2017 (2) 2016 (5) 2015 (4) 2014 (6) 2013 (8) 2012 (2) 2011 and before (22)


    MuPeXI: Prediction of neo-epitopes from tumor sequencing data
    Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC
    Cancer Immunol Immunother, 2017
    Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut
    Pipek O, Ribli D, Molnár J, Póti Á, Krzystanek M, Bodor A, Tusnády GE, Szallasi Z, Csabai I, Szüts D
    BMC Bioinformatics, 2017
    Relevant URL


    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 AJS, McGranahan N, Rosenthal R, Straten PT, Szallasi Z, Svane IM, Swanton C, Quezada SA, Jakobsen SN, Eklund AC, Hadrup SR
    Nat Biotechnol, 2016
    Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions
    Zámborszky J, Szikriszt B, Gervai JZ, Pipek O, Póti Á, Krzystanek M, Ribli D, Szalai-Gindl JM, Csabai I, Szallasi Z, Swanton C, Richardson AL, Szüts D
    Oncogene, 2016
    A comprehensive survey of the mutagenic impact of common cancer cytotoxics
    Szikriszt B, Póti Á, Pipek O, Krzystanek M, Kanu N, Molnár J, Ribli D, Szeltner Z, Tusnády GE, Csabai I, Szallasi Z, Swanton C, Szüts D
    Genome Biology, 2016
    Relevant URL
    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, 2016
    Journal link
    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., 2016
    BioMed Central


    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 Medical Genomics, 2015
    Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer
    Su Y, Subedee A, Bloushtain-Qimron N, Savova V, Krzystanek M, Li L, Marusyk A, Tabassum DP, Zak A, Flacker MJ, Li M, Lin JJ, Sukumar S, Suzuki H, Long H, Szallasi Z, Gimelbrant A, Maruyama R, Polyak K
    Cell Reports, 2015
    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
    Biomarker Research, 2015
    Biomarker Research
    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
    International journal of surgery, 2015


    Thrombocytosis portends adverse prognostic significance in patients with stage II colorectal carcinoma
    Guo T, Krzystanek M, Szallasi Z, Szallasi A
    F1000 Research, 2014
    Spatial and temporal diversity in genomic instability processes defines lung cancer evolution
    de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ, Grönroos E, Muhammad MA, Horswell S, Gerlinger M, Varela I, Jones D, Marshall J, Voet T, Van Loo P, Rassl DM, Rintoul RC, Janes SM, Lee SM, Forster M, Ahmad T, Lawrence D, Falzon M, Capitanio A, Harkins TT, Lee CC, Tom W, Teefe E, Chen SC, Begum S, Rabinowitz A, Phillimore B, Spencer-Dene B, Stamp G, Szallasi Z, Matthews N, Stewart A, Campbell P, Swanton C
    Science, 2014
    Relevant URL
    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
    Annals of Oncology, 2014
    Annals of Oncology
    Systematic Evaluation of the Prognostic Impact and Intratumour Heterogeneity of Clear Cell Renal Cell Carcinoma Biomarkers.
    Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M
    European Urology. 2014 Jul 18. pii: S0302-2838(14)00627-7., 2014
    Lactate dehydrogenase as a selection criterion for ipilimumab treatment in metastatic melanoma
    Kelderman S, Heemskerk B, van Tinteren H, van den Brom RR, Hospers GA, van den Eertwegh AJ, Kapiteijn EW, de Groot JW, Soetekouw P, Jansen RL, Fiets E, Furness AJ, Renn A, Krzystanek M, Szallasi Z, Lorigan P, Gore ME, Schumacher TN, Haanen JB, Larkin JM, Blank CU
    Cancer Immunology, Immunotherapy . 2014 May;63(5):449-58., 2014
    Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
    Dewhurst SM, McGranahan N, Burrell RA, Rowan AJ, Grönroos E, Endesfelder D, Joshi T, Mouradov D, Gibbs P, Ward RL, Hawkins NJ, Szallasi Z, Sieber OM, Swanton C
    Cancer Discovery. 2014 Feb;4(2):175-85., 2014


    Evaluation of thrombocytosis as predictive factor in colorectal cancer
    Baranyai Z, Jósa V, Krzystanek M, Eklund AC, Szász AM, Szállási Z
    Magyar Sebészet (Hungarian Journal of Surgery), 2013
    Complete genes may pass from food to human blood
    Spisák S, Solymosi N, Ittzés P, Bodor A, Kondor D, Vattay G, Barták BK, Sipos F, Galamb O, Tulassay Z, Szallasi Z, Rasmussen S, Sicheritz-Ponten T, Brunak S, Molnar B, Csabai I
    PLoS ONE 8(7):e69805 doi:10.1371/journal.pone.0069805, 2013
    The comparison of thrombocytosis and platelet-lymphocyte ratio as potential prognostic markers in colorectal cancer
    Baranyai Z, Krzystanek M, Jósa V, Dede K, Ágoston E, Szász AM, Sinkó D, Szarvas V, Salamon F, Eklund AC, Szallasi Z, Jakab F
    Thrombosis and Haemostasis, 2013
    Tumor Mutation Burden Forecasts Outcome in Ovarian Cancer with BRCA1 or BRCA2 Mutations
    Birkbak NJ, Kochupurakkal B, Izarzugaza JMG, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC
    Research Article | published 12 Nov 2013 | PLOS ONE 10.1371/journal.pone.0080023, 2013
    Parallel evolution of tumor subclones mimics diversity between tumors.
    Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell R, Rowan A, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C
    The Journal of Pathology. 230(4):356-64 doi:10.1002/path.4214, 2013
    Relevant URL
    Deconvoluting complex tissues for expression quantitative trait locus-based analyses.
    Seo JH, Li Q, Fatima A, Eklund A, Szallasi Z, Polyak K, Richardson AL, Freedman ML
    Philosophical Transactions of the Royal Society B: Biological Sciences. 368(1620):20120363 doi:10.1098/rstb.2012.0363, 2013
    Relevant URL
    Prognostic and Predictive Markers in Metastatic Renal Cell Carcinoma
    Khattak MA, Bakr F, Krzystanek M, Szallasi Z, Gerlinger M, Santos C, Swanton C, Pickering LM, Gore ME, Larkin JM
    Journal of Clinical Oncology. 31(7):971-2 doi:10.1200/JCO.2012.46.9353, 2013
    Biasogram: Visualization of Confounding Technical Bias in Gene Expression Data
    Krzystanek M, Szallasi Z, Eklund AC
    PLOS ONE, April 16 2013, 2013


    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 Discovery 2(4):366-75 doi:10.1158/2159-8290.CD-11-0206, 2012
    Intratumor heterogeneity and branched evolution revealed by multiregion sequencing
    Gerlinger M, Rowan AJ, Horswell S, 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
    Relevant URL


    Chromosomal instability confers intrinsic multidrug resistance
    Lee AJ, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, Downward J, Szallasi Z, Tomlinson IP, Howell M, Kschischo M, Swanton C
    Cancer Res. 71(5):1858-70 doi:10.1158/0008-5472.CAN-10-3604, 2011
    A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables
    Endesfelder D, McGranahan N, Birkbak NJ, Szallasi Z, Kschischo M, Graham TA, Swanton C
    Oncotarget 2(7):529-37, 2011
    CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction
    Lee AJ, Roylance R, Sander J, Gorman P, Endesfelder D, Kschischo M, Jones NP, East P, Nicke B, Spassieva S, Obeid LM, Birkbak NJ, Szallasi Z, McKnight NC, Rowan AJ, Speirs V, Hanby AM, Downward J, Tooze SA, Swanton C
    The Journal of Pathology. 226(3):482-94 doi:10.1002/path.2998, 2011
    Jetset: selecting the optimal microarray probe set to represent a gene
    Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC
    BMC Bioinformatics 12:474 doi:10.1186/1471-2105-12-474, 2011
    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, Szallasi Z, Kschischo M, Swanton C
    Cancer Epidemiol. Biomarkers Prev. 20(10):2183-94 doi:10.1158/1055-9965.EPI-11-0343, 2011
    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 12:310 doi:10.1186/1471-2105-12-310, 2011
    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. 71(10):3447-52 doi:10.1158/0008-5472.CAN-10-3667, 2011


    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 5(12):e15031 doi:10.1371/journal.pone.0015031, 2010
    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 C, Boehme KA, Volkmer H, Toschi L, Nicke B, Beck M, Szallasi Z
    Genome Med 2(8):53 doi:10.1186/gm174, 2010
    Targeting chromosomal instability and tumour heterogeneity in HER2 positive breast cancer
    Burrell RA, Juul N, Johnston SR, Reis-Filho J, Szallasi Z, Swanton C
    J. Cell. Biochem. 111(4):782-90 doi:10.1002/jcb.22781, 2010
    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. 11(4):358-65 doi:10.1016/S1470-2045(10)70018-8, 2010
    Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer
    Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, Richardson AL, Wang ZC
    Nature Medicine. 16(2):214-8 doi:10.1038/nm.2090, 2010
    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
    Journal of Clinical Oncology. 28(7):1145-53 doi:10.1200/JCO.2009.22.4725, 2010


    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. 123(3):725-31 doi:10.1007/s10549-009-0674-9, 2009
    Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
    Aron C Eklund; Pia Friis; Rasmus Wernersson; Zoltan Szallasi
    Nucleic Acids Research. 38(4):e27 doi:10.1093/nar/gkp1116, 2009
    Read article
    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 4(5):e5645 doi:10.1371/journal.pone.0005645, 2009
    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
    PNAS, Proceedings of the National Academy of Sciences U.S.A. 106(21):8671-6 doi:10.1073/pnas.0811835106, 2009


    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 7(24):3947-8, 2008
    Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer
    Swanton C, Szallasi Z, Brenton JD, Downward J
    Breast Cancer Res. 10(5):214 doi:10.1186/bcr2159, 2008
    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 F, Donahoe PK, Szallasi Z, Jensen TS, Brunak S
    Proc. Natl. Acad. Sci. U.S.A. 105(52):20870-5 doi:10.1073/pnas.0810772105, 2008
    Correction of technical bias in clinical microarray data improves concordance with known biological information
    Eklund AC, Szallasi Z
    Genome Biol. 9(2):R26 doi:10.1186/gb-2008-9-2-r26, 2008


    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. 38(9):1043-8, 2006

2017 (2) 2016 (5) 2015 (4) 2014 (6) 2013 (8) 2012 (2) 2011 and before (22)