{"entity": "researcher", "timestamp": "2026-03-16T23:46:37.001Z", "family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "affiliations": ["European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany", "Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA", "Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce"}}, "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": "127ab2b4417f4ac0ace77e0f2c278dbc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc"}}, "title": "TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.", "authors": [{"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}}, {"family": "Marques", "given": "Sueli", "initials": "S", "orcid": "0000-0003-3368-4392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36fa155444764068a6515a6ec93a7a2e.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.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": "2020-10-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "48", "issue": "18", "pages": "e104"}, "abstract": "Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5' and 3' ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5' and 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.", "doi": "10.1093/nar/gkaa691", "pmid": "32816037", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "5894951"}, {"db": "pmc", "key": "PMC7544212"}], "notes": [], "created": "2020-11-08T15:50:59.020Z", "modified": "2022-11-04T11:32:14.267Z"}, {"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"}]}