Publications

ZORA Publication List

Publications

• 2024

  • Journal Article

    • Smith, Ellery; Paloots, Rahel; Giagkos, Dimitris; Baudis, Michael; Stockinger, Kurt (2024). Data-driven information extraction and enrichment of molecular profiling data for cancer cell lines. Bioinformatics advances, 4(1):vbae045.

• 2023

  • Journal Article

    • Ladewig, Markus S; Jacobsen, Julius O B; Wagner, Alex H; Danis, Daniel; El Kassaby, Baha; Gargano, Michael; Groza, Tudor; Baudis, Michael; Steinhaus, Robin; Seelow, Dominik; Bechrakis, Nikolaos E; Mungall, Christopher J; Schofield, Paul N; Elemento, Olivier; Smith, Lindsay; McMurry, Julie A; Munoz‐Torres, Monica; Haendel, Melissa A; Robinson, Peter N (2023). GA4GH Phenopackets: A Practical Introduction. Advanced Genetics, 4(1):2200016.
    • Huang, Qingyao; Baudis, Michael (2023). Candidate targets of copy number deletion events across 17 cancer types. Frontiers in Genetics, 13:1017657.

• 2022

  • Journal Article

    • Jacobsen, Julius O B; Baudis, Michael; Baynam, Gareth S; Beckmann, Jacques S; Beltran, Sergi; Buske, Orion J; et al (2022). The GA4GH Phenopacket schema defines a computable representation of clinical data. Nature Biotechnology, 40(6):817-820.
    • Rambla, Jordi; Baudis, Michael; Ariosa, Roberto; Beck, Tim; Fromont, Lauren A; Navarro, Arcadi; Paloots, Rahel; Rueda, Manuel; Saunders, Gary; Singh, Babita; Spalding, John D; Törnroos, Juha; Vasallo, Claudia; Veal, Colin D; Brookes, Anthony J (2022). Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond. Human Mutation, 43(6):791-799.

  • Working Paper

    • Huang, Qingyao; Baudis, Michael (2022). Candidate targets of copy number deletion events across 17 cancer types. bioRxiv 498080, Cold Spring Harbor Laboratory.

• 2021

  • Journal Article

    • Rehm, Heidi L; Page, Angela J H; Smith, Lindsay; Adams, Jeremy B; Alterovitz, Gil; Babb, Lawrence J; Barkley, Maxmillian P; Baudis, Michael; Beauvais, Michael J S; Beck, Tim; Beckmann, Jacques S; Beltran, Sergi; Bernick, David; Bernier, Alexander; Bonfield, James K; Boughtwood, Tiffany F; Bourque, Guillaume; Bowers, Sarion R; Brookes, Anthony J; Brudno, Michael; Brush, Matthew H; Bujold, David; Burdett, Tony; Buske, Orion J; Cabili, Moran N; Cameron, Daniel L; Carroll, Robert J; Casas-Silva, Esmeralda; Chakravarty, Debyani; Chaudhari, Bimal P; et al (2021). GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell, 1(2):100029.
    • Thorogood, Adrian; Rehm, Heidi L; Goodhand, Peter; Page, Angela J H; Joly, Yann; Baudis, Michael; Rambla, Jordi; Navarro, Arcadi; Nyronen, Tommi H; Linden, Mikael; Dove, Edward S; Fiume, Marc; Brudno, Michael; Cline, Melissa S; Birney, Ewan (2021). International federation of genomic medicine databases using GA4GH standards. Cell, 1(2):100032.
    • Wagner, Alex H; Babb, Lawrence; Alterovitz, Gil; Baudis, Michael; et al (2021). The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. Cell Genomics, 1(2):100027.
    • Huang, Qingyao; Carrio-Cordo, Paula; Gao, Bo; Paloots, Rahel; Baudis, Michael (2021). The Progenetix oncogenomic resource in 2021. Database, 2021:baab043.
    • Gao, Bo; Baudis, Michael (2021). Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes. Frontiers in Genetics, 12:654887.

  • Working Paper

    • Jacobsen, Julius O B; Baudis, Michael; Baynam, Gareth S; Beckmann, Jacques S; Beltran, Sergi; et al (2021). The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine. medRxiv 21266944, Cold Spring Harbor Laboratory.
    • Huang, Qingyao; Carrio-Cordo, Paula; Gao, Bo; Paloots, Rahel; Baudis, Michael (2021). The Progenetix oncogenomic resource in 2021. bioRxiv 428237, Cold Spring Harbor Laboratory.
    • Wagner, Alex H; Babb, Lawrence; Alterovitz, Gil; Baudis, Michael; et al (2021). The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation. bioRxiv 426843, Cold Spring Harbor Laboratory.

• 2020

  • Journal Article

    • Cascione, Luciano; Aresu, Luca; Baudis, Michael; Bertoni, Francesco (2020). DNA Copy Number Changes in Diffuse Large B Cell Lymphomas. Frontiers in Oncology, 10:584095.
    • Salgado, David; Armean, Irina M; Baudis, Michael; et al (2020). The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research, 9:1229.
    • Gao, Bo; Baudis, Michael (2020). Minimum error calibration and normalization for genomic copy number analysis. Genomics, 112(5):3331-3341.
    • Huang, Qingyao; Baudis, Michael (2020). Enabling population assignment from cancer genomes with SNP2pop. Scientific Reports, 10:4846.
    • Putora, Paul Martin; Baudis, Michael; Beadle, Beth M; El Naqa, Issam; Giordano, Frank A; Nicolay, Nils H (2020). Oncology Informatics: Status Quo and Outlook. Oncology, 98(Suppl. 6):329-331.
    • 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.
    • Wagner, Alex H; Walsh, Brian; Mayfield, Georgia; Tamborero, David; Sonkin, Dmitriy; et al; Baudis, Michael (2020). A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants. Nature Genetics, 52:448-457.
    • Gatti, Marco; Imhof, Ralph; Huang, Qingyao; Baudis, Michael; Altmeyer, Matthias; et al (2020). The Ubiquitin Ligase TRIP12 Limits PARP1 Trapping and Constrains PARP Inhibitor Efficiency. Cell Reports Medicine, 32(5):107985.

• 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.

  • Working Paper

    • Gug, Georgiana; Huang, Qingyao; Chiticariu, Elena; Solovan, Caius; Baudis, Michael (2018). DNA copy number imbalances in primary cutaneous lymphomas (PCL). bioRxiv 417766, Cold Spring Harbor Laboratory.
    • Huang, Qingyao; Baudis, Michael (2018). Enabling population assignment from cancer genomes with SNP2pop. bioRxiv 368647, Cold Spring Harbor Laboratory.

• 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; Richter, 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.

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