Publications

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2020
- Journal Article
  - Huang, Qingyao; Baudis, Michael (2020). Enabling population assignment from cancer genomes with SNP2pop. Scientific Reports, 10:4846.
  - Carrio-Cordo, Paula; Acheson, Elise; Huang, Qingyao; Baudis, Michael (2020). Geographic assessment of cancer genome profiling studies. Database, 2020:baaa009.
  - Carrio-Cordo, Paula; Baudis, Michael (2020). Mountains and Chasms: Surveying the Oncogenomic Publication Landscape. Oncology, 98(Suppl. 6):332-343.
2019
- Journal Article
  - Saunders, Gary; Baudis, Michael; Becker, Regina; Beltran, Sergi; Béroud, Christophe; Birney, Ewan; Brooksbank, Cath; Brunak, Søren; Van den Bulcke, Marc; Drysdale, Rachel; Capella-Gutierrez, Salvador; Flicek, Paul; Florindi, Francesco; Goodhand, Peter; Gut, Ivo; Heringa, Jaap; Holub, Petr; Hooyberghs, Jef; Juty, Nick; Keane, Thomas M; Korbel, Jan O; Lappalainen, Ilkka; Leskosek, Brane; Matthijs, Gert; Mayrhofer, Michaela Th; Metspalu, Andres; Navarro, Arcadi; Newhouse, Steven; Nyrönen, Tommi; Page, Angela; et al (2019). Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews. Genetics, 20(11):693-701.
  - Gug, G; Huang, Q; Chiticariu, E; Solovan, C; Baudis, Michael (2019). DNA copy number imbalances in primary cutaneous lymphomas. Journal of the European Academy of Dermatology and Venerology, 33(6):1062-1075.
  - Fiume, Marc; Cupak, Miroslav; Keenan, Stephen; Rambla, Jordi; de la Torre, Sabela; Dyke, Stephanie O M; Brookes, Anthony J; Carey, Knox; Lloyd, David; Goodhand, Peter; Haeussler, Maximilian; Baudis, Michael; Stockinger, Heinz; Dolman, Lena; Lappalainen, Ilkka; Törnroos, Juha; Linden, Mikael; Spalding, J Dylan; Ur-Rehman, Saif; Page, Angela; Flicek, Paul; Sherry, Stephen; Haussler, David; Varma, Susheel; Saunders, Gary; Scollen, Serena (2019). Federated discovery and sharing of genomic data using Beacons. Nature Biotechnology, 37(3):220-224.
2018
- Journal Article
  - Dyke, Stephanie O M; Linden, Mikael; Lappalainen, Ilkka; De Argila, Jordi Rambla; et al; Baudis, Michael (2018). Registered access: authorizing data access. European Journal of Human Genetics, 26(12):1721-1731.
  - Marrero-Rodríguez, Daniel; Taniguchi-Ponciano, Keiko; Subramaniam, Malayannan; Hawse, John R; Pitel, Kevin S; Arreola-De la Cruz, Hugo; Huerta-Padilla, Victor; Ponce-Navarrete, Gustavo; Figueroa-Corona, Ma Del Pilar; Gomez-Virgilio, Laura; Martinez-Cuevas, Teresa I; Mendoza-Rodriguez, Monica; Rodriguez-Esquivel, Miriam; Romero-Morelos, Pablo; Ramirez-Salcedo, Jorge; Baudis, Michael; Meraz-Rios, Marco; Jimenez-Vega, Florinda; Salcedo, Mauricio (2018). Krüppel-Like Factor 10 participates in cervical cancer immunoediting through transcriptional regulation of Pregnancy-Specific Beta-1 Glycoproteins. Scientific Reports, 8(1):9445.
  - Gao, Bo; Huang, Qingyao; Baudis, Michael (2018). segment_liftover : a Python tool to convert segments between genome assemblies. F1000Research, 7:319.
2017
- Journal Article
  - Mackay, Alan; Burford, Anna; Carvalho, Diana; Izquierdo, Elisa; Fazal-Salom, Janat; Taylor, Kathryn R; Bjerke, Lynn; Clarke, Matthew; Vinci, Mara; Nandhabalan, Meera; Temelso, Sara; Popov, Sergey; Molinari, Valeria; Raman, Pichai; Waanders, Angela J; Han, Harry J; Gupta, Saumya; Marshall, Lynley; Zacharoulis, Stergios; Vaidya, Sucheta; Mandeville, Henry C; Bridges, Leslie R; Martin, Andrew J; Al-Sarraj, Safa; Chandler, Christopher; Ng, Ho-Keung; Li, Xingang; Mu, Kun; Trabelsi, Saoussen; Brahim, Dorra H'mida-Ben; Baudis, Michael; Jones, Chris; et al (2017). Integrated molecular meta-analysis of 1,000 pediatric high-grade and diffuse intrinsic pontine glioma. Cancer Cell, 32(4):520-537.e5.
2016
- Journal Article
  - Ai, Ni; Cai, Haoyang; Solovan, Caius; Baudis, Michael (2016). CNARA: reliability assessment for genomic copy number profiles. BMC Genomics, 17:799.
  - Stockinger, Heinz; Palagi, Patricia M; Durinx, Christine; Baudis, Michael; von Mering, Christian; Szövenyi, Peter; et al (2016). The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Research, 44(D1):D27-37.
  - Mackay, Alan; Burford, Anna; Salom, Janat Fazal; et al; Baudis, Michael (2016). Hg-95integrated molecular meta-analysis of 1000 paediatric high grade glioma and dipg. Neuro-Oncology, 18(suppl 3):iii70.3-iii70.
2015
- Journal Article
  - Cai, Haoyang; Gupta, Saumya; Rath, Prisni; Ai, Ni; Baudis, Michael (2015). arrayMap 2014: an updated cancer genome resource. Nucleic Acids Research, 43:D825-D830.
  - Muff, Roman; Rath, Prisni; Ram Kumar, Ram Mohan; Husmann, Knut; Born, Walter; Baudis, Michael; Fuchs, Bruno (2015). Genomic instability of osteosarcoma cell lines in culture: impact on the prediction of metastasis relevant genes. PLoS ONE, 10(5):e0125611.
2014
- Journal Article
  - Cai, Haoyang; Kumar, Nitin; Ai, Ni; Gupta, Saumya; Rath, Prisni; Baudis, Michael (2014). Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Research, 42(D1):D1055-D1062.
  - Baderca, Flavia; Chiticariu, Elena; Baudis, Michael; Solovan, Caius (2014). Biopsying parapsoriasis: quo vadis? Are morphological stains enough or are ancillary tests needed?. Romanian Journal of Morphology and Embryology = Revue Roumaine de Morphologie et Embryologie, 55(3 Suppl):1085-92.
  - Cai, Haoyang; Kumar, Nitin; Bagheri, Homayoun C; von Mering, Christian; Robinson, Mark D; Baudis, Michael (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics, 15:82.
2013
- Journal Article
  - Krieger, Michael; Roos, Andreas; Stendel, Claudia; Claeys, Kristl G; Sonmez, Fatma Mujgan; Baudis, Michael; Bauer, Peter; Bornemann, Antje; de Goede, Christian; Dufke, Andreas; Finkel, Richard S; Goebel, Hans H; Häussler, Martin; Kingston, Helen; Kirschner, Janbernd; Medne, Livija; Muschke, Petra; Rivier, François; Rudnik-Schöneborn, Sabine; Spengler, Sabrina; Inzana, Francesca; Stanzial, Franco; Benedicenti, Francesco; Synofzik, Matthis; Lia Taratuto, Ana; Pirra, Laura; Tay, Stacey Kiat-Hong; Topaloglu, Haluk; Uyanik, Gökhan; Wand, Dorothea; Williams, Denise; Zerres, Klaus; Weis, Joachim; Senderek, Jan (2013). SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome. Brain, 136(12):3634-3644.
  - Bluwstein, A; Kumar, N; Léger, K; Traenkle, J; van Oostrum, J; Rehrauer, H; Baudis, Michael; Hottiger, M O (2013). PKC signaling prevents irradiation-induced apoptosis of primary human fibroblasts. Cell Death and Disease, 4:e498.
  - Martin-Guerrero, Idoia; Salaverria, Itziar; Burkhardt, Birgit; Szczepanowski, Monika; Baudis, Michael; Bens, Susanne; de Leval, Laurence; Garcia-Orad, Africa; Horn, Heike; Lisfeld, Jasmin; Pellissery, Shoji; Klapper, Wolfram; Oschlies, Ilske; Siebert, Reiner (2013). Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas. Haematologica, 98(8):1237-1241.
  - Salaverria, Itziar; Martin-Guerrero, Idoia; Burkhardt, Birgit; Kreuz, Markus; Zenz, Thorsten; Oschlies, Ilske; Arnold, Norbert; Baudis, Michael; Bens, Susanne; García-Orad, Africa; Lisfeld, Jasmin; Schwaenen, Carsten; Szczepanowski, Monika; Wessendorf, Swen; Pfreundschuh, Michael; Trümper, Lorenz; Klapper, Wolfram; Siebert, Reiner (2013). High resolution copy number analysis of IRF4 translocation-positive diffuse large B-cell and follicular lymphomas. Genes, Chromosomes and Cancer, 52(2):150-155.
2012
- Journal Article
  - Kumar, Nitin; Cai, Haoyang; von Mering, Christian; Baudis, Michael (2012). Specific Genomic Regions Are Differentially Affected by Copy Number Alterations across Distinct Cancer Types, in Aggregated Cytogenetic Data. PLoS ONE, 7(8):e43689.
  - Eggermann, Thomas; Spengler, Sabrina; Venghaus, Andreas; Denecke, Bernd; Zerres, Klaus; Baudis, Michael; Ensenauer, Regina (2012). 2p21 Deletions in hypotonia-cystinuria syndrome. European Journal of Medical Genetics, 55(10):561-563.
  - von Bueren, André O; Gerss, Joachim; Hagel, Christian; Cai, Haoyang; Remke, Marc; Hasselblatt, Martin; Feuerstein, Burt G; Pernet, Sarah; Delattre, Olivier; Korshunov, Andrey; Rutkowski, Stefan; Pfister, Stefan M; Baudis, Michael (2012). DNA copy number alterations in central primitive neuroectodermal tumors and tumors of the pineal region: an international individual patient data meta-analysis. Journal of Neuro-Oncology, 109(2):415-423.
  - Baudis, Michael; Giefing, M; Cai, Haoyang; Kumar, Nitin; Vater, I; Ricter, J; Siebert, R (2012). Array-basierter Nachweis chromosomaler Aberrationen bei malignen Neoplasien. Medizinische Genetik, 24(2):114-122.
  - Cai, Haoyang; Kumar, Nitin; Baudis, Michael (2012). arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies. PLoS ONE, 7(5):e36944.
  - Wernstedt, Annekatrin; Valtorta, Emanuele; Armelao, Franco; Togni, Roberto; Girlando, Salvatore; Baudis, Michael; Heinimann, Karl; Messiaen, Ludwine; Staehli, Noemie; Zschocke, Johannes; Marra, Giancarlo; Wimmer, Katharina (2012). Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL. Genes, Chromosomes & Cancer, 51(9):819-831.
  - Luebke, A M; Baudis, Michael; Matthaei, H; Vashist, Y K; Verde, P E; Hosch, S B; Erbersdobler, A; Klein, C A; Izbicki, J R; Knoefel, W T; Stoecklein, N H (2012). Losses at chromosome 4q are associated with poor survival in operable ductal pancreatic adenocarcinoma. Pancreatology, 12(1):16-22.
  - Beleut, Manfred; Zimmermann, Philip; Baudis, Michael; Bruni, Nicole; Bühlmann, Peter; Laule, Oliver; Luu, Van-Duc; Gruissem, Wilhelm; Schraml, Peter; Moch, Holger (2012). Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome. BMC Cancer, 12:310.
  - Spengler, Sabrina; Begemann, Matthias; Ortiz Brüchle, Nadina; Baudis, Michael; Denecke, Bernd; Kroisel, Peter Michael; Oehl-Jaschkowitz, Barbara; Schulze, Bernd; Raabe-Meyer, Gisela; Spaich, Christiane; Blümel, Peter; Jauch, Anna; Moog, Ute; Zerres, Klaus; Eggermann, Thomas (2012). Molecular Karyotyping as a relevant diagnostic tool in children with growth retardation with Silver-Russell features. Journal of Pediatrics, 161(5):933-942.e1.
2011
- Journal Article
  - Kumar, N; Rehrauer, H; Cai, H; Baudis, Michael (2011). CDCOCA: A statistical method to define complexity dependence of co-occuring chromosomal aberrations. BMC Medical Genomics, 4:21.
  - Begemann, M; Spengler, S; Kanber, D; Haake, A; Baudis, Michael; Leisten, I; Binder, G; Markus, S; Rupprecht, T; Segerer, H; Fricke-Otto, S; Mühlenberg, R; Siebert, R; Buiting, K; Eggermann, T (2011). Silver-Russell patients showing a broad range of ICR1 and ICR2 hypomethylation in different tissues. Clinical Genetics, 80(1):83-88.
2010
- Journal Article
  - Eggermann, T; Spengler, S; Bachmann, N; Baudis, Michael; Mau-Holzmann, U A; Singer, S; Rossier, E (2010). Chromosome 11p15 duplication in Silver-Russell syndrome due to a maternally inherited translocation t(11;15). American Journal of Medical Genetics. Part A, 152A(6):1484-1487.
  - Eggermann, T; Schönherr, N; Spengler, S; Jäger, S; Denecke, B; Binder, G; Baudis, Michael (2010). Identification of a 21q22 duplication in a Silver-Russell syndrome patient further narrows down the Down syndrome critical region. American Journal of Medical Genetics. Part A, 152A(2):356-359.
  - Lacunza, E; Baudis, Michael; Colussi, A G; Segal-Eiras, A; Croce, M V; Abba, M C (2010). MUC1 oncogene amplification correlates with protein overexpression in invasive breast carcinoma cells. Cancer Genetics and Cytogenetics, 201(2):102-110.
  - Spengler, S; Schönherr, N; Binder, G; Wollmann, H; Fricke-Otto, S; Mühlenberg, R; Denecke, B; Baudis, Michael; Eggermann, T (2010). Submicroscopic chromosomal imbalances in idiopathic Silver-Russell syndrome (SRS): the SRS phenotype overlaps with the 12q14 microdeletion syndrome. Journal of Medical Genetics, 47(5):356-360.
  - Peralta, R; Baudis, Michael; Vazquez, G; Juárez, S; Ortiz, R; Decanini, H; Hernandez, D; Gallegos, F; Valdivia, A; Piña, P; Salcedo, M (2010). Increased expression of cellular retinol-binding protein 1 in laryngeal squamous cell carcinoma. Journal of Cancer Research and Clinical Oncology, 136(6):931-938.
2009
- Journal Article
  - Liu, J; Bandyopadhyay, N; Ranka, S; Baudis, Michael; Kahveci, T (2009). Inferring progression models for CGH data. Bioinformatics, 25(17):2208-2215.
  - Boerma, E G; Siebert, R; Kluin, P M; Baudis, Michael (2009). Translocations involving 8q24 in Burkitt lymphoma and other malignant lymphomas: a historical review of cytogenetics in the light of todays knowledge. Leukemia, 23(2):225-234.
  - Gerstung, M; Baudis, Michael; Moch, H; Beerenwinkel, N (2009). Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics, 25(21):2809-2815.
  - Bug, S; Dürig, J; Oyen, F; Klein-Hitpass, L; Martin-Subero, J I; Harder, L; Baudis, Michael; Arnold, N; Kordes, U; Dührsen, U; Schneppenheim, R; Siebert, R (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(1):44-47.
2008
- Journal Article
  - Roos, A; Elbracht, M; Baudis, Michael; Senderek, J; Schönherr, N; Eggermann, T; Schüler, H M (2008). A 10.7 Mb interstitial deletion of 13q21 without phenotypic effect defines a further non-pathogenic euchromatic variant.. American Journal of Medical Genetics. Part A, 146A(18):2417-2420.
  - Hoischen, A; Ehrler, M; Fassunke, J; Simon, M; Baudis, Michael; Landwehr, C; Radlwimmer, B; Lichter, P; Schramm, J; Becker, A J; Weber, R G (2008). Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH. Brain Pathology, 18(3):326-337.
  - Bauer, V L; Braselmann, H; Henke, M; Mattern, D; Walch, A; Unger, K; Baudis, Michael; Lassmann, S; Huber, R; Wienberg, J; Werner, M; Zitzelsberger, H F (2008). Chromosomal changes characterize head and neck cancer with poor prognosis. Journal of Molecular Medicine, 86(12):1353-1365.
  - Nieländer, I; Martín-Subero, J I; Wagner, F; Baudis, Michael; Gesk, S; Harder, L; Hasenclever, D; Klapper, W; Kreuzer, M; Pott, C; Martinez-Climent, J A; Dreyling, M; Arnold, N; Siebert, R (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(6):949-950.
2007
- Journal Article
  - Baudis, Michael (2007). Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer, 7:226.
  - Dürig, J; Bug, S; Klein-Hitpass, L; Boes, T; Jöns, T; Martin-Subero, J I; Harder, L; Baudis, Michael; Dührsen, U; Siebert, R (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, 21(10):2153-2163.
2006
- Journal Article
  - Liu, J; Mohammed, J; Carter, J; Ranka, S; Kahveci, T; Baudis, Michael (2006). Distance-based clustering of CGH data. Bioinformatics, 22(16):1971-1978.
  - Baudis, Michael (2006). Online database and bioinformatics toolbox to support data mining in cancer cytogenetics. BioTechniques, 40(3):269-272.

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