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Results: 1 to 20 of 125

1.

GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks.

Law B, Bader GD.

Sci Rep. 2015 Jul 13;5:12074. doi: 10.1038/srep12074.

2.

Inferring interaction type in gene regulatory networks using co-expression data.

Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Goliaei B, Bader GD.

Algorithms Mol Biol. 2015 Jul 8;10:23. doi: 10.1186/s13015-015-0054-4. eCollection 2015.

3.

Cardioprotective Signature of Short-Term Caloric Restriction.

Noyan H, El-Mounayri O, Isserlin R, Arab S, Momen A, Cheng HS, Wu J, Afroze T, Li RK, Fish JE, Bader GD, Husain M.

PLoS One. 2015 Jun 22;10(6):e0130658. doi: 10.1371/journal.pone.0130658. eCollection 2015.

4.

Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia.

Cole A, Wang Z, Coyaud E, Voisin V, Gronda M, Jitkova Y, Mattson R, Hurren R, Babovic S, Maclean N, Restall I, Wang X, Jeyaraju DV, Sukhai MA, Prabha S, Bashir S, Ramakrishnan A, Leung E, Qia YH, Zhang N, Combes KR, Ketela T, Lin F, Houry WA, Aman A, Al-Awar R, Zheng W, Wienholds E, Xu CJ, Dick J, Wang JC, Moffat J, Minden MD, Eaves CJ, Bader GD, Hao Z, Kornblau SM, Raught B, Schimmer AD.

Cancer Cell. 2015 Jun 8;27(6):864-76. doi: 10.1016/j.ccell.2015.05.004.

PMID:
26058080
5.

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Wagih O, Reimand J, Bader GD.

Nat Methods. 2015 Jun;12(6):531-3. doi: 10.1038/nmeth.3396. Epub 2015 May 4.

PMID:
25938373
6.

Metabolomic profiling in liver of adiponectin knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action.

Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, Isserlin R, Bader GD, Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G.

Biochem J. 2015 Apr 27. [Epub ahead of print]

PMID:
25915851
7.

Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes.

Ammar R, Paton TA, Torti D, Shlien A, Bader GD.

F1000Res. 2015 Jan 21;4:17. doi: 10.12688/f1000research.6037.1. eCollection 2015.

8.

Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis.

Torchia J, Picard D, Lafay-Cousin L, Hawkins CE, Kim SK, Letourneau L, Ra YS, Ho KC, Chan TS, Sin-Chan P, Dunham CP, Yip S, Ng HK, Lu JQ, Albrecht S, Pimentel J, Chan JA, Somers GR, Zielenska M, Faria CC, Roque L, Baskin B, Birks D, Foreman N, Strother D, Klekner A, Garami M, Hauser P, Hortobágyi T, Bognár L, Wilson B, Hukin J, Carret AS, Van Meter TE, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheineman K, Johnston D, Michaud J, Zelcer S, Hammond R, Ramsay DA, Fleming AJ, Lulla RR, Fangusaro JR, Sirachainan N, Larbcharoensub N, Hongeng S, Barakzai MA, Montpetit A, Stephens D, Grundy RG, Schüller U, Nicolaides T, Tihan T, Phillips J, Taylor MD, Rutka JT, Dirks P, Bader GD, Warmuth-Metz M, Rutkowski S, Pietsch T, Judkins AR, Jabado N, Bouffet E, Huang A.

Lancet Oncol. 2015 May;16(5):569-82. doi: 10.1016/S1470-2045(15)70114-2. Epub 2015 Apr 14.

PMID:
25882982
9.

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N.

Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015. Review.

10.

IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection.

Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG, Montpellier B, Kowalski PE, Voisin V, Bashir S, Bader GD, Krangel MS, Guidos CJ.

Nat Immunol. 2015 Apr;16(4):397-405. doi: 10.1038/ni.3122. Epub 2015 Mar 2.

PMID:
25729925
11.

A progesterone-CXCR4 axis controls mammary progenitor cell fate in the adult gland.

Shiah YJ, Tharmapalan P, Casey AE, Joshi PA, McKee TD, Jackson HW, Beristain AG, Chan-Seng-Yue MA, Bader GD, Lydon JP, Waterhouse PD, Boutros PC, Khokha R.

Stem Cell Reports. 2015 Mar 10;4(3):313-22. doi: 10.1016/j.stemcr.2015.01.011. Epub 2015 Feb 19.

12.

Evolutionary constraint and disease associations of post-translational modification sites in human genomes.

Reimand J, Wagih O, Bader GD.

PLoS Genet. 2015 Jan 22;11(1):e1004919. doi: 10.1371/journal.pgen.1004919. eCollection 2015 Jan.

13.

The Cytoscape app article collection.

Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T.

F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014.

14.

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity.

Meyer M, Reimand J, Lan X, Head R, Zhu X, Kushida M, Bayani J, Pressey JC, Lionel AC, Clarke ID, Cusimano M, Squire JA, Scherer SW, Bernstein M, Woodin MA, Bader GD, Dirks PB.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):851-6. doi: 10.1073/pnas.1320611111. Epub 2015 Jan 5.

15.

Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy.

Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A.

Mol Biosyst. 2015 Jan;11(1):239-51. doi: 10.1039/c4mb00265b. Epub 2014 Oct 31.

PMID:
25361207
16.

Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K.

Liu JC, Voisin V, Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-awar R, Egan SE, Bader GD, Tsao M, Mak TW, Zacksenhaus E.

EMBO Mol Med. 2014 Oct 20;6(12):1542-60. doi: 10.15252/emmm.201404402.

17.

GeneMANIA: Fast gene network construction and function prediction for Cytoscape.

Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q.

F1000Res. 2014 Jul 1;3:153. doi: 10.12688/f1000research.4572.1. eCollection 2014.

18.

Biological network exploration with cytoscape 3.

Su G, Morris JH, Demchak B, Bader GD.

Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-8.13.24. doi: 10.1002/0471250953.bi0813s47.

PMID:
25199793
19.

Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.

Isserlin R, Merico D, Voisin V, Bader GD.

F1000Res. 2014 Jul 1;3:141. doi: 10.12688/f1000research.4536.1. eCollection 2014.

20.

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.

Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM.

Nature. 2014 Jul 24;511(7510):428-34. doi: 10.1038/nature13379. Epub 2014 Jun 22.

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