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Items: 31

1.

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.

2.

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.

3.

A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling.

Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M.

Cell Syst. 2017 Dec 27;5(6):564-577.e12. doi: 10.1016/j.cels.2017.10.010. Epub 2017 Nov 8.

4.

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.

Cell Rep. 2017 Sep 12;20(11):2735-2748. doi: 10.1016/j.celrep.2017.08.074.

5.

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.

6.

Quantitative and Systems-Based Approaches for Deciphering Bacterial Membrane Interactome and Gene Function.

Deineko V, Kumar A, Vlasblom J, Babu M.

Adv Exp Med Biol. 2015;883:135-54. doi: 10.1007/978-3-319-23603-2_8. Review.

PMID:
26621466
7.

Effects of Nurses' Screening of Spiritual Needs of Hospitalized Patients on Consultation and Perceived Nurses' Support and Patients' Spiritual Well-being.

Vlasblom JP, van der Steen JT, Walton MN, Jochemsen H.

Holist Nurs Pract. 2015 Nov-Dec;29(6):346-56. doi: 10.1097/HNP.0000000000000111.

PMID:
26465624
8.

Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining.

Jessulat M, Malty RH, Nguyen-Tran DH, Deineko V, Aoki H, Vlasblom J, Omidi K, Jin K, Minic Z, Hooshyar M, Burnside D, Samanfar B, Phanse S, Freywald T, Prasad B, Zhang Z, Vizeacoumar F, Krogan NJ, Freywald A, Golshani A, Babu M.

Mol Cell Biol. 2015 Jul;35(14):2448-63. doi: 10.1128/MCB.00007-15. Epub 2015 May 11.

9.

Extracting high confidence protein interactions from affinity purification data: at the crossroads.

Pu S, Vlasblom J, Turinsky A, Marcon E, Phanse S, Trimble SS, Olsen J, Greenblatt J, Emili A, Wodak SJ.

J Proteomics. 2015 Apr 6;118:63-80. doi: 10.1016/j.jprot.2015.03.009. Epub 2015 Mar 14.

PMID:
25782749
10.

Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships.

Jin K, Musso G, Vlasblom J, Jessulat M, Deineko V, Negroni J, Mosca R, Malty R, Nguyen-Tran DH, Aoki H, Minic Z, Freywald T, Phanse S, Xiang Q, Freywald A, Aloy P, Zhang Z, Babu M.

J Proteome Res. 2015 Feb 6;14(2):1220-37. doi: 10.1021/pr501148q. Epub 2015 Jan 20.

PMID:
25546499
11.

Mitochondrial targets for pharmacological intervention in human disease.

Malty RH, Jessulat M, Jin K, Musso G, Vlasblom J, Phanse S, Zhang Z, Babu M.

J Proteome Res. 2015 Jan 2;14(1):5-21. doi: 10.1021/pr500813f. Epub 2014 Dec 12. Review.

12.

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.

13.

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.

14.

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.

Nat Biotechnol. 2014 Mar;32(3):285-290. doi: 10.1038/nbt.2831. Epub 2014 Feb 23.

15.

Exploring mitochondrial system properties of neurodegenerative diseases through interactome mapping.

Vlasblom J, Jin K, Kassir S, Babu M.

J Proteomics. 2014 Apr 4;100:8-24. doi: 10.1016/j.jprot.2013.11.008. Epub 2013 Nov 18. Review.

PMID:
24262152
16.

Protein-protein interaction networks: the puzzling riches.

Wodak SJ, Vlasblom J, Turinsky AL, Pu S.

Curr Opin Struct Biol. 2013 Dec;23(6):941-53. doi: 10.1016/j.sbi.2013.08.002. Epub 2013 Sep 2. Review.

PMID:
24007795
17.

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.

Babu M, Vlasblom J, Pu S, Guo X, Graham C, Bean BD, Burston HE, Vizeacoumar FJ, Snider J, Phanse S, Fong V, Tam YY, Davey M, Hnatshak O, Bajaj N, Chandran S, Punna T, Christopolous C, Wong V, Yu A, Zhong G, Li J, Stagljar I, Conibear E, Wodak SJ, Emili A, Greenblatt JF.

Nature. 2012 Sep 27;489(7417):585-9. doi: 10.1038/nature11354. Epub 2012 Sep 2.

PMID:
22940862
18.

A census of human soluble protein complexes.

Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A.

Cell. 2012 Aug 31;150(5):1068-81. doi: 10.1016/j.cell.2012.08.011.

19.

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.

20.

High-throughput analyses and curation of protein interactions in yeast.

Wodak SJ, Vlasblom J, Pu S.

Methods Mol Biol. 2011;759:381-406. doi: 10.1007/978-1-61779-173-4_22.

PMID:
21863499
21.

OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.

Hao Y, Merkoulovitch A, Vlasblom J, Pu S, Turinsky AL, Roudeva D, Turner B, Greenblatt J, Wodak SJ.

Bioinformatics. 2011 Mar 15;27(6):883-4. doi: 10.1093/bioinformatics/btr035. Epub 2011 Jan 20.

22.

Effects of a spiritual care training for nurses.

Vlasblom JP, van der Steen JT, Knol DL, Jochemsen H.

Nurse Educ Today. 2011 Nov;31(8):790-6. doi: 10.1016/j.nedt.2010.11.010. Epub 2010 Dec 10.

PMID:
21146259
23.

Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.

Pu S, Turinsky AL, Vlasblom J, On T, Xiong X, Emili A, Zhang Z, Greenblatt J, Parkinson J, Wodak SJ.

PLoS One. 2010 Nov 29;5(11):e14122. doi: 10.1371/journal.pone.0014122.

24.

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.

Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ.

Database (Oxford). 2010 Oct 12;2010:baq023. doi: 10.1093/database/baq023.

25.

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs.

Vlasblom J, Wodak SJ.

BMC Bioinformatics. 2009 Mar 30;10:99. doi: 10.1186/1471-2105-10-99.

26.

Challenges and rewards of interaction proteomics.

Wodak SJ, Pu S, Vlasblom J, Séraphin B.

Mol Cell Proteomics. 2009 Jan;8(1):3-18. doi: 10.1074/mcp.R800014-MCP200. Epub 2008 Sep 17. Review.

27.

Local coherence in genetic interaction patterns reveals prevalent functional versatility.

Pu S, Ronen K, Vlasblom J, Greenblatt J, Wodak SJ.

Bioinformatics. 2008 Oct 15;24(20):2376-83. doi: 10.1093/bioinformatics/btn440. Epub 2008 Aug 20.

PMID:
18718945
28.

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.

Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ.

Proteomics. 2007 Mar;7(6):944-60.

PMID:
17370254
29.

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.

Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ.

Bioinformatics. 2006 Sep 1;22(17):2178-9.

PMID:
16921162
30.

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF.

Nature. 2006 Mar 30;440(7084):637-43. Epub 2006 Mar 22.

PMID:
16554755
31.

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