{"entity": "researcher", "timestamp": "2026-08-20T20:37:13.266Z", "family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "affiliations": ["Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 17121, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6"}}, "publications": [{"entity": "publication", "iuid": "9b255b8a99944228a707e155419fd870", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b255b8a99944228a707e155419fd870.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b255b8a99944228a707e155419fd870"}}, "title": "Quest for Orthologs in the Era of Biodiversity Genomics.", "authors": [{"family": "Langschied", "given": "Felix", "initials": "F", "orcid": "0009-0004-3348-3130", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1a6e133f7fe44bf96dd05a90d8fc273.json"}}, {"family": "Bordin", "given": "Nicola", "initials": "N", "orcid": "0000-0002-6568-9035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ec6e6c9fb67478580b946a6ecae062b.json"}}, {"family": "Cosentino", "given": "Salvatore", "initials": "S", "orcid": "0000-0002-1066-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99f2695b80684c87addfbc751534e7d7.json"}}, {"family": "Fuentes-Palacios", "given": "Diego", "initials": "D", "orcid": "0000-0002-9977-6786", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc15167b6b1943a3a07e911fef77b942.json"}}, {"family": "Glover", "given": "Natasha", "initials": "N", "orcid": "0000-0003-1811-4340", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe6ec892c5404ac3a0aaf4e8ac907ee9.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Hu", "given": "Yanhui", "initials": "Y", "orcid": "0000-0003-1494-1402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d048ac84bf934c9d87774c6cab7430c6.json"}}, {"family": "Huerta-Cepas", "given": "Jaime", "initials": "J", "orcid": "0000-0003-4195-5025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c8c00b0396840c480fa3f57a376ce00.json"}}, {"family": "Coelho", "given": "Luis Pedro", "initials": "LP", "orcid": "0000-0002-9280-7885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3630792233fd4118b12a548dba98f8bc.json"}}, {"family": "Iwasaki", "given": "Wataru", "initials": "W", "orcid": "0000-0002-9169-9245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77399cc41820467ba6e32dd3ee6eaaec.json"}}, {"family": "Majidian", "given": "Sina", "initials": "S", "orcid": "0000-0001-5345-6982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a14f17e8c2dc470dae5250c36d32cb27.json"}}, {"family": "Manzano-Morales", "given": "Saioa", "initials": "S", "orcid": "0000-0001-5138-3871", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c23facda0fef49a8a038195ac49b6ee2.json"}}, {"family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}}, {"family": "Richards", "given": "Thomas A", "initials": "TA", "orcid": "0000-0002-9692-0973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4778e4e15ce4ce6af7a4f07b27943b9.json"}}, {"family": "Gabald\u00f3n", "given": "Toni", "initials": "T", "orcid": "0000-0003-0019-1735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ae849222ff5490d816ec645b9e3cda3.json"}}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}, {"family": "Thomas", "given": "Paul D", "initials": "PD", "orcid": "0000-0002-9074-3507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4af1f8a10ced487196829d162e22d314.json"}}, {"family": "Dessimoz", "given": "Christophe", "initials": "C", "orcid": "0000-0002-2170-853X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d9dc970f3da45a4a46ecfdf4ab0893f.json"}}, {"family": "Ebersberger", "given": "Ingo", "initials": "I", "orcid": "0000-0001-8187-9253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/946c40da21e441d196dd8b88ea126df0.json"}}], "type": "journal article", "published": "2024-10-09", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "10", "issn-l": "1759-6653"}, "abstract": "The era of biodiversity genomics is characterized by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life. In summary, the expanding datasets create a need for scalable gene annotation methods. To trace gene function across species, new methods must seek to increase the resolution of ortholog analyses, e.g. by extending analyses to the protein domain level and by accounting for alternative splicing. Additionally, the scope of orthology prediction should be pushed beyond well-investigated proteomes. This demands the development of specialized methods for the identification of orthologs to short proteins and noncoding RNAs and for the functional characterization of novel gene families. Furthermore, protein structures predicted by machine learning are now readily available, but this new information is yet to be integrated with orthology-based analyses. Finally, an increasing focus should be placed on making orthology assignments adhere to the findable, accessible, interoperable, and reusable (FAIR) principles. This fosters green bioinformatics by avoiding redundant computations and helps integrating diverse scientific communities sharing the need for comparative genetics and genomics information. It should also help with communicating orthology-related concepts in a format that is accessible to the public, to counteract existing misinformation about evolution.", "doi": "10.1093/gbe/evae224", "pmid": "39404012", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11523110"}, {"db": "pii", "key": "7822254"}], "notes": [], "created": "2026-08-20T09:41:22.699Z", "modified": "2026-08-20T09:41:23.293Z"}, {"entity": "publication", "iuid": "a9a869a3e5e54e9c9f401934ebd69587", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a9a869a3e5e54e9c9f401934ebd69587.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a9a869a3e5e54e9c9f401934ebd69587"}}, "title": "FunCoup 6: advancing functional association networks across species with directed links and improved user experience", "authors": [{"family": "Buzzao", "given": "Davide", "initials": "D", "orcid": "0000-0002-7521-8368", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bb0116c6ce849c2a91d9f4e96246a42.json"}}, {"family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}}, {"family": "Guala", "given": "Dimitri", "initials": "D", "orcid": "0000-0003-2245-7557", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851c00c1c0464dfa89973933c7e8e0c5.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}], "type": "posted-content", "published": "2024-09-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.09.13.612391", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:58:29.104Z", "modified": "2026-08-20T10:58:29.176Z"}, {"entity": "publication", "iuid": "280b00d630644e1499835cbcfef0ecb5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/280b00d630644e1499835cbcfef0ecb5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/280b00d630644e1499835cbcfef0ecb5"}}, "title": "InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.", "authors": [{"family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}], "type": "journal article", "published": "2022-05-13", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "38", "issue": "10", "pages": "2918-2919", "issn-l": "1367-4803"}, "abstract": "Predicting orthologs, genes in different species having shared ancestry, is an important task in bioinformatics. Orthology prediction tools are required to make accurate and fast predictions, in order to analyze large amounts of data within a feasible time frame. InParanoid is a well-known algorithm for orthology analysis, shown to perform well in benchmarks, but having the major limitation of long runtimes on large datasets. Here, we present an update to the InParanoid algorithm that can use the faster tool DIAMOND instead of BLAST for the homolog search step. We show that it reduces the runtime by 94%, while still obtaining similar performance in the Quest for Orthologs benchmark.\n\nThe source code is available at (https://bitbucket.org/sonnhammergroup/inparanoid).\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btac194", "pmid": "35561192", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9113356"}, {"db": "pii", "key": "6585430"}], "notes": [], "created": "2026-08-20T09:39:35.183Z", "modified": "2026-08-20T09:39:35.261Z"}, {"entity": "publication", "iuid": "cb820107a9644d72934e001260a8f979", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cb820107a9644d72934e001260a8f979.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cb820107a9644d72934e001260a8f979"}}, "title": "PathBIX-a web server for network-based pathway annotation with adaptive null models.", "authors": [{"family": "Castresana-Aguirre", "given": "Miguel", "initials": "M"}, {"family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}], "type": "journal article", "published": "2021-07-01", "journal": {"title": "Bioinform Adv", "issn": "2635-0041", "volume": "1", "issue": "1", "pages": "vbab010", "issn-l": null}, "abstract": "Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, utilize biological networks to gain a richer source of information as a basis of the analysis than merely the gene content. Network-based methods use the network crosstalk between the query gene set and the genes in known pathways, and compare this to a null model of random expectation.\n\nWe developed PathBIX, a novel web application for network-based pathway analysis, based on the recently published ANUBIX algorithm which has been shown to be more accurate than previous network-based methods. The PathBIX website performs pathway annotation for 21 species, and utilizes prefetched and preprocessed network data from FunCoup 5.0 networks and pathway data from three databases: KEGG, Reactome, and WikiPathways.\n\nhttps://pathbix.sbc.su.se/.\n\nerik.sonnhammer@scilifelab.se.\n\nSupplementary data are available at Bioinformatics Advances online.", "doi": "10.1093/bioadv/vbab010", "pmid": "36700096", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9710673"}, {"db": "pii", "key": "vbab010"}], "notes": [], "created": "2026-08-20T09:39:06.725Z", "modified": "2026-08-20T09:39:06.811Z"}, {"entity": "publication", "iuid": "5770ea4ec02f42038b295bb3f5382a2b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5770ea4ec02f42038b295bb3f5382a2b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5770ea4ec02f42038b295bb3f5382a2b"}}, "title": "Domainoid: domain-oriented orthology inference.", "authors": [{"family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}}, {"family": "Kaduk", "given": "Mateusz", "initials": "M"}, {"family": "Forslund", "given": "Sofia K", "initials": "SK"}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}], "type": "journal article", "published": "2019-10-28", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "20", "issue": "1", "pages": "523", "issn-l": "1471-2105"}, "abstract": "Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been shown that orthologous proteins may differ in domain architecture, creating challenges for orthology inference methods operating on full-length sequences. We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. It employs the InParanoid algorithm on single domains separately, to infer groups of orthologous domains.\n\nThis domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories. In addition to domain level analysis, protein level orthology based on the fraction of domains that are orthologous can be inferred. Domainoid orthology assignments were compared to those yielded by the conventional full-length approach InParanoid, and were validated in a standard benchmark.\n\nOur results show that domain-based orthology inference can reveal many orthologous relationships that are not found by full-length sequence approaches.\n\nhttps://bitbucket.org/sonnhammergroup/domainoid/.", "doi": "10.1186/s12859-019-3137-2", "pmid": "31660857", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6816169"}, {"db": "pii", "key": "10.1186/s12859-019-3137-2"}], "notes": [], "created": "2026-08-20T12:19:31.702Z", "modified": "2026-08-20T12:19:31.760Z"}]}