Photo of Zoltan Szallasi, MD

Zoltan Szallasi, MD

Boston Children's Hospital

Boston Children's Hospital
Phone: (617) 355-2179


zszallasi@chip.org

Photo of Zoltan Szallasi, MD

Boston Children's Hospital
Phone: (617) 355-2179


zszallasi@chip.org

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Zoltan Szallasi, MD

Boston Children's Hospital

EDUCATIONAL TITLES

  • Assistant Professor, Pediatrics, Harvard Medical School
  • Assistant Professor, Pediatrics, Boston Children's Hospital

DF/HCC PROGRAM AFFILIATION

Research Abstract

High throughput measurements, such as microarray based gene expression profiling, offers a more complete view of the biochemical changes associated with cancer. However, more data means more noise, more uncertainty and an explosion of the hypothesis space, all impeding association based learning often applied both in basic and clinical cancer research. Our group is interested in the meaningful and responsible application of high throughput measurements for cancer research. We implemented several methods that increased the reliability of microarray measurements. We are also interested in approaches that combine high throughput measurements in a manner that describe essential biology in a robust fashion, such as developing a gene expression signature of chromosomal instability.

Publications from Harvard Catalyst Profiles

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  • Kristensen NP, Heeke C, Tvingsholm SA, Borch A, Draghi A, Crowther MD, Carri I, Munk KK, Holm JS, Bjerregaard AM, Bentzen AK, Marquard AM, Szallasi Z, McGranahan N, Andersen R, Nielsen M, Jönsson GB, Donia M, Svane IM, Hadrup SR. Neoantigen-reactive CD8+ T cells affect clinical outcome of adoptive cell therapy with tumor-infiltrating lymphocytes in melanoma. J Clin Invest 2022. PubMed
  • Chen D, Gervai JZ, Póti Á, Németh E, Szeltner Z, Szikriszt B, Gyüre Z, Zámborszky J, Ceccon M, d'Adda di Fagagna F, Szallasi Z, Richardson AL, Szüts D. BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1. Nat Commun 2022; 13:226. PubMed
  • Plym A, Dióssy M, Szallasi Z, Sartor O, Silberstein J, Powell IJ, Rebbeck TR, Penney KL, Mucci LA, Pomerantz MM, Kibel AS. DNA Repair Pathways and Their Association With Lethal Prostate Cancer in African American and European American Men. JNCI Cancer Spectr 2022. PubMed
  • Miao C, Tsujino T, Takai T, Gui F, Tsutsumi T, Sztupinszki Z, Wang Z, Azuma H, Szallasi Z, Mouw KW, Zou L, Kibel AS, Jia L. loss overrides PARP inhibitor sensitivity driven by loss in prostate cancer. Sci Adv 2022; 8:eabl9794. PubMed
  • Le Naour J, Sztupinszki Z, Carbonnier V, Casiraghi O, Marty V, Galluzzi L, Szallasi Z, Kroemer G, Vacchelli E. A loss-of-function polymorphism in compromises therapeutic outcome in head and neck carcinoma patients. Oncoimmunology 2022; 11:2059878. PubMed
  • He Y, Rivera J, Diossy M, Duan H, Bowman-Colin C, Reed R, Jennings R, Novak J, Tran SV, Cohen EF, Szuts D, Giobbie-Hurder A, Bronson RT, Bass AJ, Signoretti S, Szallasi Z, Livingston DM, Pathania S. heterozygosity and replication stress drive esophageal cancer development in a mouse model. Proc Natl Acad Sci U S A 2021. PubMed
  • Sztupinszki Z, Diossy M, Börcsök J, Prosz A, Cornelius N, Kjeldsen MK, Mirza MR, Szallasi Z. Comparative Assessment of Diagnostic Homologous Recombination Deficiency associated mutational signatures in ovarian cancer. Clin Cancer Res 2021. PubMed
  • Guo J, Zhou Y, Xu C, Chen Q, Sztupinszki Z, Börcsök J, Xu C, Ye F, Tang W, Kang J, Yang L, Zhong J, Zhong T, Hu T, Yu R, Szallasi Z, Deng X, Li Q. Genetic Determinants of Somatic Selection of Mutational Processes in 3,566 Human Cancers. Cancer Res 2021. PubMed
  • Diossy M, Sztupinszki Z, Borcsok J, Krzystanek M, Tisza V, Spisak S, Rusz O, Timar J, Csabai I, Fillinger J, Moldvay J, Pedersen AG, Szuts D, Szallasi Z. A subset of lung cancer cases shows robust signs of homologous recombination deficiency associated genomic mutational signatures. NPJ Precis Oncol 2021; 5:55. PubMed
  • Diossy M, Sztupinszki Z, Krzystanek M, Borcsok J, Eklund AC, Csabai I, Pedersen AG, Szallasi Z. Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts. 2021. PubMed
  • Börcsök J, Diossy M, Sztupinszki Z, Prosz A, Tisza V, Spisak S, Rusz O, Stormoen DR, Pappot H, Csabai I, Brunak S, Mouw KW, Szallasi Z. Detection of Molecular Signatures of Homologous Recombination Deficiency in Bladder Cancer. Clin Cancer Res 2021. PubMed
  • Lindgaard SC, Sztupinszki Z, Maag E, Chen IM, Johansen AZ, Jensen BV, Bojesen SE, Nielsen DL, Hansen CP, Hasselby JP, Nielsen KR, Szallasi Z, Johansen JS. Circulating Protein Biomarkers for Use in Pancreatic Ductal Adenocarcinoma Identification. Clin Cancer Res 2021; 27:2592-2603. PubMed
  • Gieszer B, Megyesfalvi Z, Dulai V, Papay J, Kovalszky I, Timar J, Fillinger J, Harko T, Pipek O, Teglasi V, Regos E, Papp G, Szallasi Z, Laszlo V, Renyi-Vamos F, Galffy G, Bodor C, Dome B, Moldvay J. EGFR variant allele frequency predicts EGFR-TKI efficacy in lung adenocarcinoma: a multicenter study. Transl Lung Cancer Res 2021; 10:662-674. PubMed
  • Le Naour J, Liu P, Zhao L, Adjemian S, Sztupinszki Z, Taieb J, Mulot C, Silvin A, Dutertre CA, Ginhoux F, Sauvat A, Cerrato G, Castoldi F, Martins I, Stoll G, Paillet J, Mangane K, Richter C, Kepp O, Maiuri MC, Pietrocola F, Vandenabeele P, André F, Delaloge S, Szallasi Z, Laurent-Puig P, Zucman-Rossi J, Zitvogel L, Pol JG, Vacchelli E, Kroemer G. A TLR3 Ligand Reestablishes Chemotherapeutic Responses in the Context of FPR1 Deficiency. 2021; 11:408-423. PubMed
  • Mohsen H, Gunasekharan V, Qing T, Seay M, Surovtseva Y, Negahban S, Szallasi Z, Pusztai L, Gerstein MB. Network propagation-based prioritization of long tail genes in 17 cancer types. Genome Biol 2021; 22:287. PubMed
  • Börcsök J, Sztupinszki Z, Bekele R, Gao SP, Diossy M, Samant AS, Dillon KM, Tisza V, Spisák S, Rusz O, Csabai I, Pappot H, Frazier ZJ, Konieczkowski DJ, Liu D, Vasani N, Rodrigues JA, Solit DB, Hoffman-Censits JH, Plimack ER, Rosenberg JE, Lazaro JB, Taplin ME, Iyer G, Brunak S, Lozsa R, Van Allen EM, Szüts D, Mouw KW, Szallasi Z. Identification of a synthetic lethal relationship between nucleotide excision repair (NER) deficiency and irofulven sensitivity in urothelial cancer. Clin Cancer Res 2020. PubMed
  • Rojko L, Megyesfalvi Z, Czibula E, Reiniger L, Teglasi V, Szegedi Z, Szallasi Z, Dome B, Moldvay J. Longitudinal analysis of complete blood count parameters in advanced-stage lung cancer patients. Thorac Cancer 2020. PubMed
  • Watkins TBK, Lim EL, Petkovic M, Elizalde S, Birkbak NJ, Wilson GA, Moore DA, Grönroos E, Rowan A, Dewhurst SM, Demeulemeester J, Dentro SC, Horswell S, Au L, Haase K, Escudero M, Rosenthal R, Bakir MA, Xu H, Litchfield K, Lu WT, Mourikis TP, Dietzen M, Spain L, Cresswell GD, Biswas D, Lamy P, Nordentoft I, Harbst K, Castro-Giner F, Yates LR, Caramia F, Jaulin F, Vicier C, Tomlinson IPM, Brastianos PK, Cho RJ, Bastian BC, Dyrskjøt L, Jönsson GB, Savas P, Loi S, Campbell PJ, Andre F, Luscombe NM, Steeghs N, Tjan-Heijnen VCG, Szallasi Z, Turajlic S, Jamal-Hanjani M, Van Loo P, Bakhoum SF, Schwarz RF, McGranahan N, Swanton C. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 2020. PubMed
  • Valcz G, Buzás EI, Sebestyén A, Krenács T, Szállási Z, Igaz P, Molnár B. Extracellular Vesicle-Based Communication May Contribute to the Co-Evolution of Cancer Stem Cells and Cancer-Associated Fibroblasts in Anti-Cancer Therapy. Cancers (Basel) 2020. PubMed
  • Duan H, Mansour S, Reed R, Gillis MK, Parent B, Liu B, Sztupinszki Z, Birkbak N, Szallasi Z, Elia AEH, Garber JE, Pathania S. E3 ligase RFWD3 is a novel modulator of stalled fork stability in BRCA2-deficient cells. J Cell Biol 2020. PubMed
  • Sztupinszki Z, Diossy M, Krzystanek M, Börcsök J, Pomerantz MM, Tisza V, Spisák S, Rusz O, Csabai I, Freedman ML, Szallasi Z. Detection of molecular signatures of homologous recombination deficiency in prostate cancer with or without BRCA1/2 mutations. Clin Cancer Res 2020. PubMed
  • Sharad S, Dillman AA, Sztupinszki ZM, Szallasi Z, Rosner I, Cullen J, Srivastava S, Srinivasan A, Li H. Characterization of unique gene splice variants (isoforms and ) from RNA Seq profiling provides novel insights into prognostic evaluation of prostate cancer. 2020; 11:362-377. PubMed
  • Fluckiger A, Daillère R, Sassi M, Sixt BS, Liu P, Loos F, Richard C, Rabu C, Alou MT, Goubet AG, Lemaitre F, Ferrere G, Derosa L, Duong CPM, Messaoudene M, Gagné A, Joubert P, De Sordi L, Debarbieux L, Simon S, Scarlata CM, Ayyoub M, Palermo B, Facciolo F, Boidot R, Wheeler R, Boneca IG, Sztupinszki Z, Papp K, Csabai I, Pasolli E, Segata N, Lopez-Otin C, Szallasi Z, Andre F, Iebba V, Quiniou V, Klatzmann D, Boukhalil J, Khelaifia S, Raoult D, Albiges L, Escudier B, Eggermont A, Mami-Chouaib F, Nistico P, Ghiringhelli F, Routy B, Labarrière N, Cattoir V, Kroemer G, Zitvogel L. Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage. Science 2020; 369:936-942. PubMed
  • Jósa V, Brodszky V, Zaránd A, Mezei T, Szilasi Z, Merkel K, Fehér A, Szállási Z, Baranyai Z. The relationship between IL-6 and thrombocytosis accompanying gastrointestinal tumours. Prz Gastroenterol 2020; 15:215-219. PubMed
  • Saini SK, Ørskov AD, Bjerregaard AM, Unnikrishnan A, Holmberg-Thydén S, Borch A, Jensen KV, Anande G, Bentzen AK, Marquard AM, Tamhane T, Treppendahl MB, Gang AO, Dufva IH, Szallasi Z, Ternette N, Pedersen AG, Eklund AC, Pimanda J, Grønbæk K, Hadrup SR. Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers. Nat Commun 2020; 11:5660. PubMed
  • Sharad S, Sztupinszki ZM, Chen Y, Kuo C, Ravindranath L, Szallasi Z, Petrovics G, Sreenath TL, Dobi A, Rosner IL, Srinivasan A, Srivastava S, Cullen J, Li H. Analysis of Isoforms ( and ) as Selective Inhibitors of Androgen and TGF-β Signaling Reveals Distinct Biological and Prognostic Features in Prostate Cancer. Cancers (Basel) 2019. PubMed
  • Biswas D, Birkbak NJ, Rosenthal R, Hiley CT, Lim EL, Papp K, Boeing S, Krzystanek M, Djureinovic D, La Fleur L, Greco M, Döme B, Fillinger J, Brunnström H, Wu Y, Moore DA, Skrzypski M, Abbosh C, Litchfield K, Al Bakir M, Watkins TBK, Veeriah S, Wilson GA, Jamal-Hanjani M, Moldvay J, Botling J, Chinnaiyan AM, Micke P, Hackshaw A, Bartek J, Csabai I, Szallasi Z, Herrero J, McGranahan N, Swanton C, . A clonal expression biomarker associates with lung cancer mortality. Nat Med 2019; 25:1540-1548. PubMed
  • Tőkés AM, Rusz O, Cserni G, Tóth E, Rubovszky G, Tőkés T, Vízkeleti L, Reiniger L, Kószó R, Kahán Z, Kulka J, Donia M, Vörös A, Szallasi Z. Influence of mutagenic versus non-mutagenic pre-operative chemotherapy on the immune infiltration of residual breast cancer. Acta Oncol 2019. PubMed
  • Téglási V, Pipek O, Lózsa R, Berta K, Szüts D, Harkó T, Vadász P, Rojkó L, Döme B, Bagó AG, Tímár J, Moldvay J, Szállási Z, Reiniger L. PD-L1 Expression of Lung Cancer Cells, Unlike Infiltrating Immune Cells, Is Stable and Unaffected by Therapy During Brain Metastasis. Clin Lung Cancer 2019. PubMed
  • Reiniger L, Téglási V, Pipek O, Rojkó L, Glasz T, Vágvölgyi A, Kovalszky I, Gyulai M, Lohinai Z, Rásó E, Tímár J, Döme B, Szállási Z, Moldvay J. Tumor necrosis correlates with PD-L1 and PD-1 expression in lung adenocarcinoma. Acta Oncol 2019. PubMed
  • Téglási V, Csűry DT, Dezső K, Bugyik E, Szabó V, Szállási Z, Paku S, Reiniger L. Origin and Distribution of Connective Tissue and Pericytes Impacting Vascularization in Brain Metastases With Different Growth Patterns. J Neuropathol Exp Neurol 2019; 78:326-339. PubMed
  • Rosenthal R, Cadieux EL, Salgado R, Bakir MA, Moore DA, Hiley CT, Lund T, Tanić M, Reading JL, Joshi K, Henry JY, Ghorani E, Wilson GA, Birkbak NJ, Jamal-Hanjani M, Veeriah S, Szallasi Z, Loi S, Hellmann MD, Feber A, Chain B, Herrero J, Quezada SA, Demeulemeester J, Van Loo P, Beck S, McGranahan N, Swanton C, . Neoantigen-directed immune escape in lung cancer evolution. Nature 2019; 567:479-485. PubMed
  • Németh E, Krzystanek M, Reiniger L, Ribli D, Pipek O, Sztupinszki Z, Glasz T, Csabai I, Moldvay J, Szallasi Z, Szüts D. The genomic imprint of cancer therapies helps timing the formation of metastases. Int. J. Cancer 2019. PubMed
  • Valcz G, Buzás EI, Kittel Á, Krenács T, Visnovitz T, Spisák S, Török G, Homolya L, Zsigrai S, Kiszler G, Antalffy G, Pálóczi K, Szállási Z, Szabó V, Sebestyén A, Solymosi N, Kalmár A, Dede K, Lőrincz P, Tulassay Z, Igaz P, Molnár B. release of MVB-like small extracellular vesicle clusters by colorectal carcinoma cells. J Extracell Vesicles 2019; 8:1596668. PubMed
  • Póti Á, Gyergyák H, Németh E, Rusz O, Tóth S, Kovácsházi C, Chen D, Szikriszt B, Spisák S, Takeda S, Szakács G, Szallasi Z, Richardson AL, Szüts D. Correlation of homologous recombination deficiency induced mutational signatures with sensitivity to PARP inhibitors and cytotoxic agents. Genome Biol 2019; 20:240. PubMed
  • Klikovits T, Lohinai Z, Fábián K, Gyulai M, Szilasi M, Varga J, Baranya E, Pipek O, Csabai I, Szállási Z, Tímár J, Hoda MA, Laszlo V, Hegedűs B, Renyi-Vamos F, Klepetko W, Ostoros G, Döme B, Moldvay J. New insights into the impact of primary lung adenocarcinoma location on metastatic sites and sequence: A multicenter cohort study. Lung Cancer 2018; 126:139-148. PubMed
  • Póti Á, Berta K, Xiao Y, Pipek O, Klus GT, Ried T, Csabai I, Wilcoxen K, Mikule K, Szallasi Z, Szüts D. Long-term treatment with the PARP inhibitor niraparib does not increase the mutation load in cell line models and tumour xenografts. Br J Cancer 2018; 119:1392-1400. PubMed
  • Rojkó L, Reiniger L, Téglási V, Fábián K, Pipek O, Vágvölgyi A, Agócs L, Fillinger J, Kajdácsi Z, Tímár J, Döme B, Szállási Z, Moldvay J. Chemotherapy treatment is associated with altered PD-L1 expression in lung cancer patients. J Cancer Res Clin Oncol 2018; 144:1219-1226. PubMed
  • Takeda DY, Spisák S, Seo JH, Bell C, O'Connor E, Korthauer K, Ribli D, Csabai I, Solymosi N, Szállási Z, Stillman DR, Cejas P, Qiu X, Long HW, Tisza V, Nuzzo PV, Rohanizadegan M, Pomerantz MM, Hahn WC, Freedman ML. A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer. Cell 2018. PubMed
  • Rusz O, Papp O, Vízkeleti L, Molnár BÁ, Bende KC, Lotz G, Ács B, Kahán Z, Székely T, Báthori Á, Szundi C, Kulka J, Szállási Z, Tőkés AM. LAPTM4B gene copy number gain is associated with inferior response to anthracycline-based chemotherapy in hormone receptor negative breast carcinomas. Cancer Chemother Pharmacol 2018. PubMed
  • Mitchell TJ, Turajlic S, Rowan A, Nicol D, Farmery JHR, O'Brien T, Martincorena I, Tarpey P, Angelopoulos N, Yates LR, Butler AP, Raine K, Stewart GD, Challacombe B, Fernando A, Lopez JI, Hazell S, Chandra A, Chowdhury S, Rudman S, Soultati A, Stamp G, Fotiadis N, Pickering L, Au L, Spain L, Lynch J, Stares M, Teague J, Maura F, Wedge DC, Horswell S, Chambers T, Litchfield K, Xu H, Stewart A, Elaidi R, Oudard S, McGranahan N, Csabai I, Gore M, Futreal PA, Larkin J, Lynch AG, Szallasi Z, Swanton C, Campbell PJ, . Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal. Cell 2018; 173:611-623.e17. PubMed
  • Turajlic S, Xu H, Litchfield K, Rowan A, Horswell S, Chambers T, O'Brien T, Lopez JI, Watkins TBK, Nicol D, Stares M, Challacombe B, Hazell S, Chandra A, Mitchell TJ, Au L, Eichler-Jonsson C, Jabbar F, Soultati A, Chowdhury S, Rudman S, Lynch J, Fernando A, Stamp G, Nye E, Stewart A, Xing W, Smith JC, Escudero M, Huffman A, Matthews N, Elgar G, Phillimore B, Costa M, Begum S, Ward S, Salm M, Boeing S, Fisher R, Spain L, Navas C, Grönroos E, Hobor S, Sharma S, Aurangzeb I, Lall S, Polson A, Varia M, Horsfield C, Fotiadis N, Pickering L, Schwarz RF, Silva B, Herrero J, Luscombe NM, Jamal-Hanjani M, Rosenthal R, Birkbak NJ, Wilson GA, Pipek O, Ribli D, Krzystanek M, Csabai I, Szallasi Z, Gore M, McGranahan N, Van Loo P, Campbell P, Larkin J, Swanton C, . Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal. Cell 2018; 173:595-610.e11. PubMed
  • Marosvári D, Nagy N, Kriston C, Deák B, Hajdu M, Bödör C, Csala I, Bagó AG, Szállási Z, Sebestyén A, Reiniger L. Discrepancy Between Low Levels of mTOR Activity and High Levels of P-S6 in Primary Central Nervous System Lymphoma May Be Explained by PAS Domain-Containing Serine/Threonine-Protein Kinase-Mediated Phosphorylation. J Neuropathol Exp Neurol 2018; 77:268-273. PubMed
  • Sztupinszki Z, Diossy M, Krzystanek M, Reiniger L, Csabai I, Favero F, Birkbak NJ, Eklund AC, Syed A, Szallasi Z. Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer. NPJ Breast Cancer 2018; 4:16. PubMed
  • Valcz G, Buzás EI, Szállási Z, Kalmár A, Krenács T, Tulassay Z, Igaz P, Molnár B. Perspective: bidirectional exosomal transport between cancer stem cells and their fibroblast-rich microenvironment during metastasis formation. NPJ Breast Cancer 2018; 4:18. PubMed
  • Fábián K, Puskás R, Kakuk T, Prés L, Fejes D, Szegedi Z, Rojkó L, Szállási Z, Döme B, Pipek O, Moldvay J. Renal Impairment Hampers Bisphosphonate Treatment in a Quarter of Lung Cancer Patients with Bone Metastasis. Basic Clin Pharmacol Toxicol 2017. PubMed
  • Fábián K, Puskás R, Kakuk T, Prés L, Fejes D, Szegedi Z, Rojkó L, Szállási Z, Döme B, Pipek O, Moldvay J. Renal Impairment Hampers Bisphosphonate Treatment in a Quarter of Lung Cancer Patients with Bone Metastasis. Basic Clin Pharmacol Toxicol 2017. PubMed
  • Agoston AT, Srivastava A, Zheng Y, Bueno R, Odze RD, Szallasi Z. Paraneoplastic thrombocytosis is associated with increased mortality and increased rate of lymph node metastasis in oesophageal adenocarcinoma. Pathology 2017. PubMed
  • Pomerantz MM, Spisák S, Jia L, Cronin AM, Csabai I, Ledet E, Sartor AO, Rainville I, O'Connor EP, Herbert ZT, Szállási Z, Oh WK, Kantoff PW, Garber JE, Schrag D, Kibel AS, Freedman ML. The association between germline BRCA2 variants and sensitivity to platinum-based chemotherapy among men with metastatic prostate cancer. Cancer 2017. PubMed
  • 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; 7:3248. PubMed
  • 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; 545:446-451. PubMed
  • Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC. MuPeXI: prediction of neo-epitopes from tumor sequencing data. Cancer Immunol Immunother 2017. PubMed
  • Szallasi Z. Detecting mutant KRAS in liquid biopsies: A biomarker searching for a role. Ann. Oncol. 2017. PubMed
  • Téglási V, Reiniger L, Fábián K, Pipek O, Csala I, Bagó AG, Várallyai P, Vízkeleti L, Rojkó L, Tímár J, Döme B, Szállási Z, Swanton C, Moldvay J. Evaluating the significance of density, localization, and PD-1/PD-L1 immunopositivity of mononuclear cells in the clinical course of lung adenocarcinoma patients with brain metastasis. 2017. PubMed
  • Bjerregaard AM, Nielsen M, Jurtz V, Barra CM, Hadrup SR, Szallasi Z, Eklund AC. An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes. 2017; 8:1566. PubMed
  • 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; 376:2109-2121. PubMed
  • 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. PubMed
  • Baranyai Z, Jósa V, Tóth A, Szilasi Z, Tihanyi B, Zaránd A, Harsanyi L, Szállási Z. Paraneoplastic thrombocytosis in gastrointestinal cancer. Platelets 2016; 27:269-75. PubMed
  • Szendrői A, Szász AM, Kardos M, Tőkés AM, Idan R, Szűcs M, Kulka J, Nyirády P, Szendrői M, Szállási Z, Győrffy B, Tímár J. Opposite prognostic roles of HIF1α and HIF2α expressions in bone metastatic clear cell renal cell cancer. 2016. PubMed
  • Telli ML, Timms KM, Reid JE, Hennessy B, Mills GB, Jensen KC, Szallasi Z, Barry WT, Winer EP, Tung N, 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. PubMed
  • 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; 17:99. PubMed
  • 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. PubMed
  • 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. 2015. PubMed
  • Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N, , Gayther SA, Joung JK, Freedman ML. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat Med 2015. PubMed
  • Jósa V, Krzystanek M, Vass T, Lang T, Juhász V, Szilágyi K, Tihanyi B, Harsányi L, Szállási Z, Salamon F, Baranyai Z. Thrombocytosis of Liver Metastasis from Colorectal Cancer as Predictive Factor. Pathol Oncol Res 2015. PubMed
  • 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; 11:1549-63. PubMed
  • 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. PubMed
  • 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; 7:283ra54. PubMed
  • 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. PubMed
  • 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; 8:58. PubMed
  • 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. PubMed
  • 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. 2014. PubMed
  • 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; 346:251-6. PubMed
  • 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. 2014; 4:175-85. PubMed
  • 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; 230:356-64. PubMed
  • 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; 368:20120363. PubMed
  • 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:e80023. PubMed
  • 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. PubMed
  • Baranyai Z, Mersich T, Dede K, Besznyák I, Zaránd A, Teknos D, Nagy P, Salamon F, Nagy P, Nagy Z, Kótai Z, Szász M, Lukács L, Szállási Z, Jósa V, Jakab F. [From project-based sample collection to biobank]. 2011; 152:606-9. PubMed
  • 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; 71:1858-70. PubMed
  • 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; 111:782-90. PubMed
  • 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; 123:725-31. PubMed
  • 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; 11:358-65. PubMed
  • 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; 38:e27. PubMed
  • 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; 28:1145-53. PubMed
  • 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; 16:214-8. PubMed
  • 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; 5:e15031. PubMed
  • 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; 2:53. PubMed
  • 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; 106:8671-6. PubMed
  • 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; 105:20870-5. PubMed
  • 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; 7:3947-8. PubMed
  • Eklund AC, Szallasi Z. Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biol 2008; 9:R26. PubMed
  • 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; 10:214. PubMed
  • 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; 38:1043-8. PubMed
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DF/HCC members that share similar concepts* with Zoltan Szallasi, MD but have yet to coauthor a publication with this researcher.

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