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Items: 1 to 20 of 34

1.

Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut.

Leiserson MD, Tatar D, Cowen LJ, Hescott BJ.

J Comput Biol. 2011 Nov;18(11):1399-409. doi: 10.1089/cmb.2011.0191. Epub 2011 Sep 1.

2.

Membrane-trafficking sorting hubs: cooperation between PI4P and small GTPases at the trans-Golgi network.

Santiago-Tirado FH, Bretscher A.

Trends Cell Biol. 2011 Sep;21(9):515-25. doi: 10.1016/j.tcb.2011.05.005. Epub 2011 Jul 19. Review.

3.

Putting genetic interactions in context through a global modular decomposition.

Bellay J, Atluri G, Sing TL, Toufighi K, Costanzo M, Ribeiro PS, Pandey G, Baller J, VanderSluis B, Michaut M, Han S, Kim P, Brown GW, Andrews BJ, Boone C, Kumar V, Myers CL.

Genome Res. 2011 Aug;21(8):1375-87. doi: 10.1101/gr.117176.110. Epub 2011 Jun 29.

4.

Extracting between-pathway models from E-MAP interactions using expected graph compression.

Kelley DR, Kingsford C.

J Comput Biol. 2011 Mar;18(3):379-90. doi: 10.1089/cmb.2010.0268.

PMID:
21385041
5.

Identification of the first COG-CDG patient of Indian origin.

Ng BG, Sharma V, Sun L, Loh E, Hong W, Tay SK, Freeze HH.

Mol Genet Metab. 2011 Mar;102(3):364-7. doi: 10.1016/j.ymgme.2010.11.161. Epub 2010 Nov 24.

6.

A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.

Aguilar PS, Fröhlich F, Rehman M, Shales M, Ulitsky I, Olivera-Couto A, Braberg H, Shamir R, Walter P, Mann M, Ejsing CS, Krogan NJ, Walther TC.

Nat Struct Mol Biol. 2010 Jul;17(7):901-8. doi: 10.1038/nsmb.1829. Epub 2010 Jun 6.

7.

Evaluating between-pathway models with expression data.

Hescott BJ, Leiserson MD, Cowen LJ, Slonim DK.

J Comput Biol. 2010 Mar;17(3):477-87. doi: 10.1089/cmb.2009.0178.

8.

The genetic landscape of a cell.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.

Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.

9.

Next generation software for functional trend analysis.

Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP.

Bioinformatics. 2009 Nov 15;25(22):3043-4. doi: 10.1093/bioinformatics/btp498. Epub 2009 Aug 28.

10.

The COG complex, Rab6 and COPI define a novel Golgi retrograde trafficking pathway that is exploited by SubAB toxin.

Smith RD, Willett R, Kudlyk T, Pokrovskaya I, Paton AW, Paton JC, Lupashin VV.

Traffic. 2009 Oct;10(10):1502-17. doi: 10.1111/j.1600-0854.2009.00965.x. Epub 2009 Jul 21.

11.

Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.

Brady A, Maxwell K, Daniels N, Cowen LJ.

PLoS One. 2009;4(4):e5364. doi: 10.1371/journal.pone.0005364. Epub 2009 Apr 28.

12.

Multicopy suppressor analysis of thermosensitive YIP1 alleles implicates GOT1 in transport from the ER.

Lorente-Rodríguez A, Heidtman M, Barlowe C.

J Cell Sci. 2009 May 15;122(Pt 10):1540-50. doi: 10.1242/jcs.042457. Epub 2009 Apr 21.

13.

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions.

Ulitsky I, Shlomi T, Kupiec M, Shamir R.

Mol Syst Biol. 2008;4:209. doi: 10.1038/msb.2008.42. Epub 2008 Jul 15.

14.

Functional maps of protein complexes from quantitative genetic interaction data.

Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T.

PLoS Comput Biol. 2008 Apr 18;4(4):e1000065. doi: 10.1371/journal.pcbi.1000065.

15.

Mapping genetically compensatory pathways from synthetic lethal interactions in yeast.

Ma X, Tarone AM, Li W.

PLoS One. 2008 Apr 9;3(4):e1922. doi: 10.1371/journal.pone.0001922.

16.
17.

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ.

Nature. 2007 Apr 12;446(7137):806-10. Epub 2007 Feb 21.

PMID:
17314980
18.

COG-7-deficient Human Fibroblasts Exhibit Altered Recycling of Golgi Proteins.

Steet R, Kornfeld S.

Mol Biol Cell. 2006 May;17(5):2312-21. Epub 2006 Mar 1.

19.

Arf1p, Chs5p and the ChAPs are required for export of specialized cargo from the Golgi.

Trautwein M, Schindler C, Gauss R, Dengjel J, Hartmann E, Spang A.

EMBO J. 2006 Mar 8;25(5):943-54. Epub 2006 Feb 23.

20.

A DNA integrity network in the yeast Saccharomyces cerevisiae.

Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD.

Cell. 2006 Mar 10;124(5):1069-81. Epub 2006 Feb 16. Erratum in: Cell. 2013 May 23;153(5):1165.

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