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Items: 35

1.

Correction to: Sequencing and curation strategies for identifying candidate glioblastoma treatments.

Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang X, Vacic V, Bergmann EA, Moore Vogel JL, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB.

BMC Med Genomics. 2019 Aug 2;12(1):114. doi: 10.1186/s12920-019-0563-y.

2.

Sequencing and curation strategies for identifying candidate glioblastoma treatments.

Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang A, Vacic V, Bergmann EA, Vogel JLM, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB.

BMC Med Genomics. 2019 Apr 25;12(1):56. doi: 10.1186/s12920-019-0500-0. Erratum in: BMC Med Genomics. 2019 Aug 2;12(1):114.

3.

Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia.

McNeer NA, Philip J, Geiger H, Ries RE, Lavallée VP, Walsh M, Shah M, Arora K, Emde AK, Robine N, Alonzo TA, Kolb EA, Gamis AS, Smith M, Gerhard DS, Guidry-Auvil J, Meshinchi S, Kentsis A.

Leukemia. 2019 Aug;33(8):1934-1943. doi: 10.1038/s41375-019-0402-3. Epub 2019 Feb 13.

4.

Human papillomavirus and the landscape of secondary genetic alterations in oral cancers.

Gillison ML, Akagi K, Xiao W, Jiang B, Pickard RKL, Li J, Swanson BJ, Agrawal AD, Zucker M, Stache-Crain B, Emde AK, Geiger HM, Robine N, Coombes KR, Symer DE.

Genome Res. 2019 Jan;29(1):1-17. doi: 10.1101/gr.241141.118. Epub 2018 Dec 18.

5.

Genome-wide somatic variant calling using localized colored de Bruijn graphs.

Narzisi G, Corvelo A, Arora K, Bergmann EA, Shah M, Musunuri R, Emde AK, Robine N, Vacic V, Zody MC.

Commun Biol. 2018 Mar 22;1:20. doi: 10.1038/s42003-018-0023-9. eCollection 2018.

6.

Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer.

Wrzeszczynski KO, Felice V, Abhyankar A, Kozon L, Geiger H, Manaa D, London F, Robinson D, Fang X, Lin D, Lamendola-Essel MF, Khaira D, Dikoglu E, Emde AK, Robine N, Shah M, Arora K, Basturk O, Bhanot U, Kentsis A, Mansukhani MM, Bhagat G, Jobanputra V.

J Mol Diagn. 2018 Nov;20(6):822-835. doi: 10.1016/j.jmoldx.2018.06.007. Epub 2018 Aug 21.

7.

Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma.

Wrzeszczynski KO, Felice V, Shah M, Rahman S, Emde AK, Jobanputra V, O Frank M, Darnell RB.

Methods Mol Biol. 2018;1741:1-29. doi: 10.1007/978-1-4939-7659-1_1.

PMID:
29392687
8.

Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models.

Pisapia DJ, Salvatore S, Pauli C, Hissong E, Eng K, Prandi D, Sailer VW, Robinson BD, Park K, Cyrta J, Tagawa ST, Kossai M, Fontugne J, Kim R, Sigaras A, Rao R, Pancirer D, Faltas B, Bareja R, Molina AM, Nanus DM, Rajappa P, Souweidane MM, Greenfield J, Emde AK, Robine N, Elemento O, Sboner A, Demichelis F, Beltran H, Rubin MA, Mosquera JM.

JCO Precis Oncol. 2017;2017. doi: 10.1200/PO.16.00038. Epub 2017 Jun 14.

9.

Erratum: PGBD5 promotes site-specific oncogenic mutations in human tumors.

Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A.

Nat Genet. 2017 Sep 27;49(10):1558. doi: 10.1038/ng1017-1558b. No abstract available.

PMID:
28951624
10.

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.

Neurol Genet. 2017 Jul 11;3(4):e164. doi: 10.1212/NXG.0000000000000164. eCollection 2017 Aug.

11.

PGBD5 promotes site-specific oncogenic mutations in human tumors.

Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A.

Nat Genet. 2017 Jul;49(7):1005-1014. doi: 10.1038/ng.3866. Epub 2017 May 15. Erratum in: Nat Genet. 2017 Sep 27;49(10 ):1558.

12.

Modeling and predicting optimal treatment scheduling between the antiangiogenic drug sunitinib and irinotecan in preclinical settings.

Wilson S, Tod M, Ouerdani A, Emde A, Yarden Y, Adda Berkane A, Kassour S, Wei MX, Freyer G, You B, Grenier E, Ribba B.

CPT Pharmacometrics Syst Pharmacol. 2015 Dec;4(12):720-7. doi: 10.1002/psp4.12045. Epub 2015 Dec 11.

13.

Dysregulated miRNA biogenesis downstream of cellular stress and ALS-causing mutations: a new mechanism for ALS.

Emde A, Eitan C, Liou LL, Libby RT, Rivkin N, Magen I, Reichenstein I, Oppenheim H, Eilam R, Silvestroni A, Alajajian B, Ben-Dov IZ, Aebischer J, Savidor A, Levin Y, Sons R, Hammond SM, Ravits JM, Möller T, Hornstein E.

EMBO J. 2015 Nov 3;34(21):2633-51. doi: 10.15252/embj.201490493. Epub 2015 Sep 1.

14.

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.

Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA.

JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313.

15.

X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.

Hu H, Haas SA, Chelly J, Van Esch H, Raynaud M, de Brouwer AP, Weinert S, Froyen G, Frints SG, Laumonnier F, Zemojtel T, Love MI, Richard H, Emde AK, Bienek M, Jensen C, Hambrock M, Fischer U, Langnick C, Feldkamp M, Wissink-Lindhout W, Lebrun N, Castelnau L, Rucci J, Montjean R, Dorseuil O, Billuart P, Stuhlmann T, Shaw M, Corbett MA, Gardner A, Willis-Owen S, Tan C, Friend KL, Belet S, van Roozendaal KE, Jimenez-Pocquet M, Moizard MP, Ronce N, Sun R, O'Keeffe S, Chenna R, van Bömmel A, Göke J, Hackett A, Field M, Christie L, Boyle J, Haan E, Nelson J, Turner G, Baynam G, Gillessen-Kaesbach G, Müller U, Steinberger D, Budny B, Badura-Stronka M, Latos-Bieleńska A, Ousager LB, Wieacker P, Rodríguez Criado G, Bondeson ML, Annerén G, Dufke A, Cohen M, Van Maldergem L, Vincent-Delorme C, Echenne B, Simon-Bouy B, Kleefstra T, Willemsen M, Fryns JP, Devriendt K, Ullmann R, Vingron M, Wrogemann K, Wienker TF, Tzschach A, van Bokhoven H, Gecz J, Jentsch TJ, Chen W, Ropers HH, Kalscheuer VM.

Mol Psychiatry. 2016 Jan;21(1):133-48. doi: 10.1038/mp.2014.193. Epub 2015 Feb 3.

16.

Disease variants in genomes of 44 centenarians.

Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, Emde AK, Ben-Avraham D, Barzilai N, Oschwald D, Christen E, Koppel J, Greenwald B, Darnell RB, Germer S, Atzmon G, Davies P.

Mol Genet Genomic Med. 2014 Sep;2(5):438-50. doi: 10.1002/mgg3.86. Epub 2014 Jun 15.

17.

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.

Brannon AR, Vakiani E, Sylvester BE, Scott SN, McDermott G, Shah RH, Kania K, Viale A, Oschwald DM, Vacic V, Emde AK, Cercek A, Yaeger R, Kemeny NE, Saltz LB, Shia J, D'Angelica MI, Weiser MR, Solit DB, Berger MF.

Genome Biol. 2014 Aug 28;15(8):454. doi: 10.1186/s13059-014-0454-7.

18.

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone.

Trappe K, Emde AK, Ehrlich HC, Reinert K.

Bioinformatics. 2014 Dec 15;30(24):3484-90. doi: 10.1093/bioinformatics/btu431. Epub 2014 Jul 14.

PMID:
25028727
19.

miRNAs at the interface of cellular stress and disease.

Emde A, Hornstein E.

EMBO J. 2014 Jul 1;33(13):1428-37. doi: 10.15252/embj.201488142. Epub 2014 May 27. Review.

20.

Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma.

Honeyman JN, Simon EP, Robine N, Chiaroni-Clarke R, Darcy DG, Lim II, Gleason CE, Murphy JM, Rosenberg BR, Teegan L, Takacs CN, Botero S, Belote R, Germer S, Emde AK, Vacic V, Bhanot U, LaQuaglia MP, Simon SM.

Science. 2014 Feb 28;343(6174):1010-4. doi: 10.1126/science.1249484.

21.

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.

Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.

Bioinformatics. 2012 Apr 1;28(7):1024-5. doi: 10.1093/bioinformatics/bts064. Epub 2012 Feb 1.

PMID:
22302574
22.

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K.

Bioinformatics. 2012 Mar 1;28(5):619-27. doi: 10.1093/bioinformatics/bts019. Epub 2012 Jan 11.

PMID:
22238266
23.

Modeling invasive breast cancer: growth factors propel progression of HER2-positive premalignant lesions.

Pradeep CR, Zeisel A, Köstler WJ, Lauriola M, Jacob-Hirsch J, Haibe-Kains B, Amariglio N, Ben-Chetrit N, Emde A, Solomonov I, Neufeld G, Piccart M, Sagi I, Sotiriou C, Rechavi G, Domany E, Desmedt C, Yarden Y.

Oncogene. 2012 Aug 2;31(31):3569-83. doi: 10.1038/onc.2011.547. Epub 2011 Dec 5.

24.

Simultaneous Inhibition of Estrogen Receptor and the HER2 Pathway in Breast Cancer: Effects of HER2 Abundance.

Emde A, Mahlknecht G, Maslak K, Ribba B, Sela M, Possinger K, Yarden Y.

Transl Oncol. 2011 Oct;4(5):293-300. Epub 2011 Oct 1.

25.

A novel and well-defined benchmarking method for second generation read mapping.

Holtgrewe M, Emde AK, Weese D, Reinert K.

BMC Bioinformatics. 2011 May 26;12:210. doi: 10.1186/1471-2105-12-210.

26.

Combining epitope-distinct antibodies to HER2: cooperative inhibitory effects on invasive growth.

Emde A, Pradeep CR, Ferraro DA, Ben-Chetrit N, Sela M, Ribba B, Kam Z, Yarden Y.

Oncogene. 2011 Apr 7;30(14):1631-42. doi: 10.1038/onc.2010.547. Epub 2010 Dec 6.

27.

Therapeutic strategies and mechanisms of tumorigenesis of HER2-overexpressing breast cancer.

Emde A, Köstler WJ, Yarden Y; Association of Radiotherapy and Oncology of the Mediterranean arEa (AROME).

Crit Rev Oncol Hematol. 2012 Dec;84 Suppl 1:e49-57. doi: 10.1016/j.critrevonc.2010.09.002. Epub 2010 Oct 15. Review.

28.

MicroRazerS: rapid alignment of small RNA reads.

Emde AK, Grunert M, Weese D, Reinert K, Sperling SR.

Bioinformatics. 2010 Jan 1;26(1):123-4. doi: 10.1093/bioinformatics/btp601. Epub 2009 Oct 29.

PMID:
19880369
29.

RazerS--fast read mapping with sensitivity control.

Weese D, Emde AK, Rausch T, Döring A, Reinert K.

Genome Res. 2009 Sep;19(9):1646-54. doi: 10.1101/gr.088823.108. Epub 2009 Jul 10.

30.

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K.

Bioinformatics. 2009 May 1;25(9):1118-24. doi: 10.1093/bioinformatics/btp131. Epub 2009 Mar 5.

31.

Segment-based multiple sequence alignment.

Rausch T, Emde AK, Weese D, Döring A, Notredame C, Reinert K.

Bioinformatics. 2008 Aug 15;24(16):i187-92. doi: 10.1093/bioinformatics/btn281.

PMID:
18689823
32.

Anti-tumor effect of honokiol alone and in combination with other anti-cancer agents in breast cancer.

Liu H, Zang C, Emde A, Planas-Silva MD, Rosche M, Kühnl A, Schulz CO, Elstner E, Possinger K, Eucker J.

Eur J Pharmacol. 2008 Sep 4;591(1-3):43-51. doi: 10.1016/j.ejphar.2008.06.026. Epub 2008 Jun 12.

PMID:
18588872
33.

[Treatment of breast cancer: from hormones to antibodies].

Eucker J, Emde A, Possinger K.

Internist (Berl). 2006 Dec;47(12):1223-4, 1226-8. Review. German.

PMID:
17063333
34.

Analytical model of peptide mass cluster centres with applications.

Wolski WE, Farrow M, Emde AK, Lehrach H, Lalowski M, Reinert K.

Proteome Sci. 2006 Sep 23;4:18.

35.

Immunoprofiles of 11 biomarkers using tissue microarrays identify prognostic subgroups in colorectal cancer.

Knösel T, Emde A, Schlüns K, Chen Y, Jürchott K, Krause M, Dietel M, Petersen I.

Neoplasia. 2005 Aug;7(8):741-7.

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