersen RJ, Boone C.

Cell. 2006 Aug 11;126(3):611-25.

24.

Identifying transcription factor functions and targets by phenotypic activation.

Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, Hughes TR.

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12045-50. Epub 2006 Jul 31.

25.

Phenotypic activation to discover biological pathways and kinase substrates.

Sopko R, Papp B, Oliver SG, Andrews BJ.

Cell Cycle. 2006 Jul;5(13):1397-402. Epub 2006 Jul 1.

PMID:
16855397
26.

Small open reading frames: not so small anymore.

Sopko R, Andrews B.

Genome Res. 2006 Mar;16(3):314-5. No abstract available.

27.

Mapping pathways and phenotypes by systematic gene overexpression.

Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, Boone C, Andrews B.

Mol Cell. 2006 Feb 3;21(3):319-30.

28.

Global analysis of protein phosphorylation in yeast.

Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M.

Nature. 2005 Dec 1;438(7068):679-84.

PMID:
16319894
29.
30.

Global control of histone modification by the anaphase-promoting complex.

Ramaswamy V, Williams JS, Robinson KM, Sopko RL, Schultz MC.

Mol Cell Biol. 2003 Dec;23(24):9136-49.

31.

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