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Results: 1 to 20 of 128

1.

Proteome-wide remodeling of protein location and function by stress.

Lee K, Sung MK, Kim J, Kim K, Byun J, Paik H, Kim B, Huh WK, Ideker T.

Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):E3157-66. doi: 10.1073/pnas.1318881111. Epub 2014 Jul 15.

PMID:
25028499
[PubMed - in process]
2.

Inferring gene ontologies from pairwise similarity data.

Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T.

Bioinformatics. 2014 Jun 15;30(12):i34-42. doi: 10.1093/bioinformatics/btu282.

PMID:
24932003
[PubMed - in process]
Free PMC Article
3.

An integrated map of HIV-human protein complexes that facilitate viral infection.

Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T.

PLoS One. 2014 May 9;9(5):e96687. doi: 10.1371/journal.pone.0096687. eCollection 2014.

PMID:
24817247
[PubMed - in process]
Free PMC Article
4.

Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo.

Joshi S, Singh AR, Zulcic M, Bao L, Messer K, Ideker T, Dutkowski J, Durden DL.

PLoS One. 2014 Apr 25;9(4):e95893. doi: 10.1371/journal.pone.0095893. eCollection 2014.

PMID:
24770346
[PubMed - in process]
Free PMC Article
5.

Siri of the cell: what biology could learn from the iPhone.

Carvunis AR, Ideker T.

Cell. 2014 Apr 24;157(3):534-8. doi: 10.1016/j.cell.2014.03.009.

PMID:
24766803
[PubMed - indexed for MEDLINE]
6.

Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders.

Novarino G, Fenstermaker AG, Zaki MS, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel-Salam GM, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben-Omran T, Mojahedi F, Mahmoud IG, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al-Allawi N, Bindu PS, Azam M, Gunel M, Caglayan A, Bilguvar K, Tolun A, Issa MY, Schroth J, Spencer EG, Rosti RO, Akizu N, Vaux KK, Johansen A, Koh AA, Megahed H, Durr A, Brice A, Stevanin G, Gabriel SB, Ideker T, Gleeson JG.

Science. 2014 Jan 31;343(6170):506-11. doi: 10.1126/science.1247363.

PMID:
24482476
[PubMed - indexed for MEDLINE]
7.

Development of ultra-high-density screening tools for microbial "omics".

Bean GJ, Jaeger PA, Bahr S, Ideker T.

PLoS One. 2014 Jan 21;9(1):e85177. doi: 10.1371/journal.pone.0085177. eCollection 2014.

PMID:
24465499
[PubMed - in process]
Free PMC Article
8.

A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.

Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T.

Cell Rep. 2013 Dec 26;5(6):1714-24. doi: 10.1016/j.celrep.2013.11.035. Epub 2013 Dec 19.

PMID:
24360959
[PubMed - in process]
Free Article
9.

NeXO Web: the NeXO ontology database and visualization platform.

Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1269-74. doi: 10.1093/nar/gkt1192. Epub 2013 Nov 23.

PMID:
24271398
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Genotype to phenotype via network analysis.

Carter H, Hofree M, Ideker T.

Curr Opin Genet Dev. 2013 Dec;23(6):611-21. doi: 10.1016/j.gde.2013.10.003. Epub 2013 Nov 14.

PMID:
24238873
[PubMed - in process]
Free Article
11.

Using functional signature ontology (FUSION) to identify mechanisms of action for natural products.

Potts MB, Kim HS, Fisher KW, Hu Y, Carrasco YP, Bulut GB, Ou YH, Herrera-Herrera ML, Cubillos F, Mendiratta S, Xiao G, Hofree M, Ideker T, Xie Y, Huang LJ, Lewis RE, MacMillan JB, White MA.

Sci Signal. 2013 Oct 15;6(297):ra90. doi: 10.1126/scisignal.2004657.

PMID:
24129700
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Integrative approaches for finding modular structure in biological networks.

Mitra K, Carvunis AR, Ramesh SK, Ideker T.

Nat Rev Genet. 2013 Oct;14(10):719-32. doi: 10.1038/nrg3552. Review.

PMID:
24045689
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Network-based stratification of tumor mutations.

Hofree M, Shen JP, Carter H, Gross A, Ideker T.

Nat Methods. 2013 Nov;10(11):1108-15. doi: 10.1038/nmeth.2651. Epub 2013 Sep 15.

PMID:
24037242
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease.

Sharma K, Karl B, Mathew AV, Gangoiti JA, Wassel CL, Saito R, Pu M, Sharma S, You YH, Wang L, Diamond-Stanic M, Lindenmeyer MT, Forsblom C, Wu W, Ix JH, Ideker T, Kopp JB, Nigam SK, Cohen CD, Groop PH, Barshop BA, Natarajan L, Nyhan WL, Naviaux RK.

J Am Soc Nephrol. 2013 Nov;24(11):1901-12. doi: 10.1681/ASN.2013020126. Epub 2013 Oct 10.

PMID:
23949796
[PubMed - indexed for MEDLINE]
15.

Checkpoint kinases regulate a global network of transcription factors in response to DNA damage.

Jaehnig EJ, Kuo D, Hombauer H, Ideker TG, Kolodner RD.

Cell Rep. 2013 Jul 11;4(1):174-88. doi: 10.1016/j.celrep.2013.05.041. Epub 2013 Jun 27.

PMID:
23810556
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis.

Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR.

Elife (Cambridge). 2013 Jun 11;2:e00675. doi: 10.7554/eLife.00675.

PMID:
23795294
[PubMed]
Free PMC Article
17.

Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge.

Fukuyama H, Verdier Y, Guan Y, Makino-Okamura C, Shilova V, Liu X, Maksoud E, Matsubayashi J, Haddad I, Spirohn K, Ono K, Hetru C, Rossier J, Ideker T, Boutros M, Vinh J, Hoffmann JA.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10717-22. doi: 10.1073/pnas.1304380110. Epub 2013 Jun 7.

PMID:
23749869
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Proteome-wide discovery of mislocated proteins in cancer.

Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, Paek SH, Kim H, Shin HY, Ideker T, Lee B.

Genome Res. 2013 Aug;23(8):1283-94. doi: 10.1101/gr.155499.113. Epub 2013 May 14.

PMID:
23674306
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA.

PLoS Comput Biol. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9.

PMID:
23671412
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer.

Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, Wu SL, Hancock WS.

J Proteome Res. 2013 Jun 7;12(6):2805-17. doi: 10.1021/pr4001527. Epub 2013 May 22.

PMID:
23647160
[PubMed - indexed for MEDLINE]

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