{"entity": "researcher", "timestamp": "2026-09-26T10:51:45.930Z", "family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "affiliations": ["Department of Medicine Huddinge, Karolinska Institutet, Campus Flemingsberg, 141 57, Huddinge, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8445850c3b445fa943ed6ba07e067ae.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8445850c3b445fa943ed6ba07e067ae"}}, "publications": [{"entity": "publication", "iuid": "9cdf7c8a82b1465d849a66081af28154", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9cdf7c8a82b1465d849a66081af28154.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9cdf7c8a82b1465d849a66081af28154"}}, "title": "Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.", "authors": [{"family": "ElBeck", "given": "Zaher", "initials": "Z", "orcid": "0000-0002-2073-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48553b3e67484f1c9e49d739c9c0f116.json"}}, {"family": "Hossain", "given": "Mohammad Bakhtiar", "initials": "MB", "orcid": "0000-0002-4251-1912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b89cb5c684040c9a606fa9b9bb3bc6c.json"}}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8445850c3b445fa943ed6ba07e067ae.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}, {"family": "Karlsson", "given": "Fredrik", "initials": "F"}, {"family": "Lindgren", "given": "Julia", "initials": "J", "orcid": "0000-0002-3566-2069", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92fe93e1a4d74881b321eb1d5862ad13.json"}}, {"family": "Walentinsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-8100-6866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/797735271bf74245b1a10a4787f4012b.json"}}, {"family": "Koppenh\u00f6fer", "given": "Dominique", "initials": "D", "orcid": "0000-0001-5807-9645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b89f9f99c4b84c589989f487c687404e.json"}}, {"family": "Jarvis", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-7583-6548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8285affdb30e4cd1820772d117091492.json"}}, {"family": "B\u00fcrli", "given": "Roland", "initials": "R"}, {"family": "Jamier", "given": "Tanguy", "initials": "T", "orcid": "0000-0003-3014-3662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e000ba32ca3b477a94fd71158ace0ac1.json"}}, {"family": "Franssen", "given": "Elske", "initials": "E"}, {"family": "Firth", "given": "Mike", "initials": "M"}, {"family": "Degasperi", "given": "Andrea", "initials": "A", "orcid": "0000-0001-6879-0596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e573208fcac413daaa45356742b8bc7.json"}}, {"family": "Bendtsen", "given": "Claus", "initials": "C", "orcid": "0000-0002-8338-987X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a9cc68df47c421cb91251bd0ae8f044.json"}}, {"family": "Menzies", "given": "Robert I", "initials": "RI"}, {"family": "Streckfuss-B\u00f6meke", "given": "Katrin", "initials": "K"}, {"family": "Kohlhaas", "given": "Michael", "initials": "M"}, {"family": "Nickel", "given": "Alexander G", "initials": "AG"}, {"family": "Lund", "given": "Lars H", "initials": "LH"}, {"family": "Maack", "given": "Christoph", "initials": "C", "orcid": "0000-0003-3694-4559", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11b10117c83d49b3a57c747f1e06cef7.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C", "orcid": "0000-0002-8494-971X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7839aedc01354442a552955542cfc754.json"}}], "type": "journal article", "published": "2024-03-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "2358", "issn-l": "2041-1723"}, "abstract": "While excessive production of reactive oxygen species (ROS) is a characteristic hallmark of numerous diseases, clinical approaches that ameliorate oxidative stress have been unsuccessful. Here, utilizing multi-omics, we demonstrate that in cardiomyocytes, mitochondrial isocitrate dehydrogenase (IDH2) constitutes a major antioxidative defense mechanism. Paradoxically reduced expression of IDH2 associated with ventricular eccentric hypertrophy is counterbalanced by an increase in the enzyme activity. We unveil redox-dependent sex dimorphism, and extensive mutual regulation of the antioxidative activities of IDH2 and NRF2 by a feedforward network that involves 2-oxoglutarate and L-2-hydroxyglutarate and mediated in part through unconventional hydroxy-methylation of cytosine residues present in introns. Consequently, conditional targeting of ROS in a murine model of heart failure improves cardiac function in sex- and phenotype-dependent manners. Together, these insights may explain why previous attempts to treat heart failure with antioxidants have been unsuccessful and open new approaches to personalizing and, thereby, improving such treatment.", "doi": "10.1038/s41467-024-46384-8", "pmid": "38509128", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10954618"}, {"db": "pii", "key": "10.1038/s41467-024-46384-8"}], "notes": [], "created": "2026-09-23T11:24:20.939Z", "modified": "2026-09-23T11:24:21.368Z"}, {"entity": "publication", "iuid": "16036fa1c0b64ab499213e393d942cdd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/16036fa1c0b64ab499213e393d942cdd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/16036fa1c0b64ab499213e393d942cdd"}}, "title": "BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.", "authors": [{"family": "H\u00f6jer", "given": "Pontus", "initials": "P", "orcid": "0000-0001-8010-4755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afb5a8540e974734891c8f88c759621e.json"}}, {"family": "Frick", "given": "Tobias", "initials": "T", "orcid": "0000-0002-3174-2096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/617cb9ad52644d2b9a8dba637794269e.json"}}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8445850c3b445fa943ed6ba07e067ae.json"}}, {"family": "Pourbozorgi", "given": "Parham", "initials": "P", "orcid": "0000-0002-5957-627X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/955b26ba09f14bb6b24f5baa0e1f93f5.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18e3c4a868c9443c94d37c27a1b77dfb.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A", "orcid": "0000-0001-7837-8597", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2398880adbc149478b2b1c61453ca535.json"}}], "type": "journal article", "published": "2023-12-11", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "51", "issue": "22", "pages": "e114", "issn-l": "0305-1048"}, "abstract": "Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. We introduce Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10\u00d7 Genomics, TELL-seq and stLFR. Running BLR on DBS linked-reads yielded megabase-scale phasing with low (<0.2%) switch error rates. Of 13616 protein-coding genes phased in the GIAB benchmark set (v4.2.1), 98.6% matched the BLR phasing. In addition, large structural variants showed concordance with HPRC-HG002 reference assembly calls. Compared to diploid assembly with PacBio HiFi reads, BLR phasing was more continuous when considering switch errors. We further show that integrating long reads at low coverage (\u223c10\u00d7) can improve phasing contiguity and reduce switch errors in tandem repeats. When compared to Long Ranger on 10\u00d7 Genomics data, BLR showed an increase in phase block N50 with low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications. In conclusion, BLR provides a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.", "doi": "10.1093/nar/gkad1010", "pmid": "37941142", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10711428"}, {"db": "pii", "key": "7369811"}], "notes": [], "created": "2026-09-23T13:01:27.888Z", "modified": "2026-09-23T13:01:28.056Z"}, {"entity": "publication", "iuid": "306545c56c82485a9ec2b03a43e7e1f1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/306545c56c82485a9ec2b03a43e7e1f1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/306545c56c82485a9ec2b03a43e7e1f1"}}, "title": "Epigenetic modulators link mitochondrial redox homeostasis to cardiac function", "authors": [{"family": "Elbeck", "given": "Zaher", "initials": "Z", "orcid": "0000-0002-2073-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48553b3e67484f1c9e49d739c9c0f116.json"}}, {"family": "Hossain", "given": "Mohammad Bakhtiar", "initials": "MB"}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8445850c3b445fa943ed6ba07e067ae.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}, {"family": "Karlsson", "given": "Fredrik", "initials": "F"}, {"family": "Lindgren", "given": "Julia", "initials": "J", "orcid": "0000-0002-3566-2069", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92fe93e1a4d74881b321eb1d5862ad13.json"}}, {"family": "Walentinsson", "given": "Anna", "initials": "A"}, {"family": "Remedios", "given": "Cristobal Dos", "initials": "CD", "orcid": "0000-0003-1052-7490", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82a0a2bc0dfc4bd5a3b6a38e7836d855.json"}}, {"family": "Koppenh\u00f6fer", "given": "Dominique", "initials": "D"}, {"family": "Jarvis", "given": "Rebecca", "initials": "R"}, {"family": "B\u00fcrli", "given": "Roland", "initials": "R", "orcid": "0000-0001-7377-7628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89f1321756914da8aa7fcdb1bd0461e8.json"}}, {"family": "Jamier", "given": "Tanguy", "initials": "T"}, {"family": "Franssen", "given": "Elske", "initials": "E"}, {"family": "Firth", "given": "Mike", "initials": "M"}, {"family": "Degasperi", "given": "Andrea", "initials": "A", "orcid": "0000-0001-6879-0596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e573208fcac413daaa45356742b8bc7.json"}}, {"family": "Bendtsen", "given": "Claus", "initials": "C"}, {"family": "Dudek", "given": "Jan", "initials": "J"}, {"family": "Kohlhaas", "given": "Michael", "initials": "M", "orcid": "0000-0001-6132-6037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f6246ec3d140538e80a8ae471aac6d.json"}}, {"family": "Nickel", "given": "Alexander G", "initials": "AG"}, {"family": "Lund", "given": "Lars H", "initials": "LH", "orcid": "0000-0003-1411-4482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/639cd7c0a5dc40bc82dbf8ee90e0c1a0.json"}}, {"family": "Maack", "given": "Christoph", "initials": "C", "orcid": "0000-0003-3694-4559", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11b10117c83d49b3a57c747f1e06cef7.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C", "orcid": "0000-0002-8494-971X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7839aedc01354442a552955542cfc754.json"}}], "type": "posted-content", "published": "2022-03-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.03.26.485908", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:12:20.932Z", "modified": "2026-09-23T15:12:21.129Z"}]}