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Zoltan Szallasi, MD

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Computational Health Informatics Program (CHIP)
Medicine Research
Hospital Title:
Associate Scientific Researcher
Academic Title:
Assistant Professor of Pediatrics, Harvard Medical School
Research Focus Area:
Cancer Genomics
Contact Via Email
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Research Overview

We are using cancer genome analysis to understand essential and clinically relevant biology about human cancer. DNA repair pathway aberrations significantly contribute to the genomic instability underlying cancerous development  and often determine the efficacy to a particular genotoxic therapy.   We used cancer genomics to identify a DNA aberration pattern that is associated with homologous recombination incompetence and human tumors displaying this DNA aberration profile are particularly sensitive to platinum based therapy. This method is used currently undergoing clinical testing to prioritize patients for platinum based therapy. In order to identify further clinically useful DNA aberration patterns, we have developed a next generation based model model system to systematically identify mutational signatures associated with defects in the various DNA repair pathways.


Publications powered by Harvard Catalyst Profiles
  1. Martinez P, Kimberley C, BirkBak NJ, Marquard A, Szallasi Z, Graham TA. Quantification of within-sample genetic heterogeneity from SNP-array data. Sci Rep. 2017 Jun 12; 7(1):3248.
  2. Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature. 2017 Apr 26; 545(7655):446-451.
  3. Jamal-Hanjani M, Wilson GA, McGranahan N, Birkbak NJ, Watkins TBK, Veeriah S, Shafi S, Johnson DH, Mitter R, Rosenthal R, Salm M, Horswell S, Escudero M, Matthews N, Rowan A, Chambers T, Moore DA, Turajlic S, Xu H, Lee SM, Forster MD, Ahmad T, Hiley CT, Abbosh C, Falzon M, Borg E, Marafioti T, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Shah R, Joseph L, Quinn AM, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Dentro S, Taniere P, O'Sullivan B, Lowe HL, Hartley JA, Iles N, Bell H, Ngai Y, Shaw JA, Herrero J, Szallasi Z, Schwarz RF, Stewart A, Quezada SA, Le Quesne J, Van Loo P, Dive C, Hackshaw A, Swanton C. Tracking the Evolution of Non-Small-Cell Lung Cancer. N Engl J Med. 2017 06 01; 376(22):2109-2121.
  4. Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC. MuPeXI: prediction of neo-epitopes from tumor sequencing data. Cancer Immunol Immunother. 2017 Apr 20.
  5. Szallasi Z. Detecting mutant KRAS in liquid biopsies: a biomarker searching for a role. Ann Oncol. 2017 Apr 01; 28(4):677-678.
  6. Pipek O, Ribli D, Molnár J, Póti Á, Krzystanek M, Bodor A, Tusnády GE, Szallasi Z, Csabai I, Szüts D. Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut. BMC Bioinformatics. 2017 Jan 31; 18(1):73.
  7. 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. Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes. Nat Biotechnol. 2016 Oct; 34(10):1037-1045.
  8. 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. Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions. Oncogene. 2017 Feb 09; 36(6):746-755.
  9. 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. A comprehensive survey of the mutagenic impact of common cancer cytotoxics. Genome Biol. 2016 May 09; 17:99.
  10. Telli ML, Timms KM, Reid J, Hennessy B, Mills GB, Jensen KC, Szallasi Z, Barry WT, Winer EP, Tung NM, Isakoff SJ, Ryan PD, Greene-Colozzi A, Gutin A, Sangale Z, Iliev D, Neff C, Abkevich V, Jones JT, Lanchbury JS, Hartman AR, Garber JE, Ford JM, Silver DP, Richardson AL. Homologous Recombination Deficiency (HRD) Score Predicts Response to Platinum-Containing Neoadjuvant Chemotherapy in Patients with Triple-Negative Breast Cancer. Clin Cancer Res. 2016 Aug 01; 22(15):3764-73.
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  12. Krzystanek M, Moldvay J, Szüts D, Szallasi Z, Eklund AC. A robust prognostic gene expression signature for early stage lung adenocarcinoma. Biomark Res. 2016; 4:4.
  13. Szallasi Z. Another surprising role for exosomes? Improving next-generation sequencing-based cancer diagnostics in liquid biopsies. Ann Oncol. 2016 Apr; 27(4):557-8.
  14. 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. MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy. Cancer Discov. 2016 Jan; 6(1):45-58.
  15. Petrovics G, Li H, Stümpel T, Tan SH, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn IA, Freedman M, Dobi A, Srivastava S. A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men. EBioMedicine. 2015 Dec; 2(12):1957-64.
  16. 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. TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen. BMC Med Genomics. 2015 Oct 01; 8:58.
  17. 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. Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer. Cell Rep. 2015 Jun 16; 11(10):1549-63.
  18. Marquard AM, Eklund AC, Joshi T, Krzystanek M, Favero F, Wang ZC, Richardson AL, Silver DP, Szallasi Z, Birkbak NJ. Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs. Biomark Res. 2015; 3:9.
  19. McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci Transl Med. 2015 Apr 15; 7(283):283ra54.
  20. Josa V, Krzystanek M, Eklund AC, Salamon F, Zarand A, Szallasi Z, Baranyai Z. Relationship of postoperative thrombocytosis and survival of patients with colorectal cancer. Int J Surg. 2015 Jun; 18:1-6.
  21. 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. Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome. Ann Oncol. 2015 May; 26(5):880-7.
  22. Kanu N, Grönroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrík M, Rowan AJ, Patel H, Rabinowitz A, East P, Wilson G, Santos CR, McGranahan N, Gulati S, Gerlinger M, Birkbak NJ, Joshi T, Alexandrov LB, Stratton MR, Powles T, Matthews N, Bates PA, Stewart A, Szallasi Z, Larkin J, Bartek J, Swanton C. SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. Oncogene. 2015 Nov 12; 34(46):5699-708.
  23. Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol. 2015 Jan; 26(1):64-70.
  24. 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. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science. 2014 Oct 10; 346(6206):251-6.
  25. Molnár J, Póti Á, Pipek O, Krzystanek M, Kanu N, Swanton C, Tusnády GE, Szallasi Z, Csabai I, Szüts D. The genome of the chicken DT40 bursal lymphoma cell line. G3 (Bethesda). 2014 Sep 15; 4(11):2231-40.
  26. Guo T, Krzystanek M, Szallasi Z, Szallasi A. Thrombocytosis portends adverse prognostic significance in patients with stage II colorectal carcinoma. F1000Res. 2014; 3:180.
  27. 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. Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers. Eur Urol. 2014 Nov; 66(5):936-48.
  28. 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. Lactate dehydrogenase as a selection criterion for ipilimumab treatment in metastatic melanoma. Cancer Immunol Immunother. 2014 May; 63(5):449-58.
  29. 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. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov. 2014 Feb; 4(2):175-85.
  30. Birkbak NJ, Kochupurakkal B, Izarzugaza JM, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC. Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations. PLoS One. 2013; 8(11):e80023.
  31. Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell RA, Rowan AJ, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C. Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol. 2013 Aug; 230(4):356-64.
  32. Seo JH, Li Q, Fatima A, Eklund A, Szallasi Z, Polyak K, Richardson AL, Freedman ML. Deconvoluting complex tissues for expression quantitative trait locus-based analyses. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1620):20120363.
  33. Krzystanek M, Szallasi Z, Eklund AC. Biasogram: visualization of confounding technical bias in gene expression data. PLoS One. 2013; 8(4):e61872.
  34. Khattak MA, Bakr F, Krzystanek M, Szallasi Z, Gerlinger M, Santos C, Swanton C, Pickering LM, Gore ME, Larkin JM. Prognostic and predictive markers in metastatic renal cell carcinoma. J Clin Oncol. 2013 Mar 01; 31(7):971-2.
  35. Khalili JS, Hanson RW, Szallasi Z. In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census. Oncoimmunology. 2012 Nov 01; 1(8):1281-1289.
  36. 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. Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents. Cancer Discov. 2012 Apr; 2(4):366-75.
  37. 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. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012 Mar 08; 366(10):883-92.
  38. Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC. Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics. 2011 Dec 15; 12:474.
  39. 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. CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction. J Pathol. 2012 Feb; 226(3):482-94.
  40. Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z. Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinformatics. 2011 Jul 28; 12:310.
  41. 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. Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer. Cancer Epidemiol Biomarkers Prev. 2011 Oct; 20(10):2183-94.
  42. Endesfelder D, McGranahan N, Birkbak NJ, Szallasi Z, Kschischo M, Graham TA, Swanton C. 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. Oncotarget. 2011 Jul; 2(7):529-37.
  43. Lee AJ, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, Downward J, Szallasi Z, Tomlinson IP, Howell M, Kschischo M, Swanton C. Chromosomal instability confers intrinsic multidrug resistance. Cancer Res. 2011 Mar 01; 71(5):1858-70.
  44. Birkbak NJ, Eklund AC, Li Q, McClelland SE, Endesfelder D, Tan P, Tan IB, Richardson AL, Szallasi Z, Swanton C. Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res. 2011 May 15; 71(10):3447-52.
  45. Li Q, Eklund AC, Juul N, Haibe-Kains B, Workman CT, Richardson AL, Szallasi Z, Swanton C. Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status. PLoS One. 2010 Dec 01; 5(12):e15031.
  46. Burrell RA, Juul N, Johnston SR, Reis-Filho JS, Szallasi Z, Swanton C. Targeting chromosomal instability and tumour heterogeneity in HER2-positive breast cancer. J Cell Biochem. 2010 Nov 01; 111(4):782-90.
  47. 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. Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets. Genome Med. 2010 Aug 11; 2(8):53.
  48. 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. 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. Lancet Oncol. 2010 Apr; 11(4):358-65.
  49. 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. Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer. J Clin Oncol. 2010 Mar 01; 28(7):1145-53.
  50. 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. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nat Med. 2010 Feb; 16(2):214-8.
  51. Györffy B, Lanczky A, Eklund AC, Denkert C, Budczies J, Li Q, Szallasi Z. 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. Breast Cancer Res Treat. 2010 Oct; 123(3):725-31.
  52. Eklund AC, Friis P, Wernersson R, Szallasi Z. Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization. Nucleic Acids Res. 2010 Mar; 38(4):e27.
  53. Gyorffy B, Molnar B, Lage H, Szallasi Z, Eklund AC. Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples. PLoS One. 2009 May 21; 4(5):e5645.
  54. 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. Chromosomal instability determines taxane response. Proc Natl Acad Sci U S A. 2009 May 26; 106(21):8671-6.
  55. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A. 2008 Dec 30; 105(52):20870-5.
  56. Lee AJ, East P, Pepper S, Nicke B, Szallasi Z, Eklund AC, Downward J, Swanton C. Concordance of exon array and real-time PCR assessment of gene expression following cancer cell cytotoxic drug exposure. Cell Cycle. 2008 Dec 15; 7(24):3947-8.
  57. Swanton C, Szallasi Z, Brenton JD, Downward J. Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer. Breast Cancer Res. 2008; 10(5):214.
  58. Eklund AC, Szallasi Z. Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biol. 2008; 9(2):R26.
  59. 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. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006 Sep; 24(9):1151-61.
  60. Eklund AC, Turner LR, Chen P, Jensen RV, deFeo G, Kopf-Sill AR, Szallasi Z. Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat Biotechnol. 2006 Sep; 24(9):1071-3.
  61. Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006 Sep; 38(9):1043-8.
  62. Harris LN, Carter S, You F, Eklund A, Hilsenbeck S, Szallasi Z, Chang J. High level analysis of genomic data reveals complex predictors of response to trastuzumab (T) and chemotherapy for early stage breast cancer. J Clin Oncol. 2006 Jun 20; 24(18_suppl):544.
  63. Wahde M, Szallasi Z. A survey of methods for classification of gene expression data using evolutionary algorithms. Expert Rev Mol Diagn. 2006 Jan; 6(1):101-10.
  64. Draghici S, Khatri P, Eklund AC, Szallasi Z. Reliability and reproducibility issues in DNA microarray measurements. Trends Genet. 2006 Feb; 22(2):101-9.
  65. Harris LN, Perou C, Szallasi Z, Eklund A, Carter S, You F, Broadwater G, Monovich L, Winer E, Erlander M, Ellis M. Microarray profiling is feasible using archived tissue from a Cooperative Group Clinical Trial: Results from a pilot study in CALGB 9342. J Clin Oncol. 2005 Jun; 23(16_suppl):545.
  66. Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics. 2005 Apr 25; 6:107.
  67. Stelling J, Sauer U, Szallasi Z, Doyle FJ, Doyle J. Robustness of cellular functions. Cell. 2004 Sep 17; 118(6):675-85.
  68. Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane I, Mariani TJ. Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics. 2004 Aug 11; 18(3):308-15.
  69. Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 2004 May 25; 32(9):e74.
  70. Pack SD, Alper OM, Stromberg K, Augustus M, Ozdemirli M, Miermont AM, Klus G, Rusin M, Slack R, Hacker NF, Ried T, Szallasi Z, Alper O. Simultaneous suppression of epidermal growth factor receptor and c-erbB-2 reverses aneuploidy and malignant phenotype of a human ovarian carcinoma cell line. Cancer Res. 2004 Feb 01; 64(3):789-94.
  71. Szallasi Z. Build your own (virtual) cell. Trends Pharmacol Sci. 2002 Apr; 23(4):158-9.
  72. Periwal V, Szallasi Z. Trading "wet-work" for network. Nat Biotechnol. 2002 Apr; 20(4):345-6.
  73. Wahde M, Klus GT, Bittner ML, Chen Y, Szallasi Z. Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices. Bioinformatics. 2002 Mar; 18(3):389-94.
  74. Szallasi Z. Scrapie-ing' together a signal from prions. Trends Pharmacol Sci. 2001 Sep; 22(9):447.
  75. Klus GT, Rokaeus N, Bittner ML, Chen Y, Korz DM, Sukumar S, Schick A, Szallasi Z. Down-regulation of the desmosomal cadherin desmocollin 3 in human breast cancer. Int J Oncol. 2001 Jul; 19(1):169-74.
  76. Szallasi Z. The grand design. Trends Pharmacol Sci. 2001 Apr; 22(4):166-7.
  77. Szallasi Z. To kill two birds with one stone: a general concept in gene regulation? Trends Pharmacol Sci. 2001 Mar; 22(3):110.
  78. Klus GT, Song A, Schick A, Wahde M, Szallasi Z. Mutual information analysis as a tool to assess the role of aneuploidy in the generation of cancer-associated differential gene expression patterns. Pac Symp Biocomput. 2001; 42-51.
  79. Swann PG, Odom S, Zhou YJ, Szallasi Z, Blumberg PM, Draber P, Rivera J. Requirement for a negative charge at threonine 60 of the FcRgamma for complete activation of Syk. J Biol Chem. 1999 Aug 13; 274(33):23068-77.
  80. Szallasi Z. Genetic network analysis in light of massively parallel biological data acquisition. Pac Symp Biocomput. 1999; 5-16.
  81. Szallasi Z. Bioinformatics. Gene expression patterns and cancer. Nat Biotechnol. 1998 Dec; 16(13):1292-3.
  82. Mullin JM, Kampherstein JA, Laughlin KV, Clarkin CE, Miller RD, Szallasi Z, Kachar B, Soler AP, Rosson D. Overexpression of protein kinase C-delta increases tight junction permeability in LLC-PK1 epithelia. Am J Physiol. 1998 Aug; 275(2 Pt 1):C544-54.
  83. Song JS, Swann PG, Szallasi Z, Blank U, Blumberg PM, Rivera J. Tyrosine phosphorylation-dependent and -independent associations of protein kinase C-delta with Src family kinases in the RBL-2H3 mast cell line: regulation of Src family kinase activity by protein kinase C-delta. Oncogene. 1998 Jul 02; 16(26):3357-68.
  84. Gubina E, Rinaudo MS, Szallasi Z, Blumberg PM, Mufson RA. Overexpression of protein kinase C isoform epsilon but not delta in human interleukin-3-dependent cells suppresses apoptosis and induces bcl-2 expression. Blood. 1998 Feb 01; 91(3):823-9.
  85. Szallasi Z, Liang S. Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": their application for understanding carcinogenesis and assessing therapeutic strategies. Pac Symp Biocomput. 1998; 66-76.
  86. Chang EY, Szallasi Z, Acs P, Raizada V, Wolfe PC, Fewtrell C, Blumberg PM, Rivera J. Functional effects of overexpression of protein kinase C-alpha, -beta, -delta, -epsilon, and -eta in the mast cell line RBL-2H3. J Immunol. 1997 Sep 15; 159(6):2624-32.
  87. Rosson D, O'Brien TG, Kampherstein JA, Szallasi Z, Bogi K, Blumberg PM, Mullin JM. Protein kinase C-alpha activity modulates transepithelial permeability and cell junctions in the LLC-PK1 epithelial cell line. J Biol Chem. 1997 Jun 06; 272(23):14950-3.
  88. Szallasi Z, Bogi K, Gohari S, Biro T, Acs P, Blumberg PM. Non-equivalent roles for the first and second zinc fingers of protein kinase Cdelta. Effect of their mutation on phorbol ester-induced translocation in NIH 3T3 cells. J Biol Chem. 1996 Aug 02; 271(31):18299-301.
  89. Szallasi Z, Du L, Levine R, Lewin NE, Nguyen PN, Williams MD, Pettit GR, Blumberg PM. The bryostatins inhibit growth of B16/F10 melanoma cells in vitro through a protein kinase C-independent mechanism: dissociation of activities using 26-epi-bryostatin 1. Cancer Res. 1996 May 01; 56(9):2105-11.
  90. Lewin I, Jacob-Hirsch J, Zang ZC, Kupershtein V, Szallasi Z, Rivera J, Razin E. Aggregation of the Fc epsilon RI in mast cells induces the synthesis of Fos-interacting protein and increases its DNA binding-activity: the dependence on protein kinase C-beta. J Biol Chem. 1996 Jan 19; 271(3):1514-9.
  91. Lee J, Sharma R, Wang S, Milne GW, Lewin NE, Szallasi Z, Blumberg PM, George C, Marquez VE. Conformationally constrained analogues of diacylglycerol. 12. Ultrapotent protein kinase C ligands based on a chiral 4,4-disubstituted heptono-1,4-lactone template. J Med Chem. 1996 Jan 05; 39(1):36-45.
  92. Scala S, Dickstein B, Regis J, Szallasi Z, Blumberg PM, Bates SE. Bryostatin 1 affects P-glycoprotein phosphorylation but not function in multidrug-resistant human breast cancer cells. Clin Cancer Res. 1995 Dec; 1(12):1581-7.
  93. Acs P, Szallasi Z, Kazanietz MG, Blumberg PM. Differential activation of PKC isozymes by 14-3-3 zeta protein. Biochem Biophys Res Commun. 1995 Nov 02; 216(1):103-9.
  94. Haleem-Smith H, Chang EY, Szallasi Z, Blumberg PM, Rivera J. Tyrosine phosphorylation of protein kinase C-delta in response to the activation of the high-affinity receptor for immunoglobulin E modifies its substrate recognition. Proc Natl Acad Sci U S A. 1995 Sep 26; 92(20):9112-6.
  95. Szallasi Z, Denning MF, Chang EY, Rivera J, Yuspa SH, Lehel C, Olah Z, Anderson WB, Blumberg PM. Development of a rapid approach to identification of tyrosine phosphorylation sites: application to PKC delta phosphorylated upon activation of the high affinity receptor for IgE in rat basophilic leukemia cells. Biochem Biophys Res Commun. 1995 Sep 25; 214(3):888-94.
  96. Denning MF, Dlugosz AA, Williams EK, Szallasi Z, Blumberg PM, Yuspa SH. Specific protein kinase C isozymes mediate the induction of keratinocyte differentiation markers by calcium. Cell Growth Differ. 1995 Feb; 6(2):149-57.
  97. Szallasi Z, Kosa K, Smith CB, Dlugosz AA, Williams EK, Yuspa SH, Blumberg PM. Differential regulation by anti-tumor-promoting 12-deoxyphorbol-13-phenylacetate reveals distinct roles of the classical and novel protein kinase C isozymes in biological responses of primary mouse keratinocytes. Mol Pharmacol. 1995 Feb; 47(2):258-65.
  98. Blumberg PM, Acs G, Acs P, Areces LB, Kazanietz MG, Lewin NE, Szallasi Z. Protein kinase C in cell signaling: strategies for the development of selective inhibitors. Agents Actions Suppl. 1995; 47:87-100.
  99. Szallasi Z, Smith CB, Blumberg PM. Dissociation of phorbol esters leads to immediate redistribution to the cytosol of protein kinases C alpha and C delta in mouse keratinocytes. J Biol Chem. 1994 Nov 04; 269(44):27159-62.
  100. Szallasi Z, Denning MF, Smith CB, Dlugosz AA, Yuspa SH, Pettit GR, Blumberg PM. Bryostatin 1 protects protein kinase C-delta from down-regulation in mouse keratinocytes in parallel with its inhibition of phorbol ester-induced differentiation. Mol Pharmacol. 1994 Nov; 46(5):840-50.
  101. Razin E, Szallasi Z, Kazanietz MG, Blumberg PM, Rivera J. Protein kinases C-beta and C-epsilon link the mast cell high-affinity receptor for IgE to the expression of c-fos and c-jun. Proc Natl Acad Sci U S A. 1994 Aug 02; 91(16):7722-6.
  102. Szallasi Z, Smith CB, Pettit GR, Blumberg PM. Differential regulation of protein kinase C isozymes by bryostatin 1 and phorbol 12-myristate 13-acetate in NIH 3T3 fibroblasts. J Biol Chem. 1994 Jan 21; 269(3):2118-24.
  103. Blumberg PM, Acs G, Areces LB, Kazanietz MG, Lewin NE, Szallasi Z. Protein kinase C in signal transduction and carcinogenesis. Prog Clin Biol Res. 1994; 387:3-19.
  104. Szallasi Z, Krsmanovic L, Blumberg PM. Nonpromoting 12-deoxyphorbol 13-esters inhibit phorbol 12-myristate 13-acetate induced tumor promotion in CD-1 mouse skin. Cancer Res. 1993 Jun 01; 53(11):2507-12.
  105. Ozawa K, Szallasi Z, Kazanietz MG, Blumberg PM, Mischak H, Mushinski JF, Beaven MA. Ca(2+)-dependent and Ca(2+)-independent isozymes of protein kinase C mediate exocytosis in antigen-stimulated rat basophilic RBL-2H3 cells. Reconstitution of secretory responses with Ca2+ and purified isozymes in washed permeabilized cells. J Biol Chem. 1993 Jan 25; 268(3):1749-56.
  106. Szallasi Z, Krausz KW, Blumberg PM. Non-promoting 12-deoxyphorbol 13-esters as potent inhibitors of phorbol 12-myristate 13-acetate-induced acute and chronic biological responses in CD-1 mouse skin. Carcinogenesis. 1992 Nov; 13(11):2161-7.
  107. Gustafson KR, Cardellina JH, McMahon JB, Gulakowski RJ, Ishitoya J, Szallasi Z, Lewin NE, Blumberg PM, Weislow OS, Beutler JA, et al. A nonpromoting phorbol from the samoan medicinal plant Homalanthus nutans inhibits cell killing by HIV-1. J Med Chem. 1992 May 29; 35(11):1978-86.
  108. Szallasi A, Szolcsanyi J, Szallasi Z, Blumberg PM. Inhibition of [3H]resiniferatoxin binding to rat dorsal root ganglion membranes as a novel approach in evaluating compounds with capsaicin-like activity. Naunyn Schmiedebergs Arch Pharmacol. 1991 Nov; 344(5):551-6.
  109. Szallasi Z, Blumberg PM. Prostratin, a nonpromoting phorbol ester, inhibits induction by phorbol 12-myristate 13-acetate of ornithine decarboxylase, edema, and hyperplasia in CD-1 mouse skin. Cancer Res. 1991 Oct 01; 51(19):5355-60.
  110. Szolcsanyi J, Szallasi A, Szallasi Z, Joo F, Blumberg PM. Resiniferatoxin. An ultrapotent neurotoxin of capsaicin-sensitive primary afferent neurons. Ann N Y Acad Sci. 1991; 632:473-5.
  111. Szallasi A, Szallasi Z, Blumberg PM. Permanent effects of neonatally administered resiniferatoxin in the rat. Brain Res. 1990 Dec 24; 537(1-2):182-6.
  112. Szolcsanyi J, Szallasi A, Szallasi Z, Joo F, Blumberg PM. Resiniferatoxin: an ultrapotent selective modulator of capsaicin-sensitive primary afferent neurons. J Pharmacol Exp Ther. 1990 Nov; 255(2):923-8.
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