{"entity": "researcher", "timestamp": "2026-08-20T20:46:17.296Z", "family": "Morgan", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8326-6178", "affiliations": ["Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae01d9b1d3c487eb66e5379b0faa35e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae01d9b1d3c487eb66e5379b0faa35e"}}, "publications": [{"entity": "publication", "iuid": "6252faf3867b48f2a93e2961d7453c73", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6252faf3867b48f2a93e2961d7453c73.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6252faf3867b48f2a93e2961d7453c73"}}, "title": "GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data.", "authors": [{"family": "Garbulowski", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-2497-194X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98de355d5a1247cebb494b16444857e6.json"}}, {"family": "Hillerton", "given": "Thomas", "initials": "T", "orcid": "0000-0002-6362-0659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07f7f1ec854d4c309f77524357f64400.json"}}, {"family": "Morgan", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8326-6178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae01d9b1d3c487eb66e5379b0faa35e.json"}}, {"family": "Se\u00e7ilmi\u015f", "given": "Deniz", "initials": "D"}, {"family": "Sonnhammer", "given": "Lisbet", "initials": "L"}, {"family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A"}, {"family": "Nordling", "given": "Torbj\u00f6rn E M", "initials": "TEM", "orcid": "0000-0003-4867-6707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ff2e55d28354900a39b69cb1de8c532.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "6", "issue": "3", "pages": "lqae121", "issn-l": null}, "abstract": "Single-cell data is increasingly used for gene regulatory network (GRN) inference, and benchmarks for this have been developed based on simulated data. However, existing single-cell simulators cannot model the effects of gene perturbations. A further challenge lies in generating large-scale GRNs that often struggle with computational and stability issues. We present GeneSPIDER2, an update of the GeneSPIDER MATLAB toolbox for GRN benchmarking, inference, and analysis. Several software modules have improved capabilities and performance, and new functionalities have been added. A major improvement is the ability to generate large GRNs with biologically realistic topological properties in terms of scale-free degree distribution and modularity. Another major addition is a simulation of single-cell data, which is becoming increasingly popular as input for GRN inference. Specifically, we introduced the unique feature to generate single-cell data based on genetic perturbations. Finally, the simulated single-cell data was compared to real single-cell Perturb-seq data from two cell lines, showing that the synthetic and real data exhibit similar properties.", "doi": "10.1093/nargab/lqae121", "pmid": "39296931", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11409065"}, {"db": "pii", "key": "lqae121"}, {"db": "figshare", "key": "10.25452/figshare.plus.20029387.v1"}], "notes": [], "created": "2026-08-20T09:42:58.540Z", "modified": "2026-08-20T09:42:58.579Z"}, {"entity": "publication", "iuid": "f21d910ecaca414e84e9ae52c1d0f35c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f21d910ecaca414e84e9ae52c1d0f35c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f21d910ecaca414e84e9ae52c1d0f35c"}}, "title": "Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data.", "authors": [{"family": "Se\u00e7ilmi\u015f", "given": "Deniz", "initials": "D", "orcid": "0000-0001-8284-356X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66278168a97a4e54a355f2514a9773c9.json"}}, {"family": "Hillerton", "given": "Thomas", "initials": "T"}, {"family": "Morgan", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8326-6178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae01d9b1d3c487eb66e5379b0faa35e.json"}}, {"family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0064-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4d51b0b08948cd8be856ec4c0a50b2.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Nordling", "given": "Torbj\u00f6rn E M", "initials": "TEM", "orcid": "0000-0003-4867-6707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ff2e55d28354900a39b69cb1de8c532.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}], "type": "journal article", "published": "2020-11-09", "journal": {"title": "NPJ Syst Biol Appl", "issn": "2056-7189", "volume": "6", "issue": "1", "pages": "37", "issn-l": "2056-7189"}, "abstract": "The interactions among the components of a living cell that constitute the gene regulatory network (GRN) can be inferred from perturbation-based gene expression data. Such networks are useful for providing mechanistic insights of a biological system. In order to explore the feasibility and quality of GRN inference at a large scale, we used the L1000 data where ~1000 genes have been perturbed and their expression levels have been quantified in 9 cancer cell lines. We found that these datasets have a very low signal-to-noise ratio (SNR) level causing them to be too uninformative to infer accurate GRNs. We developed a gene reduction pipeline in which we eliminate uninformative genes from the system using a selection criterion based on SNR, until reaching an informative subset. The results show that our pipeline can identify an informative subset in an overall uninformative dataset, allowing inference of accurate subset GRNs. The accurate GRNs were functionally characterized and potential novel cancer-related regulatory interactions were identified.", "doi": "10.1038/s41540-020-00154-6", "pmid": "33168813", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7652823"}, {"db": "pii", "key": "10.1038/s41540-020-00154-6"}], "notes": [], "created": "2026-08-20T08:54:42.056Z", "modified": "2026-08-20T08:54:42.243Z"}, {"entity": "publication", "iuid": "ca66623f75d44a9c91f1349be35a46a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ca66623f75d44a9c91f1349be35a46a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ca66623f75d44a9c91f1349be35a46a1"}}, "title": "Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms", "authors": [{"family": "Morgan", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8326-6178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae01d9b1d3c487eb66e5379b0faa35e.json"}}, {"family": "Studham", "given": "Matthew", "initials": "M", "orcid": "0000-0001-9147-4882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3686d0959484118916f9cd826b25d9a.json"}}, {"family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0064-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4d51b0b08948cd8be856ec4c0a50b2.json"}}, {"family": "Weishaupt", "given": "Holger", "initials": "H", "orcid": "0000-0002-0364-2709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ae643d4831f469c95c3d5b3955784ea.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e673fa8c86348fb8c1a2ae34ba7ba9a.json"}}, {"family": "Nordling", "given": "Torbj\u00f6rn E M", "initials": "TEM", "orcid": "0000-0003-4867-6707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ff2e55d28354900a39b69cb1de8c532.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}], "type": "posted-content", "published": "2019-08-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/735514", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:14:40.679Z", "modified": "2026-08-20T11:14:40.832Z"}]}