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Results: 1 to 20 of 131

1.

Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress.

Shaughnessy DT, McAllister K, Worth L, Haugen AC, Meyer JN, Domann FE, Van Houten B, Mostoslavsky R, Bultman SJ, Baccarelli AA, Begley TJ, Sobol R, Hirschey MD, Ideker T, Santos JH, Copeland WC, Tice RR, Balshaw DM, Tyson FL.

Environ Health Perspect. 2014 Aug 15. [Epub ahead of print] Review.

PMID:
25127496
[PubMed - as supplied by publisher]
2.

Matrix-Metalloproteinases in Head and Neck Carcinoma-Cancer Genome Atlas Analysis and Fluorescence Imaging in Mice.

Hauff SJ, Raju SC, Orosco RK, Gross AM, Diaz-Perez JA, Savariar E, Nashi N, Hasselman J, Whitney M, Myers JN, Lippman SM, Tsien RY, Ideker T, Nguyen QT.

Otolaryngol Head Neck Surg. 2014 Aug 4. pii: 0194599814545083. [Epub ahead of print]

PMID:
25091190
[PubMed - as supplied by publisher]
3.

Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.

Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T.

Nat Genet. 2014 Aug 3. doi: 10.1038/ng.3051. [Epub ahead of print]

PMID:
25086664
[PubMed - as supplied by publisher]
4.

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]
5.

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
6.

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
7.

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
8.

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]
9.

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]
10.

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
11.

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 - indexed for MEDLINE]
Free Article
12.

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
13.

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. Review.

PMID:
24238873
[PubMed - indexed for MEDLINE]
Free Article
14.

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
15.

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
16.

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
17.

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]
18.

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
19.

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. 2013 Jun 11;2:e00675. doi: 10.7554/eLife.00675.

PMID:
23795294
[PubMed]
Free PMC Article
20.

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

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