{"entity": "researcher", "timestamp": "2026-08-20T20:43:02.203Z", "family": "Fasterius", "given": "Erik", "initials": "E", "orcid": "0000-0003-0492-9960", "affiliations": ["School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/6089752ffef34552a0b1aac7ae9dcb14.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/6089752ffef34552a0b1aac7ae9dcb14"}}, "publications": [{"entity": "publication", "iuid": "3fcd57a067db4e33a90326d550a72e4b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3fcd57a067db4e33a90326d550a72e4b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3fcd57a067db4e33a90326d550a72e4b"}}, "title": "Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.", "authors": [{"family": "Kennedy", "given": "Susan A", "initials": "SA"}, {"family": "Jarboui", "given": "Mohamed-Ali", "initials": "MA", "orcid": "0000-0002-5203-235X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66898fad22524e0eb7721b7aa71dc62a.json"}}, {"family": "Srihari", "given": "Sriganesh", "initials": "S"}, {"family": "Raso", "given": "Cinzia", "initials": "C"}, {"family": "Bryan", "given": "Kenneth", "initials": "K"}, {"family": "Dernayka", "given": "Layal", "initials": "L"}, {"family": "Charitou", "given": "Theodosia", "initials": "T"}, {"family": "Bernal-Llinares", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7368-180X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22200b3dbd6641cebc812d66163a0d55.json"}}, {"family": "Herrera-Montavez", "given": "Carlos", "initials": "C"}, {"family": "Krstic", "given": "Aleksandar", "initials": "A"}, {"family": "Matallanas", "given": "David", "initials": "D", "orcid": "0000-0002-2360-3141", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7553949877143a3a8888fcb72916d91.json"}}, {"family": "Kotlyar", "given": "Max", "initials": "M"}, {"family": "Jurisica", "given": "Igor", "initials": "I"}, {"family": "Curak", "given": "Jasna", "initials": "J"}, {"family": "Wong", "given": "Victoria", "initials": "V"}, {"family": "Stagljar", "given": "Igor", "initials": "I", "orcid": "0000-0002-5260-3327", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f52a357d31524cd88b3692d749839e0d.json"}}, {"family": "LeBihan", "given": "Thierry", "initials": "T"}, {"family": "Imrie", "given": "Lisa", "initials": "L", "orcid": "0000-0003-1115-1720", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c243c84e2b724b0fa6c1dd925fd26530.json"}}, {"family": "Pillai", "given": "Priyanka", "initials": "P"}, {"family": "Lynn", "given": "Miriam A", "initials": "MA"}, {"family": "Fasterius", "given": "Erik", "initials": "E", "orcid": "0000-0003-0492-9960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6089752ffef34552a0b1aac7ae9dcb14.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C", "orcid": "0000-0001-6990-1905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/050a127d5c354a2193d1aece35faa945.json"}}, {"family": "Breen", "given": "James", "initials": "J"}, {"family": "Kiel", "given": "Christina", "initials": "C"}, {"family": "Serrano", "given": "Luis", "initials": "L", "orcid": "0000-0002-5276-1392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f26d4773a744cb9ab7573ebfc10fdfb.json"}}, {"family": "Rauch", "given": "Nora", "initials": "N", "orcid": "0000-0001-6009-5177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7e19c1988a3480aa3f080e728b771aa.json"}}, {"family": "Rukhlenko", "given": "Oleksii", "initials": "O"}, {"family": "Kholodenko", "given": "Boris N", "initials": "BN"}, {"family": "Iglesias-Martinez", "given": "Luis F", "initials": "LF"}, {"family": "Ryan", "given": "Colm J", "initials": "CJ", "orcid": "0000-0003-2750-9854", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52c899190e7847a1ab8f45d976458fc9.json"}}, {"family": "Pilkington", "given": "Ruth", "initials": "R"}, {"family": "Cammareri", "given": "Patrizia", "initials": "P"}, {"family": "Sansom", "given": "Owen", "initials": "O", "orcid": "0000-0001-9540-3010", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/785258a0a98445669cd3593f67a7402a.json"}}, {"family": "Shave", "given": "Steven", "initials": "S", "orcid": "0000-0001-6996-3663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58f1cb976fe74d8eb9ce50465b46f4ec.json"}}, {"family": "Auer", "given": "Manfred", "initials": "M", "orcid": "0000-0001-8920-3522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cac46fc8e154326a196d64bbe41557d.json"}}, {"family": "Horn", "given": "Nicola", "initials": "N"}, {"family": "Klose", "given": "Franziska", "initials": "F"}, {"family": "Ueffing", "given": "Marius", "initials": "M"}, {"family": "Boldt", "given": "Karsten", "initials": "K", "orcid": "0000-0002-2693-689X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/902be55dfb1748079935fca1f2e7d293.json"}}, {"family": "Lynn", "given": "David J", "initials": "DJ"}, {"family": "Kolch", "given": "Walter", "initials": "W", "orcid": "0000-0001-5777-5016", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6640e523e6b847a58f5b739f5b71bfff.json"}}], "type": "journal article", "published": "2020-01-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "499", "issn-l": "2041-1723"}, "abstract": "Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.", "doi": "10.1038/s41467-019-14224-9", "pmid": "31980649", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6981206"}, {"db": "pii", "key": "10.1038/s41467-019-14224-9"}], "notes": [], "created": "2026-08-20T08:50:56.505Z", "modified": "2026-08-20T08:50:57.116Z"}, {"entity": "publication", "iuid": "1dcbe23c696745149f28d85bde14f62e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dcbe23c696745149f28d85bde14f62e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dcbe23c696745149f28d85bde14f62e"}}, "title": "seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data", "authors": [{"family": "Fasterius", "given": "Erik", "initials": "E", "orcid": "0000-0003-0492-9960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6089752ffef34552a0b1aac7ae9dcb14.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C", "orcid": "0000-0001-6990-1905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/050a127d5c354a2193d1aece35faa945.json"}}], "type": "journal-article", "published": "2019-08-12", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "7", "pages": "1466", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.16083.2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:41:33.113Z", "modified": "2026-08-20T12:41:33.186Z"}, {"entity": "publication", "iuid": "20f14a50c2a949df9c420d8a0892e6c9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/20f14a50c2a949df9c420d8a0892e6c9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/20f14a50c2a949df9c420d8a0892e6c9"}}, "title": "Single-cell RNA-seq variant analysis for exploration of genetic heterogeneity in cancer.", "authors": [{"family": "Fasterius", "given": "Erik", "initials": "E", "orcid": "0000-0003-0492-9960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6089752ffef34552a0b1aac7ae9dcb14.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C", "orcid": "0000-0001-6990-1905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/050a127d5c354a2193d1aece35faa945.json"}}], "type": "journal article", "published": "2019-07-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "9524", "issn-l": "2045-2322"}, "abstract": "Inter- and intra-tumour heterogeneity is caused by genetic and non-genetic factors, leading to severe clinical implications. High-throughput sequencing technologies provide unprecedented tools to analyse DNA and RNA in single cells and explore both genetic heterogeneity and phenotypic variation between cells in tissues and tumours. Simultaneous analysis of both DNA and RNA in the same cell is, however, still in its infancy. We have thus developed a method to extract and analyse information regarding genetic heterogeneity that affects cellular biology from single-cell RNA-seq data. The method enables both comparisons and clustering of cells based on genetic variation in single nucleotide variants, revealing cellular subpopulations corroborated by gene expression-based methods. Furthermore, the results show that lymph node metastases have lower levels of genetic heterogeneity compared to their original tumours with respect to variants affecting protein function. The analysis also revealed three previously unknown variants common across cancer cells in glioblastoma patients. These results demonstrate the power and versatility of scRNA-seq variant analysis and highlight it as a useful complement to already existing methods, enabling simultaneous investigations of both gene expression and genetic variation.", "doi": "10.1038/s41598-019-45934-1", "pmid": "31267007", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6606766"}, {"db": "pii", "key": "10.1038/s41598-019-45934-1"}], "notes": [], "created": "2026-08-20T09:04:38.112Z", "modified": "2026-08-20T09:04:38.204Z"}, {"entity": "publication", "iuid": "1ffe23527e7947daaea4323d5bbc5c3f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ffe23527e7947daaea4323d5bbc5c3f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ffe23527e7947daaea4323d5bbc5c3f"}}, "title": "seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data", "authors": [{"family": "Fasterius", "given": "Erik", "initials": "E", "orcid": "0000-0003-0492-9960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6089752ffef34552a0b1aac7ae9dcb14.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C", "orcid": "0000-0001-6990-1905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/050a127d5c354a2193d1aece35faa945.json"}}], "type": "journal-article", "published": "2018-09-14", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "7", "pages": "1466", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.16083.1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:41:31.302Z", "modified": "2026-08-20T12:41:31.396Z"}]}