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Items: 18

1.

The Modular Organization of Protein Interactions in Escherichia coli.

Peregrín-Alvarez JM, Xiong X, Su C, Parkinson J.

PLoS Comput Biol. 2009 Oct;5(10):e1000523. doi: 10.1371/journal.pcbi.1000523. Epub 2009 Oct 2.

2.

The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti.

Rodriguez-Llorente I, Caviedes MA, Dary M, Palomares AJ, Cánovas FM, Peregrín-Alvarez JM.

BMC Syst Biol. 2009 Jun 16;3:63. doi: 10.1186/1752-0509-3-63.

3.

The conservation and evolutionary modularity of metabolism.

Peregrín-Alvarez JM, Sanford C, Parkinson J.

Genome Biol. 2009;10(6):R63. doi: 10.1186/gb-2009-10-6-r63. Epub 2009 Jun 12.

4.

The origins of apicomplexan sequence innovation.

Wasmuth J, Daub J, Peregrín-Alvarez JM, Finney CA, Parkinson J.

Genome Res. 2009 Jul;19(7):1202-13. doi: 10.1101/gr.083386.108. Epub 2009 Apr 10.

5.

Phylogenomic analysis of EST datasets.

Peregrín-Alvarez JM, Parkinson J.

Methods Mol Biol. 2009;533:257-76. doi: 10.1007/978-1-60327-136-3_12.

PMID:
19277568
6.

Phylogenetic profiling.

Date SV, Peregrín-Alvarez JM.

Methods Mol Biol. 2008;453:201-16. doi: 10.1007/978-1-60327-429-6_9.

PMID:
18712304
7.

Inferring ancestral protein interaction networks.

Peregrín-Alvarez JM.

Methods Mol Biol. 2008;452:417-30. doi: 10.1007/978-1-60327-159-2_19. Review.

PMID:
18566775
8.

The comparative genomics of protein interactions.

Peregrín-Alvarez JM, Ouzounis CA.

Genome Inform. 2007;19:131-41.

PMID:
18546511
9.

The global landscape of sequence diversity.

Peregrín-Alvarez JM, Parkinson J.

Genome Biol. 2007;8(11):R238.

10.

Bacteriome.org--an integrated protein interaction database for E. coli.

Su C, Peregrin-Alvarez JM, Butland G, Phanse S, Fong V, Emili A, Parkinson J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D632-6. Epub 2007 Oct 16.

11.

Draft genome of the filarial nematode parasite Brugia malayi.

Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL.

Science. 2007 Sep 21;317(5845):1756-60.

12.

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
13.

CoGenT++: an extensive and extensible data environment for computational genomics.

Goldovsky L, Janssen P, Ahrén D, Audit B, Cases I, Darzentas N, Enright AJ, López-Bigas N, Peregrin-Alvarez JM, Smith M, Tsoka S, Kunin V, Ouzounis CA.

Bioinformatics. 2005 Oct 1;21(19):3806-10.

PMID:
16216832
14.

Interaction network containing conserved and essential protein complexes in Escherichia coli.

Butland G, Peregrín-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A.

Nature. 2005 Feb 3;433(7025):531-7.

PMID:
15690043
15.

PartiGeneDB--collating partial genomes.

Peregrín-Alvarez JM, Yam A, Sivakumar G, Parkinson J.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D303-7.

16.

An exponential core in the heart of the yeast protein interaction network.

Pereira-Leal JB, Audit B, Peregrin-Alvarez JM, Ouzounis CA.

Mol Biol Evol. 2005 Mar;22(3):421-5. Epub 2004 Oct 20. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1157.

PMID:
15496552
17.

Beyond 100 genomes.

Janssen P, Audit B, Cases I, Darzentas N, Goldovsky L, Kunin V, Lopez-Bigas N, Peregrin-Alvarez JM, Pereira-Leal JB, Tsoka S, Ouzounis CA.

Genome Biol. 2003;4(5):402. Epub 2003 Apr 28.

18.

The phylogenetic extent of metabolic enzymes and pathways.

Peregrin-Alvarez JM, Tsoka S, Ouzounis CA.

Genome Res. 2003 Mar;13(3):422-7.

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