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Items: 41

1.

Genomic Alterations Associated with Recurrence and TNBC Subtype in High-Risk Early Breast Cancers.

Wilson TR, Udyavar AR, Chang CW, Spoerke JM, Aimi J, Savage HM, Daemen A, O'Shaughnessy JA, Bourgon R, Lackner MR.

Mol Cancer Res. 2019 Jan;17(1):97-108. doi: 10.1158/1541-7786.MCR-18-0619. Epub 2018 Aug 31.

PMID:
30171174
2.

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells.

Mariathasan S, Turley SJ, Nickles D, Castiglioni A, Yuen K, Wang Y, Kadel EE III, Koeppen H, Astarita JL, Cubas R, Jhunjhunwala S, Banchereau R, Yang Y, Guan Y, Chalouni C, Ziai J, Şenbabaoğlu Y, Santoro S, Sheinson D, Hung J, Giltnane JM, Pierce AA, Mesh K, Lianoglou S, Riegler J, Carano RAD, Eriksson P, Höglund M, Somarriba L, Halligan DL, van der Heijden MS, Loriot Y, Rosenberg JE, Fong L, Mellman I, Chen DS, Green M, Derleth C, Fine GD, Hegde PS, Bourgon R, Powles T.

Nature. 2018 Feb 22;554(7693):544-548. doi: 10.1038/nature25501. Epub 2018 Feb 14.

3.

Mutation load and an effector T-cell gene signature may distinguish immunologically distinct and clinically relevant lymphoma subsets.

Bolen CR, McCord R, Huet S, Frampton GM, Bourgon R, Jardin F, Dartigues P, Punnoose EA, Szafer-Glusman E, Xerri L, Sujobert P, Salles G, Venstrom JM.

Blood Adv. 2017 Sep 27;1(22):1884-1890. doi: 10.1182/bloodadvances.2016000786. eCollection 2017 Oct 10.

4.

APPLICATIONS OF GENETICS, GENOMICS AND BIOINFORMATICS IN DRUG DISCOVERY.

Bourgon R, Dewey FE, Kan Z, Li SD.

Pac Symp Biocomput. 2018;23:1-7.

5.

High-Throughput and Sensitive Quantification of Circulating Tumor DNA by Microfluidic-Based Multiplex PCR and Next-Generation Sequencing.

Guan Y, Mayba O, Sandmann T, Lu S, Choi Y, Darbonne WC, Leveque V, Ryner L, Humke E, Tam NWR, Sujathasarma S, Cheung A, Bourgon R, Lackner MR, Wang Y.

J Mol Diagn. 2017 Nov;19(6):921-932. doi: 10.1016/j.jmoldx.2017.08.001. Epub 2017 Sep 1.

PMID:
28867605
6.

Atezolizumab as first-line treatment in cisplatin-ineligible patients with locally advanced and metastatic urothelial carcinoma: a single-arm, multicentre, phase 2 trial.

Balar AV, Galsky MD, Rosenberg JE, Powles T, Petrylak DP, Bellmunt J, Loriot Y, Necchi A, Hoffman-Censits J, Perez-Gracia JL, Dawson NA, van der Heijden MS, Dreicer R, Srinivas S, Retz MM, Joseph RW, Drakaki A, Vaishampayan UN, Sridhar SS, Quinn DI, Durán I, Shaffer DR, Eigl BJ, Grivas PD, Yu EY, Li S, Kadel EE 3rd, Boyd Z, Bourgon R, Hegde PS, Mariathasan S, Thåström A, Abidoye OO, Fine GD, Bajorin DF; IMvigor210 Study Group.

Lancet. 2017 Jan 7;389(10064):67-76. doi: 10.1016/S0140-6736(16)32455-2. Epub 2016 Dec 8. Erratum in: Lancet. 2017 Aug 26;390(10097):848.

7.

Functional screening implicates miR-371-3p and peroxiredoxin 6 in reversible tolerance to cancer drugs.

Sahu N, Stephan JP, Cruz DD, Merchant M, Haley B, Bourgon R, Classon M, Settleman J.

Nat Commun. 2016 Aug 3;7:12351. doi: 10.1038/ncomms12351.

8.

Integrated genomic analysis of colorectal cancer progression reveals activation of EGFR through demethylation of the EREG promoter.

Qu X, Sandmann T, Frierson H Jr, Fu L, Fuentes E, Walter K, Okrah K, Rumpel C, Moskaluk C, Lu S, Wang Y, Bourgon R, Penuel E, Pirzkall A, Amler L, Lackner MR, Tabernero J, Hampton GM, Kabbarah O.

Oncogene. 2016 Dec 15;35(50):6403-6415. doi: 10.1038/onc.2016.170. Epub 2016 Jun 6.

9.

Reproducible pharmacogenomic profiling of cancer cell line panels.

Haverty PM, Lin E, Tan J, Yu Y, Lam B, Lianoglou S, Neve RM, Martin S, Settleman J, Yauch RL, Bourgon R.

Nature. 2016 May 19;533(7603):333-7. doi: 10.1038/nature17987.

PMID:
27193678
10.

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial.

Rosenberg JE, Hoffman-Censits J, Powles T, van der Heijden MS, Balar AV, Necchi A, Dawson N, O'Donnell PH, Balmanoukian A, Loriot Y, Srinivas S, Retz MM, Grivas P, Joseph RW, Galsky MD, Fleming MT, Petrylak DP, Perez-Gracia JL, Burris HA, Castellano D, Canil C, Bellmunt J, Bajorin D, Nickles D, Bourgon R, Frampton GM, Cui N, Mariathasan S, Abidoye O, Fine GD, Dreicer R.

Lancet. 2016 May 7;387(10031):1909-20. doi: 10.1016/S0140-6736(16)00561-4. Epub 2016 Mar 4.

11.

Reply to T.J. Kruser et al.

Chinot OL, Taphoorn MJ, Bais C, Bourgon R, Phillips HS, Abrey LE, Wick W, Mason W, Henriksson R, Saran F, Nishikawa R, Cloughesy T.

J Clin Oncol. 2016 Apr 10;34(11):1282-3. doi: 10.1200/JCO.2015.65.2438. Epub 2016 Feb 16. No abstract available.

PMID:
26884575
12.

Patients With Proneural Glioblastoma May Derive Overall Survival Benefit From the Addition of Bevacizumab to First-Line Radiotherapy and Temozolomide: Retrospective Analysis of the AVAglio Trial.

Sandmann T, Bourgon R, Garcia J, Li C, Cloughesy T, Chinot OL, Wick W, Nishikawa R, Mason W, Henriksson R, Saran F, Lai A, Moore N, Kharbanda S, Peale F, Hegde P, Abrey LE, Phillips HS, Bais C.

J Clin Oncol. 2015 Sep 1;33(25):2735-44. doi: 10.1200/JCO.2015.61.5005. Epub 2015 Jun 29. Erratum in: J Clin Oncol. 2016 Sep 1;34(25):3113.

13.

Enhancing the antitumor efficacy of a cell-surface death ligand by covalent membrane display.

Nair PM, Flores H, Gogineni A, Marsters S, Lawrence DA, Kelley RF, Ngu H, Sagolla M, Komuves L, Bourgon R, Settleman J, Ashkenazi A.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):5679-84. doi: 10.1073/pnas.1418962112. Epub 2015 Apr 20.

14.

A resource for cell line authentication, annotation and quality control.

Yu M, Selvaraj SK, Liang-Chu MM, Aghajani S, Busse M, Yuan J, Lee G, Peale F, Klijn C, Bourgon R, Kaminker JS, Neve RM.

Nature. 2015 Apr 16;520(7547):307-11. doi: 10.1038/nature14397.

PMID:
25877200
15.

Genomic analysis of smoothened inhibitor resistance in basal cell carcinoma.

Sharpe HJ, Pau G, Dijkgraaf GJ, Basset-Seguin N, Modrusan Z, Januario T, Tsui V, Durham AB, Dlugosz AA, Haverty PM, Bourgon R, Tang JY, Sarin KY, Dirix L, Fisher DC, Rudin CM, Sofen H, Migden MR, Yauch RL, de Sauvage FJ.

Cancer Cell. 2015 Mar 9;27(3):327-41. doi: 10.1016/j.ccell.2015.02.001.

16.

Human biosample authentication using the high-throughput, cost-effective SNPtrace(TM) system.

Liang-Chu MM, Yu M, Haverty PM, Koeman J, Ziegle J, Lee M, Bourgon R, Neve RM.

PLoS One. 2015 Feb 25;10(2):e0116218. doi: 10.1371/journal.pone.0116218. eCollection 2015.

17.

A comprehensive transcriptional portrait of human cancer cell lines.

Klijn C, Durinck S, Stawiski EW, Haverty PM, Jiang Z, Liu H, Degenhardt J, Mayba O, Gnad F, Liu J, Pau G, Reeder J, Cao Y, Mukhyala K, Selvaraj SK, Yu M, Zynda GJ, Brauer MJ, Wu TD, Gentleman RC, Manning G, Yauch RL, Bourgon R, Stokoe D, Modrusan Z, Neve RM, de Sauvage FJ, Settleman J, Seshagiri S, Zhang Z.

Nat Biotechnol. 2015 Mar;33(3):306-12. doi: 10.1038/nbt.3080. Epub 2014 Dec 8.

PMID:
25485619
18.

Comparative oncogenomics identifies PSMB4 and SHMT2 as potential cancer driver genes.

Lee GY, Haverty PM, Li L, Kljavin NM, Bourgon R, Lee J, Stern H, Modrusan Z, Seshagiri S, Zhang Z, Davis D, Stokoe D, Settleman J, de Sauvage FJ, Neve RM.

Cancer Res. 2014 Jun 1;74(11):3114-26. doi: 10.1158/0008-5472.CAN-13-2683. Epub 2014 Apr 22.

19.

Discovery and development of DNA methylation-based biomarkers for lung cancer.

Walter K, Holcomb T, Januario T, Yauch RL, Du P, Bourgon R, Seshagiri S, Amler LC, Hampton GM, S Shames D.

Epigenomics. 2014 Feb;6(1):59-72. doi: 10.2217/epi.13.81.

PMID:
24579947
20.

High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing.

Bourgon R, Lu S, Yan Y, Lackner MR, Wang W, Weigman V, Wang D, Guan Y, Ryner L, Koeppen H, Patel R, Hampton GM, Amler LC, Wang Y.

Clin Cancer Res. 2014 Apr 15;20(8):2080-91. doi: 10.1158/1078-0432.CCR-13-3114. Epub 2014 Feb 26.

21.

gCMAP: user-friendly connectivity mapping with R.

Sandmann T, Kummerfeld SK, Gentleman R, Bourgon R.

Bioinformatics. 2014 Jan 1;30(1):127-8. doi: 10.1093/bioinformatics/btt592. Epub 2013 Oct 15.

PMID:
24132929
22.

Loss of NAPRT1 expression by tumor-specific promoter methylation provides a novel predictive biomarker for NAMPT inhibitors.

Shames DS, Elkins K, Walter K, Holcomb T, Du P, Mohl D, Xiao Y, Pham T, Haverty PM, Liederer B, Liang X, Yauch RL, O'Brien T, Bourgon R, Koeppen H, Belmont LD.

Clin Cancer Res. 2013 Dec 15;19(24):6912-23. doi: 10.1158/1078-0432.CCR-13-1186. Epub 2013 Oct 4.

23.

A requirement for wild-type Ras isoforms in mutant KRas-driven signalling and transformation.

Bentley C, Jurinka SS, Kljavin NM, Vartanian S, Ramani SR, Gonzalez LC, Yu K, Modrusan Z, Du P, Bourgon R, Neve RM, Stokoe D.

Biochem J. 2013 Jun 1;452(2):313-20. doi: 10.1042/BJ20121578.

PMID:
23496764
24.

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer.

Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS, Bergbower EA, Guan Y, Shin J, Guillory J, Rivers CS, Foo CK, Bhatt D, Stinson J, Gnad F, Haverty PM, Gentleman R, Chaudhuri S, Janakiraman V, Jaiswal BS, Parikh C, Yuan W, Zhang Z, Koeppen H, Wu TD, Stern HM, Yauch RL, Huffman KE, Paskulin DD, Illei PB, Varella-Garcia M, Gazdar AF, de Sauvage FJ, Bourgon R, Minna JD, Brock MV, Seshagiri S.

Nat Genet. 2012 Oct;44(10):1111-6. doi: 10.1038/ng.2405. Epub 2012 Sep 2.

25.

Recurrent R-spondin fusions in colon cancer.

Seshagiri S, Stawiski EW, Durinck S, Modrusan Z, Storm EE, Conboy CB, Chaudhuri S, Guan Y, Janakiraman V, Jaiswal BS, Guillory J, Ha C, Dijkgraaf GJ, Stinson J, Gnad F, Huntley MA, Degenhardt JD, Haverty PM, Bourgon R, Wang W, Koeppen H, Gentleman R, Starr TK, Zhang Z, Largaespada DA, Wu TD, de Sauvage FJ.

Nature. 2012 Aug 30;488(7413):660-4. doi: 10.1038/nature11282.

26.

Querying genomic databases: refining the connectivity map.

Segal MR, Xiong H, Bengtsson H, Bourgon R, Gentleman R.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(2). pii: /j/sagmb.2012.11.issue-2/1544-6115.1715/1544-6115.1715.xml. doi: 10.2202/1544-6115.1715.

PMID:
22499690
27.

DNA methylation profiling defines clinically relevant biological subsets of non-small cell lung cancer.

Walter K, Holcomb T, Januario T, Du P, Evangelista M, Kartha N, Iniguez L, Soriano R, Huw L, Stern H, Modrusan Z, Seshagiri S, Hampton GM, Amler LC, Bourgon R, Yauch RL, Shames DS.

Clin Cancer Res. 2012 Apr 15;18(8):2360-73. doi: 10.1158/1078-0432.CCR-11-2635-T. Epub 2012 Jan 19.

28.

SpeCond: a method to detect condition-specific gene expression.

Cavalli FM, Bourgon R, Vaquerizas JM, Luscombe NM.

Genome Biol. 2011 Oct 18;12(10):R101. doi: 10.1186/gb-2011-12-10-r101. Erratum in: Genome Biol. 2011;12(12):413. Huber, Wolfgang [removed].

29.

miR-221/222 targeting of trichorhinophalangeal 1 (TRPS1) promotes epithelial-to-mesenchymal transition in breast cancer.

Stinson S, Lackner MR, Adai AT, Yu N, Kim HJ, O'Brien C, Spoerke J, Jhunjhunwala S, Boyd Z, Januario T, Newman RJ, Yue P, Bourgon R, Modrusan Z, Stern HM, Warming S, de Sauvage FJ, Amler L, Yeh RF, Dornan D.

Sci Signal. 2011 Aug 9;4(186):pt5. doi: 10.1126/scisignal.2002258.

PMID:
21868360
30.

TRPS1 targeting by miR-221/222 promotes the epithelial-to-mesenchymal transition in breast cancer.

Stinson S, Lackner MR, Adai AT, Yu N, Kim HJ, O'Brien C, Spoerke J, Jhunjhunwala S, Boyd Z, Januario T, Newman RJ, Yue P, Bourgon R, Modrusan Z, Stern HM, Warming S, de Sauvage FJ, Amler L, Yeh RF, Dornan D.

Sci Signal. 2011 Jun 14;4(177):ra41. doi: 10.1126/scisignal.2001538.

31.

Genome-wide survey of post-meiotic segregation during yeast recombination.

Mancera E, Bourgon R, Huber W, Steinmetz LM.

Genome Biol. 2011;12(4):R36. doi: 10.1186/gb-2011-12-4-r36. Epub 2011 Apr 11.

32.

Diverse somatic mutation patterns and pathway alterations in human cancers.

Kan Z, Jaiswal BS, Stinson J, Janakiraman V, Bhatt D, Stern HM, Yue P, Haverty PM, Bourgon R, Zheng J, Moorhead M, Chaudhuri S, Tomsho LP, Peters BA, Pujara K, Cordes S, Davis DP, Carlton VE, Yuan W, Li L, Wang W, Eigenbrot C, Kaminker JS, Eberhard DA, Waring P, Schuster SC, Modrusan Z, Zhang Z, Stokoe D, de Sauvage FJ, Faham M, Seshagiri S.

Nature. 2010 Aug 12;466(7308):869-73. doi: 10.1038/nature09208. Epub 2010 Jul 28.

PMID:
20668451
33.

Independent filtering increases detection power for high-throughput experiments.

Bourgon R, Gentleman R, Huber W.

Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-51. doi: 10.1073/pnas.0914005107. Epub 2010 May 11.

34.

Alternative epigenetic chromatin states of polycomb target genes.

Schwartz YB, Kahn TG, Stenberg P, Ohno K, Bourgon R, Pirrotta V.

PLoS Genet. 2010 Jan;6(1):e1000805. doi: 10.1371/journal.pgen.1000805. Epub 2010 Jan 8.

35.

Genome-wide allele- and strand-specific expression profiling.

Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM.

Mol Syst Biol. 2009;5:274. doi: 10.1038/msb.2009.31. Epub 2009 Jun 16.

36.

Array-based genotyping in S.cerevisiae using semi-supervised clustering.

Bourgon R, Mancera E, Brozzi A, Steinmetz LM, Huber W.

Bioinformatics. 2009 Apr 15;25(8):1056-62. doi: 10.1093/bioinformatics/btp104. Epub 2009 Feb 23.

37.

High-resolution mapping of meiotic crossovers and non-crossovers in yeast.

Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM.

Nature. 2008 Jul 24;454(7203):479-85. doi: 10.1038/nature07135. Epub 2008 Jul 9.

38.

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD.

PLoS Biol. 2008 Feb;6(2):e27. doi: 10.1371/journal.pbio.0060027.

39.

Genome-wide analysis of Polycomb targets in Drosophila melanogaster.

Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, Biggin M, Pirrotta V.

Nat Genet. 2006 Jun;38(6):700-5. Epub 2006 May 28.

PMID:
16732288
40.

The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees.

Bourgon R, Delorenzi M, Sargeant T, Hodder AN, Crabb BS, Speed TP.

Mol Biol Evol. 2004 Nov;21(11):2161-71. Epub 2004 Aug 11.

PMID:
15306658
41.

Enzymic, phylogenetic, and structural characterization of the unusual papain-like protease domain of Plasmodium falciparum SERA5.

Hodder AN, Drew DR, Epa VC, Delorenzi M, Bourgon R, Miller SK, Moritz RL, Frecklington DF, Simpson RJ, Speed TP, Pike RN, Crabb BS.

J Biol Chem. 2003 Nov 28;278(48):48169-77. Epub 2003 Sep 17.

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