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Items: 16

1.

A reference set of curated biomedical data and metadata from clinical case reports.

Caufield JH, Zhou Y, Garlid AO, Setty SP, Liem DA, Cao Q, Lee JM, Murali S, Spendlove S, Wang W, Zhang L, Sun Y, Bui A, Hermjakob H, Watson KE, Ping P.

Sci Data. 2018 Nov 20;5:180258. doi: 10.1038/sdata.2018.258.

2.

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts.

Caufield JH, Liem DA, Garlid AO, Zhou Y, Watson K, Bui AAT, Wang W, Ping P.

J Vis Exp. 2018 Sep 20;(139). doi: 10.3791/58392.

3.

Making the Right Choice: Critical Parameters of the Y2H Systems.

Mehla J, Caufield JH, Uetz P.

Methods Mol Biol. 2018;1794:17-28. doi: 10.1007/978-1-4939-7871-7_2.

PMID:
29855948
4.

Phrase mining of textual data to analyze extracellular matrix protein patterns across cardiovascular disease.

Liem DA, Murali S, Sigdel D, Shi Y, Wang X, Shen J, Choi H, Caufield JH, Wang W, Ping P, Han J.

Am J Physiol Heart Circ Physiol. 2018 Oct 1;315(4):H910-H924. doi: 10.1152/ajpheart.00175.2018. Epub 2018 May 18.

PMID:
29775406
5.

Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori.

Wuchty S, Müller SA, Caufield JH, Häuser R, Aloy P, Kalkhof S, Uetz P.

Mol Cell Proteomics. 2018 May;17(5):961-973. doi: 10.1074/mcp.RA117.000474. Epub 2018 Feb 1.

6.

Virus-host protein-protein interactions of mycobacteriophage Giles.

Mehla J, Dedrick RM, Caufield JH, Wagemans J, Sakhawalkar N, Johnson A, Hatfull GF, Uetz P.

Sci Rep. 2017 Nov 28;7(1):16514. doi: 10.1038/s41598-017-16303-7.

7.

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.

8.

Bacterial protein meta-interactomes predict cross-species interactions and protein function.

Caufield JH, Wimble C, Shary S, Wuchty S, Uetz P.

BMC Bioinformatics. 2017 Mar 16;18(1):171. doi: 10.1186/s12859-017-1585-0.

9.

A Comparison of Two-Hybrid Approaches for Detecting Protein-Protein Interactions.

Mehla J, Caufield JH, Sakhawalkar N, Uetz P.

Methods Enzymol. 2017;586:333-358. doi: 10.1016/bs.mie.2016.10.020. Epub 2017 Jan 5.

10.

The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins.

Mehla J, Dedrick RM, Caufield JH, Siefring R, Mair M, Johnson A, Hatfull GF, Uetz P.

J Bacteriol. 2015 Aug 1;197(15):2508-16. doi: 10.1128/JB.00164-15. Epub 2015 May 18.

11.

The yeast two-hybrid system: a tool for mapping protein-protein interactions.

Mehla J, Caufield JH, Uetz P.

Cold Spring Harb Protoc. 2015 May 1;2015(5):425-30. doi: 10.1101/pdb.top083345.

PMID:
25934943
12.

Mapping protein-protein interactions using yeast two-hybrid assays.

Mehla J, Caufield JH, Uetz P.

Cold Spring Harb Protoc. 2015 May 1;2015(5):442-52. doi: 10.1101/pdb.prot086157.

PMID:
25934935
13.

Protein complexes in bacteria.

Caufield JH, Abreu M, Wimble C, Uetz P.

PLoS Comput Biol. 2015 Feb 27;11(2):e1004107. doi: 10.1371/journal.pcbi.1004107. eCollection 2015 Feb.

14.

Specific N-terminal cleavage of ribosomal protein L27 in Staphylococcus aureus and related bacteria.

Wall EA, Caufield JH, Lyons CE, Manning KA, Dokland T, Christie GE.

Mol Microbiol. 2015 Jan;95(2):258-69. doi: 10.1111/mmi.12862. Epub 2014 Dec 8.

15.

A comparison and optimization of yeast two-hybrid systems.

Caufield JH, Sakhawalkar N, Uetz P.

Methods. 2012 Dec;58(4):317-24. doi: 10.1016/j.ymeth.2012.12.001. Epub 2012 Dec 8.

16.

Studying protein complexes by the yeast two-hybrid system.

Rajagopala SV, Sikorski P, Caufield JH, Tovchigrechko A, Uetz P.

Methods. 2012 Dec;58(4):392-9. doi: 10.1016/j.ymeth.2012.07.015. Epub 2012 Jul 24.

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