{"entity": "researcher", "timestamp": "2026-08-21T23:12:13.102Z", "family": "Ulas", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9785-4197", "affiliations": ["Genomics & Immunoregulation, Life and Medical Science Institute, University of Bonn, Bonn, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/1fe5950df6e141b7aab952703e0c0c46.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/1fe5950df6e141b7aab952703e0c0c46"}}, "publications": [{"entity": "publication", "iuid": "09b1b9ba8e71494a8df546b6010120f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09b1b9ba8e71494a8df546b6010120f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09b1b9ba8e71494a8df546b6010120f5"}}, "title": "hCoCena: horizontal integration and analysis of transcriptomics datasets.", "authors": [{"family": "Oestreich", "given": "Marie", "initials": "M"}, {"family": "Holsten", "given": "Lisa", "initials": "L"}, {"family": "Agrawal", "given": "Shobhit", "initials": "S"}, {"family": "Dahm", "given": "Kilian", "initials": "K"}, {"family": "Koch", "given": "Philipp", "initials": "P"}, {"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Becker", "given": "Matthias", "initials": "M", "orcid": "0000-0002-7120-4508", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/256d327f98b84898ab42e71f18f97b51.json"}}, {"family": "Ulas", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9785-4197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1fe5950df6e141b7aab952703e0c0c46.json"}}], "type": "journal article", "published": "2022-10-14", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "38", "issue": "20", "pages": "4727-4734", "issn-l": "1367-4803"}, "abstract": "Transcriptome-based gene co-expression analysis has become a standard procedure for structured and contextualized understanding and comparison of different conditions and phenotypes. Since large study designs with a broad variety of conditions are costly and laborious, extensive comparisons are hindered when utilizing only a single dataset. Thus, there is an increased need for tools that allow the integration of multiple transcriptomic datasets with subsequent joint analysis, which can provide a more systematic understanding of gene co-expression and co-functionality within and across conditions. To make such an integrative analysis accessible to a wide spectrum of users with differing levels of programming expertise it is essential to provide user-friendliness and customizability as well as thorough documentation.\n\nThis article introduces horizontal CoCena (hCoCena: horizontal construction of co-expression networks and analysis), an R-package for network-based co-expression analysis that allows the analysis of a single transcriptomic dataset as well as the joint analysis of multiple datasets. With hCoCena, we provide a freely available, user-friendly and adaptable tool for integrative multi-study or single-study transcriptomics analyses alongside extensive comparisons to other existing tools.\n\nThe hCoCena R-package is provided together with R Markdowns that implement an exemplary analysis workflow including extensive documentation and detailed descriptions of data structures and objects. Such efforts not only make the tool easy to use but also enable the seamless integration of user-written scripts and functions into the workflow, creating a tool that provides a clear design while remaining flexible and highly customizable. The package and additional information including an extensive Wiki are freely available on GitHub: https://github.com/MarieOestreich/hCoCena. The version at the time of writing has been added to Zenodo under the following link: https://doi.org/10.5281/zenodo.6911782.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btac589", "pmid": "36018233", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9563699"}, {"db": "pii", "key": "6677225"}], "notes": [], "created": "2026-08-21T12:06:50.735Z", "modified": "2026-08-21T12:06:50.812Z"}, {"entity": "publication", "iuid": "5bb8ae8f6ba84927ace55253c2cc8ae1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5bb8ae8f6ba84927ace55253c2cc8ae1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5bb8ae8f6ba84927ace55253c2cc8ae1"}}, "title": "Tumor endothelial cell up-regulation of IDO1 is an immunosuppressive feed-back mechanism that reduces the response to CD40-stimulating immunotherapy.", "authors": [{"family": "Georganaki", "given": "Maria", "initials": "M"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Tuit", "given": "Sander", "initials": "S"}, {"family": "N\u00fa\u00f1ez", "given": "Nicol\u00e1s Gonzalo", "initials": "NG"}, {"family": "Karampatzakis", "given": "Alexandros", "initials": "A"}, {"family": "Fotaki", "given": "Grammatiki", "initials": "G"}, {"family": "van Hooren", "given": "Luuk", "initials": "L"}, {"family": "Huang", "given": "Hua", "initials": "H"}, {"family": "Lugano", "given": "Roberta", "initials": "R"}, {"family": "Ulas", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9785-4197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1fe5950df6e141b7aab952703e0c0c46.json"}}, {"family": "Kaunisto", "given": "Aura", "initials": "A"}, {"family": "Holland", "given": "Eric C", "initials": "EC"}, {"family": "Ellmark", "given": "Peter", "initials": "P"}, {"family": "Mangsbo", "given": "Sara M", "initials": "SM"}, {"family": "Schultze", "given": "Joachim", "initials": "J"}, {"family": "Essand", "given": "Magnus", "initials": "M"}, {"family": "Tugues", "given": "Sonia", "initials": "S"}, {"family": "Dimberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-4422-9125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f5d91c4b8784d8081a41604bb3d78d4.json"}}], "type": "journal article", "published": "2020-03-09", "journal": {"title": "Oncoimmunology", "issn": "2162-4011", "volume": "9", "issue": "1", "pages": "1730538", "issn-l": null}, "abstract": "CD40-stimulating immunotherapy can elicit potent anti-tumor responses by activating dendritic cells and enhancing T-cell priming. Tumor vessels orchestrate T-cell recruitment during immune response, but the effect of CD40-stimulating immunotherapy on tumor endothelial cells has not been evaluated. Here, we have investigated how tumor endothelial cells transcriptionally respond to CD40-stimulating immunotherapy by isolating tumor endothelial cells from agonistic CD40 mAb- or isotype-treated mice bearing B16-F10 melanoma, and performing RNA-sequencing. Gene set enrichment analysis revealed that agonistic CD40 mAb therapy increased interferon (IFN)-related responses in tumor endothelial cells, including up-regulation of the immunosuppressive enzyme Indoleamine 2, 3-Dioxygenase 1 (IDO1). IDO1 was predominantly expressed in endothelial cells within the tumor microenvironment, and its expression in tumor endothelium was positively correlated to T-cell infiltration and to increased intratumoral expression of IFN\u03b3. In vitro, endothelial cells up-regulated IDO1 in response to T-cell-derived IFN\u03b3, but not in response to CD40-stimulation. Combining agonistic CD40 mAb therapy with the IDO1 inhibitor epacadostat delayed tumor growth in B16-F10 melanoma, associated with increased activation of tumor-infiltrating T-cells. Hereby, we show that the tumor endothelial cells up-regulate IDO1 upon CD40-stimulating immunotherapy in response to increased IFN\u03b3-secretion by T-cells, revealing a novel immunosuppressive feedback mechanism whereby tumor vessels limit T-cell activation.", "doi": "10.1080/2162402X.2020.1730538", "pmid": "32231867", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7094447"}, {"db": "pii", "key": "1730538"}], "notes": [], "created": "2026-08-20T09:37:30.762Z", "modified": "2026-08-21T09:28:20.269Z"}]}