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References for PMC Articles for PubMed (Select 23222956)

1.

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery.

Piazza R, Pirola A, Spinelli R, Valletta S, Redaelli S, Magistroni V, Gambacorti-Passerini C.

Nucleic Acids Res. 2012 Sep;40(16):e123. doi: 10.1093/nar/gks394. Epub 2012 May 8.

2.

Setbp1 promotes the self-renewal of murine myeloid progenitors via activation of Hoxa9 and Hoxa10.

Oakley K, Han Y, Vishwakarma BA, Chu S, Bhatia R, Gudmundsson KO, Keller J, Chen X, Vasko V, Jenkins NA, Copeland NG, Du Y.

Blood. 2012 Jun 21;119(25):6099-108. doi: 10.1182/blood-2011-10-388710. Epub 2012 May 7.

3.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S.

Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933.

4.

Profiles in leukemia.

Godley LA.

N Engl J Med. 2012 Mar 22;366(12):1152-3. doi: 10.1056/NEJMe1200409. Epub 2012 Mar 14. No abstract available.

PMID:
22417205
5.

Tumor heterogeneity and personalized medicine.

Longo DL.

N Engl J Med. 2012 Mar 8;366(10):956-7. doi: 10.1056/NEJMe1200656. No abstract available.

PMID:
22397658
6.
7.

ELM--the database of eukaryotic linear motifs.

Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51. doi: 10.1093/nar/gkr1064. Epub 2011 Nov 21.

8.

Inactivation of polycomb repressive complex 2 components in myeloproliferative and myelodysplastic/myeloproliferative neoplasms.

Score J, Hidalgo-Curtis C, Jones AV, Winkelmann N, Skinner A, Ward D, Zoi K, Ernst T, Stegelmann F, Döhner K, Chase A, Cross NC.

Blood. 2012 Feb 2;119(5):1208-13. doi: 10.1182/blood-2011-07-367243. Epub 2011 Nov 3.

9.

Differential expression in RNA-seq: a matter of depth.

Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A.

Genome Res. 2011 Dec;21(12):2213-23. doi: 10.1101/gr.124321.111. Epub 2011 Sep 8.

10.

BRAF mutations in hairy-cell leukemia.

Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foà R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R, Falini B.

N Engl J Med. 2011 Jun 16;364(24):2305-15. doi: 10.1056/NEJMoa1014209. Epub 2011 Jun 11.

11.

Multicenter independent assessment of outcomes in chronic myeloid leukemia patients treated with imatinib.

Gambacorti-Passerini C, Antolini L, Mahon FX, Guilhot F, Deininger M, Fava C, Nagler A, Della Casa CM, Morra E, Abruzzese E, D'Emilio A, Stagno F, le Coutre P, Hurtado-Monroy R, Santini V, Martino B, Pane F, Piccin A, Giraldo P, Assouline S, Durosinmi MA, Leeksma O, Pogliani EM, Puttini M, Jang E, Reiffers J, Valsecchi MG, Kim DW.

J Natl Cancer Inst. 2011 Apr 6;103(7):553-61. doi: 10.1093/jnci/djr060. Epub 2011 Mar 21.

12.

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.

Xu G, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.

Source Code Biol Med. 2011 Jan 13;6(1):2. doi: 10.1186/1751-0473-6-2.

13.

Integrative genomics viewer.

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP.

Nat Biotechnol. 2011 Jan;29(1):24-6. doi: 10.1038/nbt.1754. No abstract available.

14.

Differential expression analysis for sequence count data.

Anders S, Huber W.

Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub 2010 Oct 27.

15.

Chronic myeloid leukemia: a historical perspective.

Goldman JM.

Semin Hematol. 2010 Oct;47(4):302-11. doi: 10.1053/j.seminhematol.2010.07.001. Review.

PMID:
20875546
16.

Are chronic myeloid leukemia patients more at risk for second malignancies? A population-based study.

Rebora P, Czene K, Antolini L, Gambacorti Passerini C, Reilly M, Valsecchi MG.

Am J Epidemiol. 2010 Nov 1;172(9):1028-33. doi: 10.1093/aje/kwq262. Epub 2010 Sep 22.

17.

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Goecks J, Nekrutenko A, Taylor J; Galaxy Team.

Genome Biol. 2010;11(8):R86. doi: 10.1186/gb-2010-11-8-r86. Epub 2010 Aug 25.

18.

Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders.

Ernst T, Chase AJ, Score J, Hidalgo-Curtis CE, Bryant C, Jones AV, Waghorn K, Zoi K, Ross FM, Reiter A, Hochhaus A, Drexler HG, Duncombe A, Cervantes F, Oscier D, Boultwood J, Grand FH, Cross NC.

Nat Genet. 2010 Aug;42(8):722-6. doi: 10.1038/ng.621. Epub 2010 Jul 4.

PMID:
20601953
19.

De novo mutations of SETBP1 cause Schinzel-Giedion syndrome.

Hoischen A, van Bon BW, Gilissen C, Arts P, van Lier B, Steehouwer M, de Vries P, de Reuver R, Wieskamp N, Mortier G, Devriendt K, Amorim MZ, Revencu N, Kidd A, Barbosa M, Turner A, Smith J, Oley C, Henderson A, Hayes IM, Thompson EM, Brunner HG, de Vries BB, Veltman JA.

Nat Genet. 2010 Jun;42(6):483-5. doi: 10.1038/ng.581. Epub 2010 May 2.

PMID:
20436468
20.

Transcription factor mutations in myelodysplastic/myeloproliferative neoplasms.

Ernst T, Chase A, Zoi K, Waghorn K, Hidalgo-Curtis C, Score J, Jones A, Grand F, Reiter A, Hochhaus A, Cross NC.

Haematologica. 2010 Sep;95(9):1473-80. doi: 10.3324/haematol.2010.021808. Epub 2010 Apr 26.

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