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Results: 1 to 20 of 107

1.

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.

PMID:
25075306
[PubMed]
Free Article
2.

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.

PMID:
25043047
[PubMed - in process]
3.

Intercellular network structure and regulatory motifs in the human hematopoietic system.

Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW.

Mol Syst Biol. 2014 Jul 15;10(7):741. doi: 10.15252/msb.20145141.

PMID:
25028490
[PubMed - in process]
Free Article
4.

Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction.

Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q.

Front Genet. 2014 May 16;5:123. doi: 10.3389/fgene.2014.00123. eCollection 2014.

PMID:
24904632
[PubMed]
Free PMC Article
5.

Characterizing the Late Pleistocene MSA Lithic Technology of Sibudu, KwaZulu-Natal, South Africa.

Will M, Bader GD, Conard NJ.

PLoS One. 2014 May 30;9(5):e98359. doi: 10.1371/journal.pone.0098359. eCollection 2014.

PMID:
24878544
[PubMed - in process]
Free PMC Article
6.

A draft map of the human proteome.

Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A.

Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302.

PMID:
24870542
[PubMed - indexed for MEDLINE]
7.

Mapping the cellular response to small molecules using chemogenomic fitness signatures.

Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G.

Science. 2014 Apr 11;344(6180):208-11. doi: 10.1126/science.1250217. Erratum in: Science. 2014 May 23;344(6186):1255771.

PMID:
24723613
[PubMed - indexed for MEDLINE]
8.

Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs.

Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD.

PLoS One. 2014 Apr 10;9(4):e94507. doi: 10.1371/journal.pone.0094507. eCollection 2014.

PMID:
24722214
[PubMed - in process]
Free PMC Article
9.

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery.

Leung A, Bader GD, Reimand J.

Bioinformatics. 2014 Aug 1;30(15):2230-2. doi: 10.1093/bioinformatics/btu172. Epub 2014 Apr 8.

PMID:
24713437
[PubMed - in process]
Free PMC Article
10.

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.

Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM; ICGC PedBrain Tumor Project.

Cancer Cell. 2014 Mar 17;25(3):393-405. doi: 10.1016/j.ccr.2014.02.004.

PMID:
24651015
[PubMed - indexed for MEDLINE]
11.

Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan.

Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS.

Proteomics. 2014 May;14(9):975-88. doi: 10.1002/pmic.201400041.

PMID:
24596128
[PubMed - in process]
12.

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.

Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD.

Nature. 2014 Feb 27;506(7489):445-50. doi: 10.1038/nature13108. Epub 2014 Feb 19.

PMID:
24553142
[PubMed - indexed for MEDLINE]
13.

Coordinate microRNA-mediated regulation of protein complexes in prostate cancer.

Alshalalfa M, Bader GD, Bismar TA, Alhajj R.

PLoS One. 2013 Dec 31;8(12):e84261. doi: 10.1371/journal.pone.0084261. eCollection 2013.

PMID:
24391925
[PubMed - in process]
Free PMC Article
14.

The mutational landscape of phosphorylation signaling in cancer.

Reimand J, Wagih O, Bader GD.

Sci Rep. 2013 Oct 2;3:2651. doi: 10.1038/srep02651.

PMID:
24089029
[PubMed - in process]
Free PMC Article
15.

Comprehensive identification of mutational cancer driver genes across 12 tumor types.

Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N.

Sci Rep. 2013 Oct 2;3:2650. doi: 10.1038/srep02650.

PMID:
24084849
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Using biological pathway data with paxtools.

Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.

PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19.

PMID:
24068901
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The BioPAX Validator.

Rodchenkov I, Demir E, Sander C, Bader GD.

Bioinformatics. 2013 Oct 15;29(20):2659-60. doi: 10.1093/bioinformatics/btt452. Epub 2013 Aug 5.

PMID:
23918249
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Computational approaches to identify functional genetic variants in cancer genomes.

Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.

Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562.

PMID:
23900255
[PubMed - indexed for MEDLINE]
19.

GeneMANIA prediction server 2013 update.

Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W115-22. doi: 10.1093/nar/gkt533.

PMID:
23794635
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Cytoscape app store.

Lotia S, Montojo J, Dong Y, Bader GD, Pico AR.

Bioinformatics. 2013 May 15;29(10):1350-1. doi: 10.1093/bioinformatics/btt138. Epub 2013 Apr 16.

PMID:
23595664
[PubMed - indexed for MEDLINE]
Free PMC Article

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