Zoltan Szallasi

Zoltan Szallasi

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Zoltan Szallasi

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Tumor necrosis correlates with PD-L1 and PD-1 expression in lung adenocarcinoma.

Acta Oncol 2019 Apr 19:1-8. Epub 2019 Apr 19.

b 2nd Department of Pathology, MTA-SE NAP Brain Metastasis Research Group Hungarian Academy of Sciences , Semmelweis University , Budapest , Hungary.

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https://www.tandfonline.com/doi/full/10.1080/0284186X.2019.1
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http://dx.doi.org/10.1080/0284186X.2019.1598575DOI Listing
April 2019

The genomic imprint of cancer therapies helps timing the formation of metastases.

Int J Cancer 2019 Jan 29. Epub 2019 Jan 29.

Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.

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http://doi.wiley.com/10.1002/ijc.32159
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http://dx.doi.org/10.1002/ijc.32159DOI Listing
January 2019

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 Nov 14;119(11):1392-1400. Epub 2018 Nov 14.

Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.

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http://www.nature.com/articles/s41416-018-0312-6
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http://dx.doi.org/10.1038/s41416-018-0312-6DOI Listing
November 2018

Chemotherapy treatment is associated with altered PD-L1 expression in lung cancer patients.

J Cancer Res Clin Oncol 2018 Jul 19;144(7):1219-1226. Epub 2018 Apr 19.

VI. Department of Pulmonology, National Korányi Institute of Pulmonology, Pihenő u. 1, Budapest, 1121, Hungary.

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http://dx.doi.org/10.1007/s00432-018-2642-4DOI Listing
July 2018

A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer.

Cell 2018 07 14;174(2):422-432.e13. Epub 2018 Jun 14.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183064
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http://dx.doi.org/10.1016/j.cell.2018.05.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6046260PMC
July 2018

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

Front Immunol 2018 14;9:1007. Epub 2018 May 14.

Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.

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http://dx.doi.org/10.3389/fimmu.2018.01007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961322PMC
May 2018

Universal scaling laws in metro area election results.

PLoS One 2018 22;13(2):e0192913. Epub 2018 Feb 22.

Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192913PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823399PMC
April 2018

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

Cell 2018 04 12;173(3):595-610.e11. Epub 2018 Apr 12.

Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.03.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938372PMC
April 2018

Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

Authors:
Christopher Abbosh Nicolai J Birkbak Gareth A Wilson Mariam Jamal-Hanjani Tudor Constantin Raheleh Salari John Le Quesne David A Moore Selvaraju Veeriah Rachel Rosenthal Teresa Marafioti Eser Kirkizlar Thomas B K Watkins Nicholas McGranahan Sophia Ward Luke Martinson Joan Riley Francesco Fraioli Maise Al Bakir Eva Grönroos Francisco Zambrana Raymondo Endozo Wenya Linda Bi Fiona M Fennessy Nicole Sponer Diana Johnson Joanne Laycock Seema Shafi Justyna Czyzewska-Khan Andrew Rowan Tim Chambers Nik Matthews Samra Turajlic Crispin Hiley Siow Ming Lee Martin D Forster Tanya Ahmad Mary Falzon Elaine Borg David Lawrence Martin Hayward Shyam Kolvekar Nikolaos Panagiotopoulos Sam M Janes Ricky Thakrar Asia Ahmed Fiona Blackhall Yvonne Summers Dina Hafez Ashwini Naik Apratim Ganguly Stephanie Kareht Rajesh Shah Leena Joseph Anne Marie Quinn Phil A Crosbie Babu Naidu Gary Middleton Gerald Langman Simon Trotter Marianne Nicolson Hardy Remmen Keith Kerr Mahendran Chetty Lesley Gomersall Dean A Fennell Apostolos Nakas Sridhar Rathinam Girija Anand Sajid Khan Peter Russell Veni Ezhil Babikir Ismail Melanie Irvin-Sellers Vineet Prakash Jason F Lester Malgorzata Kornaszewska Richard Attanoos Haydn Adams Helen Davies Dahmane Oukrif Ayse U Akarca John A Hartley Helen L Lowe Sara Lock Natasha Iles Harriet Bell Yenting Ngai Greg Elgar Zoltan Szallasi Roland F Schwarz Javier Herrero Aengus Stewart Sergio A Quezada Karl S Peggs Peter Van Loo Caroline Dive C Jimmy Lin Matthew Rabinowitz Hugo J W L Aerts Allan Hackshaw Jacqui A Shaw Bernhard G Zimmermann Charles Swanton

Nature 2018 02 20;554(7691):264. Epub 2017 Dec 20.

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http://dx.doi.org/10.1038/nature25161DOI Listing
February 2018

Renal Impairment Hampers Bisphosphonate Treatment in a Quarter of Lung Cancer Patients with Bone Metastasis.

Basic Clin Pharmacol Toxicol 2018 Jan 24;122(1):126-132. Epub 2017 Aug 24.

Department of Tumor Biology, National Korányi Institute of Pulmonology - Semmelweis University, Budapest, Hungary.

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http://dx.doi.org/10.1111/bcpt.12854DOI Listing
January 2018

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

Front Immunol 2017 15;8:1566. Epub 2017 Nov 15.

Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.

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http://dx.doi.org/10.3389/fimmu.2017.01566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694748PMC
November 2017

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

Cancer Immunol Immunother 2017 Sep 20;66(9):1123-1130. Epub 2017 Apr 20.

Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, 2800, Lyngby, Denmark.

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http://dx.doi.org/10.1007/s00262-017-2001-3DOI Listing
September 2017

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.

Neuro Oncol 2017 Aug;19(8):1058-1067

First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Second Department of Pathology, Semmelweis University, Budapest, Hungary; Department of Pulmonology, Semmelweis University, Budapest, Hungary; Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary; Institute of Behavioural Sciences, Semmelweis University, Budapest, Hungary; Department of Neurooncology, National Institute of Clinical Neurosciences, Budapest, Hungary; Department of Radiology, National Institute of Clinical Neurosciences, Budapest, Hungary; Sixth Department of Pulmonology, National Korányi Institute of Pulmonology, Budapest, Hungary; Hungarian Academy of Sciences-Semmelweis University, Molecular Oncology Research Unit, Budapest, Hungary; Department of Tumor Biology, National Korányi Institute of Pulmonology-Semmelweis University, Budapest, Hungary; Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary; Division of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Children's Hospital Informatics Program at the Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Francis Crick Institute, London, UK.

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http://dx.doi.org/10.1093/neuonc/now309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570158PMC
August 2017

Paraneoplastic thrombocytosis is associated with increased mortality and increased rate of lymph node metastasis in oesophageal adenocarcinoma.

Pathology 2017 Aug 28;49(5):471-475. Epub 2017 Jun 28.

Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.

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http://dx.doi.org/10.1016/j.pathol.2017.04.001DOI Listing
August 2017

Renal Impairment Hampers Bisphosphonate Treatment in a Quarter of Lung Cancer Patients with Bone Metastasis.

Basic Clin Pharmacol Toxicol 2017 Aug 21. Epub 2017 Aug 21.

Department of Tumor Biology, National Korányi Institute of Pulmonology - Semmelweis University, Budapest, Hungary.

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http://dx.doi.org/10.1111/bcpt.12876DOI Listing
August 2017

Tracking the Evolution of Non-Small-Cell Lung Cancer.

N Engl J Med 2017 06 26;376(22):2109-2121. Epub 2017 Apr 26.

From the Cancer Research UK Lung Cancer Centre of Excellence (M.J.-H., G.A.W., N. McGranahan, N.J.B., S.V., S.S., D.H.J., R.R., S.-M.L., M.D.F., C.A., S.M.J., C.D., C.S.), London and Manchester, Good Clinical Laboratory Practice Facility, University College London (UCL) Experimental Cancer Medicine Centre (H.L.L., J.A.H.), Bill Lyons Informatics Centre (J.H.), and Cancer Immunology Unit (S.A.Q.), UCL Cancer Institute, the Translational Cancer Therapeutics Laboratory (G.A.W., N. McGranahan, N.J.B., T.B.K.W., A.R., T.C., S. Turajlic, H.X., C.T.H., C.S.), Department of Bioinformatics and Biostatistics (R.M., M.S., S.H., M.E., A.S.), Advanced Sequencing Facility (N. Matthews), and Cancer Genomics Laboratory (S.D., P.V.L.), Francis Crick Institute, the Renal and Skin Units, Royal Marsden Hospital (S. Turajlic), the Departments of Medical Oncology (M.J.-H., S.-M.L., M.D.F., T.A., C.A., C.S.), Pathology (M.F., E.B., T.M.), Cardiothoracic Surgery (D.L., M.H., S. Kolvekar, N.P.), Respiratory Medicine (S.M.J., R.T.), and Radiology (A.A.), UCL Hospitals, Lungs for Living, UCL Respiratory, UCL (S.M.J.), the Department of Radiotherapy, North Middlesex University Hospital (G.A.), the Department of Respiratory Medicine, Royal Free Hospital (S. Khan), and UCL Cancer Research UK and Cancer Trials Centre (N.I., H.B., Y.N., A.H.), London, Cancer Studies, University of Leicester (D.A.M., D.A.F., J.A.S., J.L.Q.), the Department of Thoracic Surgery, Glenfield Hospital (A.N., S.R.), and the Medical Research Center Toxicology Unit (J.L.Q.), Leicester, the Institute of Cancer Studies, University of Manchester (F.B.), the Christie Hospital (F.B., Y.S.), the Departments of Cardiothoracic Surgery (R.S.) and Pathology (L.J., A.M.Q.) and the North West Lung Centre (P.A.C.), University Hospital of South Manchester, and Cancer Research UK Manchester Institute (C.D.), Manchester, the Departments of Thoracic Surgery (B.N.) and Cellular Pathology (G.L., S. Trotter), Birmingham Heartlands Hospital, Molecular Pathology Diagnostic Services, Queen Elizabeth Hospital (P.T., B.O.), and Institute of Immunology and Immunotherapy, University of Birmingham (G.M.), Birmingham, the Departments of Medical Oncology (M.N.), Cardiothoracic Surgery (H.R.), Pathology (K.K.), Respiratory Medicine (M.C.), and Radiology (L.G.), Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen, the Department of Respiratory Medicine, Barnet and Chase Farm Hospitals, Barnet (S. Khan), the Department of Respiratory Medicine, Princess Alexandra Hospital, Harlow (P.R.), the Department of Clinical Oncology, St. Luke's Cancer Centre, Guildford (V.E.), the Departments of Pathology (B.I.), Respiratory Medicine (M.I.-S.), and Radiology (V.P.), Ashford and St. Peters' Hospitals, Surrey, the Department of Clinical Oncology, Velindre Hospital (J.F.L.), the Departments of Radiology (H.A.) and Respiratory Medicine (H.D.), University Hospital Llandough, the Departments of Pathology (R.A.) and Cardiothoracic Surgery (M.K.), University Hospital of Wales, and Cardiff University (R.A.), Cardiff, and Wellcome Trust Sanger Institute, Hinxton, and Big Data Institute, University of Oxford, Oxford (S.D.) - all in the United Kingdom; the Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby (Z.S.); the Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston (Z.S.); MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary (Z.S.); Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin (R.F.S.); and the Department of Human Genetics, University of Leuven, Leuven, Belgium (P.V.L.).

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http://dx.doi.org/10.1056/NEJMoa1616288DOI Listing
June 2017

Quantification of within-sample genetic heterogeneity from SNP-array data.

Sci Rep 2017 06 12;7(1):3248. Epub 2017 Jun 12.

Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK.

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http://dx.doi.org/10.1038/s41598-017-03496-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468233PMC
June 2017

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

Authors:
Christopher Abbosh Nicolai J Birkbak Gareth A Wilson Mariam Jamal-Hanjani Tudor Constantin Raheleh Salari John Le Quesne David A Moore Selvaraju Veeriah Rachel Rosenthal Teresa Marafioti Eser Kirkizlar Thomas B K Watkins Nicholas McGranahan Sophia Ward Luke Martinson Joan Riley Francesco Fraioli Maise Al Bakir Eva Grönroos Francisco Zambrana Raymondo Endozo Wenya Linda Bi Fiona M Fennessy Nicole Sponer Diana Johnson Joanne Laycock Seema Shafi Justyna Czyzewska-Khan Andrew Rowan Tim Chambers Nik Matthews Samra Turajlic Crispin Hiley Siow Ming Lee Martin D Forster Tanya Ahmad Mary Falzon Elaine Borg David Lawrence Martin Hayward Shyam Kolvekar Nikolaos Panagiotopoulos Sam M Janes Ricky Thakrar Asia Ahmed Fiona Blackhall Yvonne Summers Dina Hafez Ashwini Naik Apratim Ganguly Stephanie Kareht Rajesh Shah Leena Joseph Anne Marie Quinn Phil A Crosbie Babu Naidu Gary Middleton Gerald Langman Simon Trotter Marianne Nicolson Hardy Remmen Keith Kerr Mahendran Chetty Lesley Gomersall Dean A Fennell Apostolos Nakas Sridhar Rathinam Girija Anand Sajid Khan Peter Russell Veni Ezhil Babikir Ismail Melanie Irvin-Sellers Vineet Prakash Jason F Lester Malgorzata Kornaszewska Richard Attanoos Haydn Adams Helen Davies Dahmane Oukrif Ayse U Akarca John A Hartley Helen L Lowe Sara Lock Natasha Iles Harriet Bell Yenting Ngai Greg Elgar Zoltan Szallasi Roland F Schwarz Javier Herrero Aengus Stewart Sergio A Quezada Karl S Peggs Peter Van Loo Caroline Dive C Jimmy Lin Matthew Rabinowitz Hugo J W L Aerts Allan Hackshaw Jacqui A Shaw Bernhard G Zimmermann Charles Swanton

Nature 2017 04;545(7655):446-451

Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK.

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http://dx.doi.org/10.1038/nature22364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812436PMC
April 2017

Paraneoplastic thrombocytosis in gastrointestinal cancer.

Platelets 2016 Jun 2;27(4):269-75. Epub 2016 May 2.

e Informatics Program, Children's Hospital , Harvard Medical School , Boston , MA , USA.

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http://dx.doi.org/10.3109/09537104.2016.1170112DOI Listing
June 2016

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

Biomark Res 2016 19;4. Epub 2016 Feb 19.

Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.

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http://dx.doi.org/10.1186/s40364-016-0058-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761211PMC
February 2016

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;6(1):45-58. Epub 2015 Nov 6.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1158/2159-8290.CD-15-0341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775099PMC
January 2016

Thrombocytosis of Liver Metastasis from Colorectal Cancer as Predictive Factor.

Pathol Oncol Res 2015 Sep 13;21(4):991-7. Epub 2015 Mar 13.

Tumorgenetika Human Biospecimen Collection and Research, 1147, Budapest, Kerékgyártó u. 36., Hungary.

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http://dx.doi.org/10.1007/s12253-015-9925-8DOI Listing
September 2015

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

Int J Surg 2015 Jun 3;18:1-6. Epub 2015 Apr 3.

Tumorgenetika Human Biospecimen Collection and Research Company, 1147 Budapest, Kerékgyártó utca 36-38, Hungary; 1st Department of Surgery, Semmelweis University, 1082 Budapest, Üllői út 78, Hungary.

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http://dx.doi.org/10.1016/j.ijsu.2015.03.005DOI Listing
June 2015

Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer.

Cell Rep 2015 Jun 4;11(10):1549-63. Epub 2015 Jun 4.

Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; BBS Program, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; The Broad Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.05.011DOI Listing
June 2015

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution.

Sci Transl Med 2015 Apr;7(283):283ra54

Cancer Research UK London Research Institute, London WC2A 3LY, UK. UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London WC1E 6DD, UK.

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http://dx.doi.org/10.1126/scitranslmed.aaa1408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636056PMC
April 2015

Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers.

Eur Urol 2014 Nov 19;66(5):936-48. Epub 2014 Jul 19.

Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK; Present address: Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.

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http://dx.doi.org/10.1016/j.eururo.2014.06.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410302PMC
November 2014

The genome of the chicken DT40 bursal lymphoma cell line.

G3 (Bethesda) 2014 Sep 15;4(11):2231-40. Epub 2014 Sep 15.

Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary

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http://dx.doi.org/10.1534/g3.114.013482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232548PMC
September 2014

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

PLoS One 2013 12;8(11):e80023. Epub 2013 Nov 12.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America ; Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080023PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827141PMC
July 2014

Thrombocytosis portends adverse prognostic significance in patients with stage II colorectal carcinoma.

F1000Res 2014 31;3:180. Epub 2014 Jul 31.

Department of Pathology, Monmouth Medical Center, Long Branch, NJ, NJ 07740, USA.

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http://dx.doi.org/10.12688/f1000research.4856.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240242PMC
July 2014

Deconvoluting complex tissues for expression quantitative trait locus-based analyses.

Philos Trans R Soc Lond B Biol Sci 2013 6;368(1620):20120363. Epub 2013 May 6.

Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA.

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http://dx.doi.org/10.1098/rstb.2012.0363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682728PMC
December 2013

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

Magy Seb 2013 Dec;66(6):331-7

Technical University of Denmark Department of Systems Biology Dánia Harvard Medical School Informatics Program, Children's Hospital Boston USA.

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http://dx.doi.org/10.1556/MaSeb.66.2013.6.5DOI Listing
December 2013

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

PLoS One 2013 16;8(4):e61872. Epub 2013 Apr 16.

Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061872PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628873PMC
November 2013

In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census.

Oncoimmunology 2012 Nov;1(8):1281-1289

Departments of Melanoma Medical Oncology and Systems Biology; University of Texas M.D. Anderson Cancer Center; Houston, TX USA.

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http://dx.doi.org/10.4161/onci.21511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518500PMC
November 2012

RecurrenceOnline: an online analysis tool to determine breast cancer recurrence and hormone receptor status using microarray data.

Breast Cancer Res Treat 2012 Apr 16;132(3):1025-34. Epub 2011 Jul 16.

Laboratory of Functional Genomics, Charité, Charitéplatz 1, 10117 Berlin, Germany.

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http://dx.doi.org/10.1007/s10549-011-1676-yDOI Listing
April 2012

Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients.

Endocr Relat Cancer 2012 Apr 10;19(2):197-208. Epub 2012 Apr 10.

Research Laboratory of Pediatrics and Nephrology, Hungarian Academy of Sciences, Budapest, Hungary.

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https://erc.bioscientifica.com/view/journals/erc/19/2/197.xm
Publisher Site
http://dx.doi.org/10.1530/ERC-11-0329DOI Listing
April 2012

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

N Engl J Med 2012 Mar;366(10):883-892

Cancer Research UK London Research Institute (M. Gerlinger, A.J.R., S.H., D.E., E.G., P.M., N.M., A.S., B.P., S.B., N.Q.M., C.R.S., B.S.-D., G.C., G.S., J.D., C.S.), Royal Marsden Hospital Department of Medicine (J.L., M.N., L.P., G.S., M. Gore), Wellcome Trust Sanger Institute (P.T., I.V., A.B., D.J., K.R., C.L., P.A.F.), Barts Cancer Institute at the Barts and the London School of Medicine and Dentistry (M. Gerlinger), and the University College London Cancer Institute (C.S.) - all in London; the Technical University of Denmark, Lyngby (A.C.E., Z.S.); and Harvard Medical School, Boston (Z.S.). Address reprint requests to Dr. Swanton at the Cancer Research UK London Research Institute, Translational Cancer Therapeutics Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom, or at

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http://dx.doi.org/10.1056/NEJMoa1113205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878653PMC
March 2012

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

BMC Bioinformatics 2011 Dec 15;12:474. Epub 2011 Dec 15.

Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.

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http://dx.doi.org/10.1186/1471-2105-12-474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266307PMC
December 2011

[From project-based sample collection to biobank].

Orv Hetil 2011 Apr;152(15):606-9

Fővárosi Önkormányzat Uzsoki Utcai Kórháza Sebészet-Érsebészeti Osztály Budapest Uzsoki u. 29. 1145 Tumorgenetika Biobank Klaszter Budapest.

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http://dx.doi.org/10.1556/OH.2011.29068DOI Listing
April 2011

Targeting chromosomal instability and tumour heterogeneity in HER2-positive breast cancer.

J Cell Biochem 2010 Nov;111(4):782-90

Translational Cancer Therapeutics Laboratory, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.

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http://dx.doi.org/10.1002/jcb.22781DOI Listing
November 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.

Breast Cancer Res Treat 2010 Oct 18;123(3):725-31. Epub 2009 Dec 18.

Joint Research Laboratory of the Hungarian Academy of Sciences and the Semmelweis University, Semmelweis University 1st Department of Pediatrics, Bokay u. 53-54, 1083, Budapest, Hungary.

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http://kmplot.com/analysis/studies/2010_Breast_Cancer_Res_Tr
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http://link.springer.com/10.1007/s10549-009-0674-9
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October 2010

Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer.

Breast Cancer Res 2008 31;10(5):214. Epub 2008 Oct 31.

Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK.

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http://breast-cancer-research.biomedcentral.com/articles/10.
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http://dx.doi.org/10.1186/bcr2159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614525PMC
February 2009

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 22;105(52):20870-5. Epub 2008 Dec 22.

Center for Biological Sequence Analysis, Kemitorvet building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark.

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http://dx.doi.org/10.1073/pnas.0810772105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2606902PMC
December 2008

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

Genome Biol 2008 4;9(2):R26. Epub 2008 Feb 4.

Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, MA 02115, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374720PMC
May 2008

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

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

Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://www.nature.com/articles/ng1861
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September 2006

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

Authors:
Leming Shi Laura H Reid Wendell D Jones Richard Shippy Janet A Warrington Shawn C Baker Patrick J Collins Francoise de Longueville Ernest S Kawasaki Kathleen Y Lee Yuling Luo Yongming Andrew Sun James C Willey Robert A Setterquist Gavin M Fischer Weida Tong Yvonne P Dragan David J Dix Felix W Frueh Frederico M Goodsaid Damir Herman Roderick V Jensen Charles D Johnson Edward K Lobenhofer Raj K Puri Uwe Schrf Jean Thierry-Mieg Charles Wang Mike Wilson Paul K Wolber Lu Zhang Shashi Amur Wenjun Bao Catalin C Barbacioru Anne Bergstrom Lucas Vincent Bertholet Cecilie Boysen Bud Bromley Donna Brown Alan Brunner Roger Canales Xiaoxi Megan Cao Thomas A Cebula James J Chen Jing Cheng Tzu-Ming Chu Eugene Chudin John Corson J Christopher Corton Lisa J Croner Christopher Davies Timothy S Davison Glenda Delenstarr Xutao Deng David Dorris Aron C Eklund Xiao-hui Fan Hong Fang Stephanie Fulmer-Smentek James C Fuscoe Kathryn Gallagher Weigong Ge Lei Guo Xu Guo Janet Hager Paul K Haje Jing Han Tao Han Heather C Harbottle Stephen C Harris Eli Hatchwell Craig A Hauser Susan Hester Huixiao Hong Patrick Hurban Scott A Jackson Hanlee Ji Charles R Knight Winston P Kuo J Eugene LeClerc Shawn Levy Quan-Zhen Li Chunmei Liu Ying Liu Michael J Lombardi Yunqing Ma Scott R Magnuson Botoul Maqsodi Tim McDaniel Nan Mei Ola Myklebost Baitang Ning Natalia Novoradovskaya Michael S Orr Terry W Osborn Adam Papallo Tucker A Patterson Roger G Perkins Elizabeth H Peters Ron Peterson Kenneth L Philips P Scott Pine Lajos Pusztai Feng Qian Hongzu Ren Mitch Rosen Barry A Rosenzweig Raymond R Samaha Mark Schena Gary P Schroth Svetlana Shchegrova Dave D Smith Frank Staedtler Zhenqiang Su Hongmei Sun Zoltan Szallasi Zivana Tezak Danielle Thierry-Mieg Karol L Thompson Irina Tikhonova Yaron Turpaz Beena Vallanat Christophe Van Stephen J Walker Sue Jane Wang Yonghong Wang Russ Wolfinger Alex Wong Jie Wu Chunlin Xiao Qian Xie Jun Xu Wen Yang Liang Zhang Sheng Zhong Yaping Zong William Slikker

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

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA.

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http://dx.doi.org/10.1038/nbt1239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272078PMC
September 2006

Reliability and reproducibility issues in DNA microarray measurements.

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

Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA.

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http://dx.doi.org/10.1016/j.tig.2005.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386979PMC
February 2006

A survey of methods for classification of gene expression data using evolutionary algorithms.

Expert Rev Mol Diagn 2006 Jan;6(1):101-10

Department of Applied Mechanics, Chalmers University of Technology, SE 412 96, Göteborg, Sweden.

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http://dx.doi.org/10.1586/14737159.6.1.101DOI Listing
January 2006

Robustness of cellular functions.

Cell 2004 Sep;118(6):675-85

Max Planck Institute for Dynamics of Complex Technical Systems, D-39106 Magdeburg, Germany.

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http://dx.doi.org/10.1016/j.cell.2004.09.008DOI Listing
September 2004

Increased measurement accuracy for sequence-verified microarray probes.

Physiol Genomics 2004 Aug 11;18(3):308-15. Epub 2004 Aug 11.

Division of Pulmonary and Critical Care Medicine, Department of Medicine and Pulmonary Bioinformatics, the Lung Biology Center, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.

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http://www.physiology.org/doi/10.1152/physiolgenomics.00066.
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August 2004

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. Epub 2004 May 25.

Division of Pulmonary and Critical Care Medicine, Department of Medicine and Pulmonary Bioinformatics, The Lung Biology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/nar/gnh071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC419626PMC
May 2004

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;64(3):789-94

Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institues of Health, Bethesda, Maryland, USA.

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February 2004

Trading "wet-work" for network.

Nat Biotechnol 2002 Apr;20(4):345-6

Children's Hospital Informatics Program, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/nbt0402-345DOI Listing
April 2002

Build your own (virtual) cell.

Authors:
Zoltan Szallasi

Trends Pharmacol Sci 2002 Apr;23(4):158-9

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April 2002

Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices.

Bioinformatics 2002 Mar;18(3):389-94

Division of Mechatronics, Chalmers University of Technology, Göteborg, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/18.3.389DOI Listing
March 2002