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Items: 29

1.

Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action.

Kintses B, Jangir PK, Fekete G, Számel M, Méhi O, Spohn R, Daruka L, Martins A, Hosseinnia A, Gagarinova A, Kim S, Phanse S, Csörgő B, Györkei Á, Ari E, Lázár V, Nagy I, Babu M, Pál C, Papp B.

Nat Commun. 2019 Dec 16;10(1):5731. doi: 10.1038/s41467-019-13618-z.

2.

Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis.

Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M.

iScience. 2019 Sep 27;19:1114-1132. doi: 10.1016/j.isci.2019.08.057. Epub 2019 Sep 4.

3.

A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli.

Kumar A, Hosseinnia A, Gagarinova A, Phanse S, Kim S, Aly KA, Zilles S, Babu M.

Bioinformatics. 2020 Feb 1;36(3):880-889. doi: 10.1093/bioinformatics/btz673.

PMID:
31504172
4.

Legionella pneumophila effector Lem4 is a membrane-associated protein tyrosine phosphatase.

Beyrakhova K, Li L, Xu C, Gagarinova A, Cygler M.

J Biol Chem. 2018 Aug 24;293(34):13044-13058. doi: 10.1074/jbc.RA118.003845. Epub 2018 Jul 5.

5.

Global landscape of cell envelope protein complexes in Escherichia coli.

Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A.

Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27.

6.

Insights from protein-protein interaction studies on bacterial pathogenesis.

Gagarinova A, Phanse S, Cygler M, Babu M.

Expert Rev Proteomics. 2017 Sep;14(9):779-797. doi: 10.1080/14789450.2017.1365603. Epub 2017 Sep 8. Review.

PMID:
28786313
7.

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery.

Gagarinova A, Stewart G, Samanfar B, Phanse S, White CA, Aoki H, Deineko V, Beloglazova N, Yakunin AF, Golshani A, Brown ED, Babu M, Emili A.

Cell Rep. 2016 Oct 11;17(3):904-916. doi: 10.1016/j.celrep.2016.09.040.

8.

Novel Interactome of Saccharomyces cerevisiae Myosin Type II Identified by a Modified Integrated Membrane Yeast Two-Hybrid (iMYTH) Screen.

Santiago E, Akamine P, Snider J, Wong V, Jessulat M, Deineko V, Gagarinova A, Aoki H, Minic Z, Phanse S, San Antonio A, Cubano LA, Rymond BC, Babu M, Stagljar I, Rodriguez-Medina JR.

G3 (Bethesda). 2016 May 3;6(5):1469-74. doi: 10.1534/g3.115.026609.

9.

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M.

Cell Rep. 2016 Jan 26;14(3):648-661. doi: 10.1016/j.celrep.2015.12.060. Epub 2016 Jan 8.

10.

Investigating Bacterial Protein Synthesis Using Systems Biology Approaches.

Gagarinova A, Emili A.

Adv Exp Med Biol. 2015;883:21-40. doi: 10.1007/978-3-319-23603-2_2. Review.

PMID:
26621460
11.

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli.

Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M.

Bioinformatics. 2015 Feb 1;31(3):306-10. doi: 10.1093/bioinformatics/btu671. Epub 2014 Oct 13.

12.

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A.

PLoS Genet. 2014 Feb 20;10(2):e1004120. doi: 10.1371/journal.pgen.1004120. eCollection 2014 Feb.

13.

Investigating the Ustilago maydis/Zea mays pathosystem: transcriptional responses and novel functional aspects of a fungal calcineurin regulatory B subunit.

Donaldson ME, Meng S, Gagarinova A, Babu M, Lambie SC, Swiadek AA, Saville BJ.

Fungal Genet Biol. 2013 Sep-Oct;58-59:91-104. doi: 10.1016/j.fgb.2013.08.006. Epub 2013 Aug 22.

PMID:
23973481
14.

Mapping bacterial functional networks and pathways in Escherichia Coli using synthetic genetic arrays.

Gagarinova A, Babu M, Greenblatt J, Emili A.

J Vis Exp. 2012 Nov 12;(69). pii: 4056. doi: 10.3791/4056.

15.

Genome-scale genetic manipulation methods for exploring bacterial molecular biology.

Gagarinova A, Emili A.

Mol Biosyst. 2012 Jun;8(6):1626-38. doi: 10.1039/c2mb25040c. Epub 2012 Apr 19. Review.

PMID:
22517266
16.

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.

Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A.

PLoS Genet. 2011 Nov;7(11):e1002377. doi: 10.1371/journal.pgen.1002377. Epub 2011 Nov 17.

17.

Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.

Babu M, Gagarinova A, Emili A.

Methods Mol Biol. 2011;781:99-126. doi: 10.1007/978-1-61779-276-2_7.

PMID:
21877280
18.

Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.

Babu M, Gagarinova A, Greenblatt J, Emili A.

Methods Mol Biol. 2011;765:125-53. doi: 10.1007/978-1-61779-197-0_9.

PMID:
21815091
19.

Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation.

Babu M, Aoki H, Chowdhury WQ, Gagarinova A, Graham C, Phanse S, Laliberte B, Sunba N, Jessulat M, Golshani A, Emili A, Greenblatt JF, Ganoza MC.

PLoS One. 2011 Apr 27;6(4):e18510. doi: 10.1371/journal.pone.0018510.

20.

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.

Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF.

Mol Microbiol. 2011 Jan;79(2):484-502. doi: 10.1111/j.1365-2958.2010.07465.x. Epub 2010 Dec 7.

21.

Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes.

Gagarinova AG, Babu M, Strömvik MV, Wang A.

Virol J. 2008 Nov 26;5:143. doi: 10.1186/1743-422X-5-143.

22.

Identification and molecular characterization of two naturally occurring Soybean mosaic virus isolates that are closely related but differ in their ability to overcome Rsv4 resistance.

Gagarinova AG, Babu M, Poysa V, Hill JH, Wang A.

Virus Res. 2008 Dec;138(1-2):50-6. doi: 10.1016/j.virusres.2008.08.010. Epub 2008 Sep 30.

PMID:
18793685
23.

eSGA: E. coli synthetic genetic array analysis.

Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, Emili A.

Nat Methods. 2008 Sep;5(9):789-95. doi: 10.1038/nmeth.1239.

PMID:
18677321
24.

Association of the transcriptional response of soybean plants with soybean mosaic virus systemic infection.

Babu M, Gagarinova AG, Brandle JE, Wang A.

J Gen Virol. 2008 Apr;89(Pt 4):1069-1080. doi: 10.1099/vir.0.83531-0.

PMID:
18343851
25.

[A method of preparing antibody erythrocytic diagnostic means for detecting viruses].

Zhumatov KKh, Bagasheva SS, Kiriushchenko TV, Saiatov MKh, Karimov SK, Gagarinova AV.

Vopr Virusol. 1994 Sep-Oct;39(5):235-8. Russian.

PMID:
7716912
26.

[Blood protein spectrum during hemodialysis of kidney transplant patients].

Gagarinova AV, Chernyshov VP.

Vrach Delo. 1981 Apr;(4):65-7. Russian. No abstract available.

PMID:
7023047
27.

[Serum proteins in chronic kidney failure patients under treatment with programmed dialysis].

Gagarinova AV, Chernyshov VP.

Vrach Delo. 1980 Oct;(10):87-91. Russian. No abstract available.

PMID:
7434715
28.

[Blood serum immunoglobulin level in chronic renal insufficiency treated by hemodialysis].

Gagarinova AV, Chernyshov VP.

Urol Nefrol (Mosk). 1980 Jan-Feb;(1):58-60. Russian. No abstract available.

PMID:
7368442
29.

[Effect of hemodialysis on the serum free amino acid level in patients with chronic renal failure].

Gagarinova AV, Levchenko IV.

Vrach Delo. 1977 Dec;(12):46-9. Russian. No abstract available.

PMID:
605593

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