Publications

ZORA Publication List

Publications

• 2026

  • Journal Article

    • Yang, Z., & Baudis, M. (2026). CNAttention: an attention-based deep multiple-instance method for uncovering copy number aberration signatures across cancers Briefings in Bioinformatics, 27, bbaf696. https://doi.org/10.1093/bib/bbaf696

• 2025

  • Journal Article

    • Zhao, H., & Baudis, M. (2025). CNAdjust: enhancing CNA calling accuracy through systematic baseline adjustment Frontiers in Genetics, 16, 1674138. https://doi.org/10.3389/fgene.2025.1674138

• 2024

  • Journal Article

    • Yang, Z., Carrio-Cordo, P., & Baudis, M. (2024). Copy number variation heterogeneity reveals biological inconsistency in hierarchical cancer classifications Molecular Cytogenetics, 17, 26. https://doi.org/10.1186/s13039-024-00692-2
    • Paloots, R., & Baudis, M. (2024). cancercelllines.org-a novel resource for genomic variants in cancer cell lines Database, 2024, baae030. https://doi.org/10.1093/database/baae030
    • Smith, E., Paloots, R., Giagkos, D., Baudis, M., & Stockinger, K. (2024). Data-driven information extraction and enrichment of molecular profiling data for cancer cell lines Bioinformatics Advances, 4, vbae045. https://doi.org/10.1093/bioadv/vbae045
    • Zhao, H., & Baudis, M. (2024). labelSeg : Segment Annotation for Tumor Copy Number Alteration Profiles. Briefings in Bioinformatics, 25, bbad541. https://doi.org/10.1093/bib/bbad541
    • van Baardwijk, M. N., Heijnen, L. S. E. M., Zhao, H., Baudis, M., & Stubbs, A. P. (2024). A systematic benchmark of copy number variation detection tools for high density SNP genotyping arrays Genomics, 116, 110962. https://doi.org/10.1016/j.ygeno.2024.110962
    • Fromont, L. A., Moldes, M., Baudis, M., Brookes, A. J., Navarro, A., & Rambla, J. (2024). Twelve quick tips for deploying a Beacon PLoS Computational Biology, 20, e1011817. https://doi.org/10.1371/journal.pcbi.1011817

• 2023

  • Journal Article

    • Ladewig, M. S., Jacobsen, J. O. B., Wagner, A. H., Danis, D., El Kassaby, B., Gargano, M., Groza, T., Baudis, M., Steinhaus, R., Seelow, D., Bechrakis, N. E., Mungall, C. J., Schofield, P. N., Elemento, O., Smith, L., McMurry, J. A., Munoz‐Torres, M., Haendel, M. A., & Robinson, P. N. (2023). GA4GH Phenopackets: A Practical Introduction Advanced Genetics, 4, 2200016. https://doi.org/10.1002/ggn2.202200016
    • Huang, Q., & Baudis, M. (2023). Candidate targets of copy number deletion events across 17 cancer types Frontiers in Genetics, 13, 1017657. https://doi.org/10.3389/fgene.2022.1017657

• 2022

  • Journal Article

    • Rambla, J., Baudis, M., Ariosa, R., Beck, T., Fromont, L. A., Navarro, A., Paloots, R., Rueda, M., Saunders, G., Singh, B., Spalding, J. D., Törnroos, J., Vasallo, C., Veal, C. D., & Brookes, A. J. (2022). Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond. Human Mutation, 43, 791–799. https://doi.org/10.1002/humu.24369
    • Jacobsen, J. O. B., Baudis, M., Baynam, G. S., Beckmann, J. S., Beltran, S., Buske, O. J., & et al. (2022). The GA4GH Phenopacket schema defines a computable representation of clinical data Nature Biotechnology, 40, 817–820. https://doi.org/10.1038/s41587-022-01357-4

  • Working Paper

    • Huang, Q., & Baudis, M. (2022). Candidate targets of copy number deletion events across 17 cancer types (No. 498080; BioRxiv). https://doi.org/10.1101/2022.06.29.498080

• 2021

  • Journal Article

    • Wagner, A. H., Babb, L., Alterovitz, G., Baudis, M., & et al. (2021). The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification Cell Genomics, 1, 100027. https://doi.org/10.1016/j.xgen.2021.100027
    • Thorogood, A., Rehm, H. L., Goodhand, P., Page, A. J. H., Joly, Y., Baudis, M., Rambla, J., Navarro, A., Nyronen, T. H., Linden, M., Dove, E. S., Fiume, M., Brudno, M., Cline, M. S., & Birney, E. (2021). International federation of genomic medicine databases using GA4GH standards Cell, 1, 100032. https://doi.org/10.1016/j.xgen.2021.100032
    • Rehm, H. L., Page, A. J. H., Smith, L., Adams, J. B., Alterovitz, G., Babb, L. J., Barkley, M. P., Baudis, M., Beauvais, M. J. S., Beck, T., Beckmann, J. S., Beltran, S., Bernick, D., Bernier, A., Bonfield, J. K., Boughtwood, T. F., Bourque, G., Bowers, S. R., Brookes, A. J., … et al. (2021). GA4GH: International policies and standards for data sharing across genomic research and healthcare Cell, 1, 100029. https://doi.org/10.1016/j.xgen.2021.100029
    • Huang, Q., Carrio-Cordo, P., Gao, B., Paloots, R., & Baudis, M. (2021). The Progenetix oncogenomic resource in 2021 Database, 2021, baab043. https://doi.org/10.1093/database/baab043
    • Gao, B., & Baudis, M. (2021). Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes Frontiers in Genetics, 12, 654887. https://doi.org/10.3389/fgene.2021.654887

  • Working Paper

    • Jacobsen, J. O. B., Baudis, M., Baynam, G. S., Beckmann, J. S., Beltran, S., & et al. (2021). The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine (No. 21266944; MedRxiv). https://doi.org/10.1101/2021.11.27.21266944
    • Huang, Q., Carrio-Cordo, P., Gao, B., Paloots, R., & Baudis, M. (2021). The Progenetix oncogenomic resource in 2021 (No. 428237; BioRxiv). https://doi.org/10.1101/2021.02.15.428237
    • Wagner, A. H., Babb, L., Alterovitz, G., Baudis, M., & et al. (2021). The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation (No. 426843; BioRxiv). https://doi.org/10.1101/2021.01.15.426843

• 2020

  • Journal Article

    • Cascione, L., Aresu, L., Baudis, M., & Bertoni, F. (2020). DNA Copy Number Changes in Diffuse Large B Cell Lymphomas Frontiers in Oncology, 10, 584095. https://doi.org/10.3389/fonc.2020.584095
    • Salgado, D., Armean, I. M., Baudis, M., & et al. (2020). The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research F1000Research, 9, 1229. https://doi.org/10.12688/f1000research.24887.1
    • Gao, B., & Baudis, M. (2020). Minimum error calibration and normalization for genomic copy number analysis Genomics, 112, 3331–3341. https://doi.org/10.1016/j.ygeno.2020.05.008
    • Huang, Q., & Baudis, M. (2020). Enabling population assignment from cancer genomes with SNP2pop Scientific Reports, 10, 4846. https://doi.org/10.1038/s41598-020-61854-x
    • Putora, P. M., Baudis, M., Beadle, B. M., El Naqa, I., Giordano, F. A., & Nicolay, N. H. (2020). Oncology Informatics: Status Quo and Outlook Oncology, 98, 329–331. https://doi.org/10.1159/000507586
    • Carrio-Cordo, P., Acheson, E., Huang, Q., & Baudis, M. (2020). Geographic assessment of cancer genome profiling studies Database, 2020, baaa009. https://doi.org/10.1093/database/baaa009
    • Carrio-Cordo, P., & Baudis, M. (2020). Mountains and Chasms: Surveying the Oncogenomic Publication Landscape Oncology, 98, 332–343. https://doi.org/10.1159/000493192
    • Wagner, A. H., Walsh, B., Mayfield, G., Tamborero, D., Sonkin, D., et al, & Baudis, M. (2020). A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants Nature Genetics, 52, 448–457. https://doi.org/10.1101/366856
    • Gatti, M., Imhof, R., Huang, Q., Baudis, M., Altmeyer, M., & et al. (2020). The Ubiquitin Ligase TRIP12 Limits PARP1 Trapping and Constrains PARP Inhibitor Efficiency Cell Reports Medicine, 32, 107985. https://doi.org/10.1016/j.celrep.2020.107985

• 2019

  • Journal Article

    • Saunders, G., Baudis, M., Becker, R., Beltran, S., Béroud, C., Birney, E., Brooksbank, C., Brunak, S., Van den Bulcke, M., Drysdale, R., Capella-Gutierrez, S., Flicek, P., Florindi, F., Goodhand, P., Gut, I., Heringa, J., Holub, P., Hooyberghs, J., Juty, N., … et al. (2019). Leveraging European infrastructures to access 1 million human genomes by 2022 Nature Reviews. Genetics, 20, 693–701. https://doi.org/10.1038/s41576-019-0156-9
    • Gug, G., Huang, Q., Chiticariu, E., Solovan, C., & Baudis, M. (2019). DNA copy number imbalances in primary cutaneous lymphomas Journal of the European Academy of Dermatology and Venerology, 33, 1062–1075. https://doi.org/10.1111/jdv.15442
    • Fiume, M., Cupak, M., Keenan, S., Rambla, J., de la Torre, S., Dyke, S. O. M., Brookes, A. J., Carey, K., Lloyd, D., Goodhand, P., Haeussler, M., Baudis, M., Stockinger, H., Dolman, L., Lappalainen, I., Törnroos, J., Linden, M., Spalding, J. D., Ur-Rehman, S., … Scollen, S. (2019). Federated discovery and sharing of genomic data using Beacons Nature Biotechnology, 37, 220–224. https://doi.org/10.1038/s41587-019-0046-x

• 2018

  • Journal Article

    • Marrero-Rodríguez, D., Taniguchi-Ponciano, K., Subramaniam, M., Hawse, J. R., Pitel, K. S., Arreola-De la Cruz, H., Huerta-Padilla, V., Ponce-Navarrete, G., Figueroa-Corona, M. D. P., Gomez-Virgilio, L., Martinez-Cuevas, T. I., Mendoza-Rodriguez, M., Rodriguez-Esquivel, M., Romero-Morelos, P., Ramirez-Salcedo, J., Baudis, M., Meraz-Rios, M., Jimenez-Vega, F., & Salcedo, M. (2018). Krüppel-Like Factor 10 participates in cervical cancer immunoediting through transcriptional regulation of Pregnancy-Specific Beta-1 Glycoproteins Scientific Reports, 8, 9445. https://doi.org/10.1038/s41598-018-27711-8
    • Dyke, S. O. M., Linden, M., Lappalainen, I., De Argila, J. R., et al, & Baudis, M. (2018). Registered access: authorizing data access European Journal of Human Genetics, 26, 1721–1731. https://doi.org/10.1038/s41431-018-0219-y
    • Gao, B., Huang, Q., & Baudis, M. (2018). segment_liftover : a Python tool to convert segments between genome assemblies. F1000Research, 7, 319. https://doi.org/10.12688/f1000research.14148.1

  • Working Paper

    • Gug, G., Huang, Q., Chiticariu, E., Solovan, C., & Baudis, M. (2018). DNA copy number imbalances in primary cutaneous lymphomas (PCL) (No. 417766; BioRxiv). https://doi.org/10.1101/417766
    • Huang, Q., & Baudis, M. (2018). Enabling population assignment from cancer genomes with SNP2pop (No. 368647; BioRxiv). https://doi.org/10.1101/368647

• 2017

  • Journal Article

    • Mackay, A., Burford, A., Carvalho, D., Izquierdo, E., Fazal-Salom, J., Taylor, K. R., Bjerke, L., Clarke, M., Vinci, M., Nandhabalan, M., Temelso, S., Popov, S., Molinari, V., Raman, P., Waanders, A. J., Han, H. J., Gupta, S., Marshall, L., Zacharoulis, S., … et al. (2017). Integrated molecular meta-analysis of 1,000 pediatric high-grade and diffuse intrinsic pontine glioma Cancer Cell, 32, 520-537.e5. https://doi.org/10.1016/j.ccell.2017.08.017

• 2016

  • Journal Article

    • Ai, N., Cai, H., Solovan, C., & Baudis, M. (2016). CNARA: reliability assessment for genomic copy number profiles BMC Genomics, 17, 799. https://doi.org/10.1186/s12864-016-3074-7
    • Stockinger, H., Palagi, P. M., Durinx, C., Baudis, M., von Mering, C., Szövenyi, P., & et al. (2016). The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Research, 44, D27-37. https://doi.org/10.1093/nar/gkv1310
    • Mackay, A., Burford, A., Salom, J. F., et al, & Baudis, M. (2016). Hg-95integrated molecular meta-analysis of 1000 paediatric high grade glioma and dipg Neuro-Oncology, 18, iii70.3-iii70. https://doi.org/10.1093/neuonc/now073.91

• 2015

  • Journal Article

    • Cai, H., Gupta, S., Rath, P., Ai, N., & Baudis, M. (2015). arrayMap 2014: an updated cancer genome resource Nucleic Acids Research, 43, D825–D830. https://doi.org/10.1093/nar/gku1123
    • Muff, R., Rath, P., Ram Kumar, R. M., Husmann, K., Born, W., Baudis, M., & Fuchs, B. (2015). Genomic instability of osteosarcoma cell lines in culture: impact on the prediction of metastasis relevant genes PLoS ONE, 10, e0125611. https://doi.org/10.1371/journal.pone.0125611

• 2014

  • Journal Article

    • Cai, H., Kumar, N., Ai, N., Gupta, S., Rath, P., & Baudis, M. (2014). Progenetix: 12 years of oncogenomic data curation Nucleic Acids Research, 42, D1055–D1062. https://doi.org/10.1093/nar/gkt1108
    • Cai, H., Kumar, N., Bagheri, H. C., von Mering, C., Robinson, M. D., & Baudis, M. (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens BMC Genomics, 15, 82. https://doi.org/10.1186/1471-2164-15-82
    • Baderca, F., Chiticariu, E., Baudis, M., & Solovan, C. (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, 1085–1092. http://www.ncbi.nlm.nih.gov/pubmed/25607389

• 2013

  • Journal Article

    • Krieger, M., Roos, A., Stendel, C., Claeys, K. G., Sonmez, F. M., Baudis, M., Bauer, P., Bornemann, A., de Goede, C., Dufke, A., Finkel, R. S., Goebel, H. H., Häussler, M., Kingston, H., Kirschner, J., Medne, L., Muschke, P., Rivier, F., Rudnik-Schöneborn, S., … Senderek, J. (2013). SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome Brain : A Journal of Neurology, 136, 3634–3644. https://doi.org/10.1093/brain/awt283
    • Martin-Guerrero, I., Salaverria, I., Burkhardt, B., Szczepanowski, M., Baudis, M., Bens, S., de Leval, L., Garcia-Orad, A., Horn, H., Lisfeld, J., Pellissery, S., Klapper, W., Oschlies, I., & Siebert, R. (2013). Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas Haematologica, 98, 1237–1241. https://doi.org/10.3324/haematol.2012.073916
    • Salaverria, I., Martin-Guerrero, I., Burkhardt, B., Kreuz, M., Zenz, T., Oschlies, I., Arnold, N., Baudis, M., Bens, S., García-Orad, A., Lisfeld, J., Schwaenen, C., Szczepanowski, M., Wessendorf, S., Pfreundschuh, M., Trümper, L., Klapper, W., & Siebert, R. (2013). High resolution copy number analysis of IRF4 translocation-positive diffuse large B-cell and follicular lymphomas Genes, Chromosomes and Cancer, 52, 150–155. https://doi.org/10.1002/gcc.22014

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