%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
% Baudis group %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{Marrero-Rodríguez_1018_KLF10,
author = {Marrero-Rodríguez, D and Taniguchi-Ponciano, K and Subramaniam, M and Hawse, JR and Pitel, KS and Arreola-De la Cruz, H and Huerta-Padilla, V and Ponce-Navarrete, G and Figueroa-Corona, MDP and Gomez-Virgilio, L and Martinez-Cuevas, TI and Mendoza-Rodriguez, M and Rodriguez-Esquivel, M and Romero-Morelos, P and Ramirez-Salcedo, J and Baudis, M and Meraz-Rios, M and Jimenez-Vega, F and Salcedo, M}, 
title = {Krüppel-Like Factor 10 participates in cervical cancer immunoediting through transcriptional regulation of Pregnancy-Specific Beta-1 Glycoproteins.}, 
journal = {Sci Rep}, 
volume = {8}, 
number = {1}, 
pages = {9445}, 
year = {2018}, 
location = {Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Departamento de Biomedicina Molecular, CINVESTAV, CDMX, Mexico. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA. Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA. Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Departamento de Biomedicina Molecular, CINVESTAV, CDMX, Mexico. Departamento de Biomedicina Molecular, CINVESTAV, CDMX, Mexico. Departamento de Biomedicina Molecular, CINVESTAV, CDMX, Mexico. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Departamento de Biomedicina Molecular, CINVESTAV, CDMX, Mexico. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. Unidad de Microarreglos de DNA, Instituto de Fisiologia Celular, UNAM, CDMX, Mexico. Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland. Departamento de Biomedicina Molecular, CINVESTAV, CDMX, Mexico. Laboratorio de Biotecnología, Universidad Autonóma de Ciudad Juárez, Ciudad Juárez, Chihuahua, Mexico. fjimenez@uacj.mx. Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN-SXXI. IMSS, CDMX, Mexico. masava89@gmail.com.}, 
keywords = {}}

@Article{gao_segment_liftover_f1000_2018,
AUTHOR = { Gao, B and Huang, Q and Baudis, M},
TITLE = {segment\_liftover : a Python tool to convert segments between genome assemblies [version 1; referees: awaiting peer review] },
JOURNAL = {F1000Research},
VOLUME = {7},
YEAR = {2018},
NUMBER = {319},
DOI = {10.12688/f1000research.14148.1}
}

@Article{sib_resources_2016,
 author = {SIB, Swiss Institute of Bioinformatics Members}, 
 title = {The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases.}, 
 journal = {Nucleic Acids Res}, 
 volume = {44}, 
 number = {D1}, 
 pages = {D27–37}, 
 year = {2016}, 
 keywords = {}, 
}

@Article{bevilacqua_2010_role,
 author = {Bevilacqua, G and Bosman, F and Dassesse, T and Höfler, H and Janin, A and Langer, R and Larsimont, D and Morente, MM and Riegman, P and Schirmacher, P and Stanta, G and Zatloukal, K and Caboux, E and Hainaut, P}, 
 title = {The role of the pathologist in tissue banking: European Consensus Expert Group Report.}, 
 journal = {Virchows Arch}, 
 volume = {456}, 
 number = {4}, 
 pages = {449–454}, 
 year = {2010}, 
 keywords = {}, 
}

@Article{casali_2014_rare,
 author = {Casali, PG}, 
 title = {Rare cancers: work in progress in Europe.}, 
 journal = {Ann Oncol}, 
 volume = {25}, 
 number = {4}, 
 pages = {914}, 
 year = {2014}, 
 keywords = {}, 
}

@Article{dove_2015_genomic,
 author = {Dove, ES}, 
 title = {Biobanks, Data Sharing, and the Drive for a Global Privacy Governance Framework.}, 
 journal = {J Law Med Ethics}, 
 volume = {43}, 
 number = {4}, 
 pages = {675–689}, 
 year = {2015}, 
 keywords = {}, 
}

@Article{helmy_2016_limited,
 author = {Helmy, M and Awad, M and Mosa, KA}, 
 title = {Limited resources of genome sequencing in developing countries: Challenges and solutions.}, 
 journal = {Appl Transl Genom}, 
 volume = {9}, 
 number = {}, 
 pages = {15–19}, 
 year = {2016}, 
 keywords = {}, 
}

@Article{muff_osteosarcoma_2015,
 author = {Muff, R and Rath, P and Ram Kumar, RM and Husmann, K and Born, W and Baudis, M and Fuchs, B}, 
 title = {Genomic instability of osteosarcoma cell lines in culture: impact on the prediction of metastasis relevant genes.}, 
 journal = {PLoS One}, 
 volume = {10}, 
 number = {5}, 
 pages = {e0125611}, 
 year = {2015}, 
 keywords = {}, 
}

@Article{cai_progenetix_2014,
author = {Cai, H and Kumar, N and Ai, N and Gupta, S and Rath, P and Baudis, M}, 
title = {Progenetix: 12 years of oncogenomic data curation.}, 
journal = {Nucleic Acids Res}, 
volume = {42}, 
number = {Database issue}, 
pages = {D1055-62}, 
year = {2014}, 
abstract = {}, 
keywords = {}}

@article{cai_arraymap_2012,
  Abstract = {},
  Author = {Cai, H and Kumar, N and Baudis, M},
  Journal = {PLoS One},
  Location = {Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.},
  Number = {5},
  Pages = {e36944},
  Title = {arrayMap: a reference resource for genomic copy number imbalances in human malignancies.},
  Volume = {7},
  Year = {2012}
}


@Article{liu_clustering_cgh_2006,
author = {Liu, J and Mohammed, J and Carter, J and Ranka, S and Kahveci, T and Baudis, M}, 
title = {Distance-based clustering of CGH data.}, 
journal = {Bioinformatics}, 
volume = {22}, 
number = {16}, 
pages = {1971-1978}, 
year = {2006}, 
abstract = {}, 
location = {Computer and Information Science and Engineering, University of Florida Gainesville, FL 32611, USA. juliu@cise.ufl.edu}, 
keywords = {}}

@Article{baudis_imbalances_5918_2007,
author = {Baudis, M}, 
title = {Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data.}, 
journal = {BMC Cancer}, 
volume = {7}, 
number = {1}, 
pages = {226}, 
year = {2007}, 
location = {}, 
keywords = {}}

@Article{vonbueren_pnet_2012,
author = {von Bueren, AO and Gerss, J and Hagel, C and Cai, H and Remke, M and Hasselblatt, M and Feuerstein, BG and Pernet, S and Delattre, O and Korshunov, A and Rutkowski, S and Pfister, SM and Baudis, M}, 
title = {DNA copy number alterations in central primitive neuroectodermal tumors and tumors of the pineal region: an international individual patient data meta-analysis.}, 
journal = {J Neurooncol}, 
volume = {109}, 
number = {2}, 
pages = {415-423}, 
year = {2012}, 
location = {Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany. a.von-bueren@uke.de}, 
keywords = {}}

@Article{kumar_cdcoca_2011,
author = {Kumar, N and Rehrauer, H and Cai, H and Baudis, M}, 
title = {CDCOCA: a statistical method to define complexity dependence of co-occuring chromosomal aberrations.}, 
journal = {BMC Med Genomics}, 
volume = {4}, 
number = {}, 
pages = {21}, 
year = {2011}, 
location = {Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.}, 
keywords = {}}

@Article{kumar_differential_cna_2012,
author = {Kumar, N and Cai, H and von Mering, C and Baudis, M}, 
title = {Specific genomic regions are differentially affected by copy number alterations across distinct cancer types, in aggregated cytogenetic data.}, 
journal = {PLoS One}, 
volume = {7}, 
number = {8}, 
pages = {e43689}, 
year = {2012}, 
location = {Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.}, 
keywords = {}}

@Article{cai_chromothripsis_2014,
author = {Cai, H and Kumar, N and Bagheri, HC and von Mering, C and Robinson, MD and Baudis, M}, 
title = {Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.}, 
journal = {BMC Genomics}, 
volume = {15}, 
number = {1}, 
pages = {82}, 
year = {2014}, 
location = {}, 
keywords = {}}

@Article{ai_cnara_2016,
author = {Ai, N and Cai, H and Solovan, C and Baudis, M}, 
title = {CNARA: reliability assessment for genomic copy number profiles.}, 
journal = {BMC Genomics}, 
volume = {17}, 
number = {1}, 
pages = {799}, 
year = {2016}, 
keywords = {}}

@Article{baudis_progenetix_2001,
author = {Baudis, M and Cleary, ML}, 
title = {Progenetix.net: an online repository for molecular cytogenetic aberration data.}, 
journal = {Bioinformatics}, 
volume = {17}, 
number = {12}, 
pages = {1228-1229}, 
year = {2001}, 
abstract = {}, 
location = {Medizinische Klinik und Poliklinik V der Universitat Heidelberg, Germany. mbaudis@stanford.edu}, 
keywords = {}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
% collaborations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{beleut_2015_biobank,
 author = {Beleut, M and Seclaman, E and Baudis, M and Nicula, A and Solovan, C}, 
 title = {A Biobank Supporting Rare Disease Research In Dermatopathology. Our Experience In Establishing A Biobank.}, 
 journal = {RoJCED}, 
 volume = {2}, 
 number = {3}, 
 pages = {202–206}, 
 year = {2015}, 
 keywords = {}, 
}

@Article{bluwstein_pkc_2013,
 author = {Bluwstein, A and Kumar, N and Leger, K and Traenkle, J and Oostrum, Jv and Rehrauer, H and Baudis, M and Hottiger, MO}, 
 title = {PKC signaling prevents irradiation-induced apoptosis of primary human fibroblasts.}, 
 journal = {Cell Death Dis}, 
 volume = {4}, 
 number = {}, 
 pages = {e498}, 
 year = {2013}, 
 keywords = {}, 
}

@Article{salaverria_irf4_2013,
 author = {Salaverria, I and Martin-Guerrero, I and Burkhardt, B and Kreuz, M and Zenz, T and Oschlies, I and Arnold, N and Baudis, M and Bens, S and Garcia-Orad, A and Lisfeld, J and Schwaenen, C and Szczepanowski, M and Wessendorf, S and Pfreundschuh, M and Trumper, L and Klapper, W and Siebert, R}, 
 title = {High resolution copy number analysis of IRF4 translocation-positive diffuse large B-cell and follicular lymphomas.}, 
 journal = {Genes Chromosomes Cancer}, 
 volume = {52}, 
 number = {2}, 
 pages = {150–155}, 
 year = {2013}, 
 keywords = {}, 
}

@Article{luebke_paadca_2012,
 author = {Luebke, AM and Baudis, M and Matthaei, H and Vashist, YK and Verde, PE and Hosch, SB and Erbersdobler, A and Klein, CA and Izbicki, JR and Knoefel, WT and Stoecklein, NH}, 
 title = {Losses at chromosome 4q are associated with poor survival in operable ductal pancreatic adenocarcinoma.}, 
 journal = {Pancreatology}, 
 volume = {12}, 
 number = {1}, 
 pages = {16–22}, 
 year = {2012}, 
 keywords = {}, 
}

@Article{beleut_renal_2012,
 author = {Beleut, M and Zimmermann, P and Baudis, M and Bruni, N and Buhlmann, P and Laule, O and Luu, VD and Gruissem, W and Schraml, P and Moch, H}, 
 title = {Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome.}, 
 journal = {BMC Cancer}, 
 volume = {12}, 
 number = {1}, 
 pages = {310}, 
 year = {2012}, 
 keywords = {}, 
}

@Article{martin-guerrero_irf4_2013,
 author = {Martin-Guerrero, I and Salaverria, I and Burkhardt, B and Szczepanowski, M and Baudis, M and Bens, S and de Leval, L and Garcia-Orad, A and Horn, H and Lisfeld, J and Pellissery, S and Klapper, W and Oschlies, I and Siebert, R}, 
 title = {Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas.}, 
 journal = {Haematologica}, 
 volume = {98}, 
 number = {8}, 
 pages = {1237–1241}, 
 year = {2013}, 
 keywords = {}, 
}

@Article{lacunza_muc1_2010,
 author = {Lacunza, E and Baudis, M and Colussi, AG and Segal-Eiras, A and Croce, MV and Abba, MC}, 
 title = {MUC1 oncogene amplification correlates with protein overexpression in invasive breast carcinoma cells.}, 
 journal = {Cancer Genet Cytogenet}, 
 volume = {201}, 
 number = {2}, 
 pages = {102–110}, 
 year = {2010}, 
 keywords = {}, 
}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
% big data collections %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{hapmap_2003,
  author = {{International HapMap Consortium}}, 
  title = {The International HapMap Project.}, 
  journal = {Nature}, 
  volume = {426}, 
  number = {6968}, 
  pages = {789–796}, 
  year = {2003}, 
  location = {}, 
  keywords = {}
}

@Article{edgar_2002_GEO,
  author = {Edgar, R and Domrachev, M and Lash, AE}, 
  title = {Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.}, 
  journal = {Nucleic Acids Res}, 
  volume = {30}, 
  number = {1}, 
  pages = {207–210}, 
  year = {2002}, 
  location = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA.}, 
  keywords = {}
}



@Article{tcga_2008,
author = {Cancer Genome Atlas Research Network}, 
title = {Comprehensive genomic characterization defines human glioblastoma genes and core pathways.}, 
journal = {Nature}, 
volume = {455}, 
number = {7216}, 
pages = {1061-1068}, 
year = {2008}, 
abstract = {}, 
location = {}, 
keywords = {}
}


@Article{icgc_2010,
author = {Hudson, TJ and International Cancer Genome Consortium}, 
title = {International network of cancer genome projects.}, 
journal = {Nature}, 
volume = {464}, 
number = {7291}, 
pages = {993-998}, 
year = {2010}, 
abstract = {},
authorlist = {},
location = {}, 
keywords = {}
}

@Article{tcga_2013,
author = {{Cancer Genome Atlas Research Network} and Weinstein, JN and Collisson, EA and Mills, GB and Shaw, KR and Ozenberger, BA and Ellrott, K and Shmulevich, I and Sander, C and Stuart, JM}, 
title = {The Cancer Genome Atlas Pan-Cancer analysis project.}, 
journal = {Nat Genet}, 
volume = {45}, 
number = {10}, 
pages = {1113–1120}, 
year = {2013}, 
location = {Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.}, 
keywords = {}}

@Article{1000_genomes_2015,
author = {Auton, A and Brooks, LD and Durbin, RM and Garrison, EP and Kang, HM and Korbel, JO and Marchini, JL and McCarthy, S and McVean, GA and Abecasis, GR and Consortium, {1000 Genomes Project}}, 
title = {A global reference for human genetic variation.}, 
journal = {Nature}, 
volume = {526}, 
number = {7571}, 
pages = {68–74}, 
year = {2015}, 
location = {}, 
keywords = {}}


@article{campbell_pcawg_biorxiv_2017,
	author = {Campbell, Peter J. and Getz, Gad and Stuart, Joshua M. and Korbel, Jan O. and Stein, Lincoln D. and {ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net}},
	title = {Pan-cancer analysis of whole genomes},
	year = {2017},
	doi = {10.1101/162784},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {We report the integrative analysis of more than 2,600 whole cancer genomes and their matching normal tissues across 39 distinct tumour types. By studying whole genomes we have been able to catalogue non-coding cancer driver events, study patterns of structural variation, infer tumour evolution, probe the interactions among variants in the germline genome, the tumour genome and the transcriptome, and derive an understanding of how coding and non-coding variations together contribute to driving individual patient{\textquoteright}s tumours. This work represents the most comprehensive look at cancer whole genomes to date. NOTE TO READERS: This is an incomplete draft of the marker paper for the Pan-Cancer Analysis of Whole Genomes Project, and is intended to provide the background information for a series of in-depth papers that will be posted to BioRixv during the summer of 2017.},
	URL = {https://www.biorxiv.org/content/early/2017/07/12/162784},
	eprint = {https://www.biorxiv.org/content/early/2017/07/12/162784.full.pdf},
	journal = {bioRxiv}
}

@Article{mackay_dipg_2017,
author = {Mackay, A and Burford, A and Carvalho, D and Izquierdo, E and Fazal-Salom, J and Taylor, KR and Bjerke, L and Clarke, M and Vinci, M and Nandhabalan, M and Temelso, S and Popov, S and Molinari, V and Raman, P and Waanders, AJ and Han, HJ and Gupta, S and Marshall, L and Zacharoulis, S and Vaidya, S and Mandeville, HC and Bridges, LR and Martin, AJ and Al-Sarraj, S and Chandler, C and Ng, HK and Li, X and Mu, K and Trabelsi, S and Brahim, DH and Kisljakov, AN and Konovalov, DM and Moore, AS and Carcaboso, AM and Sunol, M and de Torres, C and Cruz, O and Mora, J and Shats, LI and Stavale, JN and Bidinotto, LT and Reis, RM and Entz-Werle, N and Farrell, M and Cryan, J and Crimmins, D and Caird, J and Pears, J and Monje, M and Debily, MA and Castel, D and Grill, J and Hawkins, C and Nikbakht, H and Jabado, N and Baker, SJ and Pfister, SM and Jones, DTW and Fouladi, M and von Bueren, AO and Baudis, M and Resnick, A and Jones, C}, 
title = {Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma.}, 
journal = {Cancer Cell}, 
volume = {32}, 
number = {4}, 
pages = {520â-537.e5}, 
year = {2017}, 
location = {}, 
keywords = {}}


@Article{gao_segment_liftover_biorxiv_2018,
author = {Gao, Bo and Huang, Qingyao and Baudis, Michael}, 
title = {segment\_liftover: a Python tool to convert segments between genome assemblies}, 
journal = {bioRxiv}, 
volume = {}, 
number = {}, 
pages = {}, 
year = {2018}, 
location = {}, 
keywords = {}}


@Article{danaei_cancer_risk_world_2005,
author = {Danaei, G and Vander Hoorn, S and Lopez, AD and Murray, CJ and Ezzati, M and Comparative, Risk Assessment collaborating group (Cancers}, 
title = {Causes of cancer in the world: comparative risk assessment of nine behavioural and environmental risk factors.}, 
journal = {Lancet}, 
volume = {366}, 
number = {9499}, 
pages = {1784-1793}, 
year = {2005}, 
abstract = {}, 
location = {Harvard School of Public Health, Boston, MA 02115, USA.}, 
keywords = {}}


@article{siegel_cancer_statistics_2017,
Abstract = {},
Author = {Siegel, RL and Miller, KD and Jemal, A},
Journal = {CA Cancer J Clin},
Number = {1},
Pages = {7--30},
Title = {Cancer Statistics, 2017.},
Volume = {67},
Year = {2017}}


@online{mitelman_database,
  author = {Mitelman F, Johansson B and Mertens F (Eds.)},
  title = {Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer},
  year = 2018,
  url = http://cgap.nci.nih.gov/Chromosomes/Mitelman},
  urldate = {2018-04-24}
}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
% cancer mutations overviews && classics %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{hanahan_hallmarks_2011,
 author = {Hanahan, D and Weinberg, RA}, 
 title = {Hallmarks of cancer: the next generation.}, 
 journal = {Cell}, 
 volume = {144}, 
 number = {5}, 
 pages = {646–674}, 
 year = {2011}, 
 keywords = {}, 
}

@Article{groebner_childhood_cancer_mutations_2018,
 author = {Gröbner, SN and Worst, BC and Weischenfeldt, J and Buchhalter, I and Kleinheinz, K and Rudneva, VA and Johann, PD and Balasubramanian, GP and Segura-Wang, M and Brabetz, S and Bender, S and Hutter, B and Sturm, D and Pfaff, E and Hübschmann, D and Zipprich, G and Heinold, M and Eils, J and Lawerenz, C and Erkek, S and Lambo, S and Waszak, S and Blattmann, C and Borkhardt, A and Kuhlen, M and Eggert, A and Fulda, S and Gessler, M and Wegert, J and Kappler, R and Baumhoer, D and Burdach, S and Kirschner-Schwabe, R and Kontny, U and Kulozik, AE and Lohmann, D and Hettmer, S and Eckert, C and Bielack, S and Nathrath, M and Niemeyer, C and Richter, GH and Schulte, J and Siebert, R and Westermann, F and Molenaar, JJ and Vassal, G and Witt, H and ICGC, PedBrain-Seq Project and ICGC, MMML-Seq Project and Burkhardt, B and Kratz, CP and Witt, O and van Tilburg, CM and Kramm, CM and Fleischhack, G and Dirksen, U and Rutkowski, S and Frühwald, M and von Hoff, K and Wolf, S and Klingebiel, T and Koscielniak, E and Landgraf, P and Koster, J and Resnick, AC and Zhang, J and Liu, Y and Zhou, X and Waanders, AJ and Zwijnenburg, DA and Raman, P and Brors, B and Weber, UD and Northcott, PA and Pajtler, KW and Kool, M and Piro, RM and Korbel, JO and Schlesner, M and Eils, R and Jones, DTW and Lichter, P and Chavez, L and Zapatka, M and Pfister, SM}, 
 title = {The landscape of genomic alterations across childhood cancers.}, 
 journal = {Nature}, 
 volume = {555}, 
 number = {7696}, 
 pages = {321–327}, 
 year = {2018}, 
 keywords = {}, 
}


@Article{futreal_1994_brca1,
 author = {Futreal, PA and Liu, Q and Shattuck-Eidens, D and Cochran, C and Harshman, K and Tavtigian, S and Bennett, LM and Haugen-Strano, A and Swensen, J and Miki, Y}, 
 title = {BRCA1 mutations in primary breast and ovarian carcinomas.}, 
 journal = {Science}, 
 volume = {266}, 
 number = {5182}, 
 pages = {120–122}, 
 year = {1994}, 
 keywords = {}, 
}


@Article{miki_1994_BRCA1,
 author = {Miki, Y and Swensen, J and Shattuck-Eidens, D and Futreal, PA and Harshman, K and Tavtigian, S and Liu, Q and Cochran, C and Bennett, LM and Ding, W}, 
 title = {A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1.}, 
 journal = {Science}, 
 volume = {266}, 
 number = {5182}, 
 pages = {66–71}, 
 year = {1994}, 
 keywords = {}, 
}




@Article{yunis_mutations_fcl_1987,
author = {Yunis, JJ and Frizzera, G and Oken, MM and McKenna, J and Theologides, A and Arnesen, M}, 
title = {Multiple recurrent genomic defects in follicular lymphoma. A possible model for cancer.}, 
journal = {N Engl J Med}, 
volume = {316}, 
number = {2}, 
pages = {79–84}, 
year = {1987}, 
location = {}, 
keywords = {}}


@Article{vogelstein_multistep_1993,
author = {Vogelstein, B and Kinzler, KW}, 
title = {The multistep nature of cancer.}, 
journal = {Trends Genet}, 
volume = {4}, 
number = {9}, 
pages = {138â-141}, 
year = {1993}, 
location = {Johns Hopkins Oncology Center, Baltimore, MD 21231.}, 
keywords = {Adult; Aged; Aged, 80 and over; Animals; Animals, Genetically Modified; Cell Transformation, Neoplastic/*genetics; Gene Expression Regulation, Neoplastic; Humans; Mice; Middle Aged; Mutation; Neoplasms/epidemiology/*genetics; Oncogenes}}

@Article{vogelstein_cancer_genome_landscape_2013,
author = {Vogelstein, B and Papadopoulos, N and Velculescu, VE and Zhou, S and Diaz, LA and Kinzler, KW}, 
title = {Cancer genome landscapes.}, 
journal = {Science}, 
volume = {339}, 
number = {6127}, 
pages = {1546â-1558}, 
year = {2013}, 
location = {The Ludwig Center and The Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21287, USA.}, 
keywords = {}}

@Article{sjoeblom_breast_colorectal_sequencing_2006,
 author = {Sjöblom, T and Jones, S and Wood, LD and Parsons, DW and Lin, J and Barber, TD and Mandelker, D and Leary, RJ and Ptak, J and Silliman, N and Szabo, S and Buckhaults, P and Farrell, C and Meeh, P and Markowitz, SD and Willis, J and Dawson, D and Willson, JK and Gazdar, AF and Hartigan, J and Wu, L and Liu, C and Parmigiani, G and Park, BH and Bachman, KE and Papadopoulos, N and Vogelstein, B and Kinzler, KW and Velculescu, VE}, 
 title = {The consensus coding sequences of human breast and colorectal cancers.}, 
 journal = {Science}, 
 volume = {314}, 
 number = {5797}, 
 pages = {268–274}, 
 year = {2006}, 
 keywords = {}, 
}

@Article{szabo_1997_brca1_2_populations,
 author = {Szabo, CI and King, MC}, 
 title = {Population genetics of BRCA1 and BRCA2.}, 
 journal = {Am J Hum Genet}, 
 volume = {60}, 
 number = {5}, 
 pages = {1013–1020}, 
 year = {1997}, 
 keywords = {}, 
}

@Article{knuutila_1998_amplifications,
 author = {Knuutila, S and Bjorkqvist, AM and Autio, K and Tarkkanen, M and Wolf, M and Monni, O and Szymanska, J and Larramendy, ML and Tapper, J and Pere, H and El-Rifai, W and Hemmer, S and Wasenius, VM and Vidgren, V and Zhu, Y}, 
 title = {DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies.}, 
 journal = {Am J Pathol}, 
 volume = {152}, 
 number = {5}, 
 pages = {1107–1123}, 
 year = {1998}, 
 keywords = {}, 
}


@Article{stilgenbauer_1997_atm,
 author = {Stilgenbauer, S and Schaffner, C and Litterst, A and Liebisch, P and Gilad, S and Bar-Shira, A and James, MR and Lichter, P and Döhner, H}, 
 title = {Biallelic mutations in the ATM gene in T-prolymphocytic leukemia.}, 
 journal = {Nat Med}, 
 volume = {3}, 
 number = {10}, 
 pages = {1155–1159}, 
 year = {1997}, 
 keywords = {}, 
}



@Article{spirio_1992_APC,
 author = {Spirio, L and Otterud, B and Stauffer, D and Lynch, H and Lynch, P and Watson, P and Lanspa, S and Smyrk, T and Cavalieri, J and Howard, L}, 
 title = {Linkage of a variant or attenuated form of adenomatous polyposis coli to the adenomatous polyposis coli (APC) locus.}, 
 journal = {Am J Hum Genet}, 
 volume = {51}, 
 number = {1}, 
 pages = {92–100}, 
 year = {1992}, 
 keywords = {}, 
}

@Article{malkin_1990_tp53,
 author = {Malkin, D and Li, FP and Strong, LC and Fraumeni, JF and Nelson, CE and Kim, DH and Kassel, J and Gryka, MA and Bischoff, FZ and Tainsky, MA}, 
 title = {Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms.}, 
 journal = {Science}, 
 volume = {250}, 
 number = {4985}, 
 pages = {1233–1238}, 
 year = {1990}, 
 keywords = {}, 
}





@Article{lynch_1979_AFP,
 author = {Lynch, HT and Lynch, PM and Follett, KL and Harris, RE}, 
 title = {Familial polyposis coli: heterogeneous polyp expression in 2 kindreds.}, 
 journal = {J Med Genet}, 
 volume = {16}, 
 number = {1}, 
 pages = {1–7}, 
 year = {1979}, 
 keywords = {}, 
}




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
% CNA in cancer %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{jones_2012_medulloblastoma,
 author = {Jones, DT and Jager, N and Kool, M and Zichner, T and Hutter, B and Sultan, M and Cho, YJ and Pugh, TJ and Hovestadt, V and Stutz, AM and Rausch, T and Warnatz, HJ and Ryzhova, M and Bender, S and Sturm, D and Pleier, S and Cin, H and Pfaff, E and Sieber, L and Wittmann, A and Remke, M and Witt, H and Hutter, S and Tzaridis, T and Weischenfeldt, J and Raeder, B and Avci, M and Amstislavskiy, V and Zapatka, M and Weber, UD and Wang, Q and Lasitschka, B and Bartholomae, CC and Schmidt, M and von Kalle, C and Ast, V and Lawerenz, C and Eils, J and Kabbe, R and Benes, V and van Sluis, P and Koster, J and Volckmann, R and Shih, D and Betts, MJ and Russell, RB and Coco, S and Tonini, GP and Schuller, U and Hans, V and Graf, N and Kim, YJ and Monoranu, C and Roggendorf, W and Unterberg, A and Herold-Mende, C and Milde, T and Kulozik, AE and von Deimling, A and Witt, O and Maass, E and Rossler, J and Ebinger, M and Schuhmann, MU and Fruhwald, MC and Hasselblatt, M and Jabado, N and Rutkowski, S and von Bueren, AO and Williamson, D and Clifford, SC and McCabe, MG and Collins, VP and Wolf, S and Wiemann, S and Lehrach, H and Brors, B and Scheurlen, W and Felsberg, J and Reifenberger, G and Northcott, PA and Taylor, MD and Meyerson, M and Pomeroy, SL and Yaspo, ML and Korbel, JO and Korshunov, A and Eils, R and Pfister, SM and Lichter, P}, 
 title = {Dissecting the genomic complexity underlying medulloblastoma.}, 
 journal = {Nature}, 
 volume = {488}, 
 number = {7409}, 
 pages = {100–105}, 
 year = {2012}, 
 keywords = {}, 
}




@Article{jonsson_2010_breast_subtypes,
 author = {Jonsson, G and Staaf, J and Vallon-Christersson, J and Ringner, M and Holm, K and Hegardt, C and Gunnarsson, H and Fagerholm, R and Strand, C and Agnarsson, BA and Kilpivaara, O and Luts, L and Heikkila, P and Aittomaki, K and Blomqvist, C and Loman, N and Malmstrom, P and Olsson, H and Johannsson, OT and Arason, A and Nevanlinna, H and Barkardottir, RB and Borg, A}, 
 title = {Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics.}, 
 journal = {Breast Cancer Res}, 
 volume = {12}, 
 number = {3}, 
 pages = {R42}, 
 year = {2010}, 
 keywords = {}, 
}


@Article{lapointe_2007_prostate_subtypes,
 author = {Lapointe, J and Li, C and Giacomini, CP and Salari, K and Huang, S and Wang, P and Ferrari, M and Hernandez-Boussard, T and Brooks, JD and Pollack, JR}, 
 title = {Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis.}, 
 journal = {Cancer Res}, 
 volume = {67}, 
 number = {18}, 
 pages = {8504–8510}, 
 year = {2007}, 
 keywords = {}, 
}


@Article{vandesompele_neuroblastoma_2005,
 author = {Vandesompele, J and Baudis, M and De Preter, K and Van Roy, N and Ambros, P and Bown, N and Brinkschmidt, C and Christiansen, H and Combaret, V and Lastowska, M and Nicholson, J and O’Meara, A and Plantaz, D and Stallings, R and Brichard, B and Van den Broecke, C and De Bie, S and De Paepe, A and Laureys, G and Speleman, F}, 
 title = {Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma.}, 
 journal = {J Clin Oncol}, 
 volume = {23}, 
 number = {10}, 
 pages = {2280–2299}, 
 year = {2005}, 
 keywords = {}, 
}




@Article{houldsworth_1996_REL,
 author = {Houldsworth, J and Mathew, S and Rao, PH and Dyomina, K and Louie, DC and Parsa, N and Offit, K and Chaganti, RS}, 
 title = {REL proto-oncogene is frequently amplified in extranodal diffuse large cell lymphoma.}, 
 journal = {Blood}, 
 volume = {87}, 
 number = {1}, 
 pages = {25–29}, 
 year = {1996}, 
 keywords = {}, 
}

@Article{monni_1997_bcl2,
 author = {Monni, O and Joensuu, H and Franssila, K and Klefstrom, J and Alitalo, K and Knuutila, S}, 
 title = {BCL2 overexpression associated with chromosomal amplification in diffuse large B-cell lymphoma.}, 
 journal = {Blood}, 
 volume = {90}, 
 number = {3}, 
 pages = {1168–1174}, 
 year = {1997}, 
 keywords = {}, 
}

@Article{tapper_1997_ovarian,
 author = {Tapper, J and Butzow, R and Wahlstrom, T and Seppala, M and Knuutila, S}, 
 title = {Evidence for divergence of DNA copy number changes in serous, mucinous and endometrioid ovarian carcinomas.}, 
 journal = {Br J Cancer}, 
 volume = {75}, 
 number = {12}, 
 pages = {1782–1787}, 
 year = {1997}, 
 keywords = {}, 
}


@Article{weber_meningiomas_1997,
 author = {Weber, RG and Bostrom, J and Wolter, M and Baudis, M and Collins, VP and Reifenberger, G and Lichter, P}, 
 title = {Analysis of genomic alterations in benign, atypical, and anaplastic meningiomas: toward a genetic model of meningioma progression.}, 
 journal = {Proc Natl Acad Sci U S A}, 
 volume = {26}, 
 number = {94}, 
 pages = {14719–14724}, 
 year = {1997}, 
 keywords = {}, 
}




@Article{werner_high_level_cna_b-nhl_1997,
author = {Werner, CA and Dohner, H and Joos, S and Trumper, LH and Baudis, M and Barth, TF and Ott, G and Moller, P and Lichter, P and Bentz, M}, 
title = {High-level DNA amplifications are common genetic aberrations in B-cell neoplasms.}, 
journal = {Am J Pathol}, 
volume = {151}, 
number = {2}, 
pages = {335â-342}, 
year = {1997}, 
location = {Medizinische Klinik und Poliklinik V, Universitat Heidelberg, Germany.}, 
keywords = {}}

@Article{sarlomo_rikala_1998_gist_patterns,
 author = {Sarlomo-Rikala, M and El-Rifai, W and Lahtinen, T and Andersson, LC and Miettinen, M and Knuutila, S}, 
 title = {Different patterns of DNA copy number changes in gastrointestinal stromal tumors, leiomyomas, and schwannomas.}, 
 journal = {Hum Pathol}, 
 volume = {29}, 
 number = {5}, 
 pages = {476–481}, 
 year = {1998}, 
 keywords = {}, 
}



	
@Article{chiang_focal_cna_hcc_2008,
author = {Chiang, DY and Villanueva, A and Hoshida, Y and Peix, J and Newell, P and Minguez, B and LeBlanc, AC and Donovan, DJ and Thung, SN and Sole, M and Tovar, V and Alsinet, C and Ramos, AH and Barretina, J and Roayaie, S and Schwartz, M and Waxman, S and Bruix, J and Mazzaferro, V and Ligon, AH and Najfeld, V and Friedman, SL and Sellers, WR and Meyerson, M and Llovet, JM}, 
title = {Focal gains of VEGFA and molecular classification of hepatocellular carcinoma.}, 
journal = {Cancer Res}, 
volume = {68}, 
number = {16}, 
pages = {6779â-6788}, 
year = {2008}, 
location = {Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA.}, 
keywords = {}}


@Article{beroukhim_cna_landscape_cancer_2010,
author = {Beroukhim, R and Mermel, CH and Porter, D and Wei, G and Raychaudhuri, S and Donovan, J and Barretina, J and Boehm, JS and Dobson, J and Urashima, M and Mc Henry, KT and Pinchback, RM and Ligon, AH and Cho, YJ and Haery, L and Greulich, H and Reich, M and Winckler, W and Lawrence, MS and Weir, BA and Tanaka, KE and Chiang, DY and Bass, AJ and Loo, A and Hoffman, C and Prensner, J and Liefeld, T and Gao, Q and Yecies, D and Signoretti, S and Maher, E and Kaye, FJ and Sasaki, H and Tepper, JE and Fletcher, JA and Tabernero, J and Baselga, J and Tsao, MS and Demichelis, F and Rubin, MA and Janne, PA and Daly, MJ and Nucera, C and Levine, RL and Ebert, BL and Gabriel, S and Rustgi, AK and Antonescu, CR and Ladanyi, M and Letai, A and Garraway, LA and Loda, M and Beer, DG and True, LD and Okamoto, A and Pomeroy, SL and Singer, S and Golub, TR and Lander, ES and Getz, G and Sellers, WR and Meyerson, M}, 
title = {The landscape of somatic copy-number alteration across human cancers.}, 
journal = {Nature}, 
volume = {463}, 
number = {7283}, 
pages = {899â-905}, 
year = {2010}, 
location = {Cancer Program and Medical and Population Genetics Group, The Broad Institute of M.I.T. and Harvard, 7 Cambridge Center.}, 
keywords = {}}

@Article{paugh_gene_amplifications_dipg_2011,
author = {Paugh, BS and Broniscer, A and Qu, C and Miller, CP and Zhang, J and Tatevossian, RG and Olson, JM and Geyer, JR and Chi, SN and da Silva, NS and Onar-Thomas, A and Baker, JN and Gajjar, A and Ellison, DW and Baker, SJ}, 
title = {Genome-wide analyses identify recurrent amplifications of receptor tyrosine kinases and cell-cycle regulatory genes in diffuse intrinsic pontine glioma.}, 
journal = {J Clin Oncol}, 
volume = {29}, 
number = {30}, 
pages = {3999â-4006}, 
year = {2011}, 
location = {St Jude Children's Research Hospital, Memphis, TN 38105, USA.}, 
keywords = {}}


@Article{hirsch_focal_cna_chromothripsis_melanoma_2013,
author = {Hirsch, D and Kemmerling, R and Davis, S and Camps, J and Meltzer, PS and Ried, T and Gaiser, T}, 
title = {Chromothripsis and Focal Copy Number Alterations Determine Poor Outcome in Malignant Melanoma.}, 
journal = {Cancer Res}, 
volume = {}, 
number = {}, 
pages = {}, 
year = {2013}, 
location = {Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland; Institute of Pathology, Paracelsus Medical University, Salzburg, Austria; and Institute of Pathology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.}, 
keywords = {}}


%% Chromothripsis

@Article{meyerson_chromothripsis_2011,
author = {Meyerson, M and Pellman, D}, 
title = {Cancer genomes evolve by pulverizing single chromosomes.}, 
journal = {Cell}, 
volume = {144}, 
number = {1}, 
pages = {9–10}, 
year = {2011}, 
location = {Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. matthew_meyerson@dfci.harvard.edu}, 
keywords = {}}

@Article{kloostermann_chromothripsis_crc,
 author = {Kloosterman, WP and Hoogstraat, M and Paling, O and Tavakoli-Yaraki, M and Renkens, I and Vermaat, JS and van Roosmalen, MJ and van Lieshout, S and Nijman, IJ and Roessingh, W and van ‘t Slot, R and van de Belt, J and Guryev, V and Koudijs, M and Voest, E and Cuppen, E}, 
 title = {Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer.}, 
 journal = {Genome Biol}, 
 volume = {12}, 
 number = {10}, 
 pages = {R103}, 
 year = {2011}, 
 keywords = {}, 
}

@Article{northcott_medulloblastoma_subgroups_2012,
 author = {Northcott, PA and Shih, DJ and Peacock, J and Garzia, L and Morrissy, AS and Zichner, T and Stutz, AM and Korshunov, A and Reimand, J and Schumacher, SE and Beroukhim, R and Ellison, DW and Marshall, CR and Lionel, AC and Mack, S and Dubuc, A and Yao, Y and Ramaswamy, V and Luu, B and Rolider, A and Cavalli, FM and Wang, X and Remke, M and Wu, X and Chiu, RY and Chu, A and Chuah, E and Corbett, RD and Hoad, GR and Jackman, SD and Li, Y and Lo, A and Mungall, KL and Nip, KM and Qian, JQ and Raymond, AG and Thiessen, NT and Varhol, RJ and Birol, I and Moore, RA and Mungall, AJ and Holt, R and Kawauchi, D and Roussel, MF and Kool, M and Jones, DT and Witt, H and Fernandez-L, A and Kenney, AM and Wechsler-Reya, RJ and Dirks, P and Aviv, T and Grajkowska, WA and Perek-Polnik, M and Haberler, CC and Delattre, O and Reynaud, SS and Doz, FF and Pernet-Fattet, SS and Cho, BK and Kim, SK and Wang, KC and Scheurlen, W and Eberhart, CG and Fevre-Montange, M and Jouvet, A and Pollack, IF and Fan, X and Muraszko, KM and Gillespie, GY and Di Rocco, C and Massimi, L and Michiels, EM and Kloosterhof, NK and French, PJ and Kros, JM and Olson, JM and Ellenbogen, RG and Zitterbart, K and Kren, L and Thompson, RC and Cooper, MK and Lach, B and McLendon, RE and Bigner, DD and Fontebasso, A and Albrecht, S and Jabado, N and Lindsey, JC and Bailey, S and Gupta, N and Weiss, WA and Bognar, L and Klekner, A and Van Meter, TE and Kumabe, T and Tominaga, T and Elbabaa, SK and Leonard, JR and Rubin, JB and Liau, LM and Van Meir, EG and Fouladi, M and Nakamura, H and Cinalli, G and Garami, M and Hauser, P and Saad, AG and Iolascon, A and Jung, S and Carlotti, CG and Vibhakar, R and Ra, YS and Robinson, S and Zollo, M and Faria, CC and Chan, JA and Levy, ML and Sorensen, PH and Meyerson, M and Pomeroy, SL and Cho, YJ and Bader, GD and Tabori, U and Hawkins, CE and Bouffet, E and Scherer, SW and Rutka, JT and Malkin, D and Clifford, SC and Jones, SJ and Korbel, JO and Pfister, SM and Marra, MA and Taylor, MD}, 
 title = {Subgroup-specific structural variation across 1,000 medulloblastoma genomes.}, 
 journal = {Nature}, 
 volume = {488}, 
 number = {7409}, 
 pages = {49–56}, 
 year = {2012}, 
 keywords = {}, 
}

@Article{CLCGP_2013_lung_cancer,
 author = {Clinical Lung Cancer Genome Project (CLCGP) and Network Genomic Medicine (NGM)}, 
 title = {A genomics-based classification of human lung tumors.}, 
 journal = {Science translational medicine}, 
 volume = {5}, 
 number = {209}, 
 pages = {209ra153}, 
 year = {2013}, 
 keywords = {}, 
}


@Article{holland_2011_breast,
 author = {Holland, DG and Burleigh, A and Git, A and Goldgraben, MA and Perez-Mancera, PA and Chin, SF and Hurtado, A and Bruna, A and Ali, HR and Greenwood, W and Dunning, MJ and Samarajiwa, S and Menon, S and Rueda, OM and Lynch, AG and McKinney, S and Ellis, IO and Eaves, CJ and Carroll, JS and Curtis, C and Aparicio, S and Caldas, C}, 
 title = {ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium.}, 
 journal = {EMBO Mol Med}, 
 volume = {3}, 
 number = {3}, 
 pages = {167–180}, 
 year = {2011}, 
 keywords = {}, 
}




@Article{rausch_medullobastoma_2012,
 author = {Rausch, T and Jones, DT and Zapatka, M and Stutz, AM and Zichner, T and Weischenfeldt, J and Jager, N and Remke, M and Shih, D and Northcott, PA and Pfaff, E and Tica, J and Wang, Q and Massimi, L and Witt, H and Bender, S and Pleier, S and Cin, H and Hawkins, C and Beck, C and von Deimling, A and Hans, V and Brors, B and Eils, R and Scheurlen, W and Blake, J and Benes, V and Kulozik, AE and Witt, O and Martin, D and Zhang, C and Porat, R and Merino, DM and Wasserman, J and Jabado, N and Fontebasso, A and Bullinger, L and Rucker, FG and Dohner, K and Dohner, H and Koster, J and Molenaar, JJ and Versteeg, R and Kool, M and Tabori, U and Malkin, D and Korshunov, A and Taylor, MD and Lichter, P and Pfister, SM and Korbel, JO}, 
 title = {Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations.}, 
 journal = {Cell}, 
 volume = {148}, 
 number = {1-2}, 
 pages = {59–71}, 
 year = {2012}, 
 keywords = {}, 
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
%%  germline or ethnicity and cancer %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{heath_2018_racial,
 author = {Heath, EI and Lynce, F and Xiu, J and Ellerbrock, A and Reddy, SK and Obeid, E and Liu, SV and Bollig-Fischer, A and Separovic, D and Vanderwalde, A}, 
 title = {Racial Disparities in the Molecular Landscape of Cancer.}, 
 journal = {Anticancer Res}, 
 volume = {38}, 
 number = {4}, 
 pages = {2235–2240}, 
 year = {2018}, 
 keywords = {}, 
}



@Article{zhang_germline_cancer_2016,
 author = {Zhang, J and Nichols, KE and Downing, JR}, 
 title = {Germline Mutations in Predisposition Genes in Pediatric Cancer.}, 
 journal = {N Engl J Med}, 
 volume = {374}, 
 number = {14}, 
 pages = {1391}, 
 year = {2016}, 
 keywords = {}, 
}

@article{bach_early_lung_cancer_treatment_race_1999,
author = {Bach ,  Peter B.  and  Cramer ,  Laura D.  and  Warren ,  Joan L.  and  Begg ,  Colin B. },
title = {Racial Differences in the Treatment of Early-Stage Lung Cancer},
journal = {New England Journal of Medicine},
volume = {341},
number = {16},
pages = {1198-1205},
year = {1999},
doi = {10.1056/NEJM199910143411606},
note ={PMID: 10519898},
URL = {http://dx.doi.org/10.1056/NEJM199910143411606},
eprint = {http://dx.doi.org/10.1056/NEJM199910143411606}
}

@Article{li_aldh2_geography_2009,
author = {Li, H and Borinskaya, S and Yoshimura, K and Kal’ina, N and Marusin, A and Stepanov, VA and Qin, Z and Khaliq, S and Lee, MY and Yang, Y and Mohyuddin, A and Gurwitz, D and Mehdi, SQ and Rogaev, E and Jin, L and Yankovsky, NK and Kidd, JR and Kidd, KK}, 
title = {Refined geographic distribution of the oriental ALDH2*504Lys (nee 487Lys) variant.}, 
journal = {Ann Hum Genet}, 
volume = {73}, 
number = {Pt 3}, 
pages = {335–345}, 
year = {2009}, 
location = {Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520-8005, USA.}, 
keywords = {}}

@Article{alexander_admixture_2009,
author = {Alexander, DH and Novembre, J and Lange, K}, 
title = {Fast model-based estimation of ancestry in unrelated individuals.}, 
journal = {Genome Res}, 
volume = {19}, 
number = {9}, 
pages = {1655–1664}, 
year = {2009}, 
location = {Department of Biomathematics, University of California at Los Angeles, Los Angeles, California 90095, USA. dalexander@ucla.edu}, 
keywords = {}}


@article{kim_gastric_cancer_ethnicity_survival_2010,
author = {Kim, J. and Sun, C.-L. and Mailey, B. and Prendergast, C. and Artinyan, A. and Bhatia, S. and Pigazzi, A. and Ellenhorn, J. D. I.},
title = {Race and ethnicity correlate with survival in patients with gastric adenocarcinoma},
journal = {Annals of Oncology},
volume = {21},
number = {1},
pages = {152-160},
year = {2010},
doi = {10.1093/annonc/mdp290},
URL = { + http://dx.doi.org/10.1093/annonc/mdp290},
eprint = {/oup/backfile/content_public/journal/annonc/21/1/10.1093/annonc/mdp290/2/mdp290.pdf}
}

@Article{maher_2008_missing_heritability,
 author = {Maher, B}, 
 title = {Personal genomes: The case of the missing heritability.}, 
 journal = {Nature}, 
 volume = {456}, 
 number = {7218}, 
 pages = {18–21}, 
 year = {2008}, 
 keywords = {}, 
}

@Article{tan_cancer_genomics_ethnicity_2015,
author = {Tan, DS and Mok, TS and Rebbeck, TR}, 
title = {Cancer Genomics: Diversity and Disparity Across Ethnicity and Geography.}, 
journal = {J Clin Oncol}, 
volume = {34}, 
number = {1}, 
pages = {91â-101}, 
year = {2016}, 
keywords = {}}


@article{keenan_breast_cancer_biology_race_2015,
author = {Tanya Keenan and Beverly Moy and Edmund A. Mroz and Kenneth Ross and Andrzej Niemierko and James W. Rocco and Steven Isakoff and Leif W. Ellisen and Aditya Bardia},
title = {Comparison of the Genomic Landscape Between Primary Breast Cancer in African American Versus White Women and the Association of Racial Differences With Tumor Recurrence},
journal = {Journal of Clinical Oncology},
volume = {33},
number = {31},
pages = {3621-3627},
year = {2015},
doi = {10.1200/JCO.2015.62.2126},
note ={PMID: 26371147},
URL = {https://doi.org/10.1200/JCO.2015.62.2126},
eprint = {https://doi.org/10.1200/JCO.2015.62.2126},
abstract = { Purpose African American women are more likely to die as a result of breast cancer than white women. The influence of somatic genomic profiles on this racial disparity is unclear. We aimed to compare the racial distribution of tumor genomic characteristics and breast cancer recurrence. Methods We assessed white and African American women with stage I to III breast cancer diagnosed from 1988 to 2013 and primary tumors submitted to The Cancer Genome Atlas from 2010 to 2014. We used Cox proportional hazards models to evaluate the association of race and genetic traits with tumor recurrence. Results We investigated exome sequencing and gene expression data in 663 and 711 white and 105 and 159 African American women, respectively. African Americans had more TP53 mutations (42.9\% v 27.6\%; P = .003) and fewer PIK3CA mutations (20.0\% v 33.9\%; P = .008). Intratumor genetic heterogeneity was greater in African American than white tumors overall by 5.1 units (95\% CI, 2.4 to 7.7) and within triple-negative tumors by 4.1 units (95\% CI, 1.4 to 6.8). African Americans had more basal tumors by the 50-gene set predictor using the predication analysis of microarray method (PAM50; 39.0\% v 18.6\%; P < .001) and fewer PAM50 luminal A tumors (17.0\% v 34.7\%; P < .001). Among triple-negative subtypes, African Americans had more basal-like 1 and mesenchymal stem-like tumors. African Americans had a higher risk of tumor recurrence than whites (hazard ratio, 2.22; 95\% CI, 1.05 to 4.67). Racial differences in TP53 mutation, PAM50 basal subtype, and triple-negative tumor prevalence but not intratumor genetic heterogeneity influenced the magnitude and significance of the racial disparity in tumor recurrence. Conclusion African Americans had greater intratumor genetic heterogeneity and more basal gene expression tumors, even within triple-negative breast cancer. This pattern suggests more aggressive tumor biology in African Americans than whites, which could contribute to racial disparity in breast cancer outcome. }
}


@Article{deng_esophagus_cancer_chinese_2017,
author={Deng, Jiaying and Chen, Hu and Zhou, Daizhan and Zhang, Junhua and Chen, Yun and Liu, Qi and Ai, Dashan and Zhu, Hanting and Chu, Li and Ren, Wenjia and Zhang, Xiaofei and Xia, Yi and Sun, Menghong and Zhang, Huiwen and Li, Jun and Peng, Xinxin and Li, Liang and Han, Leng and Lin, Hui and Cai, Xiujun and Xiang, Jiaqing and Chen, Shufeng and Sun, Yihua and Zhang, Yawei and Zhang, Jie and Chen, Haiquan and Zhang, Shijian and Zhao, Yi and Liu, Yun and Liang, Han and Zhao, Kuaile},
title={Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations},
journal={Nature Communications},
year={2017},
volume={8},
number={1},
pages={1533},
abstract={Esophageal squamous cell carcinoma is a major histological type of esophageal cancer, with distinct incidence and survival patterns among races. Although previous studies have characterized somatic mutations in this disease, a rigorous comparison between different patient populations has not been conducted. Here we sequence the samples of 316 Chinese patients, combine them with those from The Cancer Genome Atlas, and perform a comparative analysis between Asian and Caucasian patients. We find that mutated CSMD3 is associated with better prognosis in Asian patients. Applying a robust computational strategy that adjusts for both technical and biological confounding factors, we find that TP53, EP300, and NFE2L2 show higher mutational frequencies in Asian patients. Moreover, NFE2L2 mutations correlate with the allele status of a nearby high-Fst SNP, suggesting their potential interaction. Our study provides insights into the molecular basis underlying the striking racial disparities of this disease, and represents a general computational framework for such a cross-population comparison.},
issn={2041-1723},
doi={10.1038/s41467-017-01730-x},
url={https://doi.org/10.1038/s41467-017-01730-x}
}

@Article{zhang_tcga_mutation_burden_race_2017,
author={Zhang, Wensheng
and Edwards, Andrea
and Flemington, Erik K.
and Zhang, Kun},
title={Racial disparities in patient survival and tumor mutation burden, and the association between tumor mutation burden and cancer incidence rate},
journal={Scientific Reports},
year={2017},
volume={7},
number={1},
pages={13639},
abstract={},
issn={2045-2322},
doi={10.1038/s41598-017-13091-y},
url={https://doi.org/10.1038/s41598-017-13091-y}
}


@Article{boffetta_2003_environmental,
 author = {Boffetta, P and Nyberg, F}, 
 title = {Contribution of environmental factors to cancer risk.}, 
 journal = {Br Med Bull}, 
 volume = {68}, 
 number = {}, 
 pages = {71–94}, 
 year = {2003}, 
 keywords = {}, 
}

@Article{johansson_1991_geographic,
 author = {Johansson, B and Mertens, F and Mitelman, F}, 
 title = {Geographic heterogeneity of neoplasia-associated chromosome aberrations.}, 
 journal = {Genes Chromosomes Cancer}, 
 volume = {3}, 
 number = {1}, 
 pages = {1–7}, 
 year = {1991}, 
 keywords = {}, 
}




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% familial
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{popejoy_2018_race,
 author = {Popejoy, Alice B and Ritter, Deborah I and Crooks, Kristy and Currey, Erin and Fullerton, Stephanie M and Hindorff, Lucia A and Koenig, Barbara and Ramos, Erin M and Sorokin, Elena P and Wand, Hannah and Wright, Matthew W and Zou, James and Gignoux, Christopher R and Bonham, Vence L and Plon, Sharon E and Bustamante, Carlos D}, 
 title = {The Clinical Imperative for Inclusivity: Race, Ethnicity, and Ancestry (REA) in Genomics}, 
 journal = {bioRxiv}, 
 volume = {}, 
 number = {}, 
 pages = {}, 
 year = {2018}, 
 keywords = {}, 
}



@Article{lynch_hereditary_crc_2003,
  author = {Lynch, HT and de la Chapelle, A}, 
  title = {Hereditary colorectal cancer.}, 
  journal = {N Engl J Med}, 
  volume = {348}, 
  number = {10}, 
  pages = {919–932}, 
  year = {2003}, 
  location = {Department of Preventive Medicine and Public Health, Creighton University School of Medicine, Omaha, Nebr 68178, USA. htlynch@creighton.edu}, 
  keywords = {}
}


@Article{olopade_1996_familial_AML,
 author = {Olopade, OI and Roulston, D and Baker, T and Narvid, S and Le Beau, MM and Freireich, EJ and Larson, RA and Golomb, HM}, 
 title = {Familial myeloid leukemia associated with loss of the long arm of chromosome 5.}, 
 journal = {Leukemia}, 
 volume = {10}, 
 number = {4}, 
 pages = {669–674}, 
 year = {1996}, 
 keywords = {}, 
}

@Article{siebert_1995_familial_AML,
 author = {Siebert, R and Jhanwar, S and Brown, K and Berman, E and Offit, K}, 
 title = {Familial acute myeloid leukemia and DiGuglielmo syndrome.}, 
 journal = {Leukemia}, 
 volume = {9}, 
 number = {6}, 
 pages = {1091–1094}, 
 year = {1995}, 
 keywords = {}, 
}

@Article{lynch_1993_FAMMM,
 author = {Lynch, HT and Fusaro, RM and Sandberg, AA and Bixenman, HA and Johnsen, LR and Lynch, JF and Ramesh, KH and Leppert, M}, 
 title = {Chromosome instability and the FAMMM syndrome.}, 
 journal = {Cancer Genet Cytogenet}, 
 volume = {71}, 
 number = {1}, 
 pages = {27–39}, 
 year = {1993}, 
 keywords = {}, 
}





%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% environmental
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{vandenberghe_1979_benzene_leukemia,
 author = {Van den Berghe, H and Louwagie, A and Broeckaert-Van Orshoven, A and David, G and Verwilghen, R}, 
 title = {Chromosome analysis in two unusual malignant blood disorders presumably induced by benzene.}, 
 journal = {Blood}, 
 volume = {53}, 
 number = {4}, 
 pages = {558–566}, 
 year = {1979}, 
 keywords = {}, 
}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Databases etc.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{chakravarty_oncokb_2017,
author = {Chakravarty, D and Gao, J and Phillips, SM and Kundra, R and Zhang, H and Wang, J and Rudolph, JE and Yaeger, R and Soumerai, T and Nissan, MH and Chang, MT and Chandarlapaty, S and Traina, TA and Paik, PK and Ho, AL and Hantash, FM and Grupe, A and Baxi, SS and Callahan, MK and Snyder, A and Chi, P and Danila, D and Gounder, M and Harding, JJ and Hellmann, MD and Iyer, G and Janjigian, Y and Kaley, T and Levine, DA and Lowery, M and Omuro, A and Postow, MA and Rathkopf, D and Shoushtari, AN and Shukla, N and Voss, M and Paraiso, E and Zehir, A and Berger, MF and Taylor, BS and Saltz, LB and Riely, GJ and Ladanyi, M and Hyman, DM and Baselga, J and Sabbatini, P and Solit, DB and Schultz, N}, 
title = {OncoKB: A Precision Oncology Knowledge Base.}, 
journal = {JCO Precis Oncol}, 
volume = {2017}, 
number = {}, 
pages = {}, 
year = {2017}, 
location = {}, 
keywords = {}}

@Article{griffith_civic_2017,
author = {Griffith, M and Spies, NC and Krysiak, K and McMichael, JF and Coffman, AC and Danos, AM and Ainscough, BJ and Ramirez, CA and Rieke, DT and Kujan, L and Barnell, EK and Wagner, AH and Skidmore, ZL and Wollam, A and Liu, CJ and Jones, MR and Bilski, RL and Lesurf, R and Feng, YY and Shah, NM and Bonakdar, M and Trani, L and Matlock, M and Ramu, A and Campbell, KM and Spies, GC and Graubert, AP and Gangavarapu, K and Eldred, JM and Larson, DE and Walker, JR and Good, BM and Wu, C and Su, AI and Dienstmann, R and Margolin, AA and Tamborero, D and Lopez-Bigas, N and Jones, SJ and Bose, R and Spencer, DH and Wartman, LD and Wilson, RK and Mardis, ER and Griffith, OL}, 
title = {CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.}, 
journal = {Nat Genet}, 
volume = {49}, 
number = {2}, 
pages = {170–174}, 
year = {2017}, 
location = {}, 
keywords = {}}

@Article{ng_fasmic_2018,
  title = {Systematic Functional Annotation of Somatic Mutations in Cancer.}, 
  author = {Ng, PK and Li, J and Jeong, KJ and Shao, S and Chen, H and Tsang, YH and Sengupta, S and Wang, Z and Bhavana, VH and Tran, R and Soewito, S and Minussi, DC and Moreno, D and Kong, K and Dogruluk, T and Lu, H and Gao, J and Tokheim, C and Zhou, DC and Johnson, AM and Zeng, J and Ip, CKM and Ju, Z and Wester, M and Yu, S and Li, Y and Vellano, CP and Schultz, N and Karchin, R and Ding, L and Lu, Y and Cheung, LWT and Chen, K and Shaw, KR and Meric-Bernstam, F and Scott, KL and Yi, S and Sahni, N and Liang, H and Mills, GB}, 
  journal = {Cancer Cell}, 
  volume = {33}, 
  number = {3}, 
  pages = {450–462.e10}, 
  year = {2018}, 
  location = {}, 
  keywords = {}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% bioinformatics
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{beroukhim_2007_GISTIC,
 author = {Beroukhim, R and Getz, G and Nghiemphu, L and Barretina, J and Hsueh, T and Linhart, D and Vivanco, I and Lee, JC and Huang, JH and Alexander, S and Du, J and Kau, T and Thomas, RK and Shah, K and Soto, H and Perner, S and Prensner, J and Debiasi, RM and Demichelis, F and Hatton, C and Rubin, MA and Garraway, LA and Nelson, SF and Liau, L and Mischel, PS and Cloughesy, TF and Meyerson, M and Golub, TA and Lander, ES and Mellinghoff, IK and Sellers, WR}, 
 title = {Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma.}, 
 journal = {Proc Natl Acad Sci U S A}, 
 volume = {104}, 
 number = {50}, 
 pages = {20007–20012}, 
 year = {2007}, 
 keywords = {}, 
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CGH, arrays, sequencing technology references
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{wang_2015_CNV_WES,
 author = {Wang, W and Sun, W and Crowley, JJ and Szatkiewicz, JP}, 
 title = {Allele-specific copy-number discovery from whole-genome and whole-exome sequencing.}, 
 journal = {Nucleic Acids Res}, 
 volume = {43}, 
 number = {14}, 
 pages = {e90}, 
 year = {2015}, 
 keywords = {}, 
}

@Article{amarasinghe_2013_CNV_WES,
 author = {Amarasinghe, KC and Li, J and Halgamuge, SK}, 
 title = {CoNVEX: copy number variation estimation in exome sequencing data using HMM.}, 
 journal = {BMC Bioinformatics}, 
 volume = {14 Suppl 2}, 
 number = {}, 
 pages = {S2}, 
 year = {2013}, 
 keywords = {}, 
}

@Article{delight_2013_CNV_WES,
 author = {de Ligt, J and Boone, PM and Pfundt, R and Vissers, LE and Richmond, T and Geoghegan, J and O’Moore, K and de Leeuw, N and Shaw, C and Brunner, HG and Lupski, JR and Veltman, JA and Hehir-Kwa, JY}, 
 title = {Detection of clinically relevant copy number variants with whole-exome sequencing.}, 
 journal = {Hum Mutat}, 
 volume = {34}, 
 number = {10}, 
 pages = {1439–1448}, 
 year = {2013}, 
 keywords = {}, 
}



@Article{parsons_2011_MBL,
 author = {Parsons, DW and Li, M and Zhang, X and Jones, S and Leary, RJ and Lin, JC and Boca, SM and Carter, H and Samayoa, J and Bettegowda, C and Gallia, GL and Jallo, GI and Binder, ZA and Nikolsky, Y and Hartigan, J and Smith, DR and Gerhard, DS and Fults, DW and VandenBerg, S and Berger, MS and Marie, SK and Shinjo, SM and Clara, C and Phillips, PC and Minturn, JE and Biegel, JA and Judkins, AR and Resnick, AC and Storm, PB and Curran, T and He, Y and Rasheed, BA and Friedman, HS and Keir, ST and McLendon, R and Northcott, PA and Taylor, MD and Burger, PC and Riggins, GJ and Karchin, R and Parmigiani, G and Bigner, DD and Yan, H and Papadopoulos, N and Vogelstein, B and Kinzler, KW and Velculescu, VE}, 
 title = {The genetic landscape of the childhood cancer medulloblastoma.}, 
 journal = {Science}, 
 volume = {331}, 
 number = {6016}, 
 pages = {435–439}, 
 year = {2011}, 
 keywords = {}, 
}

@Article{timmermann_2010_WES,
 author = {Timmermann, Bernd and Kerick, Martin and Roehr, Christina and Fischer, Axel and Isau, Melanie and Boerno, Stefan T and Wunderlich, Andrea and Barmeyer, Christian and Seemann, Petra and Koenig, Jana and Lappe, Michael and Kuss, Andreas W and Garshasbi, Masoud and Bertram, Lars and Trappe, Kathrin and Werber, Martin and Herrmann, Bernhard G and Zatloukal, Kurt and Lehrach, Hans and Schweiger, Michal R}, 
 title = {Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis.}, 
 journal = {PLoS ONE}, 
 volume = {5}, 
 number = {12}, 
 pages = {e15661}, 
 year = {2010}, 
 keywords = {}, 
}


@Article{meyerson_2010_WES_review,
 author = {Meyerson, M. and Gabriel, S. and Getz, G.}, 
 title = {Advances in understanding cancer genomes through second-generation sequencing}, 
 journal = {Nat Rev Genet}, 
 volume = {11}, 
 number = {10}, 
 pages = {685–696}, 
 year = {2010}, 
 keywords = {Genome-Wide Association Study; Genomics; Genome: Human; Neoplasms; Sequence Analysis: DNA; Gene Expression Profiling; Computational Biology; Humans; Exons; Mutation}, 
}

@Article{campbell_2008_WES,
 author = {Campbell, PJ and Stephens, PJ and Pleasance, ED and O’Meara, S and Li, H and Santarius, T and Stebbings, LA and Leroy, C and Edkins, S and Hardy, C and Teague, JW and Menzies, A and Goodhead, I and Turner, DJ and Clee, CM and Quail, MA and Cox, A and Brown, C and Durbin, R and Hurles, ME and Edwards, PA and Bignell, GR and Stratton, MR and Futreal, PA}, 
 title = {Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.}, 
 journal = {Nat Genet}, 
 volume = {40}, 
 number = {6}, 
 pages = {722–729}, 
 year = {2008}, 
 keywords = {}, 
}


@Article{ley_2008_WGS,
 author = {Ley, TJ and Mardis, ER and Ding, L and Fulton, B and McLellan, MD and Chen, K and Dooling, D and Dunford-Shore, BH and McGrath, S and Hickenbotham, M and Cook, L and Abbott, R and Larson, DE and Koboldt, DC and Pohl, C and Smith, S and Hawkins, A and Abbott, S and Locke, D and Hillier, LW and Miner, T and Fulton, L and Magrini, V and Wylie, T and Glasscock, J and Conyers, J and Sander, N and Shi, X and Osborne, JR and Minx, P and Gordon, D and Chinwalla, A and Zhao, Y and Ries, RE and Payton, JE and Westervelt, P and Tomasson, MH and Watson, M and Baty, J and Ivanovich, J and Heath, S and Shannon, WD and Nagarajan, R and Walter, MJ and Link, DC and Graubert, TA and DiPersio, JF and Wilson, RK}, 
 title = {DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.}, 
 journal = {Nature}, 
 volume = {456}, 
 number = {7218}, 
 pages = {66–72}, 
 year = {2008}, 
 keywords = {}, 
}



@Article{malcolm_1982_in-situ,
 author = {Malcolm, S and Barton, P and Murphy, C and Ferguson-Smith, MA and Bentley, DL and Rabbitts, TH}, 
 title = {Localization of human immunoglobulin kappa light chain variable region genes to the short arm of chromosome 2 by in situ hybridization.}, 
 journal = {Proc Natl Acad Sci U S A}, 
 volume = {79}, 
 number = {16}, 
 pages = {4957–4961}, 
 year = {1982}, 
 keywords = {}, 
}

@Article{lichter_fish_1988,
 author = {Lichter, P and Cremer, T and Borden, J and Manuelidis, L and Ward, DC}, 
 title = {Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries.}, 
 journal = {Hum Genet}, 
 volume = {80}, 
 number = {3}, 
 pages = {224–234}, 
 year = {1988}, 
 keywords = {}, 
}

@Article{cremer_1988_FISH,
 author = {Cremer, T and Lichter, P and Borden, J and Ward, DC and Manuelidis, L}, 
 title = {Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes.}, 
 journal = {Hum Genet}, 
 volume = {80}, 
 number = {3}, 
 pages = {235–246}, 
 year = {1988}, 
 keywords = {}, 
}

@Article{kallioniemi_1992_CGH,
 author = {Kallioniemi, A and Kallioniemi, OP and Sudar, D and Rutovitz, D and Gray, JW and Waldman, F and Pinkel, D}, 
 title = {Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors.}, 
 journal = {Science}, 
 volume = {5083}, 
 number = {258}, 
 pages = {818–821}, 
 year = {1992}, 
 keywords = {}, 
}

@Article{joos_1993_pre_cgh,
 author = {Joos, S and Scherthan, H and Speicher, MR and Schlegel, J and Cremer, T and Lichter, P}, 
 title = {Detection of amplified DNA sequences by reverse chromosome painting using genomic tumor DNA as probe.}, 
 journal = {Hum Genet}, 
 volume = {90}, 
 number = {6}, 
 pages = {584–589}, 
 year = {1993}, 
 keywords = {}, 
}

@Article{speicher_1993_CGH,
 author = {Speicher, MR and du Manoir, S and Schrock, E and Holtgreve-Grez, H and Schoell, B and Lengauer, C and Cremer, T and Ried, T}, 
 title = {Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by comparative genomic hybridization after universal DNA-amplification.}, 
 journal = {Hum Mol Genet}, 
 volume = {11}, 
 number = {2}, 
 pages = {1907–1914}, 
 year = {1993}, 
 keywords = {}, 
}

@Article{speicher_1993_CGH,
 author = {Speicher, MR and du Manoir, S and Schrock, E and Holtgreve-Grez, H and Schoell, B and Lengauer, C and Cremer, T and Ried, T}, 
 title = {Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by comparative genomic hybridization after universal DNA-amplification.}, 
 journal = {Hum Mol Genet}, 
 volume = {11}, 
 number = {2}, 
 pages = {1907–1914}, 
 year = {1993}, 
 keywords = {}, 
}


@Article{suijkerbuijk_1993_multiple_FISH,
 author = {Suijkerbuijk, RF and Sinke, RJ and Meloni, AM and Parrington, JM and van Echten, J and de Jong, B and Oosterhuis, JW and Sandberg, AA and Geurts van Kessel, A}, 
 title = {Overrepresentation of chromosome 12p sequences and karyotypic evolution in i(12p)-negative testicular germ-cell tumors revealed by fluorescence in situ hybridization.}, 
 journal = {Cancer Genet Cytogenet}, 
 volume = {70}, 
 number = {2}, 
 pages = {85–93}, 
 year = {1993}, 
 keywords = {}, 
}

@Article{isola_1994_paraffin_CGH,
 author = {Isola, J and DeVries, S and Chu, L and Ghazvini, S and Waldman, F}, 
 title = {Analysis of changes in DNA sequence copy number by comparative genomic hybridization in archival paraffin-embedded tumor samples.}, 
 journal = {Am J Pathol}, 
 volume = {6}, 
 number = {145}, 
 pages = {1301–1308}, 
 year = {1994}, 
 keywords = {}, 
}


@Article{speicher_1996_M-FISH,
 author = {Speicher, MR and Gwyn Ballard, S and Ward, DC}, 
 title = {Karyotyping human chromosomes by combinatorial multi-fluor FISH.}, 
 journal = {Nat Genet}, 
 volume = {12}, 
 number = {4}, 
 pages = {368–375}, 
 year = {1996}, 
 keywords = {Chromosome Aberrations/genetics; Chromosomes, Artificial, Yeast; Chromosomes, Human/*genetics/ultrastructure; DNA Probes; Female; Fluorescent Dyes; Gene Rearrangement; Humans; Image Processing, Computer-Assisted; In Situ Hybridization, Fluorescence/*methods; Karyotyping/*methods; Male; Research Support, Non-U.S. Gov’t; Research Support, U.S. Gov’t, Non-P.H.S.; Software; Tumor Cells, Cultured}, 
}


@Article{veldman_1997_spectral,
 author = {Veldman, T and Vignon, C and Schrock, E and Rowley, JD and Ried, T}, 
 title = {Hidden chromosome abnormalities in haematological malignancies detected by multicolour spectral karyotyping.}, 
 journal = {Nat Genet}, 
 volume = {15}, 
 number = {4}, 
 pages = {406–410}, 
 year = {1997}, 
 keywords = {}, 
}

@Article{solinas_toldo_matrix_cgh_1997,
 author = {Solinas-Toldo, S and Lampel, S and Stilgenbauer, S and Nickolenko, J and Benner, A and Dohner, H and Cremer, T and Lichter, P}, 
 title = {Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances.}, 
 journal = {Genes Chromosomes Cancer}, 
 volume = {4}, 
 number = {20}, 
 pages = {399–407}, 
 year = {1997}, 
 keywords = {}, 
}

@Article{werner_amplifications_1997,
 author = {Werner, CA and Dohner, H and Joos, S and Trumper, LH and Baudis, M and Barth, TF and Ott, G and Moller, P and Lichter, P and Bentz, M}, 
 title = {High-level DNA amplifications are common genetic aberrations in B-cell neoplasms.}, 
 journal = {Am J Pathol}, 
 volume = {151}, 
 number = {2}, 
 pages = {335–342}, 
 year = {1997}, 
 keywords = {}, 
}



@Article{bentz_1998_CGH_resolution,
 author = {Bentz, M and Plesch, A and Stilgenbauer, S and Dohner, H and Lichter, P}, 
 title = {Minimal sizes of deletions detected by comparative genomic hybridization.}, 
 journal = {Genes Chromosomes Cancer}, 
 volume = {2}, 
 number = {21}, 
 pages = {172–175}, 
 year = {1998}, 
 keywords = {Chromosome Deletion; Chromosome Mapping; Chromosomes, Human, Pair 11/*genetics; Comparative Study; Humans; Leukemia, B-Cell/genetics/pathology; Nucleic Acid Hybridization/*genetics; Research Support, Non-U.S. Gov’t}, 
}



@Article{pinkel_dna_microarrays_1998,
 author = {Pinkel, D and Segraves, R and Sudar, D and Clark, S and Poole, I and Kowbel, D and Collins, C and Kuo, WL and Chen, C and Zhai, Y and Dairkee, SH and Ljung, BM and Gray, JW and Albertson, DG}, 
 title = {High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays.}, 
 journal = {Nat Genet}, 
 volume = {2}, 
 number = {20}, 
 pages = {207–211}, 
 year = {1998}, 
 keywords = {}, 
}

@Article{wang_1998_SNP_arrays,
 author = {Wang, DG and Fan, JB and Siao, CJ and Berno, A and Young, P and Sapolsky, R and Ghandour, G and Perkins, N and Winchester, E and Spencer, J and Kruglyak, L and Stein, L and Hsie, L and Topaloglou, T and Hubbell, E and Robinson, E and Mittmann, M and Morris, MS and Shen, N and Kilburn, D and Rioux, J and Nusbaum, C and Rozen, S and Hudson, TJ and Lipshutz, R and Chee, M and Lander, ES}, 
 title = {Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.}, 
 journal = {Science}, 
 volume = {280}, 
 number = {5366}, 
 pages = {1077–1082}, 
 year = {1998}, 
 keywords = {}, 
}



@Article{pollack_cdna_arrays_1999,
 author = {Pollack, JR and Perou, CM and Alizadeh, AA and Eisen, MB and Pergamenschikov, A and Williams, CF and Jeffrey, SS and Botstein, D and Brown, PO}, 
 title = {Genome-wide analysis of DNA copy-number changes using cDNA microarrays.}, 
 journal = {Nat Genet}, 
 volume = {1}, 
 number = {23}, 
 pages = {41–46}, 
 year = {1999}, 
 keywords = {}, 
}


@Article{zhao_meyerson_cnloh_2004,
 author = {Zhao, X and Li, C and Paez, JG and Chin, K and Jänne, PA and Chen, TH and Girard, L and Minna, J and Christiani, D and Leo, C and Gray, JW and Sellers, WR and Meyerson, M}, 
 title = {An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays.}, 
 journal = {Cancer Res}, 
 volume = {64}, 
 number = {9}, 
 pages = {3060–3071}, 
 year = {2004}, 
 keywords = {}, 
}

@Article{snijders_acgh_2001,
 author = {Snijders, AM and Nowak, N and Segraves, R and Blackwood, S and Brown, N and Conroy, J and Hamilton, G and Hindle, AK and Huey, B and Kimura, K and Law, S and Myambo, K and Palmer, J and Ylstra, B and Yue, JP and Gray, JW and Jain, AN and Pinkel, D and Albertson, DG}, 
 title = {Assembly of microarrays for genome-wide measurement of DNA copy number.}, 
 journal = {Nat Genet}, 
 volume = {29}, 
 number = {3}, 
 pages = {263–264}, 
 year = {2001}, 
 keywords = {}, 
}

@Article{tkachuk_1990_CML_FISH,
 author = {Tkachuk, DC and Westbrook, CA and Andreeff, M and Donlon, TA and Cleary, ML and Suryanarayan, K and Homge, M and Redner, A and Gray, J and Pinkel, D}, 
 title = {Detection of bcr-abl fusion in chronic myelogeneous leukemia by in situ hybridization.}, 
 journal = {Science}, 
 volume = {250}, 
 number = {4980}, 
 pages = {559–562}, 
 year = {1990}, 
 keywords = {}, 
}

@Article{pearson_2006_history_genome_screening,
 author = {Pearson, PL}, 
 title = {Historical development of analysing large-scale changes in the human genome.}, 
 journal = {Cytogenet Genome Res S}, 
 volume = {115}, 
 number = {3-4}, 
 pages = {198–204}, 
 year = {2006}, 
 keywords = {}, 
}

@Article{calkins_1914_science_review_boveri,
  title = {Zur Frage der Entstehung maligner Tumoren},
  author = {Calkins, GN},
  journal = {Science}, 
  volume = {40}, 
  number = {1041}, 
  pages = {857-859}, 
  year = {1914}, 
}

@Article{nowell_1960_philadelphia,
 author = {Nowell, PC and Hungerford, DA}, 
 title = {A minute chromosome in chronic granulocytic leukemia.}, 
 journal = {Science}, 
 volume = {132}, 
 number = {}, 
 pages = {1497}, 
 year = {1960}, 
 keywords = {}, 
}


@Article{zang_1967_chromosome_meningiomas,
 author = {Zang, KD and Singer, H}, 
 title = {Chromosomal consitution of meningiomas.}, 
 journal = {Nature}, 
 volume = {216}, 
 number = {5110}, 
 pages = {84–85}, 
 year = {1967}, 
 keywords = {}, 
}

@Article{mitelman_1974_banding_polyps,
 author = {Mitelman, F and Mark, J and Nilsson, PG and Dencker, H and Norryd, C and Tranberg, KG}, 
 title = {Chromosome banding pattern in human colonic polyps.}, 
 journal = {Hereditas}, 
 volume = {78}, 
 number = {1}, 
 pages = {63–68}, 
 year = {1974}, 
 keywords = {}, 
}

@Article{rowley_1973_CML,
 author = {Rowley, JD}, 
 title = {Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining.}, 
 journal = {Nature}, 
 volume = {243}, 
 number = {5405}, 
 pages = {290–293}, 
 year = {1973}, 
 keywords = {}, 
}

@Article{schwab_1984_MYCN,
 author = {Schwab, M and Ellison, J and Busch, M and Rosenau, W and Varmus, HE and Bishop, JM}, 
 title = {Enhanced expression of the human gene N-myc consequent to amplification of DNA may contribute to malignant progression of neuroblastoma.}, 
 journal = {Proc Natl Acad Sci U S A}, 
 volume = {15}, 
 number = {81}, 
 pages = {4940–4944}, 
 year = {1984}, 
 keywords = {Cell Line; Gene Amplification; Gene Expression Regulation; Humans; Neuroblastoma/*genetics/pathology; Oncogenes; RNA, Messenger/genetics; Research Support, Non-U.S. Gov’t; Research Support, U.S. Gov’t, P.H.S.}, 
}


@Article{lebeau_1985_SRC,
 author = {Le Beau, MM and Westbrook, CA and Diaz, MO and Rowley, JD}, 
 title = {c-src is consistently conserved in the chromosomal deletion (20q) observed in myeloid disorders.}, 
 journal = {Proc Natl Acad Sci U S A}, 
 volume = {82}, 
 number = {19}, 
 pages = {6692–6696}, 
 year = {1985}, 
 keywords = {}, 
}

@Article{alitalo_bishop_cmyc_oncogene_1983,
 author = {Alitalo, K and Schwab, M and Lin, CC and Varmus, HE and Bishop, JM}, 
 title = {Homogeneously staining chromosomal regions contain amplified copies of an abundantly expressed cellular oncogene (c-myc) in malignant neuroendocrine cells from a human colon carcinoma.}, 
 journal = {Proc Natl Acad Sci U S A}, 
 volume = {6}, 
 number = {80}, 
 pages = {1707–1711}, 
 year = {1983}, 
 keywords = {Apudoma/*genetics; Chromosome Mapping; Chromosomes/ultrastructure; Colonic Neoplasms/*genetics; Gene Amplification; Humans; Karyotyping; Neoplasms, Nerve Tissue/genetics; Oncogenes; Research Support, Non-U.S. Gov’t; Research Support, U.S. Gov’t, P.H.S.; Translocation, Genetic}, 
}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%etc.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@Article{lawler_ga4gh_2015,
 author = {Lawler, M and Siu, LL and Rehm, HL and Chanock, SJ and Alterovitz, G and Burn, J and Calvo, F and Lacombe, D and Teh, BT and North, KN and Sawyers, CL and Clinical Working Group of the Global Alliance for Genomics and Health, (GA4GH}, 
 title = {All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health.}, 
 journal = {Cancer Discov}, 
 volume = {5}, 
 number = {11}, 
 pages = {1133–1136}, 
 year = {2015}, 
 keywords = {}, 
}

@Article{ga4gh_science_2016,
 author = {{Global Alliance for Genomics and Health}}, 
 title = {GENOMICS. A federated ecosystem for sharing genomic, clinical data.}, 
 journal = {Science}, 
 volume = {352}, 
 number = {6291}, 
 pages = {1278–1280}, 
 year = {2016}, 
 keywords = {}, 
}



@Article{bergamaschi_breast_ca_subtypes_2006,
 author = {Bergamaschi, A and Kim, YH and Wang, P and Sorlie, T and Hernandez-Boussard, T and Lonning, PE and Tibshirani, R and Borresen-Dale, AL and Pollack, JR}, 
 title = {Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer.}, 
 journal = {Genes Chromosomes Cancer}, 
 volume = {45}, 
 number = {11}, 
 pages = {1033–1040}, 
 year = {2006}, 
 keywords = {}, 
}


@Article{bertucci_breast_expression_2006,
 author = {Bertucci, F and Finetti, P and Cervera, N and Charafe-Jauffret, E and Mamessier, E and Adélaïde, J and Debono, S and Houvenaeghel, G and Maraninchi, D and Viens, P and Charpin, C and Jacquemier, J and Birnbaum, D}, 
 title = {Gene expression profiling shows medullary breast cancer is a subgroup of basal breast cancers.}, 
 journal = {Cancer Res}, 
 volume = {66}, 
 number = {9}, 
 pages = {4636–4644}, 
 year = {2006}, 
 keywords = {}, 
}

@Article{alizadeh_dlbcl_expression_2000,
 author = {Alizadeh, AA and Eisen, MB and Davis, RE and Ma, C and Lossos, IS and Rosenwald, A and Boldrick, JC and Sabet, H and Tran, T and Yu, X and Powell, JI and Yang, L and Marti, GE and Moore, T and Hudson, J Jr and Lu, L and Lewis, DB and Tibshirani, R and Sherlock, G and Chan, WC and Greiner, TC and Weisenburger, DD and Armitage, JO and Warnke, R and Levy, R and Wilson, W and Grever, MR and Byrd, JC and Botstein, D and Brown, PO and Staudt, LM}, 
 title = {Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.}, 
 journal = {Nature}, 
 volume = {403}, 
 number = {6769}, 
 pages = {503–511}, 
 year = {2000}, 
 keywords = {}, 
}


@Article{ciriello_signatures_2013,
author = {Ciriello, Giovanni and Miller, Martin L and Aksoy, Bulent Arman and Senbabaoglu, Yasin and Schultz, Nikolaus and Sander, Chris}, 
title = {Emerging landscape of oncogenic signatures across human cancers}, 
journal = {Nat Genet}, 
volume = {45}, 
number = {10}, 
pages = {1127--1133}, 
year = {2013}, 
abstract = {Cancer therapy is challenged by the diversity of molecular implementations of oncogenic processes and by the resulting variation in therapeutic responses. Projects such as The Cancer Genome Atlas (TCGA) provide molecular tumor maps in unprecedented detail. The interpretation of these maps remains a major challenge. Here we distilled thousands of genetic and epigenetic features altered in cancers to [sim]500 selected functional events (SFEs). Using this simplified description, we derived a hierarchical classification of 3,299 TCGA tumors from 12 cancer types. The top classes are dominated by either mutations (M class) or copy number changes (C class). This distinction is clearest at the extremes of genomic instability, indicating the presence of different oncogenic processes. The full hierarchy shows functional event patterns characteristic of multiple cross-tissue groups of tumors, termed oncogenic signature classes. Targetable functional events in a tumor class are suggestive of class-specific combination therapy. These results may assist in the definition of clinical trials to match actionable oncogenic signatures with personalized therapies.}, 
location = {}, 
keywords = {}}


@Article{pon_drivers_2015,
author = {Pon, Julia R. and Marra, Marco A.}, 
title = {Driver and Passenger Mutations in Cancer}, 
journal = {Annual Review of Pathology: Mechanisms of Disease
Annu. Rev. Pathol. Mech. Dis.}, 
volume = {10}, 
number = {1}, 
pages = {25--50}, 
year = {2015}, 
abstract = {Next-generation sequencing has allowed identification of millions of somatic mutations and epigenetic changes in cancer cells. A key challenge in interpreting cancer genomes and epigenomes is distinguishing which genetic and epigenetic changes are drivers of cancer development. Frequency-based and function-based approaches have been developed to identify candidate drivers; we discuss the advantages and drawbacks of these methods as well as their latest refinements. We focus particularly on identification of the types of drivers most likely to be missed, such as genes affected by copy number alterations, mutations in noncoding regions, dysregulation of microRNA, epigenetic changes, and mutations in chromatin modifiers.}, 
location = {}, 
keywords = {}}

@Proceedings{baldi_autoencoders_2012,
author = {Baldi, Pierre}, 
editor = {}, 
title = {Autoencoders, unsupervised learning, and deep architectures Proceedings of ICML Workshop on Unsupervised and Transfer Learning}, 
booktitle = {Autoencoders, unsupervised learning, and deep architectures Proceedings of ICML Workshop on Unsupervised and Transfer Learning}, 
volume = {}, 
publisher = {}, 
address = {}, 
pages = {37-49}, 
year = {2012}, 
abstract = {}, 
keywords = {}}

@Article{li_autoencoder_2015,
author = {Li, J. and Luong, M.-T. and Jurafsky, D.}, 
title = {A Hierarchical Neural Autoencoder for Paragraphs and Documents}, 
journal = {ArXiv e-prints}, 
volume = {}, 
number = {}, 
pages = {}, 
year = {015 un}, 
abstract = {}, 
location = {}, 
keywords = {Computer Science - Computation and Language}}


@Article{xu_autoencoder_2016,
author = {J., Xu and L., Xiang and Q., Liu and H., Gilmore and J., Wu and J., Tang and A., Madabhushi}, 
title = {Stacked Sparse Autoencoder (SSAE) for Nuclei Detection on Breast Cancer Histopathology Images}, 
journal = {IEEE Transactions on Medical Imaging}, 
volume = {35}, 
number = {1}, 
pages = {119--130}, 
year = {2016}, 
abstract = {}, 
location = {}, 
keywords = {biological tissues; cancer; image classification; image coding; image representation; image resolution; learning (artificial intelligence); medical image processing; Nottingham histologic score system; automated grading; automated nuclear detection; average area under Precision-Recall curve; breast cancer tissue specimens; computer assisted pathology related image analysis algorithms; deep learning strategy; high resolution digitized pathology images; high-level features; high-resolution breast cancer histopathological images; image classifier; image patch representation; nuclei detection; pixel intensity; sliding window operation; stacked sparse autoencoder; Breast cancer; Decoding; Feature extraction; Image color analysis; Pathology; Training; Automated nuclei detection; breast cancer histopathology; deep learning; digital pathology; feature representation learning; stacked sparse autoencoder; Algorithms; Breast Neoplasms; Cell Nucleus; Female; Histocytochemistry; Humans; Image Processing, Computer-Assisted; Machine Learning}}


@Article{madhavan_clingen_2018,
 author = {Madhavan, S and Ritter, D and Micheel, C and Rao, S and Roy, A and Sonkin, D and Mccoy, M and Griffith, M and Griffith, OL and Mcgarvey, P and Kulkarni, S}, 
 title = {ClinGen Cancer Somatic Working Group - standardizing and democratizing access to cancer molecular diagnostic data to drive translational research.}, 
 journal = {Pac Symp Biocomput}, 
 volume = {23}, 
 number = {}, 
 pages = {247–258}, 
 year = {2018}, 
 keywords = {}, 
}

@Article{mallick_simons_diversity_2016,
 author = {Mallick, S and Li, H and Lipson, M and Mathieson, I and Gymrek, M and Racimo, F and Zhao, M and Chennagiri, N and Nordenfelt, S and Tandon, A and Skoglund, P and Lazaridis, I and Sankararaman, S and Fu, Q and Rohland, N and Renaud, G and Erlich, Y and Willems, T and Gallo, C and Spence, JP and Song, YS and Poletti, G and Balloux, F and van Driem, G and de Knijff, P and Romero, IG and Jha, AR and Behar, DM and Bravi, CM and Capelli, C and Hervig, T and Moreno-Estrada, A and Posukh, OL and Balanovska, E and Balanovsky, O and Karachanak-Yankova, S and Sahakyan, H and Toncheva, D and Yepiskoposyan, L and Tyler-Smith, C and Xue, Y and Abdullah, MS and Ruiz-Linares, A and Beall, CM and Di Rienzo, A and Jeong, C and Starikovskaya, EB and Metspalu, E and Parik, J and Villems, R and Henn, BM and Hodoglugil, U and Mahley, R and Sajantila, A and Stamatoyannopoulos, G and Wee, JT and Khusainova, R and Khusnutdinova, E and Litvinov, S and Ayodo, G and Comas, D and Hammer, MF and Kivisild, T and Klitz, W and Winkler, CA and Labuda, D and Bamshad, M and Jorde, LB and Tishkoff, SA and Watkins, WS and Metspalu, M and Dryomov, S and Sukernik, R and Singh, L and Thangaraj, K and Pääbo, S and Kelso, J and Patterson, N and Reich, D}, 
 title = {The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.}, 
 journal = {Nature}, 
 volume = {538}, 
 number = {7624}, 
 pages = {201–206}, 
 year = {2016}, 
 keywords = {}, 
}


@Article{clarke_igsr_2017,
 author = {Clarke, L and Fairley, S and Zheng-Bradley, X and Streeter, I and Perry, E and Lowy, E and Tassé, AM and Flicek, P}, 
 title = {The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.}, 
 journal = {Nucleic Acids Res}, 
 volume = {45}, 
 number = {D1}, 
 pages = {D854–D859}, 
 year = {2017}, 
 keywords = {}, 
}


@Article{forstberg_post-zygotic_mutations_2013,
 author = {Forsberg, LA and Absher, D and Dumanski, JP}, 
 title = {Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.}, 
 journal = {J Med Genet}, 
 volume = {50}, 
 number = {1}, 
 pages = {1–10}, 
 year = {2013}, 
 keywords = {}, 
}



@Article{editorial_census_race_2000,
 author = {}, 
 title = {Census, race and science.}, 
 journal = {Nat Genet}, 
 volume = {24}, 
 number = {2}, 
 pages = {97–98}, 
 year = {2000}, 
 keywords = {}, 
}


@Article{dyke_2016_consent_codes,
 author = {Dyke, SO and Philippakis, AA and Rambla De Argila, J and Paltoo, DN and Luetkemeier, ES and Knoppers, BM and Brookes, AJ and Spalding, JD and Thompson, M and Roos, M and Boycott, KM and Brudno, M and Hurles, M and Rehm, HL and Matern, A and Fiume, M and Sherry, ST}, 
 title = {Consent Codes: Upholding Standard Data Use Conditions.}, 
 journal = {PLoS Genet}, 
 volume = {12}, 
 number = {1}, 
 pages = {e1005772}, 
 year = {2016}, 
 keywords = {}, 
}


@misc{ga4gh_framework_data_sharing,
  author = {{Global Alliance for Genomics and Health}},
  title = {Framework for Responsible Sharing of Genomic and Health-Related Data},
  howpublished = {\url{https://www.ga4gh.org/ga4ghtoolkit/regulatoryandethics/framework-for-responsible-sharing-genomic-and-health-related-data/}},
  note = {Accessed: 2018-05-07}
}

@misc{brca_exchange,
  author = {{BRCA Exchange}},
  title = {BRCA Exchange of the Global Alliance for Genomics and Health},
  howpublished = {\url{http://brcaexchange.org}},
  note = {Accessed: 2018-05-07}
}

@misc{elixir_beacon,
  author = {{ELIXIR}},
  title = {ELIXIR Beacon},
  howpublished = {\url{https://www.elixir-europe.org/about-us/implementation-studies/beacons}},
  note = {Accessed: 2018-05-07}
}


@Book{fritz_2000_ICD-O-3,
author = {}, 
title = {International Classification of Diseases for Oncology (ICD-O), Third Edition}, 
volume = {}, 
pages = {}, 
editor = {Fritz, A and Percy, C and Jack, A and Sobin, LH and Parkin, MD}, 
publisher = {World Health Organization}, 
address = {Geneva}, 
year = {2000}, 
abstract = {}, 
keywords = {}}


@misc{NCBI_GEO,
  author = {NCBI}, 
  title = {NCBI Gene Expression Omnibus}, 
  howpublished = {\url{www.ncbi.nlm.nih.gov/geo/}},
  note = {Accessed: 2017-06-30}
 keywords = {}, 
}

@Article{arrayexpress,
 author = {EMBL-EBI}, 
 title = {EMBL-EBI ArrayExpress}, 
  howpublished = {\url{www.ebi.ac.uk/microarray-as/aer/}},
  note = {Accessed: 2017-06-30}
 keywords = {}, 
}

@misc{seerstat,
  author = {{National Cancer Institute}},
  title = {{Surveillance, Epidemiology, and End Results Program}},
  howpublished = {\url{https://seer.cancer.gov/statfacts/}},
  year={2018}, 
  note="Online; accessed May-2018”}
}


@Article{haendel_2018_disease_ontologies,
 author = {Haendel, Melissa and McMurry, Julie and Relevo, Rose and Mungall, Chris and Robinson, Peter and Chute, Christopher G.}, 
 title = {A Census of Disease Ontologies}, 
 journal = {Annual Review of Biomedical Data Science
Annu. Rev. Biomed. Data Sci.}, 
 volume = {14}, 
 number = {5}, 
 pages = {305–331}, 
 year = {2018}, 
 keywords = {}, 
}


@article{iliopoulos2013algorithms,
  title={Algorithms For Next-Generation Sequencing Data},
  author={Iliopoulos, Costas S and Pissis, Solon P},
  journal={Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data},
  pages={251--280},
  year={2013},
  publisher={John Wiley \& Sons, Inc.}
}


