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Items: 44

1.

Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes.

Espinosa-Cantú A, Ascencio D, Herrera-Basurto S, Xu J, Roguev A, Krogan NJ, DeLuna A.

Genetics. 2018 Jan;208(1):419-431. doi: 10.1534/genetics.117.300377. Epub 2017 Nov 10.

2.

DNA Preparation from Schizosaccharomyces pombe.

Roguev A, Xu J, Krogan NJ.

Cold Spring Harb Protoc. 2018 Jan 2;2018(1):pdb.prot091959. doi: 10.1101/pdb.prot091959.

PMID:
28733411
3.

Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast.

Roguev A, Ryan CJ, Xu J, Colson I, Hartsuiker E, Krogan N.

Cold Spring Harb Protoc. 2018 Feb 1;2018(2):pdb.prot091983. doi: 10.1101/pdb.prot091983.

PMID:
28733406
4.

High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe.

Roguev A, Ryan CJ, Hartsuiker E, Krogan NJ.

Cold Spring Harb Protoc. 2018 Feb 1;2018(2):pdb.top079905. doi: 10.1101/pdb.top079905.

PMID:
28733404
5.

Transformation of Schizosaccharomyces pombe in a 96-Well Format.

Roguev A, Xu J, Krogan NJ.

Cold Spring Harb Protoc. 2018 Jan 2;2018(1):pdb.prot091942. doi: 10.1101/pdb.prot091942.

PMID:
28733397
6.

Genetic Interaction Mapping in Schizosaccharomyces pombe Using the Pombe Epistasis Mapper (PEM) System and a ROTOR HDA Colony Replicating Robot in a 1536 Array Format.

Roguev A, Xu J, Krogan N.

Cold Spring Harb Protoc. 2018 Feb 1;2018(2):pdb.prot091975. doi: 10.1101/pdb.prot091975.

PMID:
28733394
7.

Genetic interaction mapping in mammalian cells using CRISPR interference.

Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ.

Nat Methods. 2017 Jun;14(6):577-580. doi: 10.1038/nmeth.4286. Epub 2017 May 8.

8.

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P.

Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225. Epub 2017 Mar 20.

9.

Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells.

Ding L, Paszkowski-Rogacz M, Winzi M, Chakraborty D, Theis M, Singh S, Ciotta G, Poser I, Roguev A, Chu WK, Choudhary C, Mann M, Stewart AF, Krogan N, Buchholz F.

Cell Syst. 2015 Aug 26;1(2):141-51. doi: 10.1016/j.cels.2015.08.002. Epub 2015 Aug 26.

10.

Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.

Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C.

PLoS Genet. 2015 Mar 31;11(3):e1005074. doi: 10.1371/journal.pgen.1005074. eCollection 2015 Mar.

11.

Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants.

Sánchez A, Roguev A, Krogan NJ, Russell P.

G3 (Bethesda). 2015 Mar 19;5(5):953-62. doi: 10.1534/g3.115.017251.

12.

Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells.

Tosti E, Katakowski JA, Schaetzlein S, Kim HS, Ryan CJ, Shales M, Roguev A, Krogan NJ, Palliser D, Keogh MC, Edelmann W.

Genome Med. 2014 Sep 17;6(9):68. doi: 10.1186/s13073-014-0068-4. eCollection 2014.

13.

Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.

Anver S, Roguev A, Zofall M, Krogan NJ, Grewal SI, Harmer SL.

EMBO Rep. 2014 Aug;15(8):894-902. doi: 10.15252/embr.201438902. Epub 2014 Jun 23.

14.

Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function.

Kim HS, Mukhopadhyay R, Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Ryan CJ, Xu J, Jahari H, Hardwick KG, Greenblatt JF, Krogan NJ, Fillingham JS, Strahl BD, Bouhassira EE, Edelmann W, Keogh MC.

Cell Rep. 2014 Mar 13;6(5):892-905. doi: 10.1016/j.celrep.2014.01.029. Epub 2014 Feb 22.

15.

A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability.

Kriegenburg F, Jakopec V, Poulsen EG, Nielsen SV, Roguev A, Krogan N, Gordon C, Fleig U, Hartmann-Petersen R.

PLoS Genet. 2014 Jan 30;10(1):e1004140. doi: 10.1371/journal.pgen.1004140. eCollection 2014 Jan.

16.

A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation.

Kabeche R, Roguev A, Krogan NJ, Moseley JB.

J Cell Sci. 2014 Mar 15;127(Pt 6):1318-26. doi: 10.1242/jcs.143545. Epub 2014 Jan 16.

17.

Quantitative genetic-interaction mapping in mammalian cells.

Roguev A, Talbot D, Negri GL, Shales M, Cagney G, Bandyopadhyay S, Panning B, Krogan NJ.

Nat Methods. 2013 May;10(5):432-7. doi: 10.1038/nmeth.2398. Epub 2013 Feb 13.

18.

Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant.

Sánchez A, Sharma S, Rozenzhak S, Roguev A, Krogan NJ, Chabes A, Russell P.

Mol Cell Biol. 2012 Nov;32(21):4445-54. doi: 10.1128/MCB.01062-12. Epub 2012 Aug 27.

19.

Hierarchical modularity and the evolution of genetic interactomes across species.

Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ.

Mol Cell. 2012 Jun 8;46(5):691-704. doi: 10.1016/j.molcel.2012.05.028.

20.

Hho1p, the linker histone of Saccharomyces cerevisiae, is important for the proper chromatin organization in vivo.

Georgieva M, Roguev A, Balashev K, Zlatanova J, Miloshev G.

Biochim Biophys Acta. 2012 May;1819(5):366-74. doi: 10.1016/j.bbagrm.2011.12.003. Epub 2011 Dec 20.

PMID:
22200500
21.

Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex.

Stewart EV, Nwosu CC, Tong Z, Roguev A, Cummins TD, Kim DU, Hayles J, Park HO, Hoe KL, Powell DW, Krogan NJ, Espenshade PJ.

Mol Cell. 2011 Apr 22;42(2):160-71. doi: 10.1016/j.molcel.2011.02.035.

22.

Quantitative genetic interaction mapping using the E-MAP approach.

Collins SR, Roguev A, Krogan NJ.

Methods Enzymol. 2010;470:205-31. doi: 10.1016/S0076-6879(10)70009-4. Epub 2010 Mar 1.

23.

An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.

Kim HS, Vanoosthuyse V, Fillingham J, Roguev A, Watt S, Kislinger T, Treyer A, Carpenter LR, Bennett CS, Emili A, Greenblatt JF, Hardwick KG, Krogan NJ, Bähler J, Keogh MC.

Nat Struct Mol Biol. 2009 Dec;16(12):1286-93. doi: 10.1038/nsmb.1688. Epub 2009 Nov 15.

24.

The Schizosaccharomyces pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains.

Buchanan L, Durand-Dubief M, Roguev A, Sakalar C, Wilhelm B, Strålfors A, Shevchenko A, Aasland R, Shevchenko A, Ekwall K, Francis Stewart A.

PLoS Genet. 2009 Nov;5(11):e1000726. doi: 10.1371/journal.pgen.1000726. Epub 2009 Nov 13.

25.

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.

Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ.

PLoS Biol. 2009 Jun 16;7(6):e1000134. doi: 10.1371/journal.pbio.1000134. Epub 2009 Jun 23. Erratum in: PLoS Biol. 2009 Nov;7(11). doi: 10.1371/annotation/66479889-5e57-4213-bf25-c4e8cf3d933b.

26.

Thioredoxin-related Protein 32 is an arsenite-regulated Thiol Reductase of the proteasome 19 S particle.

Wiseman RL, Chin KT, Haynes CM, Stanhill A, Xu CF, Roguev A, Krogan NJ, Neubert TA, Ron D.

J Biol Chem. 2009 May 29;284(22):15233-45. doi: 10.1074/jbc.M109.002121. Epub 2009 Apr 6.

27.

Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.

Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, Stewart AF.

Genome Biol. 2008;9(11):R167. doi: 10.1186/gb-2008-9-11-r167. Epub 2008 Nov 28.

28.

Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, Krogan NJ.

Science. 2008 Oct 17;322(5900):405-10. doi: 10.1126/science.1162609. Epub 2008 Sep 25.

29.

BAC to the future: functional genomics in mammals.

Roguev A, Krogan NJ.

Nat Methods. 2008 May;5(5):383-4. doi: 10.1038/nmeth0508-383. No abstract available.

30.

High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe.

Roguev A, Wiren M, Weissman JS, Krogan NJ.

Nat Methods. 2007 Oct;4(10):861-6. Epub 2007 Sep 23.

PMID:
17893680
31.

SIN-fully silent: HDAC complexes in fission yeast.

Roguev A, Krogan NJ.

Nat Struct Mol Biol. 2007 May;14(5):358-9. No abstract available.

PMID:
17473877
32.

CCR4/NOT complex associates with the proteasome and regulates histone methylation.

Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD.

Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5836-41. Epub 2007 Mar 26.

33.

Stability of mRNA/DNA and DNA/DNA duplexes affects mRNA transcription.

Kraeva RI, Krastev DB, Roguev A, Ivanova A, Nedelcheva-Veleva MN, Stoynov SS.

PLoS One. 2007 Mar 14;2(3):e290.

34.

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ.

Nature. 2007 Apr 12;446(7137):806-10. Epub 2007 Feb 21.

PMID:
17314980
35.

A recombineering pipeline for functional genomics applied to Caenorhabditis elegans.

Sarov M, Schneider S, Pozniakovski A, Roguev A, Ernst S, Zhang Y, Hyman AA, Stewart AF.

Nat Methods. 2006 Oct;3(10):839-44.

PMID:
16990816
36.

Protein interactions within the Set1 complex and their roles in the regulation of histone 3 lysine 4 methylation.

Dehé PM, Dichtl B, Schaft D, Roguev A, Pamblanco M, Lebrun R, Rodríguez-Gil A, Mkandawire M, Landsberg K, Shevchenko A, Shevchenko A, Rosaleny LE, Tordera V, Chávez S, Stewart AF, Géli V.

J Biol Chem. 2006 Nov 17;281(46):35404-12. Epub 2006 Aug 18.

37.

Uncoupling of unwinding from DNA synthesis implies regulation of MCM helicase by Tof1/Mrc1/Csm3 checkpoint complex.

Nedelcheva MN, Roguev A, Dolapchiev LB, Shevchenko A, Taskov HB, Shevchenko A, Stewart AF, Stoynov SS.

J Mol Biol. 2005 Apr 1;347(3):509-21.

PMID:
15755447
38.

A comparative analysis of an orthologous proteomic environment in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe.

Roguev A, Shevchenko A, Schaft D, Thomas H, Stewart AF, Shevchenko A.

Mol Cell Proteomics. 2004 Feb;3(2):125-32. Epub 2003 Nov 15.

39.

The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation.

Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KM, Stewart AF.

Nucleic Acids Res. 2003 May 15;31(10):2475-82.

40.

High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in budding and fission yeasts.

Roguev A, Schaft D, Shevchenko A, Aasland R, Shevchenko A, Stewart AF.

J Biol Chem. 2003 Mar 7;278(10):8487-93. Epub 2002 Dec 17.

41.

Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry: analytical perspective.

Shevchenko A, Schaft D, Roguev A, Pijnappel WW, Stewart AF, Shevchenko A.

Mol Cell Proteomics. 2002 Mar;1(3):204-12.

42.

The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4.

Roguev A, Schaft D, Shevchenko A, Pijnappel WW, Wilm M, Aasland R, Stewart AF.

EMBO J. 2001 Dec 17;20(24):7137-48.

43.

The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program.

Pijnappel WW, Schaft D, Roguev A, Shevchenko A, Tekotte H, Wilm M, Rigaut G, Séraphin B, Aasland R, Stewart AF.

Genes Dev. 2001 Nov 15;15(22):2991-3004.

44.

Two-wavelength fluorescence assay for DNA repair.

Roguev A, Russev G.

Anal Biochem. 2000 Dec 15;287(2):313-8.

PMID:
11112279

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