{"entity": "researcher", "timestamp": "2026-08-08T15:45:03.930Z", "family": "Das", "given": "Jyotirmoy", "initials": "J", "orcid": "0000-0002-5649-4658", "affiliations": ["Bioinformatics, Core Facility, Division of Cell Biology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Link\u00f6ping University, 58183 Link\u00f6ping, Sweden.", "Clinical Genomics Link\u00f6ping, SciLife Laboratory, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Link\u00f6ping University, 58183 Link\u00f6ping, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ebcbc4237c1c48aeb6bdd446fd8d2c8a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ebcbc4237c1c48aeb6bdd446fd8d2c8a"}}, "publications": [{"entity": "publication", "iuid": "83a77d8160924330b81be0f9c36ddd00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83a77d8160924330b81be0f9c36ddd00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83a77d8160924330b81be0f9c36ddd00"}}, "title": "Altered DNA Methylation Pattern Contributes to Differential Epigenetic Immune Signaling in the Upper Respiratory Airway of Unvaccinated COVID-19 Patients", "authors": [{"family": "Govender", "given": "Melissa", "initials": "M", "orcid": "0000-0001-8327-5517", "researcher": {"href": "https://publications.scilifelab.se/researcher/0283324530c24dc59a856cc26f202884.json"}}, {"family": "Das", "given": "Jyotirmoy", "initials": "J", "orcid": "0000-0002-5649-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebcbc4237c1c48aeb6bdd446fd8d2c8a.json"}}, {"family": "Hopkins", "given": "Francis R", "initials": "FR"}, {"family": "Svanberg", "given": "Cecilia", "initials": "C"}, {"family": "Nordgren", "given": "Johan", "initials": "J", "orcid": "0000-0002-5349-2569", "researcher": {"href": "https://publications.scilifelab.se/researcher/81437aaae3b44d148e838a184c455f2b.json"}}, {"family": "Hagbom", "given": "Marie", "initials": "M", "orcid": "0000-0002-9770-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0555f8ab1b2d42fc9bead5f4c0240ec9.json"}}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Nilsdotter-Augustinsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-5719-5601", "researcher": {"href": "https://publications.scilifelab.se/researcher/129ff8d1d877437fbf37f4180ea19fb4.json"}}, {"family": "Yong", "given": "Yean K", "initials": "YK"}, {"family": "Velu", "given": "Vijayakumar", "initials": "V", "orcid": "0000-0003-4238-1924", "researcher": {"href": "https://publications.scilifelab.se/researcher/61fbbd07ba5341f087bfcc958246792a.json"}}, {"family": "Raju", "given": "Sivadoss", "initials": "S"}, {"family": "Sj\u00f6wall", "given": "Johanna", "initials": "J", "orcid": "0000-0001-5622-866X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6442643a54484b3e9a6bfd586f2c27dc.json"}}, {"family": "Shankar", "given": "Esaki M", "initials": "EM", "orcid": "0000-0002-7866-9818", "researcher": {"href": "https://publications.scilifelab.se/researcher/1edec2d2bca84f3499109c5135436309.json"}}, {"family": "Nystr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0002-0145-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/93a23955db724558abca4e7ed1265067.json"}}, {"family": "Larsson", "given": "Marie", "initials": "M", "orcid": "0000-0002-4524-0177", "researcher": {"href": "https://publications.scilifelab.se/researcher/46874786a8de48668401faba73165750.json"}}], "type": "journal-article", "published": "2025-10-27", "journal": {"title": "Cells", "issn": "2073-4409", "issn-l": "2073-4409", "volume": "14", "issue": "21", "pages": "1673"}, "abstract": null, "doi": "10.3390/cells14211673", "pmid": null, "labels": {"Clinical Genomics": "Service", "Clinical Genomics Link\u00f6ping": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-30T12:39:09.525Z", "modified": "2025-10-30T12:40:16.743Z"}, {"entity": "publication", "iuid": "4e17395031e840d18135c925fc1214da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e17395031e840d18135c925fc1214da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e17395031e840d18135c925fc1214da"}}, "title": "methylR: a graphical interface for comprehensive DNA methylation array data analysis.", "authors": [{"family": "Volpe", "given": "Massimiliano", "initials": "M", "orcid": "0000-0003-4184-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/72a3bf9590054279985a2fbb287ef8ce.json"}}, {"family": "Das", "given": "Jyotirmoy", "initials": "J", "orcid": "0000-0002-5649-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebcbc4237c1c48aeb6bdd446fd8d2c8a.json"}}], "type": "journal article", "published": "2023-04-03", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "39", "issue": "4", "issn-l": "1367-4803"}, "abstract": "DNA methylation analysis using arrays is a widely used method in research and clinical studies to study Epigenetics. Although several packages have been published to incur the results, most of them require a deep computational knowledge to perform the analysis. To resolve the limitation and to offer an easily accessible solution for researchers, we developed methylR a graphical tool that can analyze not only the raw data but also performs different downstream analyses with a few mouse clicks.\n\nWe used standard and established open-source published packages or pipelines in methylR. We evaluated a publicly available dataset and compared the published results with those obtained with our tool. We implemented eight downstream analysis modules that can perform multidimensional analyses to pathway enrichment. Although the main application is designed for Illumina DNA methylation array data analysis, we made the accessory modules suitable for other kinds of data analysis as well.\n\nFreely available at Github: https://github.com/JD2112/methylr; Webserver: https://methylr.research.liu.se.", "doi": "10.1093/bioinformatics/btad184", "pmid": "37039839", "labels": {"Clinical Genomics Link\u00f6ping": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC10125902"}, {"db": "pii", "key": "7114023"}], "notes": [], "created": "2023-12-03T06:05:10.029Z", "modified": "2023-12-03T06:05:10.070Z"}, {"entity": "publication", "iuid": "b5b1cf7954344c1788417ce16b90c590", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b1cf7954344c1788417ce16b90c590.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b1cf7954344c1788417ce16b90c590"}}, "title": "miRNome and Proteome Profiling of Human Keratinocytes and Adipose Derived Stem Cells Proposed miRNA-Mediated Regulations of Epidermal Growth Factor and Interleukin 1-Alpha.", "authors": [{"family": "Shahin", "given": "Hady", "initials": "H", "orcid": "0000-0003-3894-6849", "researcher": {"href": "https://publications.scilifelab.se/researcher/19bc3853696c459980e4d71f4ba66687.json"}}, {"family": "Abdallah", "given": "Sallam", "initials": "S"}, {"family": "Das", "given": "Jyotirmoy", "initials": "J", "orcid": "0000-0002-5649-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebcbc4237c1c48aeb6bdd446fd8d2c8a.json"}}, {"family": "He", "given": "Weihai", "initials": "W"}, {"family": "El-Serafi", "given": "Ibrahim", "initials": "I", "orcid": "0000-0002-0463-1518", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3cc7696eeb4c82ac5115342730d11c.json"}}, {"family": "Steinvall", "given": "Ingrid", "initials": "I"}, {"family": "Sj\u00f6berg", "given": "Folke", "initials": "F"}, {"family": "Elmasry", "given": "Moustafa", "initials": "M"}, {"family": "El-Serafi", "given": "Ahmed T", "initials": "AT"}], "type": "journal article", "published": "2023-03-04", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "24", "issue": "5", "issn-l": null}, "abstract": "Wound healing is regulated by complex crosstalk between keratinocytes and other cell types, including stem cells. In this study, a 7-day direct co-culture model of human keratinocytes and adipose-derived stem cells (ADSCs) was proposed to study the interaction between the two cell types, in order to identify regulators of ADSCs differentiation toward the epidermal lineage. As major mediators of cell communication, miRNome and proteome profiles in cell lysates of cultured human keratinocytes and ADSCs were explored through experimental and computational analyses. GeneChip\u00ae miRNA microarray, identified 378 differentially expressed miRNAs; of these, 114 miRNAs were upregulated and 264 miRNAs were downregulated in keratinocytes. According to miRNA target prediction databases and the Expression Atlas database, 109 skin-related genes were obtained. Pathway enrichment analysis revealed 14 pathways including vesicle-mediated transport, signaling by interleukin, and others. Proteome profiling showed a significant upregulation of the epidermal growth factor (EGF) and Interleukin 1-alpha (IL-1\u03b1) compared to ADSCs. Integrated analysis through cross-matching the differentially expressed miRNA and proteins suggested two potential pathways for regulations of epidermal differentiation; the first is EGF-based through the downregulation of miR-485-5p and miR-6765-5p and/or the upregulation of miR-4459. The second is mediated by IL-1\u03b1 overexpression through four isomers of miR-30-5p and miR-181a-5p.", "doi": "10.3390/ijms24054956", "pmid": "36902387", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10002856"}, {"db": "pii", "key": "ijms24054956"}], "notes": [], "created": "2023-12-03T05:51:58.814Z", "modified": "2023-12-03T06:11:02.288Z"}]}