{"entity": "researcher", "timestamp": "2026-07-20T22:11:39.233Z", "family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "affiliations": ["SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodav\u00e4gen 23A, 17165, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee"}}, "publications": [{"entity": "publication", "iuid": "76699bd557614e69bccb6e73592cd4a7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76699bd557614e69bccb6e73592cd4a7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76699bd557614e69bccb6e73592cd4a7"}}, "title": "Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs.", "authors": [{"family": "Tayyab", "given": "Muhammad", "initials": "M", "orcid": "0000-0002-4372-504X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fbced44ff6847fab3b50a830f44abc4.json"}}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "van Riel", "given": "Gijs", "initials": "G"}, {"family": "Liu", "given": "Shujing", "initials": "S", "orcid": "0000-0002-5783-4204", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efd66c143bda4ad68ba21cd6e2319e15.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Scharfe", "given": "Curt", "initials": "C", "orcid": "0000-0001-6322-2039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/151a81585ba4445793d52cf41934b10e.json"}}, {"family": "Griffin", "given": "Peter", "initials": "P"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Javanmard", "given": "Mehdi", "initials": "M", "orcid": "0000-0002-6297-392X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1208a771a4fa451d92a74c76aa6032b2.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2023-09-08", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "36", "pages": "eadi4997", "issn-l": "2375-2548"}, "abstract": "Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, \u03b2-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour).", "doi": "10.1126/sciadv.adi4997", "pmid": "37672583", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10482329"}], "notes": [], "created": "2023-11-23T09:13:47.169Z", "modified": "2023-11-23T09:13:47.417Z"}, {"entity": "publication", "iuid": "c0cf16af36db4481865c4c6ccffb5d75", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c0cf16af36db4481865c4c6ccffb5d75.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c0cf16af36db4481865c4c6ccffb5d75"}}, "title": "Atlas of mRNA translation and decay for bacteria.", "authors": [{"family": "Huch", "given": "Susanne", "initials": "S", "orcid": "0000-0003-3956-7197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0b94cf87e4243efa8e6229f49403d0f.json"}}, {"family": "Nersisyan", "given": "Lilit", "initials": "L", "orcid": "0000-0001-8525-420X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c77363d1fa7f4ea6b50c22590c23a163.json"}}, {"family": "Ropat", "given": "Maria", "initials": "M"}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "Wu", "given": "Mengjun", "initials": "M"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Valeriano", "given": "Valerie D", "initials": "VD", "orcid": "0000-0002-4396-346X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c444998f561a43e8a8a8295b5ead218b.json"}}, {"family": "Vardazaryan", "given": "Nelli", "initials": "N", "orcid": "0000-0002-7972-8912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dabc3fd207b54423bf21dcbee3ca03ee.json"}}, {"family": "Huerta-Cepas", "given": "Jaime", "initials": "J", "orcid": "0000-0003-4195-5025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c8c00b0396840c480fa3f57a376ce00.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2023-05-22", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276"}, "abstract": "Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA decay intermediates (5'P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5'-3' exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5'-3' exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5'P degradome) sequencing approach, we characterize 5'P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5'P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.", "doi": "10.1038/s41564-023-01393-z", "pmid": "37217719", "labels": {"SciLifeLab Fellow": null, "Vicent Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-023-01393-z"}], "notes": [], "created": "2023-05-29T07:36:18.693Z", "modified": "2023-05-29T07:36:18.872Z"}, {"entity": "publication", "iuid": "9be1ae6123ae437e8fde8d91b37b6931", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9be1ae6123ae437e8fde8d91b37b6931.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9be1ae6123ae437e8fde8d91b37b6931"}}, "title": "OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.", "authors": [{"family": "Alekseenko", "given": "Alisa", "initials": "A", "orcid": "0000-0002-4269-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85f8ac2ec1a54cf79e4b1fbfc8a44aaf.json"}}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "4", "issue": "2", "pages": "lqac048", "issn-l": null}, "abstract": "Detection of low-frequency DNA variants (below 1%) is becoming increasingly important in biomedical research and clinical practice, but is challenging to do with standard sequencing approaches due to high error rates. The use of double-stranded unique molecular identifiers (dsUMIs) allows correction of errors by comparing reads arising from the same original DNA duplex. However, the implementation of such approaches is still challenging. Here, we present a novel method, one-pot dsUMI sequencing (OPUSeq), which allows incorporation of dsUMIs in the same reaction as the library PCR. This obviates the need for adapter pre-synthesis or additional enzymatic steps. OPUSeq can be incorporated into standard DNA library preparation approaches and coupled with hybridization target capture. We demonstrate successful error correction and detection of variants down to allele frequency of 0.01%. Using OPUSeq, we also show that the use of enzymatic fragmentation can lead to the appearance of spurious double-stranded variants, interfering with detection of variant fractions below 0.1%.", "doi": "10.1093/nargab/lqac048", "pmid": "35769342", "labels": {"SciLifeLab Fellow": null, "Vicent Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC9235115"}, {"db": "pii", "key": "lqac048"}], "notes": [], "created": "2022-11-25T19:21:46.596Z", "modified": "2022-11-25T19:21:46.668Z"}, {"entity": "publication", "iuid": "b07323c92b2a46a7abf1df532fe692c2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b07323c92b2a46a7abf1df532fe692c2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b07323c92b2a46a7abf1df532fe692c2"}}, "title": "Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples.", "authors": [{"family": "Alekseenko", "given": "Alisa", "initials": "A", "orcid": "0000-0002-4269-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85f8ac2ec1a54cf79e4b1fbfc8a44aaf.json"}}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "Pareja-Sanchez", "given": "Yerma", "initials": "Y", "orcid": "0000-0003-2008-5390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Strandback", "given": "Emilia", "initials": "E"}, {"family": "Ampah-Korsah", "given": "Henry", "initials": "H", "orcid": "0000-0002-8363-1697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5f166b865a7483c88415aa9c607d039.json"}}, {"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U", "orcid": "0000-0001-5889-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0ab87a8712f4ad886da61c1edcf679f.json"}}, {"family": "Zuniga-Veliz", "given": "Silvia", "initials": "S"}, {"family": "Klenov", "given": "Alexander", "initials": "A"}, {"family": "Malloo", "given": "Jayshna", "initials": "J"}, {"family": "Ye", "given": "Shenglong", "initials": "S"}, {"family": "Liu", "given": "Xiyang", "initials": "X"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faaf7145e4044091a2fed9069f56b92e.json"}}, {"family": "Nyman", "given": "Tomas", "initials": "T"}, {"family": "Sandh", "given": "Gustaf", "initials": "G"}, {"family": "Yin", "given": "Xiushan", "initials": "X", "orcid": "0000-0001-8124-7387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10f57a1b340547ebb74092bd2c6acdfe.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2021-01-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "1820", "issn-l": "2045-2322"}, "abstract": "RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.", "doi": "10.1038/s41598-020-80352-8", "pmid": "33469065", "labels": {"Vicent Pelechano": null, "Simon Els\u00e4sser": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-80352-8"}, {"db": "pmc", "key": "PMC7815738"}], "notes": [], "created": "2021-12-02T18:33:50.940Z", "modified": "2022-11-04T11:32:13.725Z"}]}