{"entity": "researcher", "timestamp": "2026-06-17T06:42:04.818Z", "family": "Pareja Sanchez", "given": "Yerma", "initials": "Y", "orcid": "0000-0003-2008-5390", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e"}}, "publications": [{"entity": "publication", "iuid": "f5f0ff606e2a4674a4f16cdfe99c6a19", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f5f0ff606e2a4674a4f16cdfe99c6a19.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f5f0ff606e2a4674a4f16cdfe99c6a19"}}, "title": "Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells.", "authors": [{"family": "Geng", "given": "Keyi", "initials": "K", "orcid": "0000-0003-0892-7460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a56ac387ab324409b2c0dc24b9be5d73.json"}}, {"family": "Merino", "given": "Lara G", "initials": "LG", "orcid": "0000-0002-7208-953X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e989808f60c4a60861c99df3ec9ac25.json"}}, {"family": "Wedemann", "given": "Linda", "initials": "L", "orcid": "0000-0003-1096-9037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ed2d03a9efe42838005d02101aa1591.json"}}, {"family": "Martens", "given": "Aniek", "initials": "A", "orcid": "0000-0002-0291-0281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9fa7441c1f24c4689fa884748cb1722.json"}}, {"family": "Sobota", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Sanchez", "given": "Yerma P", "initials": "YP", "orcid": "0000-0003-2008-5390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e.json"}}, {"family": "S\u00f8ndergaard", "given": "Jonas N\u00f8rskov", "initials": "JN", "orcid": "0000-0002-4438-6756", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85be14546c6e4c28a3171880521ed29c.json"}}, {"family": "White", "given": "Robert J", "initials": "RJ", "orcid": "0000-0002-9631-7760", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a36167f04c94e29a973b9155083e6d9.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4c9dcde56304ab2a99bb1032e4ce834.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Genome Res", "issn": "1549-5469", "volume": "32", "issue": "10", "pages": "1876-1891", "issn-l": "1088-9051"}, "abstract": "The CRISPR-Cas9 system is widely used to permanently delete genomic regions via dual guide RNAs. Genomic rearrangements induced by CRISPR-Cas9 can occur, but continuous technical developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Furthermore, we found that these genomic alterations led to functional aberrant DNA fragments and can alter cell proliferation. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations, and introduce a data-driven workflow enabling detailed dissection of the on-target sequence content with superior resolution.", "doi": "10.1101/gr.276901.122", "pmid": "36180232", "labels": {"SciLifeLab Fellow": null, "Claudia Kutter": null}, "xrefs": [{"db": "pii", "key": "gr.276901.122"}], "notes": [], "created": "2022-11-28T11:18:35.200Z", "modified": "2022-11-28T11:18:35.507Z"}, {"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"}, {"entity": "publication", "iuid": "5ae608853bc545c9b08e1b8c6a0abab9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae608853bc545c9b08e1b8c6a0abab9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae608853bc545c9b08e1b8c6a0abab9"}}, "title": "Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.", "authors": [{"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Hennig", "given": "Bianca P", "initials": "BP", "orcid": "0000-0002-7733-8160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c64ef90520aa408c8c2ed17fae8fd95c.json"}}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Zhang", "given": "Yujie", "initials": "Y", "orcid": "0000-0002-4926-028X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782.json"}}, {"family": "Piazza", "given": "Ilaria", "initials": "I", "orcid": "0000-0001-5895-6134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5258dce396444d9a8f5e5bc2fd13b282.json"}}, {"family": "Pareja Sanchez", "given": "Yerma", "initials": "Y", "orcid": "0000-0003-2008-5390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e.json"}}, {"family": "Chabbert", "given": "Christophe D", "initials": "CD", "orcid": "0000-0001-7851-4640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/490051f9ae674750a4dd3ee10c27b2b0.json"}}, {"family": "Adjalley", "given": "Sophie H", "initials": "SH", "orcid": "0000-0002-5666-7088", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0ba3a91cf9b4039a83e915d1698e581.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.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": "2019-12-00", "journal": {"title": "Genome Res", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "29", "issue": "12", "pages": "1974-1984"}, "abstract": "Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site (TSS) usage, chromatin organization, and posttranscriptional consequences in Saccharomyces cerevisiae We show that TSSs of chromatin-sensitive internal cryptic transcripts retain comparable features of canonical TSSs in terms of DNA sequence, directionality, and chromatin accessibility. We define the 5' and 3' boundaries of cryptic transcripts and show that, contrary to RNA degradation-sensitive ones, they often overlap with the end of the gene, thereby using the canonical polyadenylation site, and associate to polyribosomes. We show that chromatin-sensitive cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Finally, we confirm the presence of the predicted polypeptides by reanalyzing N-terminal proteomic data sets. Our work suggests that a fraction of chromatin-sensitive internal cryptic promoters initiates the transcription of alternative truncated mRNA isoforms. The expression of these chromatin-sensitive isoforms is conserved from yeast to human, expanding the functional consequences of cryptic transcription and proteome complexity.", "doi": "10.1101/gr.243378.118", "pmid": "31740578", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "gr.243378.118"}, {"db": "pmc", "key": "PMC6886497"}], "notes": [], "created": "2020-11-08T15:49:22.722Z", "modified": "2022-11-04T11:32:15.727Z"}]}