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Items: 1 to 50 of 61

1.

Identifying Pseudomonas syringae Type III Secreted Effector Function via a Yeast Genomic Screen.

Huei-Yi Lee A, Bastedo DP, Youn JY, Lo T, Middleton MA, Kireeva I, Lee JY, Sharifpoor S, Baryshnikova A, Zhang J, Wang PW, Peisajovich SG, Costanzo M, Andrews BJ, Boone CM, Desveaux D, Guttman DS.

G3 (Bethesda). 2018 Dec 20. pii: g3.200877.2018. doi: 10.1534/g3.118.200877. [Epub ahead of print]

2.

Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks.

Baryshnikova A.

Methods Mol Biol. 2018;1819:249-268. doi: 10.1007/978-1-4939-8618-7_12.

PMID:
30421408
3.

A Genome-Wide Screen Reveals a Role for the HIR Histone Chaperone Complex in Preventing Mislocalization of Budding Yeast CENP-A.

Ciftci-Yilmaz S, Au WC, Mishra PK, Eisenstatt JR, Chang J, Dawson AR, Zhu I, Rahman M, Bilke S, Costanzo M, Baryshnikova A, Myers CL, Meltzer PS, Landsman D, Baker RE, Boone C, Basrai MA.

Genetics. 2018 Sep;210(1):203-218. doi: 10.1534/genetics.118.301305. Epub 2018 Jul 16.

PMID:
30012561
4.

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome.

Ho B, Baryshnikova A, Brown GW.

Cell Syst. 2018 Feb 28;6(2):192-205.e3. doi: 10.1016/j.cels.2017.12.004. Epub 2018 Jan 17.

PMID:
29361465
5.

Errata: Functional annotation of chemical libraries across diverse biological processes.

Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C.

Nat Chem Biol. 2017 Nov 21;13(12):1286. doi: 10.1038/nchembio1217-1286a.

PMID:
29161247
6.

Errata: Functional annotation of chemical libraries across diverse biological processes.

Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C.

Nat Chem Biol. 2017 Nov 21;13(12):1286. doi: 10.1038/nchembio1217-1286b.

PMID:
29161244
7.

Functional annotation of chemical libraries across diverse biological processes.

Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C.

Nat Chem Biol. 2017 Sep;13(9):982-993. doi: 10.1038/nchembio.2436. Epub 2017 Jul 24. Erratum in: Nat Chem Biol. 2017 Nov 21;13(12 ):1286. Nat Chem Biol. 2017 Nov 21;13(12 ):1286.

8.

Exploring genetic suppression interactions on a global scale.

van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, van Lieshout N, McNee M, San Luis BJ, Shaeri F, Shuteriqi E, Sun S, Yang L, Youn JY, Yuen M, Costanzo M, Gingras AC, Aloy P, Oostenbrink C, Murray A, Graham TR, Myers CL, Andrews BJ, Roth FP, Boone C.

Science. 2016 Nov 4;354(6312). pii: aag0839.

9.

A global genetic interaction network maps a wiring diagram of cellular function.

Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C.

Science. 2016 Sep 23;353(6306). pii: aaf1420.

10.

Systematic Functional Annotation and Visualization of Biological Networks.

Baryshnikova A.

Cell Syst. 2016 Jun 22;2(6):412-21. doi: 10.1016/j.cels.2016.04.014. Epub 2016 May 26.

11.

Exploratory Analysis of Biological Networks through Visualization, Clustering, and Functional Annotation in Cytoscape.

Baryshnikova A.

Cold Spring Harb Protoc. 2016 Jun 1;2016(6). doi: 10.1101/pdb.prot077644.

PMID:
26988373
12.

trappc11 is required for protein glycosylation in zebrafish and humans.

DeRossi C, Vacaru A, Rafiq R, Cinaroglu A, Imrie D, Nayar S, Baryshnikova A, Milev MP, Stanga D, Kadakia D, Gao N, Chu J, Freeze HH, Lehrman MA, Sacher M, Sadler KC.

Mol Biol Cell. 2016 Apr 15;27(8):1220-34. doi: 10.1091/mbc.E15-08-0557. Epub 2016 Feb 24.

13.

Chromosome-Specific and Global Effects of Aneuploidy in Saccharomyces cerevisiae.

Dodgson SE, Kim S, Costanzo M, Baryshnikova A, Morse DL, Kaiser CA, Boone C, Amon A.

Genetics. 2016 Apr;202(4):1395-409. doi: 10.1534/genetics.115.185660. Epub 2016 Feb 2.

14.

Synthetic genetic array analysis for global mapping of genetic networks in yeast.

Kuzmin E, Sharifpoor S, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C.

Methods Mol Biol. 2014;1205:143-68. doi: 10.1007/978-1-4939-1363-3_10.

PMID:
25213244
15.

ER-associated retrograde SNAREs and the Dsl1 complex mediate an alternative, Sey1p-independent homotypic ER fusion pathway.

Rogers JV, McMahon C, Baryshnikova A, Hughson FM, Rose MD.

Mol Biol Cell. 2014 Nov 1;25(21):3401-12. doi: 10.1091/mbc.E14-07-1220. Epub 2014 Sep 3.

16.

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities.

Vizeacoumar FJ, Arnold R, Vizeacoumar FS, Chandrashekhar M, Buzina A, Young JT, Kwan JH, Sayad A, Mero P, Lawo S, Tanaka H, Brown KR, Baryshnikova A, Mak AB, Fedyshyn Y, Wang Y, Brito GC, Kasimer D, Makhnevych T, Ketela T, Datti A, Babu M, Emili A, Pelletier L, Wrana J, Wainberg Z, Kim PM, Rottapel R, O'Brien CA, Andrews B, Boone C, Moffat J.

Mol Syst Biol. 2013 Oct 8;9:696. doi: 10.1038/msb.2013.54.

17.

Global linkage map connects meiotic centromere function to chromosome size in budding yeast.

Baryshnikova A, VanderSluis B, Costanzo M, Myers CL, Cha RS, Andrews B, Boone C.

G3 (Bethesda). 2013 Oct 3;3(10):1741-51. doi: 10.1534/g3.113.007377.

18.

Genetic interaction networks: toward an understanding of heritability.

Baryshnikova A, Costanzo M, Myers CL, Andrews B, Boone C.

Annu Rev Genomics Hum Genet. 2013;14:111-33. doi: 10.1146/annurev-genom-082509-141730. Epub 2013 Jun 26. Review.

PMID:
23808365
19.

[State of collective immunity against poliomyelitis in some regions of Russia].

Seĭbil' VB, Malyshkina LP, Khishtova SN, Lesnikova MV, Baryshnikova AS, Konopleva TN, Mnozhina EG, Agafonova TV, Vladimirova LA.

Zh Mikrobiol Epidemiol Immunobiol. 2013 Mar-Apr;(2):56-64. Russian.

PMID:
23805674
20.

SGAtools: one-stop analysis and visualization of array-based genetic interaction screens.

Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W591-6. doi: 10.1093/nar/gkt400. Epub 2013 May 15.

21.

[Antiproliferative activity of diclofenac at tumor cell cultures].

Smirnova AV, Lazebnik LB, Trubitsina IE, Tkachenko EV, Varvarina GG, Drozdov VN, Kim VA, Baryshnikova AIu, Sokolova ZA.

Eksp Klin Gastroenterol. 2012;(5):66-9. Russian.

PMID:
23402174
22.

Global gene deletion analysis exploring yeast filamentous growth.

Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin ZY, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzmüller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras AC, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C.

Science. 2012 Sep 14;337(6100):1353-6. doi: 10.1126/science.1224339.

23.

Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae.

Cheng E, Vaisica JA, Ou J, Baryshnikova A, Lu Y, Roth FP, Brown GW.

Genetics. 2012 Sep;192(1):147-60. doi: 10.1534/genetics.112.141051. Epub 2012 Jun 5.

24.

Exploring the yeast acetylome using functional genomics.

Kaluarachchi Duffy S, Friesen H, Baryshnikova A, Lambert JP, Chong YT, Figeys D, Andrews B.

Cell. 2012 May 11;149(4):936-48. doi: 10.1016/j.cell.2012.02.064.

25.

Neighboring-gene effect: a genetic uncertainty principle.

Baryshnikova A, Andrews B.

Nat Methods. 2012 Mar 27;9(4):341, 343. doi: 10.1038/nmeth.1936. No abstract available.

PMID:
22453910
26.

Restoring methicillin-resistant Staphylococcus aureus susceptibility to β-lactam antibiotics.

Tan CM, Therien AG, Lu J, Lee SH, Caron A, Gill CJ, Lebeau-Jacob C, Benton-Perdomo L, Monteiro JM, Pereira PM, Elsen NL, Wu J, Deschamps K, Petcu M, Wong S, Daigneault E, Kramer S, Liang L, Maxwell E, Claveau D, Vaillancourt J, Skorey K, Tam J, Wang H, Meredith TC, Sillaots S, Wang-Jarantow L, Ramtohul Y, Langlois E, Landry F, Reid JC, Parthasarathy G, Sharma S, Baryshnikova A, Lumb KJ, Pinho MG, Soisson SM, Roemer T.

Sci Transl Med. 2012 Mar 21;4(126):126ra35. doi: 10.1126/scitranslmed.3003592.

27.

Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs.

Sharifpoor S, van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC, Youn JY, VanderSluis B, Myers CL, Papp B, Boone C, Andrews BJ.

Genome Res. 2012 Apr;22(4):791-801. doi: 10.1101/gr.129213.111. Epub 2012 Jan 26.

28.

Systematic exploration of synergistic drug pairs.

Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP.

Mol Syst Biol. 2011 Nov 8;7:544. doi: 10.1038/msb.2011.71.

29.

A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis.

Lissina E, Young B, Urbanus ML, Guan XL, Lowenson J, Hoon S, Baryshnikova A, Riezman I, Michaut M, Riezman H, Cowen LE, Wenk MR, Clarke SG, Giaever G, Nislow C.

PLoS Genet. 2011 Oct;7(10):e1002332. doi: 10.1371/journal.pgen.1002332. Epub 2011 Oct 20.

30.

An integrated approach to characterize genetic interaction networks in yeast metabolism.

Szappanos B, Kovács K, Szamecz B, Honti F, Costanzo M, Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, Andrews BJ, Boone C, Oliver SG, Pál C, Papp B.

Nat Genet. 2011 May 29;43(7):656-62. doi: 10.1038/ng.846.

31.

Mms1 and Mms22 stabilize the replisome during replication stress.

Vaisica JA, Baryshnikova A, Costanzo M, Boone C, Brown GW.

Mol Biol Cell. 2011 Jul 1;22(13):2396-408. doi: 10.1091/mbc.E10-10-0848. Epub 2011 May 18.

32.

Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell.

Magtanong L, Ho CH, Barker SL, Jiao W, Baryshnikova A, Bahr S, Smith AM, Heisler LE, Choy JS, Kuzmin E, Andrusiak K, Kobylianski A, Li Z, Costanzo M, Basrai MA, Giaever G, Nislow C, Andrews B, Boone C.

Nat Biotechnol. 2011 May 15;29(6):505-11. doi: 10.1038/nbt.1855.

PMID:
21572441
33.

Systematic exploration of essential yeast gene function with temperature-sensitive mutants.

Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, Vandersluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C.

Nat Biotechnol. 2011 Apr;29(4):361-7. doi: 10.1038/nbt.1832. Epub 2011 Mar 27.

34.

Protein complexes are central in the yeast genetic landscape.

Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD.

PLoS Comput Biol. 2011 Feb;7(2):e1001092. doi: 10.1371/journal.pcbi.1001092. Epub 2011 Feb 24.

35.

Charting the genetic interaction map of a cell.

Costanzo M, Baryshnikova A, Myers CL, Andrews B, Boone C.

Curr Opin Biotechnol. 2011 Feb;22(1):66-74. doi: 10.1016/j.copbio.2010.11.001. Epub 2010 Nov 24. Review.

PMID:
21111604
36.

Combining functional genomics and chemical biology to identify targets of bioactive compounds.

Ho CH, Piotrowski J, Dixon SJ, Baryshnikova A, Costanzo M, Boone C.

Curr Opin Chem Biol. 2011 Feb;15(1):66-78. doi: 10.1016/j.cbpa.2010.10.023. Epub 2010 Nov 17. Review.

PMID:
21093351
37.

Genetic interactions reveal the evolutionary trajectories of duplicate genes.

VanderSluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL.

Mol Syst Biol. 2010 Nov 16;6:429. doi: 10.1038/msb.2010.82.

38.

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.

Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL.

Nat Methods. 2010 Dec;7(12):1017-24. doi: 10.1038/nmeth.1534. Epub 2010 Nov 14.

39.

Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C.

Methods Enzymol. 2010;470:145-79. doi: 10.1016/S0076-6879(10)70007-0. Epub 2010 Mar 1.

PMID:
20946810
40.

The genetic landscape of a cell.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.

Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.

41.

DRYGIN: a database of quantitative genetic interaction networks in yeast.

Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C.

Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. doi: 10.1093/nar/gkp820. Epub 2009 Oct 30.

42.

You too can play with an edge.

Costanzo M, Baryshnikova A, Nislow C, Andrews B, Boone C.

Nat Methods. 2009 Nov;6(11):797-8. doi: 10.1038/nmeth1109-797. No abstract available.

PMID:
19876015
43.

Systematic mapping of genetic interaction networks.

Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C.

Annu Rev Genet. 2009;43:601-25. doi: 10.1146/annurev.genet.39.073003.114751. Review.

PMID:
19712041
44.

Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes.

Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, Toufighi K, Baryshnikova A, Hayles J, Hoe KL, Kim DU, Park HO, Myers CL, Pandey A, Durocher D, Andrews BJ, Boone C.

Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16653-8. doi: 10.1073/pnas.0806261105. Epub 2008 Oct 17.

45.

[Cancer vaccinotherapy: from the experiment to clinical application].

Baryshnikova AIu, Demidov LV, Mikhaĭlova IN, Petenko NN.

Vestn Ross Akad Med Nauk. 2007;(10):46-8. Review. Russian.

PMID:
18050681
46.

The human F-Box DNA helicase FBH1 faces Saccharomyces cerevisiae Srs2 and postreplication repair pathway roles.

Chiolo I, Saponaro M, Baryshnikova A, Kim JH, Seo YS, Liberi G.

Mol Cell Biol. 2007 Nov;27(21):7439-50. Epub 2007 Aug 27.

47.

Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase.

Liberi G, Maffioletti G, Lucca C, Chiolo I, Baryshnikova A, Cotta-Ramusino C, Lopes M, Pellicioli A, Haber JE, Foiani M.

Genes Dev. 2005 Feb 1;19(3):339-50.

48.

[Case of multiple foreign bodies in the respiratory tract].

Tymchak IV, Baryshnikova AV.

Vestn Otorinolaringol. 1976 Nov-Dec;(6):70-1. Russian. No abstract available.

PMID:
1020167
49.

[Cryotherapy of chronic tonsillitis in children].

Fotin AV, Shuster MA, Chireshkin DG, Reidman LB, Baryshnikova AV.

Vestn Otorinolaringol. 1974 Jan-Feb;(1):66-70. Russian. No abstract available.

PMID:
4467383
50.

[Hemodynamic indices in experimental acute pancreatitis].

Baryshnikova AD, Zavetnaia GL.

Patol Fiziol Eksp Ter. 1971 Nov-Dec;15(6):56-9. Russian. No abstract available.

PMID:
5146500

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