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Items: 39

1.

Evaluating the quality of the 1000 genomes project data.

Belsare S, Levy-Sakin M, Mostovoy Y, Durinck S, Chaudhuri S, Xiao M, Peterson AS, Kwok PY, Seshagiri S, Wall JD.

BMC Genomics. 2019 Aug 16;20(1):620. doi: 10.1186/s12864-019-5957-x.

2.

Adaptive adipose tissue stromal plasticity in response to cold stress and antibody-based metabolic therapy.

Chang JC, Durinck S, Chen MZ, Martinez-Martin N, Zhang JA, Lehoux I, Li H, Lin M, Wu J, Bainbridge TW, Ernst JA, Ramani SR, Paduchuri S, Kates L, Solon M, Buechler MB, Castiglioni A, Thai M, Breart B, Modrusan Z, Peterson AS, Turley SJ, Sonoda J.

Sci Rep. 2019 Jun 20;9(1):8833. doi: 10.1038/s41598-019-45354-1.

3.

Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations.

Pahuja KB, Nguyen TT, Jaiswal BS, Prabhash K, Thaker TM, Senger K, Chaudhuri S, Kljavin NM, Antony A, Phalke S, Kumar P, Mravic M, Stawiski EW, Vargas D, Durinck S, Gupta R, Khanna-Gupta A, Trabucco SE, Sokol ES, Hartmaier RJ, Singh A, Chougule A, Trivedi V, Dutt A, Patil V, Joshi A, Noronha V, Ziai J, Banavali SD, Ramprasad V, DeGrado WF, Bueno R, Jura N, Seshagiri S.

Cancer Cell. 2018 Nov 12;34(5):792-806.e5. doi: 10.1016/j.ccell.2018.09.010. Epub 2018 Oct 25.

4.

Adverse Outcome Pathway-Driven Analysis of Liver Steatosis in Vitro: A Case Study with Cyproconazole.

Luckert C, Braeuning A, de Sousa G, Durinck S, Katsanou ES, Konstantinidou P, Machera K, Milani ES, Peijnenburg AACM, Rahmani R, Rajkovic A, Rijkers D, Spyropoulou A, Stamou M, Stoopen G, Sturla S, Wollscheid B, Zucchini-Pascal N, Lampen A.

Chem Res Toxicol. 2018 Aug 20;31(8):784-798. doi: 10.1021/acs.chemrestox.8b00112. Epub 2018 Jul 11.

PMID:
29995386
5.

An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors.

Wang T, Lu R, Kapur P, Jaiswal BS, Hannan R, Zhang Z, Pedrosa I, Luke JJ, Zhang H, Goldstein LD, Yousuf Q, Gu YF, McKenzie T, Joyce A, Kim MS, Wang X, Luo D, Onabolu O, Stevens C, Xie Z, Chen M, Filatenkov A, Torrealba J, Luo X, Guo W, He J, Stawiski E, Modrusan Z, Durinck S, Seshagiri S, Brugarolas J.

Cancer Discov. 2018 Sep;8(9):1142-1155. doi: 10.1158/2159-8290.CD-17-1246. Epub 2018 Jun 8.

6.

CRISPR off-target analysis in genetically engineered rats and mice.

Anderson KR, Haeussler M, Watanabe C, Janakiraman V, Lund J, Modrusan Z, Stinson J, Bei Q, Buechler A, Yu C, Thamminana SR, Tam L, Sowick MA, Alcantar T, O'Neil N, Li J, Ta L, Lima L, Roose-Girma M, Rairdan X, Durinck S, Warming S.

Nat Methods. 2018 Jul;15(7):512-514. doi: 10.1038/s41592-018-0011-5. Epub 2018 May 21.

7.

ERK Mutations and Amplification Confer Resistance to ERK-Inhibitor Therapy.

Jaiswal BS, Durinck S, Stawiski EW, Yin J, Wang W, Lin E, Moffat J, Martin SE, Modrusan Z, Seshagiri S.

Clin Cancer Res. 2018 Aug 15;24(16):4044-4055. doi: 10.1158/1078-0432.CCR-17-3674. Epub 2018 May 14.

8.

Homozygous KSR1 deletion attenuates morbidity but does not prevent tumor development in a mouse model of RAS-driven pancreatic cancer.

Germino EA, Miller JP, Diehl L, Swanson CJ, Durinck S, Modrusan Z, Miner JH, Shaw AS.

PLoS One. 2018 Mar 29;13(3):e0194998. doi: 10.1371/journal.pone.0194998. eCollection 2018.

9.

Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia.

Cuellar TL, Herzner AM, Zhang X, Goyal Y, Watanabe C, Friedman BA, Janakiraman V, Durinck S, Stinson J, Arnott D, Cheung TK, Chaudhuri S, Modrusan Z, Doerr JM, Classon M, Haley B.

J Cell Biol. 2017 Nov 6;216(11):3535-3549. doi: 10.1083/jcb.201612160. Epub 2017 Sep 8.

10.

Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types.

Chen YJ, Friedman BA, Ha C, Durinck S, Liu J, Rubenstein JL, Seshagiri S, Modrusan Z.

Sci Rep. 2017 Mar 31;7:45656. doi: 10.1038/srep45656.

11.

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.

Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, Gnad F, Nguyen TT, Jaiswal BS, Chirieac LR, Sciaranghella D, Dao N, Gustafson CE, Munir KJ, Hackney JA, Chaudhuri A, Gupta R, Guillory J, Toy K, Ha C, Chen YJ, Stinson J, Chaudhuri S, Zhang N, Wu TD, Sugarbaker DJ, de Sauvage FJ, Richards WG, Seshagiri S.

Nat Genet. 2016 Apr;48(4):407-16. doi: 10.1038/ng.3520. Epub 2016 Feb 29.

PMID:
26928227
12.

Targeting PTPRK-RSPO3 colon tumours promotes differentiation and loss of stem-cell function.

Storm EE, Durinck S, de Sousa e Melo F, Tremayne J, Kljavin N, Tan C, Ye X, Chiu C, Pham T, Hongo JA, Bainbridge T, Firestein R, Blackwood E, Metcalfe C, Stawiski EW, Yauch RL, Wu Y, de Sauvage FJ.

Nature. 2016 Jan 7;529(7584):97-100. doi: 10.1038/nature16466. Epub 2015 Dec 23.

PMID:
26700806
13.

Erratum to: Modeling precision treatment of breast cancer.

Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, Van't Veer LJ, Spellman PT, Gray JW.

Genome Biol. 2015 May 12;16:95. doi: 10.1186/s13059-015-0658-5.

14.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98. doi: 10.1093/nar/gkv350. Epub 2015 Apr 20.

15.

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
16.

Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes.

Durinck S, Stawiski EW, Pavía-Jiménez A, Modrusan Z, Kapur P, Jaiswal BS, Zhang N, Toffessi-Tcheuyap V, Nguyen TT, Pahuja KB, Chen YJ, Saleem S, Chaudhuri S, Heldens S, Jackson M, Peña-Llopis S, Guillory J, Toy K, Ha C, Harris CJ, Holloman E, Hill HM, Stinson J, Rivers CS, Janakiraman V, Wang W, Kinch LN, Grishin NV, Haverty PM, Chow B, Gehring JS, Reeder J, Pau G, Wu TD, Margulis V, Lotan Y, Sagalowsky A, Pedrosa I, de Sauvage FJ, Brugarolas J, Seshagiri S.

Nat Genet. 2015 Jan;47(1):13-21. doi: 10.1038/ng.3146. Epub 2014 Nov 17.

17.

Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer.

Liu J, McCleland M, Stawiski EW, Gnad F, Mayba O, Haverty PM, Durinck S, Chen YJ, Klijn C, Jhunjhunwala S, Lawrence M, Liu H, Wan Y, Chopra V, Yaylaoglu MB, Yuan W, Ha C, Gilbert HN, Reeder J, Pau G, Stinson J, Stern HM, Manning G, Wu TD, Neve RM, de Sauvage FJ, Modrusan Z, Seshagiri S, Firestein R, Zhang Z.

Nat Commun. 2014 May 8;5:3830. doi: 10.1038/ncomms4830.

18.

Modeling precision treatment of breast cancer.

Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, van't Veer LJ, Spellman PT, Gray JW.

Genome Biol. 2013;14(10):R110. Erratum in: Genome Biol. 2015;16:95.

19.

Oncogenic ERBB3 mutations in human cancers.

Jaiswal BS, Kljavin NM, Stawiski EW, Chan E, Parikh C, Durinck S, Chaudhuri S, Pujara K, Guillory J, Edgar KA, Janakiraman V, Scholz RP, Bowman KK, Lorenzo M, Li H, Wu J, Yuan W, Peters BA, Kan Z, Stinson J, Mak M, Modrusan Z, Eigenbrot C, Firestein R, Stern HM, Rajalingam K, Schaefer G, Merchant MA, Sliwkowski MX, de Sauvage FJ, Seshagiri S.

Cancer Cell. 2013 May 13;23(5):603-17. doi: 10.1016/j.ccr.2013.04.012. Erratum in: Cancer Cell. 2014 Apr 14;25(4):543-4.

20.

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.

21.

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.

22.

Conditional activation of Pik3ca(H1047R) in a knock-in mouse model promotes mammary tumorigenesis and emergence of mutations.

Yuan W, Stawiski E, Janakiraman V, Chan E, Durinck S, Edgar KA, Kljavin NM, Rivers CS, Gnad F, Roose-Girma M, Haverty PM, Fedorowicz G, Heldens S, Soriano RH, Zhang Z, Wallin JJ, Johnson L, Merchant M, Modrusan Z, Stern HM, Seshagiri S.

Oncogene. 2013 Jan 17;32(3):318-26. doi: 10.1038/onc.2012.53. Epub 2012 Feb 27.

23.

Subtype and pathway specific responses to anticancer compounds in breast cancer.

Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2724-9. doi: 10.1073/pnas.1018854108. Epub 2011 Oct 14.

24.

Temporal dissection of tumorigenesis in primary cancers.

Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, Pons J, Chan SW, Lam ET, Chu C, Park K, Hong SW, Hur JS, Huh N, Neuhaus IM, Yu SS, Grekin RC, Mauro TM, Cleaver JE, Kwok PY, LeBoit PE, Getz G, Cibulskis K, Aster JC, Huang H, Purdom E, Li J, Bolund L, Arron ST, Gray JW, Spellman PT, Cho RJ.

Cancer Discov. 2011 Jul;1(2):137-43. doi: 10.1158/2159-8290.CD-11-0028. Epub 2011 Jun 29.

25.

Exon-level microarray analyses identify alternative splicing programs in breast cancer.

Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW.

Mol Cancer Res. 2010 Jul;8(7):961-74. doi: 10.1158/1541-7786.MCR-09-0528. Epub 2010 Jul 6.

26.

Prediction of epigenetically regulated genes in breast cancer cell lines.

Loss LA, Sadanandam A, Durinck S, Nautiyal S, Flaucher D, Carlton VE, Moorhead M, Lu Y, Gray JW, Faham M, Spellman P, Parvin B.

BMC Bioinformatics. 2010 Jun 4;11:305. doi: 10.1186/1471-2105-11-305.

27.

microRNA profiling identifies cancer-specific and prognostic signatures in pediatric malignancies.

Wei JS, Johansson P, Chen QR, Song YK, Durinck S, Wen X, Cheuk AT, Smith MA, Houghton P, Morton C, Khan J.

Clin Cancer Res. 2009 Sep 1;15(17):5560-8. doi: 10.1158/1078-0432.CCR-08-3287. Epub 2009 Aug 25.

28.

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.

Durinck S, Spellman PT, Birney E, Huber W.

Nat Protoc. 2009;4(8):1184-91. doi: 10.1038/nprot.2009.97. Epub 2009 Jul 23.

29.

GenomeGraphs: integrated genomic data visualization with R.

Durinck S, Bullard J, Spellman PT, Dudoit S.

BMC Bioinformatics. 2009 Jan 6;10:2. doi: 10.1186/1471-2105-10-2.

30.

Pre-processing of microarray data and analysis of differential expression.

Durinck S.

Methods Mol Biol. 2008;452:89-110. doi: 10.1007/978-1-60327-159-2_4. Review.

PMID:
18563370
31.

In vitro differential sensitivity of melanomas to phenothiazines is based on the presence of codon 600 BRAF mutation.

Ikediobi ON, Reimers M, Durinck S, Blower PE, Futreal AP, Stratton MR, Weinstein JN.

Mol Cancer Ther. 2008 Jun;7(6):1337-46. doi: 10.1158/1535-7163.MCT-07-2308. Epub 2008 Jun 4.

32.

The MYCN oncogene is a direct target of miR-34a.

Wei JS, Song YK, Durinck S, Chen QR, Cheuk AT, Tsang P, Zhang Q, Thiele CJ, Slack A, Shohet J, Khan J.

Oncogene. 2008 Sep 4;27(39):5204-13. doi: 10.1038/onc.2008.154. Epub 2008 May 26.

33.

Molecular effectors and modulators of hypericin-mediated cell death in bladder cancer cells.

Buytaert E, Matroule JY, Durinck S, Close P, Kocanova S, Vandenheede JR, de Witte PA, Piette J, Agostinis P.

Oncogene. 2008 Mar 20;27(13):1916-29. Epub 2007 Oct 22.

PMID:
17952126
34.

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.

Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M.

Plant Physiol. 2005 Oct;139(2):632-6.

35.

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.

Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W.

Bioinformatics. 2005 Aug 15;21(16):3439-40.

PMID:
16082012
36.

Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis.

Allemeersch J, Durinck S, Vanderhaeghen R, Alard P, Maes R, Seeuws K, Bogaert T, Coddens K, Deschouwer K, Van Hummelen P, Vuylsteke M, Moreau Y, Kwekkeboom J, Wijfjes AH, May S, Beynon J, Hilson P, Kuiper MT.

Plant Physiol. 2005 Feb;137(2):588-601.

37.

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, Bhalerao RP, Bitton F, Caboche M, Cannoot B, Chardakov V, Cognet-Holliger C, Colot V, Crowe M, Darimont C, Durinck S, Eickhoff H, de Longevialle AF, Farmer EE, Grant M, Kuiper MT, Lehrach H, Léon C, Leyva A, Lundeberg J, Lurin C, Moreau Y, Nietfeld W, Paz-Ares J, Reymond P, Rouzé P, Sandberg G, Segura MD, Serizet C, Tabrett A, Taconnat L, Thareau V, Van Hummelen P, Vercruysse S, Vuylsteke M, Weingartner M, Weisbeek PJ, Wirta V, Wittink FR, Zabeau M, Small I.

Genome Res. 2004 Oct;14(10B):2176-89.

38.

Importing MAGE-ML format microarray data into BioConductor.

Durinck S, Allemeersch J, Carey VJ, Moreau Y, De Moor B.

Bioinformatics. 2004 Dec 12;20(18):3641-2. Epub 2004 Jul 15.

PMID:
15256416
39.

Expression Profiler: next generation--an online platform for analysis of microarray data.

Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W465-70.

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