{"entity": "researcher", "timestamp": "2026-08-23T22:16:56.075Z", "family": "Merkenschlager", "given": "Matthias", "initials": "M", "orcid": "0000-0003-2889-3288", "affiliations": ["Lymphocyte Development Group, MRC London Institute of Medical Sciences, London, United Kingdom.", "Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/6257840a1b0c4478a38ec31b070fb13c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/6257840a1b0c4478a38ec31b070fb13c"}}, "publications": [{"entity": "publication", "iuid": "f80c6b93948c4440b080c6423a4e63d3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f80c6b93948c4440b080c6423a4e63d3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f80c6b93948c4440b080c6423a4e63d3"}}, "title": "Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.", "authors": [{"family": "Jansen", "given": "Camden", "initials": "C"}, {"family": "Ramirez", "given": "Ricardo N", "initials": "RN", "orcid": "0000-0002-1259-5406", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/606cf67d57f441008ecb07b0e3e4705d.json"}}, {"family": "El-Ali", "given": "Nicole C", "initials": "NC"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}, {"family": "Tegner", "given": "Jesper", "initials": "J"}, {"family": "Merkenschlager", "given": "Matthias", "initials": "M", "orcid": "0000-0003-2889-3288", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6257840a1b0c4478a38ec31b070fb13c.json"}}, {"family": "Conesa", "given": "Ana", "initials": "A"}, {"family": "Mortazavi", "given": "Ali", "initials": "A", "orcid": "0000-0002-4259-6362", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bf4e09c681848b693ee5eaddde1ef3e.json"}}], "type": "journal article", "published": "2019-11-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "15", "issue": "11", "pages": "e1006555", "issn-l": "1553-734X"}, "abstract": "Rapid advances in single-cell assays have outpaced methods for analysis of those data types. Different single-cell assays show extensive variation in sensitivity and signal to noise levels. In particular, scATAC-seq generates extremely sparse and noisy datasets. Existing methods developed to analyze this data require cells amenable to pseudo-time analysis or require datasets with drastically different cell-types. We describe a novel approach using self-organizing maps (SOM) to link scATAC-seq regions with scRNA-seq genes that overcomes these challenges and can generate draft regulatory networks. Our SOMatic package generates chromatin and gene expression SOMs separately and combines them using a linking function. We applied SOMatic on a mouse pre-B cell differentiation time-course using controlled Ikaros over-expression to recover gene ontology enrichments, identify motifs in genomic regions showing similar single-cell profiles, and generate a gene regulatory network that both recovers known interactions and predicts new Ikaros targets during the differentiation process. The ability of linked SOMs to detect emergent properties from multiple types of highly-dimensional genomic data with very different signal properties opens new avenues for integrative analysis of heterogeneous data.", "doi": "10.1371/journal.pcbi.1006555", "pmid": "31682608", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6855564"}, {"db": "pii", "key": "PCOMPBIOL-D-18-01711"}], "notes": [], "created": "2026-08-21T12:43:43.904Z", "modified": "2026-08-21T12:43:44.018Z"}, {"entity": "publication", "iuid": "42a4d22ee30e48ccac0ec0cf1a9a3fa1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/42a4d22ee30e48ccac0ec0cf1a9a3fa1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/42a4d22ee30e48ccac0ec0cf1a9a3fa1"}}, "title": "Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.", "authors": [{"family": "Ferreir\u00f3s-Vidal", "given": "Isabel", "initials": "I"}, {"family": "Carroll", "given": "Thomas", "initials": "T"}, {"family": "Zhang", "given": "Tianyi", "initials": "T"}, {"family": "Lagani", "given": "Vincenzo", "initials": "V"}, {"family": "Ramirez", "given": "Ricardo N", "initials": "RN"}, {"family": "Ing-Simmons", "given": "Elizabeth", "initials": "E"}, {"family": "G\u00f3mez-Valad\u00e9s", "given": "Alicia G", "initials": "AG"}, {"family": "Cooper", "given": "Lee", "initials": "L"}, {"family": "Liang", "given": "Ziwei", "initials": "Z"}, {"family": "Papoutsoglou", "given": "Georgios", "initials": "G"}, {"family": "Dharmalingam", "given": "Gopuraja", "initials": "G"}, {"family": "Guo", "given": "Ya", "initials": "Y"}, {"family": "Tarazona", "given": "Sonia", "initials": "S"}, {"family": "Fernandes", "given": "Sunjay J", "initials": "SJ"}, {"family": "Noori", "given": "Peri", "initials": "P"}, {"family": "Silberberg", "given": "Gilad", "initials": "G"}, {"family": "Fisher", "given": "Amanda G", "initials": "AG"}, {"family": "Tsamardinos", "given": "Ioannis", "initials": "I"}, {"family": "Mortazavi", "given": "Ali", "initials": "A"}, {"family": "Lenhard", "given": "Boris", "initials": "B"}, {"family": "Conesa", "given": "Ana", "initials": "A"}, {"family": "Tegner", "given": "Jesper", "initials": "J"}, {"family": "Merkenschlager", "given": "Matthias", "initials": "M", "orcid": "0000-0003-2889-3288", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6257840a1b0c4478a38ec31b070fb13c.json"}}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}], "type": "journal article", "published": "2019-04-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "17", "issue": "4", "pages": "e2006506", "issn-l": "1544-9173"}, "abstract": "The differentiation of self-renewing progenitor cells requires not only the regulation of lineage- and developmental stage-specific genes but also the coordinated adaptation of housekeeping functions from a metabolically active, proliferative state toward quiescence. How metabolic and cell-cycle states are coordinated with the regulation of cell type-specific genes is an important question, because dissociation between differentiation, cell cycle, and metabolic states is a hallmark of cancer. Here, we use a model system to systematically identify key transcriptional regulators of Ikaros-dependent B cell-progenitor differentiation. We find that the coordinated regulation of housekeeping functions and tissue-specific gene expression requires a feedforward circuit whereby Ikaros down-regulates the expression of Myc. Our findings show how coordination between differentiation and housekeeping states can be achieved by interconnected regulators. Similar principles likely coordinate differentiation and housekeeping functions during progenitor cell differentiation in other cell lineages.", "doi": "10.1371/journal.pbio.2006506", "pmid": "30978178", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6481923"}, {"db": "pii", "key": "pbio.2006506"}], "notes": [], "created": "2026-08-21T12:43:29.153Z", "modified": "2026-08-21T12:43:29.228Z"}]}