{"entity": "researcher", "timestamp": "2026-08-20T20:45:49.087Z", "family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0064-1791", "affiliations": ["Bioinformatics, Department of Physics, Chemistry and Biology, Link\u00f6ping University, Link\u00f6ping, Sweden.", "Department of Biology, Center For Genomics and Systems Biology, New York University, New York, NY, 10008, USA.", "Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4d51b0b08948cd8be856ec4c0a50b2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4d51b0b08948cd8be856ec4c0a50b2"}}, "publications": [{"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": "7c1cb7d6bb354c10bd7b51364f4bb4d1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7c1cb7d6bb354c10bd7b51364f4bb4d1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7c1cb7d6bb354c10bd7b51364f4bb4d1"}}, "title": "Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder.", "authors": [{"family": "Dwivedi", "given": "Sanjiv K", "initials": "SK", "orcid": "0000-0003-3400-4133", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa4b2a4afa3942beac5115b5ab505825.json"}}, {"family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0064-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4d51b0b08948cd8be856ec4c0a50b2.json"}}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J", "orcid": "0000-0002-9568-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b115e5faf68a4acbb6f947c711fd37ec.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d87fbeece2db4a9dbaf2254bfd9a1100.json"}}], "type": "journal article", "published": "2020-02-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "856", "issn-l": "2041-1723"}, "abstract": "Disease modules in molecular interaction maps have been useful for characterizing diseases. Yet biological networks, that commonly define such modules are incomplete and biased toward some well-studied disease genes. Here we ask whether disease-relevant modules of genes can be discovered without prior knowledge of a biological network, instead training a deep autoencoder from large transcriptional data. We hypothesize that modules could be discovered within the autoencoder representations. We find a statistically significant enrichment of genome-wide association studies (GWAS) relevant genes in the last layer, and to a successively lesser degree in the middle and first layers respectively. In contrast, we find an opposite gradient where a modular protein-protein interaction signal is strongest in the first layer, but then vanishing smoothly deeper in the network. We conclude that a data-driven discovery approach is sufficient to discover groups of disease-related genes.", "doi": "10.1038/s41467-020-14666-6", "pmid": "32051402", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7016183"}, {"db": "pii", "key": "10.1038/s41467-020-14666-6"}], "notes": [], "created": "2026-08-20T08:51:03.573Z", "modified": "2026-08-20T08:51:03.799Z"}, {"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"}]}