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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. Vlasblom J, et al. Among authors: kumar a. Bioinformatics. 2015 Feb 1;31(3):306-10. doi: 10.1093/bioinformatics/btu671. Epub 2014 Oct 13. Bioinformatics. 2015. PMID: 25316676 Free PMC article.
The binary protein-protein interaction landscape of Escherichia coli.
Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P. Rajagopala SV, et al. Among authors: kumar a. Nat Biotechnol. 2014 Mar;32(3):285-290. doi: 10.1038/nbt.2831. Epub 2014 Feb 23. Nat Biotechnol. 2014. PMID: 24561554 Free PMC article.
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. Babu M, et al. Among authors: kumar a. PLoS Genet. 2014 Feb 20;10(2):e1004120. doi: 10.1371/journal.pgen.1004120. eCollection 2014 Feb. PLoS Genet. 2014. PMID: 24586182 Free PMC article.
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. Kumar A, et al. Cell Rep. 2016 Jan 26;14(3):648-661. doi: 10.1016/j.celrep.2015.12.060. Epub 2016 Jan 8. Cell Rep. 2016. PMID: 26774489 Free article.
Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping.
Rizzolo K, Huen J, Kumar A, Phanse S, Vlasblom J, Kakihara Y, Zeineddine HA, Minic Z, Snider J, Wang W, Pons C, Seraphim TV, Boczek EE, Alberti S, Costanzo M, Myers CL, Stagljar I, Boone C, Babu M, Houry WA. Rizzolo K, et al. Among authors: kumar a. Cell Rep. 2017 Sep 12;20(11):2735-2748. doi: 10.1016/j.celrep.2017.08.074. Cell Rep. 2017. PMID: 28903051 Free article.
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. Babu M, et al. Among authors: kumar a. Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27. Nat Biotechnol. 2018. PMID: 29176613 Free PMC article.
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