{"entity": "researcher", "timestamp": "2026-08-20T19:46:13.322Z", "family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "affiliations": ["Department of Immunotechnology, Lund University, Lund, Sweden.", "National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c"}}, "publications": [{"entity": "publication", "iuid": "2691943b505045888090b9a21c80fda0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2691943b505045888090b9a21c80fda0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2691943b505045888090b9a21c80fda0"}}, "title": "Effects of acute cold and heat shocks on the protein profile of crayfish hemolymph: Implications for crustacean adaptation to thermal stress", "authors": [{"family": "Mengal", "given": "Kifayatullah", "initials": "K"}, {"family": "Kor", "given": "Golara", "initials": "G"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Niksirat", "given": "Hamid", "initials": "H", "orcid": "0000-0003-3782-4954", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04537c6d5bbd494dac909ea633c3dc20.json"}}], "type": "journal-article", "published": "2026-03-00", "journal": {"title": "Aquaculture Reports", "issn": "2352-5134", "volume": "46", "pages": "103265", "issn-l": null}, "abstract": null, "doi": "10.1016/j.aqrep.2025.103265", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:42:29.797Z", "modified": "2026-08-20T09:36:12.560Z"}, {"entity": "publication", "iuid": "c71c4efd6da042d3a605ae0b9a03e558", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c71c4efd6da042d3a605ae0b9a03e558.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c71c4efd6da042d3a605ae0b9a03e558"}}, "title": "Considerations and Software for Successful Immune Cell Deconvolution Using Proteomics Data.", "authors": [{"family": "Zamore", "given": "M\u00e5ns", "initials": "M", "orcid": "0000-0002-8108-1097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07cf9b490bd94f01acb56bcfac8cd0da.json"}}, {"family": "Junior", "given": "Sergio Mosquim", "initials": "SM"}, {"family": "Andree", "given": "Sebastian L", "initials": "SL"}, {"family": "Altunbulakli", "given": "Can", "initials": "C"}, {"family": "Lindstedt", "given": "Malin", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2025-08-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "8", "pages": "3751-3761", "issn-l": "1535-3893"}, "abstract": "Inferring the cell-type composition of bulk samples can provide biological insight. While bulk transcriptomics data has been extensively used for this purpose, the use of proteomics data has remained unexplored until recently. This study evaluates computational approaches for estimating immune cell composition using bulk sample proteomics data. Leveraging defined immune cell populations and simulated mixtures, we assess the impact of preprocessing methods and software tools on cell deconvolution outcomes. Our findings demonstrate the feasibility of using proteomics data for cell-type deconvolution, with Pearson correlations for estimated proportions in simulated sample mixtures above 0.9 when employing optimal missing value imputation and reference matrix generation parameters. We further provide an R package, proteoDeconv, to facilitate the preprocessing of proteomics data for deconvolution and parsing of results. This study highlights the feasibility of using proteomics for analyzing cell-type composition in biological samples.", "doi": "10.1021/acs.jproteome.4c00868", "pmid": "40657748", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12322953"}], "notes": [], "created": "2026-08-20T08:11:58.900Z", "modified": "2026-08-20T08:11:58.994Z"}, {"entity": "publication", "iuid": "f4d8d306cc8340e09e37b45ecd1cd98e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f4d8d306cc8340e09e37b45ecd1cd98e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f4d8d306cc8340e09e37b45ecd1cd98e"}}, "title": "Sex programs functional protein level dimorphism in the zebrafish gastrointestinal tract", "authors": [{"family": "Niksirat", "given": "Hamid", "initials": "H"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Steinbach", "given": "Christoph", "initials": "C"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "Aquaculture Reports", "issn": "2352-5134", "volume": "42", "pages": "102775", "issn-l": null}, "abstract": null, "doi": "10.1016/j.aqrep.2025.102775", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:42:27.840Z", "modified": "2026-08-20T06:42:27.893Z"}, {"entity": "publication", "iuid": "9ff913d912d34f9a8d8e78ea5577c8bd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ff913d912d34f9a8d8e78ea5577c8bd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ff913d912d34f9a8d8e78ea5577c8bd"}}, "title": "Multiomic profiling of metastatic potential in estrogen receptor-positive human epidermal growth factor-negative breast cancer", "authors": [{"family": "Mosquim", "given": "Sergio", "initials": "S", "orcid": "0000-0002-1537-7252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08836688b1b74eeab88cda7b3ed3e488.json"}}, {"family": "Zamore", "given": "M\u00e5ns", "initials": "M"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a79aa63d75d4ffbb4228bc7c3e16ac4.json"}}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e40f8cbccd87481991010cc506b901fa.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "posted-content", "published": "2025-01-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.01.22.25320944", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:00:36.538Z", "modified": "2026-08-20T11:00:36.663Z"}, {"entity": "publication", "iuid": "62a99fdbaecc406ba1c205c490123d10", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62a99fdbaecc406ba1c205c490123d10.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62a99fdbaecc406ba1c205c490123d10"}}, "title": "Automated multiplexed affinity-based enrichment of peptides for LC-MS/MS plasma proteomics.", "authors": [{"family": "Junior", "given": "Sergio Mosquim", "initials": "SM"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "24", "issue": "21-22", "pages": "e2400049", "issn-l": "1615-9853"}, "abstract": "Plasma proteomics offers high potential for biomarker discovery, as plasma is collected through a minimally invasive procedure and constitutes the most complex human-derived proteome. However, the wide dynamic range poses a significant challenge. Here, we propose a semi-automated method based on the use of multiple single chain variable fragment antibodies, each enriching for peptides found in up to a few hundred proteins. This approach allows for the analysis of a complementary fraction compared to full proteome analysis. Proteins from pooled plasma were extracted and digested before testing the performance of 29 different antibodies with the aim of reproducibly maximizing peptide enrichment. Our results demonstrate the enrichment of 3662 peptides not detected in neat plasma or negative controls. Moreover, most antibodies were able to enrich for at least 155 peptides across different levels of abundance in plasma. To further reduce analysis time, a combination of antibodies was used in a multiplexed setting. Repeated sample analyses showed low coefficients of variation, and the method is flexible in terms of affinity binders. It does not impose drastic increases in instrument time, thus showing excellent potential for usage in large scale discovery projects.", "doi": "10.1002/pmic.202400049", "pmid": "39192483", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:34:53.004Z", "modified": "2026-08-20T06:34:53.097Z"}, {"entity": "publication", "iuid": "3bdf9df99988436aa514c33ba81f0de5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3bdf9df99988436aa514c33ba81f0de5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3bdf9df99988436aa514c33ba81f0de5"}}, "title": "OmicLoupe: Facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons", "authors": [{"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "posted-content", "published": "2020-10-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.10.22.349944", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:59:36.844Z", "modified": "2026-08-20T09:59:56.088Z"}]}