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Items: 1 to 50 of 55

1.

Individual and structural factors predicting HIV testing among Latinx MSM: substance use as a moderator.

Eklund AC, Dillon FR, Ebersole RC.

AIDS Care. 2019 May 19:1-9. doi: 10.1080/09540121.2019.1619664. [Epub ahead of print]

PMID:
31104481
2.

Bifidobacteriumbreve Bif195 Protects Against Small-Intestinal Damage Caused by Acetylsalicylic Acid in Healthy Volunteers.

Mortensen B, Murphy C, O'Grady J, Lucey M, Elsafi G, Barry L, Westphal V, Wellejus A, Lukjancenko O, Eklund AC, Nielsen HB, Baker A, Damholt A, van Hylckama Vlieg JET, Shanahan F, Buckley M.

Gastroenterology. 2019 Sep;157(3):637-646.e4. doi: 10.1053/j.gastro.2019.05.008. Epub 2019 May 13.

3.

Corrigendum to: Breast cancer brain metastases show increased levels of genomic aberration-based homologous recombination deficiency scores relative to their corresponding primary tumors.

Diossy M, Reiniger L, Sztupinszki Z, Krzystanek M, Timms KM, Neff C, Solimeno C, Pruss D, Eklund AC, Tóth E, Kiss O, Rusz O, Cserni G, Zombori T, Székely B, Kulka J, Tímár J, Csabai I, Szallasi Z.

Ann Oncol. 2019 Mar 30. pii: mdz081. doi: 10.1093/annonc/mdz081. [Epub ahead of print] No abstract available.

4.

Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer.

Sztupinszki Z, Diossy M, Krzystanek M, Reiniger L, Csabai I, Favero F, Birkbak NJ, Eklund AC, Syed A, Szallasi Z.

NPJ Breast Cancer. 2018 Jul 2;4:16. doi: 10.1038/s41523-018-0066-6. eCollection 2018.

5.

Breast cancer brain metastases show increased levels of genomic aberration-based homologous recombination deficiency scores relative to their corresponding primary tumors.

Diossy M, Reiniger L, Sztupinszki Z, Krzystanek M, Timms KM, Neff C, Solimeno C, Pruss D, Eklund AC, Tóth E, Kiss O, Rusz O, Cserni G, Zombori T, Székely B, Tímár J, Csabai I, Szallasi Z.

Ann Oncol. 2018 Sep 1;29(9):1948-1954. doi: 10.1093/annonc/mdy216. Erratum in: Ann Oncol. 2019 Mar 30;:.

6.

Corrigendum: An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes.

Bjerregaard AM, Nielsen M, Jurtz V, Barra CM, Hadrup SR, Szallasi Z, Eklund AC.

Front Immunol. 2018 May 14;9:1007. doi: 10.3389/fimmu.2018.01007. eCollection 2018.

7.

Computational prediction of neoantigens: do we need more data or new approaches?

Eklund AC, Szallasi Z.

Ann Oncol. 2018 Apr 1;29(4):799-801. doi: 10.1093/annonc/mdy070. No abstract available.

PMID:
29481589
8.

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes.

Bjerregaard AM, Nielsen M, Jurtz V, Barra CM, Hadrup SR, Szallasi Z, Eklund AC.

Front Immunol. 2017 Nov 15;8:1566. doi: 10.3389/fimmu.2017.01566. eCollection 2017. Erratum in: Front Immunol. 2018 May 14;9:1007.

9.

MuPeXI: prediction of neo-epitopes from tumor sequencing data.

Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC.

Cancer Immunol Immunother. 2017 Sep;66(9):1123-1130. doi: 10.1007/s00262-017-2001-3. Epub 2017 Apr 20.

PMID:
28429069
10.

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.

Bentzen AK, Marquard AM, Lyngaa R, Saini SK, Ramskov S, Donia M, Such L, Furness AJ, McGranahan N, Rosenthal R, Straten PT, Szallasi Z, Svane IM, Swanton C, Quezada SA, Jakobsen SN, Eklund AC, Hadrup SR.

Nat Biotechnol. 2016 Oct;34(10):1037-1045. doi: 10.1038/nbt.3662. Epub 2016 Aug 29.

PMID:
27571370
11.

A robust prognostic gene expression signature for early stage lung adenocarcinoma.

Krzystanek M, Moldvay J, Szüts D, Szallasi Z, Eklund AC.

Biomark Res. 2016 Feb 19;4:4. doi: 10.1186/s40364-016-0058-3. eCollection 2016.

12.

MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy.

Neupane M, Clark AP, Landini S, Birkbak NJ, Eklund AC, Lim E, Culhane AC, Barry WT, Schumacher SE, Beroukhim R, Szallasi Z, Vidal M, Hill DE, Silver DP.

Cancer Discov. 2016 Jan;6(1):45-58. doi: 10.1158/2159-8290.CD-15-0341. Epub 2015 Nov 6.

13.

TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen.

Marquard AM, Birkbak NJ, Thomas CE, Favero F, Krzystanek M, Lefebvre C, Ferté C, Jamal-Hanjani M, Wilson GA, Shafi S, Swanton C, André F, Szallasi Z, Eklund AC.

BMC Med Genomics. 2015 Oct 1;8:58. doi: 10.1186/s12920-015-0130-0.

14.

Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs.

Marquard AM, Eklund AC, Joshi T, Krzystanek M, Favero F, Wang ZC, Richardson AL, Silver DP, Szallasi Z, Birkbak NJ.

Biomark Res. 2015 May 1;3:9. doi: 10.1186/s40364-015-0033-4. eCollection 2015.

15.

Relationship of postoperative thrombocytosis and survival of patients with colorectal cancer.

Josa V, Krzystanek M, Eklund AC, Salamon F, Zarand A, Szallasi Z, Baranyai Z.

Int J Surg. 2015 Jun;18:1-6. doi: 10.1016/j.ijsu.2015.03.005. Epub 2015 Apr 3.

16.

Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome.

Favero F, McGranahan N, Salm M, Birkbak NJ, Sanborn JZ, Benz SC, Becq J, Peden JF, Kingsbury Z, Grocok RJ, Humphray S, Bentley D, Spencer-Dene B, Gutteridge A, Brada M, Roger S, Dietrich PY, Forshew T, Gerlinger M, Rowan A, Stamp G, Eklund AC, Szallasi Z, Swanton C.

Ann Oncol. 2015 May;26(5):880-7. doi: 10.1093/annonc/mdv127. Epub 2015 Mar 2.

17.

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC.

Ann Oncol. 2015 Jan;26(1):64-70. doi: 10.1093/annonc/mdu479. Epub 2014 Oct 15.

18.

[Evaluation of thrombocytosis as predictive factor in colorectal cancer].

Baranyai Z, Jósa V, Krzystanek M, Eklund AC, Szász AM, Szállási Z.

Magy Seb. 2013 Dec;66(6):331-7. doi: 10.1556/MaSeb.66.2013.6.5. Hungarian.

PMID:
24333978
19.

The comparison of thrombocytosis and platelet-lymphocyte ratio as potential prognostic markers in colorectal cancer.

Baranyai Z, Krzystanek M, Jósa V, Dede K, Agoston E, Szász AM, Sinkó D, Szarvas V, Salamon F, Eklund AC, Szállási Z, Jakab F.

Thromb Haemost. 2014 Mar 3;111(3):483-90. doi: 10.1160/TH13-08-0632. Epub 2013 Nov 28.

PMID:
24285160
20.

Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations.

Birkbak NJ, Kochupurakkal B, Izarzugaza JM, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC.

PLoS One. 2013 Nov 12;8(11):e80023. doi: 10.1371/journal.pone.0080023. eCollection 2013.

21.

Biasogram: visualization of confounding technical bias in gene expression data.

Krzystanek M, Szallasi Z, Eklund AC.

PLoS One. 2013 Apr 16;8(4):e61872. doi: 10.1371/journal.pone.0061872. Print 2013.

22.

The CIN4 chromosomal instability qPCR classifier defines tumor aneuploidy and stratifies outcome in grade 2 breast cancer.

Szász AM, Li Q, Eklund AC, Sztupinszki Z, Rowan A, Tőkés AM, Székely B, Kiss A, Szendrői M, Győrffy B, Szállási Z, Swanton C, Kulka J.

PLoS One. 2013;8(2):e56707. doi: 10.1371/journal.pone.0056707. Epub 2013 Feb 26.

23.

Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents.

Birkbak NJ, Wang ZC, Kim JY, Eklund AC, Li Q, Tian R, Bowman-Colin C, Li Y, Greene-Colozzi A, Iglehart JD, Tung N, Ryan PD, Garber JE, Silver DP, Szallasi Z, Richardson AL.

Cancer Discov. 2012 Apr;2(4):366-375. doi: 10.1158/2159-8290.CD-11-0206. Epub 2012 Mar 22. Erratum in: Cancer Discov. 2013 Aug;3(8):952.

24.

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

Gerlinger M, Rowan AJ, Horswell S, Math M, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal PA, Swanton C.

N Engl J Med. 2012 Mar 8;366(10):883-892. doi: 10.1056/NEJMoa1113205. Erratum in: N Engl J Med. 2012 Sep 6;367(10):976.

25.

Jetset: selecting the optimal microarray probe set to represent a gene.

Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC.

BMC Bioinformatics. 2011 Dec 15;12:474. doi: 10.1186/1471-2105-12-474.

26.

Prediction of drug efficacy for cancer treatment based on comparative analysis of chemosensitivity and gene expression data.

Wan P, Li Q, Larsen JE, Eklund AC, Parlesak A, Rigina O, Nielsen SJ, Björkling F, Jónsdóttir SÓ.

Bioorg Med Chem. 2012 Jan 1;20(1):167-76. doi: 10.1016/j.bmc.2011.11.019. Epub 2011 Nov 22.

PMID:
22154557
27.

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response.

Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z.

BMC Bioinformatics. 2011 Jul 28;12:310. doi: 10.1186/1471-2105-12-310.

28.

Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer.

Roylance R, Endesfelder D, Gorman P, Burrell RA, Sander J, Tomlinson I, Hanby AM, Speirs V, Richardson AL, Birkbak NJ, Eklund AC, Downward J, Kschischo M, Szallasi Z, Swanton C.

Cancer Epidemiol Biomarkers Prev. 2011 Oct;20(10):2183-94. doi: 10.1158/1055-9965.EPI-11-0343. Epub 2011 Jul 22.

29.

Paradoxical relationship between chromosomal instability and survival outcome in cancer.

Birkbak NJ, Eklund AC, Li Q, McClelland SE, Endesfelder D, Tan P, Tan IB, Richardson AL, Szallasi Z, Swanton C.

Cancer Res. 2011 May 15;71(10):3447-52. doi: 10.1158/0008-5472.CAN-10-3667. Epub 2011 Jan 26.

30.

Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status.

Li Q, Eklund AC, Juul N, Haibe-Kains B, Workman CT, Richardson AL, Szallasi Z, Swanton C.

PLoS One. 2010 Dec 1;5(12):e15031. doi: 10.1371/journal.pone.0015031.

31.

PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease.

Zheng B, Liao Z, Locascio JJ, Lesniak KA, Roderick SS, Watt ML, Eklund AC, Zhang-James Y, Kim PD, Hauser MA, Grünblatt E, Moran LB, Mandel SA, Riederer P, Miller RM, Federoff HJ, Wüllner U, Papapetropoulos S, Youdim MB, Cantuti-Castelvetri I, Young AB, Vance JM, Davis RL, Hedreen JC, Adler CH, Beach TG, Graeber MB, Middleton FA, Rochet JC, Scherzer CR; Global PD Gene Expression (GPEX) Consortium.

Sci Transl Med. 2010 Oct 6;2(52):52ra73. doi: 10.1126/scitranslmed.3001059.

32.

Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets.

Swanton C, Larkin JM, Gerlinger M, Eklund AC, Howell M, Stamp G, Downward J, Gore M, Futreal PA, Escudier B, Andre F, Albiges L, Beuselinck B, Oudard S, Hoffmann J, Gyorffy B, Torrance CJ, Boehme KA, Volkmer H, Toschi L, Nicke B, Beck M, Szallasi Z.

Genome Med. 2010 Aug 11;2(8):53. doi: 10.1186/gm174.

33.

Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials.

Juul N, Szallasi Z, Eklund AC, Li Q, Burrell RA, Gerlinger M, Valero V, Andreopoulou E, Esteva FJ, Symmans WF, Desmedt C, Haibe-Kains B, Sotiriou C, Pusztai L, Swanton C.

Lancet Oncol. 2010 Apr;11(4):358-65. doi: 10.1016/S1470-2045(10)70018-8. Epub 2010 Feb 26.

34.

Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer.

Silver DP, Richardson AL, Eklund AC, Wang ZC, Szallasi Z, Li Q, Juul N, Leong CO, Calogrias D, Buraimoh A, Fatima A, Gelman RS, Ryan PD, Tung NM, De Nicolo A, Ganesan S, Miron A, Colin C, Sgroi DC, Ellisen LW, Winer EP, Garber JE.

J Clin Oncol. 2010 Mar 1;28(7):1145-53. doi: 10.1200/JCO.2009.22.4725. Epub 2010 Jan 25.

35.

An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients.

Györffy B, Lanczky A, Eklund AC, Denkert C, Budczies J, Li Q, Szallasi Z.

Breast Cancer Res Treat. 2010 Oct;123(3):725-31. doi: 10.1007/s10549-009-0674-9. Epub 2009 Dec 18.

PMID:
20020197
36.

Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization.

Eklund AC, Friis P, Wernersson R, Szallasi Z.

Nucleic Acids Res. 2010 Mar;38(4):e27. doi: 10.1093/nar/gkp1116. Epub 2009 Dec 6.

37.

Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples.

Gyorffy B, Molnar B, Lage H, Szallasi Z, Eklund AC.

PLoS One. 2009 May 21;4(5):e5645. doi: 10.1371/journal.pone.0005645.

38.

Chromosomal instability determines taxane response.

Swanton C, Nicke B, Schuett M, Eklund AC, Ng C, Li Q, Hardcastle T, Lee A, Roy R, East P, Kschischo M, Endesfelder D, Wylie P, Kim SN, Chen JG, Howell M, Ried T, Habermann JK, Auer G, Brenton JD, Szallasi Z, Downward J.

Proc Natl Acad Sci U S A. 2009 May 26;106(21):8671-6. doi: 10.1073/pnas.0811835106. Epub 2009 May 19.

39.

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes.

Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S.

Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20870-5. doi: 10.1073/pnas.0810772105. Epub 2008 Dec 22.

40.

Concordance of exon array and real-time PCR assessment of gene expression following cancer cell cytotoxic drug exposure.

Lee AJ, East P, Pepper S, Nicke B, Szallasi Z, Eklund AC, Downward J, Swanton C.

Cell Cycle. 2008 Dec 15;7(24):3947-8. Epub 2008 Dec 17. No abstract available.

PMID:
19066460
41.

MicroRNA profile analysis of human prostate cancers.

Tong AW, Fulgham P, Jay C, Chen P, Khalil I, Liu S, Senzer N, Eklund AC, Han J, Nemunaitis J.

Cancer Gene Ther. 2009 Mar;16(3):206-16. doi: 10.1038/cgt.2008.77. Epub 2008 Oct 24.

PMID:
18949015
42.

GATA transcription factors directly regulate the Parkinson's disease-linked gene alpha-synuclein.

Scherzer CR, Grass JA, Liao Z, Pepivani I, Zheng B, Eklund AC, Ney PA, Ng J, McGoldrick M, Mollenhauer B, Bresnick EH, Schlossmacher MG.

Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10907-12. doi: 10.1073/pnas.0802437105. Epub 2008 Jul 31.

43.

Are designer guppies inbred? Microsatellite variation in five strains of ornamental guppies, Poecilia reticulata, used for behavioral research.

Bleakley BH, Eklund AC, Brodie ED.

Zebrafish. 2008 Spring;5(1):39-48. doi: 10.1089/zeb.2007.0513.

PMID:
18361681
44.

Correction of technical bias in clinical microarray data improves concordance with known biological information.

Eklund AC, Szallasi Z.

Genome Biol. 2008;9(2):R26. doi: 10.1186/gb-2008-9-2-r26. Epub 2008 Feb 4.

45.

Molecular markers of early Parkinson's disease based on gene expression in blood.

Scherzer CR, Eklund AC, Morse LJ, Liao Z, Locascio JJ, Fefer D, Schwarzschild MA, Schlossmacher MG, Hauser MA, Vance JM, Sudarsky LR, Standaert DG, Growdon JH, Jensen RV, Gullans SR.

Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):955-60. Epub 2007 Jan 10.

46.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr.

Nat Biotechnol. 2006 Sep;24(9):1151-61.

47.

Replacing cRNA targets with cDNA reduces microarray cross-hybridization.

Eklund AC, Turner LR, Chen P, Jensen RV, deFeo G, Kopf-Sill AR, Szallasi Z.

Nat Biotechnol. 2006 Sep;24(9):1071-3. No abstract available.

PMID:
16964210
48.

A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers.

Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z.

Nat Genet. 2006 Sep;38(9):1043-8. Epub 2006 Aug 20.

PMID:
16921376
49.

Male 11-ketotestosterone levels change as a result of being watched in Siamese fighting fish, Betta splendens.

Dzieweczynski TL, Eklund AC, Rowland WJ.

Gen Comp Endocrinol. 2006 Jun;147(2):184-9. Epub 2006 Feb 13.

PMID:
16473353
50.

Reliability and reproducibility issues in DNA microarray measurements.

Draghici S, Khatri P, Eklund AC, Szallasi Z.

Trends Genet. 2006 Feb;22(2):101-9. Epub 2005 Dec 27. Review.

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