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Items: 18

1.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P; IMEx Consortium contributing authors.

Nat Commun. 2019 Jan 2;10(1):10. doi: 10.1038/s41467-018-07709-6.

2.

A resource of variant effect predictions of single nucleotide variants in model organisms.

Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P.

Mol Syst Biol. 2018 Dec 20;14(12):e8430. doi: 10.15252/msb.20188430.

3.

Phenotype inference in an Escherichia coli strain panel.

Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P.

Elife. 2017 Dec 27;6. pii: e31035. doi: 10.7554/eLife.31035.

4.

ggseqlogo: a versatile R package for drawing sequence logos.

Wagih O.

Bioinformatics. 2017 Nov 15;33(22):3645-3647. doi: 10.1093/bioinformatics/btx469.

PMID:
29036507
5.

Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.

Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y.

J Proteome Res. 2017 Apr 7;16(4):1825-1830. doi: 10.1021/acs.jproteome.7b00087. Epub 2017 Mar 15.

PMID:
28287266
6.

Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii.

Chen Y, Farrer RA, Giamberardino C, Sakthikumar S, Jones A, Yang T, Tenor JL, Wagih O, Van Wyk M, Govender NP, Mitchell TG, Litvintseva AP, Cuomo CA, Perfect JR.

MBio. 2017 Mar 7;8(2). pii: e00166-17. doi: 10.1128/mBio.00166-17.

7.

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J.

PLoS Comput Biol. 2017 Jan 10;13(1):e1005297. doi: 10.1371/journal.pcbi.1005297. eCollection 2017 Jan.

8.

Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.

Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP.

Genome Biol. 2016 Mar 8;17:45. doi: 10.1186/s13059-016-0900-9.

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.

Genetic Interaction Scoring Procedure for Bacterial Species.

Wagih O, Parts L.

Adv Exp Med Biol. 2015;883:169-85. doi: 10.1007/978-3-319-23603-2_10. Review.

PMID:
26621468
11.

Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.

Wagih O, Sugiyama N, Ishihama Y, Beltrao P.

Mol Cell Proteomics. 2016 Jan;15(1):236-45. doi: 10.1074/mcp.M115.052357. Epub 2015 Nov 16.

12.

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004362. doi: 10.1371/journal.pcbi.1004362. eCollection 2015 Aug.

13.

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Wagih O, Reimand J, Bader GD.

Nat Methods. 2015 Jun;12(6):531-3. doi: 10.1038/nmeth.3396. Epub 2015 May 4.

PMID:
25938373
14.

Evolutionary constraint and disease associations of post-translational modification sites in human genomes.

Reimand J, Wagih O, Bader GD.

PLoS Genet. 2015 Jan 22;11(1):e1004919. doi: 10.1371/journal.pgen.1004919. eCollection 2015 Jan.

15.

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.

16.

gitter: a robust and accurate method for quantification of colony sizes from plate images.

Wagih O, Parts L.

G3 (Bethesda). 2014 Mar 20;4(3):547-52. doi: 10.1534/g3.113.009431.

17.

The mutational landscape of phosphorylation signaling in cancer.

Reimand J, Wagih O, Bader GD.

Sci Rep. 2013 Oct 2;3:2651. doi: 10.1038/srep02651.

18.

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.

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