Citation of the website & software tool usage

For any use of the Progenetix data, e.g. as a reference for aberration frequencies in a certain locus, it is necessary to cite both the website and the original Bioinformatics publication:

  1. Baudis, M., & Cleary, M. L. (2001). Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics, 17(12), 1228-1229.
  2. Progenetix oncogenomic online resource: www.progenetix.net. Baudis, M. (2009)

(Randomly) selected articles using Progenetix as reference or making use of the online tools

Cao, Q., M. Zhou, X. Wang, C. A. Meyer, Y. Zhang, Z. Chen, C. Li, and X. S. Liu. 2010. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic acids research . PDF
Bug, S., J. Dürig, F. Oyen, L. Klein-Hitpass, J. Martin-Subero, L. Harder, M. Baudis, N. Arnold, U. Kordes, U. Dührsen, R. Schneppenheim, and R. Siebert. 2009. Recurrent loss, but lack of mutations, of the SMARCB1 tumor suppressor gene in T-cell prolymphocytic leukemia with TCL1A-TCRAD juxtaposition. Cancer Genetics and Cytogenetics 192, no. 1: 44-47. PDF
Savola, S., A. Klami, A. Tripathi, T. Niini, M. Serra, P. Picci, S. Kaski, D. Zambelli, K. Scotlandi, and S. Knuutila. 2009. Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors. BMC Cancer 9, 17. PDF
Paulson, K. G., B. D. Lemos, B. Feng, N. Jaimes, P. F. Peñas, X. Bi, E. Maher, L. Cohen, J. H. Leonard, S. R. Granter, L. Chin, and P. Nghiem. 2008. Array-CGH Reveals Recurrent Genomic Changes in Merkel Cell Carcinoma Including Amplification of L-Myc. J. Invest. Dermatol. . PDF
Boerma, E. G., R. Siebert, P. M. Kluin, and M. Baudis. 2008. Translocations involving 8q24 in Burkitt lymphoma and other malignant lymphomas: a historical review of cytogenetics in the light of todays knowledge. Leukemia . PDF
Bauer, V. L., H. Braselmann, M. Henke, D. Mattern, A. Walch, K. Unger, M. Baudis, S. Lassmann, R. Huber, J. Wienberg, M. Werner, and H. F. Zitzelsberger. 2008. Chromosomal changes characterize head and neck cancer with poor prognosis. J. Mol. Med. . PDF
Booman, M., K. Szuhai, A. Rosenwald, E. Hartmann, H. Kluin-Nelemans, D. De Jong, E. Schuuring, and P. Kluin. 2008. Genomic alterations and gene expression in primary diffuse large B-cell lymphomas of immune-privileged sites: the importance of apoptosis and immunomodulatory pathways. J Pathol 216, no. 2: 209-217. PDF
Liu, J., S. Ranka, and T. Kahveci. 2008. Classification and feature selection algorithms for multi-class CGH data. Bioinformatics 24, no. 13: i86-95. PDF
Nielander, I., J. I. Martin-Subero, F. Wagner, M. Baudis, S. Gesk, L. Harder, D. Hasenclever, W. Klapper, M. Kreuz, C. Pott, J. A. Martinez-Climent, M. Dreyling, N. Arnold, and R. Siebert. 2008. Recurrent loss of the Y chromosome and homozygous deletions within the pseudoautosomal region 1: association with male predominance in mantle cell lymphoma. Haematologica 93, no. 6: 949. PDF
Myllykangas, S., J. Tikka, T. Böhling, S. Knuutila, and J. Hollmén. 2008. Classification of human cancers based on DNA copy number amplification modeling. BMC medical genomics 1, 15. PDF
Hoischen, A., M. Ehrler, J. Fassunke, M. Simon, M. Baudis, C. Landwehr, B. Radlwimmer, P. Lichter, J. Schramm, A. J. Becker, and R. G. Weber. 2008. Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH. Brain Pathol 18, no. 3: 326-337. PDF
Lacunza, E., M. Baudis, A. G. Colussi, A. Segal-Eiras, M. V. Croce, and M. C. Abba. 2010. MUC1 oncogene amplification correlates with protein overexpression in invasive breast carcinoma cells. Cancer Genetics and Cytogenetics 201, no. 2: 102-110. PDF
Lindholm, P. M., K. Salmenkivi, H. Vauhkonen, A. G. Nicholson, S. Anttila, V. L. Kinnula, and S. Knuutila. 2007. Gene copy number analysis in malignant pleural mesothelioma using oligonucleotide array CGH. Cytogenet Genome Res 119, no. 1-2: 46-52. PDF
Baudis, M. 2007. Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer 7, no. 1: 226. PDF
Bläker, H., G. Mechtersheimer, C. Sutter, C. Hertkorn, M. A. Kern, R. J. Rieker, R. Penzel, P. Schirmacher, and M. Kloor. 2007. Recurrent deletions at 6q in early age of onset non-HNPCC- and non-FAP-associated intestinal carcinomas. Evidence for a novel cancer susceptibility locus at 6q14-q22. Genes Chromosomes Cancer 47, no. 2: 159-164. PDF
Stallings, R. L. 2007. Origin and functional significance of large-scale chromosomal imbalances in neuroblastoma. Cytogenet. Genome Res. 118, no. 2-4: 110-115. PDF
Dürig, J., S. Bug, L. Klein-Hitpass, T. Boes, T. Jöns, J. I. Martin-Subero, L. Harder, M. Baudis, U. Dührsen, and R. Siebert. 2007. Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32). Leukemia . PDF
Gorringe, K. L., S. Jacobs, E. R. Thompson, A. Sridhar, W. Qiu, D. Y. Choong, and I. G. Campbell. 2007. High-resolution single nucleotide polymorphism array analysis of epithelial ovarian cancer reveals numerous microdeletions and amplifications. Clin. Cancer Res. 13, no. 16: 4731-4739. PDF
Ghazani, A. A., N. Arneson, K. Warren, M. Pintilie, J. Bayani, J. A. Squire, and S. J. Done. 2007. Genomic alterations in sporadic synchronous primary breast cancer using array and metaphase comparative genomic hybridization. Neoplasia 9, no. 6: 511-520. PDF
Corson, T. W., C. Q. Zhu, S. K. Lau, F. A. Shepherd, M. S. Tsao, and B. L. Gallie. 2007. KIF14 messenger RNA expression is independently prognostic for outcome in lung cancer. Clin Cancer Res 13, no. 11: 3229-3234. PDF
Stallings, R. L. 2007. Are chromosomal imbalances important in cancer? Trends Genet 23, no. 6: 278-283. PDF
Assämäki, R., M. Sarlomo-Rikala, J. A. Lopez-Guerrero, J. Lasota, L. C. Andersson, A. Llombart-Bosch, M. Miettinen, and S. Knuutila. 2007. Array comparative genomic hybridization analysis of chromosomal imbalances and their target genes in gastrointestinal stromal tumors. Genes Chromosomes Cancer 46, no. 6: 564-576. PDF
Chari, R., K. Thu, I. Wilson, W. W. Lockwood, K. Lonergan, B. P. Coe, C. Malloff, A. F. Gazdar, S. Lam, C. Garnis, C. Macaulay, C. Alvarez, and W. L. Lam. 2010. Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. Cancer Metastasis Rev . PDF
Chen, W., M. Salto-Tellez, N. Palanisamy, K. Ganesan, Q. Hou, L. K. Tan, L. H. Sii, K. Ito, B. Tan, J. Wu, A. Tay, K. C. Tan, E. Ang, B. K. Tan, P. H. Tan, Y. Ito, and P. Tan. 2007. Targets of genome copy number reduction in primary breast cancers identified by integrative genomics. Genes Chromosomes Cancer 46, no. 3: 288-301. PDF
Liu, J., S. Ranka, and T. Kahveci. 2007. Markers improve clustering of CGH data. Bioinformatics 23, no. 4: 450-457. PDF
Varshavsky, R. 2007. Mining large-scale Genomic and Proteomic Data: Algorithms, Tools and Inference. PDF
Helou, K., H. Padilla-Nash, D. Wangsa, E. Karlsson, L. Osterberg, P. Karlsson, T. Ried, and T. Knutsen. 2006. Comparative genome hybridization reveals specific genomic imbalances during the genesis from benign through borderline to malignant ovarian tumors. Cancer Genet. Cytogenet. 170, no. 1: 1-8. PDF
van Beijnum, J. R., R. P. Dings, E. van der Linden, B. M. Zwaans, F. C. Ramaekers, K. H. Mayo, and A. W. Griffioen. 2006. Gene expression of tumor angiogenesis dissected: specific targeting of colon cancer angiogenic vasculature. Blood 108, no. 7: 2339-2348. PDF
Santos, G. C., M. Zielenska, M. Prasad, and J. A. Squire. 2007. Chromosome 6p amplification and cancer progression. J. Clin. Pathol. 60, no. 1: 1-7. PDF
Järvinen, A. K., R. Autio, S. Haapa-Paananen, M. Wolf, M. Saarela, R. Grénman, I. Leivo, O. Kallioniemi, A. A. Mäkitie, and O. Monni. 2006. Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene 25, no. 52: 6997-7008. PDF
Liu, J., J. Mohammed, J. Carter, S. Ranka, T. Kahveci, and M. Baudis. 2006. Distance-based clustering of CGH data. Bioinformatics 22, no. 16: 1971-1978. PDF
Mao, X., R. A. Hamoudi, I. C. Talbot, and M. Baudis. 2006. Allele-specific loss of heterozygosity in multiple colorectal adenomas: toward an integrated molecular cytogenetic map II. Cancer Genet. Cytogenet. 167, no. 1: 1-14. PDF
Baudis, M. 2006. Online database and bioinformatics toolbox to support data mining in cancer cytogenetics. BioTechniques 40, no. 3: 269-70, 272. PDF
Eggermann, T., N. Schönherr, S. Spengler, S. Jäger, B. Denecke, G. Binder, and M. Baudis. 2010. Identification of a 21q22 duplication in a Silver-Russell syndrome patient further narrows down the Down syndrome critical region. Am. J. Med. Genet. 152A, no. 2: 356-359. PDF
Diep, C. B., K. Kleivi, F. R. Ribeiro, M. R. Teixeira, O. C. Lindgjaerde, and R. A. Lothe. 2006. The order of genetic events associated with colorectal cancer progression inferred from meta-analysis of copy number changes. Genes Chromosomes Cancer 45, no. 1: 31-41. PDF
Schubert, F., B. Tausch, S. Joos, and R. Eils. 2005. CGH-Profiler: data mining based on genomic aberration profiles. BMC Bioinformatics 6, 188. PDF
Bernardini, M., C. H. Lee, B. Beheshti, M. Prasad, M. Albert, P. Marrano, H. Begley, P. Shaw, A. Covens, J. Murphy, B. Rosen, S. Minkin, J. A. Squire, and P. F. Macgregor. 2005. High-resolution mapping of genomic imbalance and identification of gene expression profiles associated with differential chemotherapy response in serous epithelial ovarian cancer. Neoplasia 7, no. 6: 603-613. PDF
Hidalgo, A., M. Baudis, I. Petersen, H. Arreola, P. Piña, G. Vázquez-Ortiz, D. Hernández, J. González, M. Lazos, R. López, C. Pérez, J. García, K. Vázquez, B. Alatorre, and M. Salcedo. 2005. Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma. BMC Cancer 5, 77. PDF
Mao, X., R. A. Hamoudi, P. Zhao, and M. Baudis. 2005. Genetic losses in breast cancer: toward an integrated molecular cytogenetic map. Cancer Genet. Cytogenet. 160, no. 2: 141-151. PDF
Knutsen, T., V. Gobu, R. Knaus, H. Padilla-Nash, M. Augustus, R. L. Strausberg, I. R. Kirsch, K. Sirotkin, and T. Ried. 2005. The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence. Genes Chromosomes Cancer 44, no. 1: 52-64. PDF
Vandesompele, J., M. Baudis, K. De Preter, N. Van Roy, P. Ambros, N. Bown, C. Brinkschmidt, H. Christiansen, V. Combaret, M. Lastowska, J. Nicholson, A. O'Meara, D. Plantaz, R. Stallings, B. Brichard, C. Van den Broecke, S. De Bie, A. De Paepe, G. Laureys, and F. Speleman. 2005. Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma. J Clin Oncol 23, no. 10: 2280-2299. PDF
Junker, K., I. Romics, A. Szendroi, P. Riesz, P. Moravek, W. Hindermann, R. Winter, and J. Schubert. 2004. Genetic profile of bone metastases in renal cell carcinoma. Eur Urol 45, no. 3: 320-324. PDF
Garnis, C., T. P. Buys, and W. L. Lam. 2004. Genetic alteration and gene expression modulation during cancer progression. Mol Cancer 3, 9. PDF
Baudis, M., and M. L. Cleary. 2001. Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics 17, no. 12: 1228-1229. PDF
de Vreeze, R., D. de Jong, P. Nederlof, H. J. Ruijter, L. Boerrigter, R. Haas, and F. van Coevorden. 2010. Multifocal Myxoid Liposarcoma: Metastasis or Second Primary Tumor? A Molecular Biological Analysis. The Journal of molecular diagnostics : JMD . PDF
Knutsen, T., H. Padilla-Nash, D. Wangsa, L. Barenboim-Stapleton, J. Camps, N. Mcneil, M. Difilippantonio, and T. Ried. 2010. Definitive molecular cytogenetic characterization of 15 colorectal cancer cell lines. Genes Chromosomes Cancer 49, no. 3: 204-223. PDF
Spengler, S., N. Schönherr, G. Binder, H. Wollmann, S. Fricke-Otto, R. Mühlenberg, B. Denecke, M. Baudis, and T. Eggermann. 2009. Submicroscopic chromosomal imbalances in idiopathic Silver-Russell syndrome (SRS): the SRS phenotype overlaps with the 12q14 microdeletion syndrome. Journal of Medical Genetics . PDF
Gerstung, M., M. Baudis, H. Moch, and N. Beerenwinkel. 2009. Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics . PDF
Liu, J., N. Bandyopadhyay, S. Ranka, M. Baudis, and T. Kahveci. 2009. Inferring Progression Models for CGH data. Bioinformatics . PDF