{"entity": "researcher", "timestamp": "2026-08-20T20:39:20.350Z", "family": "Wilmes", "given": "Paul", "initials": "P", "orcid": "0000-0002-6478-2924", "affiliations": ["Luxembourg Centre for Systems Biomedicine , University of Luxembourg , 6 avenue du Swing , L-4367 Belvaux , Luxembourg."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/e169727cc0f9482baf98944388a77b24.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/e169727cc0f9482baf98944388a77b24"}}, "publications": [{"entity": "publication", "iuid": "91405623b285409eabccccde8100a0bc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/91405623b285409eabccccde8100a0bc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/91405623b285409eabccccde8100a0bc"}}, "title": "Integration of multiple flexible electrodes for real-time detection of barrier formation with spatial resolution in a gut-on-chip system.", "authors": [{"family": "Lucchetti", "given": "Mara", "initials": "M", "orcid": "0000-0002-3057-983X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a64adffc16d94185884350098ebb11dd.json"}}, {"family": "Werr", "given": "Gabriel", "initials": "G", "orcid": "0000-0001-9503-5481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90e0ce9e278f4c44b8125dd84758f573.json"}}, {"family": "Johansson", "given": "Sofia", "initials": "S", "orcid": "0000-0003-3672-9883", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d976bdc17d7248d6b60c4f7a47fc84c7.json"}}, {"family": "Barbe", "given": "Laurent", "initials": "L", "orcid": "0000-0003-4475-6478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9b28e1a0e95432881ff25ae35da88d4.json"}}, {"family": "Grandmougin", "given": "L\u00e9a", "initials": "L"}, {"family": "Wilmes", "given": "Paul", "initials": "P", "orcid": "0000-0002-6478-2924", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e169727cc0f9482baf98944388a77b24.json"}}, {"family": "Tenje", "given": "Maria", "initials": "M", "orcid": "0000-0002-1264-1337", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd13273274574923b354ca9c605efc8f.json"}}], "type": "journal article", "published": "2024-01-24", "journal": {"title": "Microsyst. Nanoeng.", "issn": "2055-7434", "volume": "10", "pages": "18", "issn-l": null}, "abstract": "In healthy individuals, the intestinal epithelium forms a tight barrier to prevent gut bacteria from reaching blood circulation. To study the effect of probiotics, dietary compounds and drugs on gut barrier formation and disruption, human gut epithelial and bacterial cells can be cocultured in an in vitro model called the human microbial crosstalk (HuMiX) gut-on-a-chip system. Here, we present the design, fabrication and integration of thin-film electrodes into the HuMiX platform to measure transepithelial electrical resistance (TEER) as a direct readout on barrier tightness in real-time. As various aspects of the HuMiX platform have already been set in their design, such as multiple compressible layers, uneven surfaces and nontransparent materials, a novel fabrication method was developed whereby thin-film metal electrodes were first deposited on flexible substrates and sequentially integrated with the HuMiX system via a transfer-tape approach. Moreover, to measure localized TEER along the cell culture chamber, we integrated multiple electrodes that were connected to an impedance analyzer via a multiplexer. We further developed a dynamic normalization method because the active measurement area depends on the measured TEER levels. The fabrication process and system setup can be applicable to other barrier-on-chip systems. As a proof-of-concept, we measured the barrier formation of a cancerous Caco-2 cell line in real-time, which was mapped at four spatially separated positions along the HuMiX culture area.", "doi": "10.1038/s41378-023-00640-x", "pmid": "38268774", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10805851"}, {"db": "pii", "key": "640"}], "notes": [], "created": "2026-08-20T08:48:03.488Z", "modified": "2026-08-20T08:48:03.647Z"}, {"entity": "publication", "iuid": "ea525cca041145b7bdfe210040715780", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780"}}, "title": "Expanding the Use of Spectral Libraries in Proteomics.", "authors": [{"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Chalkley", "given": "Robert J", "initials": "RJ"}, {"family": "Wilhelm", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9224-3258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eda8473072c48639cbd09676ed17cfe.json"}}, {"family": "Tate", "given": "Stephen", "initials": "S"}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Walzer", "given": "Mathias", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Delanghe", "given": "Bernard", "initials": "B"}, {"family": "B\u00f6cker", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9304-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c71ab14b72a540f3be202f873d6c7dea.json"}}, {"family": "Schymanski", "given": "Emma L", "initials": "EL", "orcid": "0000-0001-6868-8145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc533a4744624b80960f4cf28cabdd64.json"}}, {"family": "Wilmes", "given": "Paul", "initials": "P", "orcid": "0000-0002-6478-2924", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e169727cc0f9482baf98944388a77b24.json"}}, {"family": "Dorfer", "given": "Viktoria", "initials": "V", "orcid": "0000-0002-5332-5701", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2a0a15b0b2945238e7a39343b5c2a29.json"}}, {"family": "Kuster", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9094-1677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5196477f29b345ccb3f4a8fc32c9fac4.json"}}, {"family": "Volders", "given": "Pieter-Jan", "initials": "PJ", "orcid": "0000-0002-2685-2637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fac44563b164dae90052b9764a8f9ab.json"}}, {"family": "Jehmlich", "given": "Nico", "initials": "N", "orcid": "0000-0002-5638-6868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1c3e5702c6740c6a4d553b60eee62e3.json"}}, {"family": "Vissers", "given": "Johannes P C", "initials": "JPC", "orcid": "0000-0001-6283-8456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cde55fba2234534a8ce709f13478e42.json"}}, {"family": "Wolan", "given": "Dennis W", "initials": "DW", "orcid": "0000-0001-9879-8353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/635cea76374a4c90a9514aa845b7f59c.json"}}, {"family": "Wang", "given": "Ana Y", "initials": "AY"}, {"family": "Mendoza", "given": "Luis", "initials": "L", "orcid": "0000-0003-0128-8643", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6e8a7feab0f481eaf6acd7ec097c5c5.json"}}, {"family": "Shofstahl", "given": "Jim", "initials": "J"}, {"family": "Dowsey", "given": "Andrew W", "initials": "AW", "orcid": "0000-0002-7404-9128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1cb70e527d84d32b1e995014007efb8.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Salek", "given": "Reza M", "initials": "RM", "orcid": "0000-0001-8604-1732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62799f5748ef484b816827380b723b2c.json"}}, {"family": "Neumann", "given": "Steffen", "initials": "S", "orcid": "0000-0002-7899-7192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fd85c99a6364305ba466010ed3012ec.json"}}, {"family": "Binz", "given": "Pierre-Alain", "initials": "PA", "orcid": "0000-0002-0045-7698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f857e16ce82b4242ab0e780c8bec9539.json"}}, {"family": "Lam", "given": "Henry", "initials": "H", "orcid": "0000-0001-7928-0364", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f27cfbc77fe4122977457e89968814c.json"}}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81245410f3234e658147bc94f6b3dad2.json"}}, {"family": "Bandeira", "given": "Nuno", "initials": "N"}, {"family": "R\u00f6st", "given": "Hannes", "initials": "H", "orcid": "0000-0003-0990-7488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4579af772375404da76c447b23c658a3.json"}}], "type": "journal article", "published": "2018-12-07", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "17", "issue": "12", "pages": "4051-4060", "issn-l": "1535-3893"}, "abstract": "The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.", "doi": "10.1021/acs.jproteome.8b00485", "pmid": "30270626", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1015163"}, {"db": "pmc", "key": "PMC6443480"}], "notes": [], "created": "2026-08-20T08:12:14.655Z", "modified": "2026-08-20T08:12:15.306Z"}]}