{"entity": "label", "iuid": "f584b7687e784e24846e86c11d779923", "timestamp": "2026-09-25T10:36:01.280Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/label/Sina%20Majidian.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/label/Sina%20Majidian"}}, "value": "Sina Majidian", "created": "2026-09-22T09:24:39.886Z", "modified": "2026-09-22T09:24:39.890Z", "accounts": [{"entity": "account", "iuid": "4869cac89efa4395ababeb15e93296c8", "timestamp": "2026-09-25T10:36:01.280Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/sina.majidian%40chalmers.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/sina.majidian%40chalmers.se"}}, "email": "sina.majidian@chalmers.se", "name": "Sina Majidian", "orcid": "0000-0001-5345-6982", "role": "curator", "status": "enabled", "login": "2026-09-22T09:52:03.085Z", "created": "2026-09-22T09:29:22.123Z", "modified": "2026-09-22T09:52:03.085Z"}], "publications_count": 4, "publications": [{"entity": "publication", "iuid": "78eccb6848ac4f06a062d6477b8da5ec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/78eccb6848ac4f06a062d6477b8da5ec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/78eccb6848ac4f06a062d6477b8da5ec"}}, "title": "Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.", "authors": [{"family": "Majidian", "given": "Sina", "initials": "S"}, {"family": "Hadziahmetovic", "given": "Armin", "initials": "A"}, {"family": "Langschied", "given": "Felix", "initials": "F"}, {"family": "Pascarelli", "given": "Stefano", "initials": "S"}, {"family": "Prieto-Ba\u00f1os", "given": "Silvia", "initials": "S"}, {"family": "Rojas-Vargas", "given": "Jorge", "initials": "J"}, {"family": "Quest for Orthologs Consortium", "given": "", "initials": ""}, {"family": "Braun", "given": "Edward L", "initials": "EL"}, {"family": "Dessimoz", "given": "Christophe", "initials": "C"}, {"family": "Diallo", "given": "Abdoulaye Banir\u00e9", "initials": "AB"}, {"family": "Durand", "given": "Dannie", "initials": "D"}, {"family": "Fang", "given": "Gang", "initials": "G"}, {"family": "Gabald\u00f3n", "given": "Toni", "initials": "T"}, {"family": "Glover", "given": "Natasha", "initials": "N"}, {"family": "Liberles", "given": "David A", "initials": "DA"}, {"family": "McWhite", "given": "Claire", "initials": "C"}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}, {"family": "Thomas", "given": "Paul D", "initials": "PD"}, {"family": "Ouangraoua", "given": "A\u00efda", "initials": "A"}, {"family": "Julca", "given": "Irene", "initials": "I", "orcid": "0000-0002-1332-7948", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ede1363f1a34109844cd5672b82991d.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "J. Mol. Evol.", "issn": "1432-1432", "volume": "93", "issue": "6", "pages": "702-719", "issn-l": "0022-2844"}, "abstract": "The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthology plays a crucial role in understanding evolutionary patterns of genes and their functions. At the last Quest for Orthologs meeting (Montr\u00e9al, Canada-2024), we discussed recent advances in orthology inference, with a focus on the impact of artificial intelligence (AI), protein structures, RNA splicing isoforms, and protein domain evolution together with other evolutionary considerations. A long-standing challenge in the field is the functional annotation of paralogs, for which we present novel approaches. The meeting also emphasised strategies for integrating diverse genetic features into the concept of orthology, encouraging frameworks that account for elements like alternative splicing, domain organisation, and regulatory sequences. We discuss various applications of orthology and paralogy to environmental research, agriculture, and comparative genomics. Additionally, we report recent progress in orthology inference methodologies and resources. This work represents a collaborative synthesis of insights and innovations presented at the 8th Quest for Orthologs meeting, highlighting current progress while outlining future directions for orthology research.", "doi": "10.1007/s00239-025-10272-6", "pmid": "41085653", "labels": {"Sina Majidian": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12756340"}, {"db": "pii", "key": "10.1007/s00239-025-10272-6"}], "notes": [], "created": "2026-08-20T06:39:19.074Z", "modified": "2026-09-23T11:34:22.079Z"}, {"entity": "publication", "iuid": "0f940366e32a487088053ca05174d12e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0f940366e32a487088053ca05174d12e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0f940366e32a487088053ca05174d12e"}}, "title": "Accurate and Robust Characterization of Structural Variants at Low Coverages with ARCLID", "authors": [{"family": "Tavakoli", "given": "Sajad", "initials": "S", "orcid": "0000-0002-0510-6491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5aae5d84417c4fc0a0ece3be48bd1d5d.json"}}, {"family": "Frandsen", "given": "Rasmus John Normand", "initials": "RJN", "orcid": "0000-0002-3799-6062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee6354f31a7549d78b3ab988338d58d0.json"}}, {"family": "Majidian", "given": "Sina", "initials": "S", "orcid": "0000-0001-5345-6982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a14f17e8c2dc470dae5250c36d32cb27.json"}}, {"family": "Mansourvar", "given": "Marjan", "initials": "M", "orcid": "0000-0001-6492-7858", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d5ba9c3906e4b9babd2e839a86d0e8b.json"}}], "type": "posted-content", "published": "2025-10-13", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.10.10.681591", "pmid": null, "labels": {"Sina Majidian": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T15:51:54.433Z", "modified": "2026-09-23T15:51:54.585Z"}, {"entity": "publication", "iuid": "5e29e009d86b4cb781d38abaee53167a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5e29e009d86b4cb781d38abaee53167a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5e29e009d86b4cb781d38abaee53167a"}}, "title": "New developments for the Quest for Orthologs benchmark service.", "authors": [{"family": "Altenhoff", "given": "Adrian", "initials": "A"}, {"family": "Nevers", "given": "Yannis", "initials": "Y", "orcid": "0000-0002-8604-2943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e5e2aea9cc2433c880a3d650d4d0d5b.json"}}, {"family": "Tran", "given": "Vinh", "initials": "V"}, {"family": "Jyothi", "given": "Dushyanth", "initials": "D"}, {"family": "Martin", "given": "Maria", "initials": "M"}, {"family": "Cosentino", "given": "Salvatore", "initials": "S"}, {"family": "Majidian", "given": "Sina", "initials": "S", "orcid": "0000-0001-5345-6982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a14f17e8c2dc470dae5250c36d32cb27.json"}}, {"family": "Marcet-Houben", "given": "Marina", "initials": "M"}, {"family": "Fuentes-Palacios", "given": "Diego", "initials": "D"}, {"family": "Persson", "given": "Emma", "initials": "E"}, {"family": "Walsh", "given": "Thomas", "initials": "T"}, {"family": "Lecompte", "given": "Odile", "initials": "O"}, {"family": "Gabald\u00f3n", "given": "Toni", "initials": "T"}, {"family": "Kelly", "given": "Steven", "initials": "S"}, {"family": "Hu", "given": "Yanhui", "initials": "Y", "orcid": "0000-0003-1494-1402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d048ac84bf934c9d87774c6cab7430c6.json"}}, {"family": "Iwasaki", "given": "Wataru", "initials": "W"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S", "orcid": "0000-0002-0309-604X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c76a6ff4986b42f58a0be702993eef42.json"}}, {"family": "Dessimoz", "given": "Christophe", "initials": "C", "orcid": "0000-0002-2170-853X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d9dc970f3da45a4a46ecfdf4ab0893f.json"}}, {"family": "Thomas", "given": "Paul D", "initials": "PD", "orcid": "0000-0002-9074-3507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4af1f8a10ced487196829d162e22d314.json"}}, {"family": "Ebersberger", "given": "Ingo", "initials": "I", "orcid": "0000-0001-8187-9253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/946c40da21e441d196dd8b88ea126df0.json"}}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "6", "issue": "4", "pages": "lqae167", "issn-l": null}, "abstract": "The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose.", "doi": "10.1093/nargab/lqae167", "pmid": "39664814", "labels": {"Sina Majidian": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11632614"}, {"db": "pii", "key": "lqae167"}], "notes": [], "created": "2026-08-20T09:43:00.453Z", "modified": "2026-09-23T11:26:36.697Z"}, {"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": {"Sina Majidian": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11523110"}, {"db": "pii", "key": "7822254"}], "notes": [], "created": "2026-08-20T09:41:22.699Z", "modified": "2026-09-23T09:05:59.758Z"}]}