{"entity": "researcher", "timestamp": "2026-08-20T20:46:19.585Z", "family": "Sonnhammer", "given": "Erik L L", "initials": "ELL", "orcid": "0000-0002-9015-5588", "affiliations": ["Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden. erik.sonnhammer@scilifelab.se."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa"}}, "publications": [{"entity": "publication", "iuid": "db266b1ccdd74049aadbab1e57b95d65", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/db266b1ccdd74049aadbab1e57b95d65.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/db266b1ccdd74049aadbab1e57b95d65"}}, "title": "BiGSM: Bayesian inference of gene regulatory network via sparse modelling.", "authors": [{"family": "Qin", "given": "Hang", "initials": "H", "orcid": "0009-0009-0631-9382", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25090177f60341548b6cfb7fd7f99c23.json"}}, {"family": "Garbulowski", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-2497-194X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98de355d5a1247cebb494b16444857e6.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}, {"family": "Chatterjee", "given": "Saikat", "initials": "S", "orcid": "0000-0003-2638-6047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74fbfe174a984d059993042bdaace4fe.json"}}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "41", "issue": "6", "issn-l": "1367-4803"}, "abstract": "Inference of gene regulatory network (GRN) is challenging due to the inherent sparsity of the GRN matrix and noisy expression data, often leading to a high possibility of false positive or negative predictions. To address this, it is essential to leverage the sparsity of the GRN matrix and develop a robust method capable of handling varying levels of noise in the data. Moreover, most existing GRN inference methods produce only fixed point estimates, which lack the flexibility and informativeness for comprehensive network analysis. In contrast, a Bayesian approach that yields closed-form posterior distributions allows probabilistic link selection, offering insights into the statistical confidence of each possible link. Consequently, it is important to engineer a Bayesian GRN inference method and rigorously execute a benchmark evaluation compared to state-of-the-art methods.\n\nWe propose a method-Bayesian inference of GRN via Sparse Modelling (BiGSM). BiGSM effectively exploits the sparsity of the GRN matrix and infers the posterior distributions of GRN links from noisy expression data by using the maximum likelihood based learning. We thoroughly benchmarked BiGSM using biological and simulated datasets including GeneNetWeaver, GeneSPIDER, and GRNbenchmark. The benchmark test evaluates its accuracy and robustness across varying noise levels and data models. Using point-estimate based performance measures, BiGSM provides an overall best performance in comparison with several state-of-the-art methods including GENIE3, LASSO, LSCON, and Zscore. Additionally, BiGSM is the only method in the set of competing methods that provides posteriors for the GRN weights, helping to decipher confidence across predictions.\n\nCode implemented via MATLAB and Python are available at Github: https://github.com/SachLab/BiGSM and archived at zenodo.", "doi": "10.1093/bioinformatics/btaf318", "pmid": "40484997", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12151459"}, {"db": "pii", "key": "8158397"}], "notes": [], "created": "2026-08-20T09:40:03.146Z", "modified": "2026-08-20T09:40:03.268Z"}, {"entity": "publication", "iuid": "27e51c5d49b84d9a8e5d54b690400a59", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/27e51c5d49b84d9a8e5d54b690400a59.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/27e51c5d49b84d9a8e5d54b690400a59"}}, "title": "Topology-based metrics for finding the optimal sparsity in gene regulatory network inference.", "authors": [{"family": "Lundqvist", "given": "Nils", "initials": "N", "orcid": "0009-0004-7638-5979", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e3ded13534544249e258b6c63858cb1.json"}}, {"family": "Garbulowski", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-2497-194X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98de355d5a1247cebb494b16444857e6.json"}}, {"family": "Hillerton", "given": "Thomas", "initials": "T", "orcid": "0000-0002-6362-0659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07f7f1ec854d4c309f77524357f64400.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": "2025-05-06", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "41", "issue": "5", "issn-l": "1367-4803"}, "abstract": "Gene regulatory network (GRN) inference is a complex task aiming to unravel regulatory interactions between genes in a cell. A major shortcoming of most GRN inference methods is that they do not attempt to find the optimal sparsity, i.e. the single best GRN, which is important when applying GRN inference in a real situation. Instead, the sparsity tends to be controlled by an arbitrarily set hyperparameter.\n\nIn this paper, two new methods for predicting the optimal sparsity of GRNs are formulated and benchmarked on simulated perturbation-based gene expression data using four GRN inference methods: LASSO, Zscore, LSCON, and GENIE3. Both sparsity prediction methods are defined using the hypothesis that the topology of real GRNs is scale-free, and are evaluated based on their ability to predict the sparsity of the true GRN. The results show that the new topology-based approaches reliably predict a sparsity close to the true one. This ability is valuable for real-world applications where a single GRN is inferred from real data. In such situations, it is vital to be able to infer a GRN with the correct sparsity.\n\nhttps://bitbucket.org/sonnhammergrni/powerlaw_sparsity/ and https://codeocean.com/capsule/4393635/.", "doi": "10.1093/bioinformatics/btaf120", "pmid": "40127172", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12057811"}, {"db": "pii", "key": "8092552"}], "notes": [], "created": "2026-08-20T09:40:01.145Z", "modified": "2026-08-20T09:40:01.286Z"}, {"entity": "publication", "iuid": "ff35da2bc4f4453dae33069270afe937", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ff35da2bc4f4453dae33069270afe937.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ff35da2bc4f4453dae33069270afe937"}}, "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"}, {"family": "Guala", "given": "Dimitri", "initials": "D"}, {"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": "2025-01-06", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "D1", "pages": "D658-D671", "issn-l": "0305-1048"}, "abstract": "FunCoup 6 (https://funcoup.org) represents a significant advancement in global functional association networks, aiming to provide researchers with a comprehensive view of the functional coupling interactome. This update introduces novel methodologies and integrated tools for improved network inference and analysis. Major new developments in FunCoup 6 include vastly expanding the coverage of gene regulatory links, a new framework for bin-free Bayesian training and a new website. FunCoup 6 integrates a new tool for disease and drug target module identification using the TOPAS algorithm. To expand the utility of the resource for biomedical research, it incorporates pathway enrichment analysis using the ANUBIX and EASE algorithms. The unique comparative interactomics analysis in FunCoup provides insights of network conservation, now allowing users to align orthologs only or query each species network independently. Bin-free training was applied to 23 primary species, and in addition, networks were generated for all remaining 618 species in InParanoiDB 9. Accompanying these advancements, FunCoup 6 features a new redesigned website, together with updated API functionalities, and represents a pivotal step forward in functional genomics research, offering unique capabilities for exploring the complex landscape of protein interactions.", "doi": "10.1093/nar/gkae1021", "pmid": "39530220", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11701656"}, {"db": "pii", "key": "7893320"}], "notes": [], "created": "2026-08-20T09:50:02.208Z", "modified": "2026-08-20T09:50:02.262Z"}, {"entity": "publication", "iuid": "0245120d20b649f2a28ecde4508af4ce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0245120d20b649f2a28ecde4508af4ce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0245120d20b649f2a28ecde4508af4ce"}}, "title": "The FunCoup Cytoscape App: multi-species network analysis and visualization.", "authors": [{"family": "Buzzao", "given": "Davide", "initials": "D", "orcid": "0000-0002-7521-8368", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bb0116c6ce849c2a91d9f4e96246a42.json"}}, {"family": "Steininger", "given": "Lukas", "initials": "L"}, {"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": "journal article", "published": "2024-12-26", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "41", "issue": "1", "issn-l": "1367-4803"}, "abstract": "Functional association networks, such as FunCoup, are crucial for analyzing complex gene interactions. To facilitate the analysis and visualization of such genome-wide networks, there is a need for seamless integration with powerful network analysis tools like Cytoscape.\n\nThe FunCoup Cytoscape App integrates the FunCoup web service API with Cytoscape, allowing users to visualize and analyze gene interaction networks for 640 species. Users can input gene identifiers and customize search parameters, using various network expansion algorithms like group or independent gene search, MaxLink, and TOPAS. The app maintains consistent visualizations with the FunCoup website, providing detailed node and link information, including tissue and pathway gene annotations. The integration with Cytoscape plugins, such as ClusterMaker2, enhances the analytical capabilities of FunCoup, as exemplified by the identification of the Myasthenia gravis disease module along with potential new therapeutic targets.\n\nThe FunCoup Cytoscape App is developed using the Java OSGi framework, with UI components implemented in Java Swing and build support from Maven. The App is available as a JAR file at https://bitbucket.org/sonnhammergroup/funcoup_cytoscape/ repository, and can be downloaded from the Cytoscape App store https://apps.cytoscape.org/apps/funcoup.", "doi": "10.1093/bioinformatics/btae739", "pmid": "39700425", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11684335"}, {"db": "pii", "key": "7928839"}], "notes": [], "created": "2026-08-20T09:39:59.488Z", "modified": "2026-08-20T09:39:59.581Z"}, {"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": [], "xrefs": [{"db": "pmc", "key": "PMC11632614"}, {"db": "pii", "key": "lqae167"}], "notes": [], "created": "2026-08-20T09:43:00.453Z", "modified": "2026-08-20T09:43:00.602Z"}, {"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": "1a7101928225491895d8be1199482d92", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a7101928225491895d8be1199482d92.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a7101928225491895d8be1199482d92"}}, "title": "Benchmarking enrichment analysis methods with the disease pathway network", "authors": [{"family": "Buzzao", "given": "Davide", "initials": "D", "orcid": "0000-0002-7521-8368", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bb0116c6ce849c2a91d9f4e96246a42.json"}}, {"family": "Castresana-Aguirre", "given": "Miguel", "initials": "M", "orcid": "0000-0002-4665-6537", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/feea5e97a7094459a210636193ddf551.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": "2023-09-30", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.09.29.560169", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:48:12.556Z", "modified": "2026-08-20T10:48:12.661Z"}, {"entity": "publication", "iuid": "5ce610c132e144b3a80a22801a4af51f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ce610c132e144b3a80a22801a4af51f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ce610c132e144b3a80a22801a4af51f"}}, "title": "GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.", "authors": [{"family": "Se\u00e7ilmi\u015f", "given": "Deniz", "initials": "D", "orcid": "0000-0001-8284-356X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66278168a97a4e54a355f2514a9773c9.json"}}, {"family": "Hillerton", "given": "Thomas", "initials": "T", "orcid": "0000-0002-6362-0659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07f7f1ec854d4c309f77524357f64400.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": "2022-07-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "50", "issue": "W1", "pages": "W398-W404", "issn-l": "0305-1048"}, "abstract": "Accurate inference of gene regulatory networks (GRN) is an essential component of systems biology, and there is a constant development of new inference methods. The most common approach to assess accuracy for publications is to benchmark the new method against a selection of existing algorithms. This often leads to a very limited comparison, potentially biasing the results, which may stem from tuning the benchmark's properties or incorrect application of other methods. These issues can be avoided by a web server with a broad range of data properties and inference algorithms, that makes it easy to perform comprehensive benchmarking of new methods, and provides a more objective assessment. Here we present https://GRNbenchmark.org/ - a new web server for benchmarking GRN inference methods, which provides the user with a set of benchmarks with several datasets, each spanning a range of properties including multiple noise levels. As soon as the web server has performed the benchmarking, the accuracy results are made privately available to the user via interactive summary plots and underlying curves. The user can then download these results for any purpose, and decide whether or not to make them public to share with the community.", "doi": "10.1093/nar/gkac377", "pmid": "35609981", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9252735"}, {"db": "pii", "key": "6591524"}], "notes": [], "created": "2026-08-20T09:49:50.136Z", "modified": "2026-08-20T09:49:50.212Z"}, {"entity": "publication", "iuid": "9a81cb729e1c42df987c6cc4b52e6bba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9a81cb729e1c42df987c6cc4b52e6bba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9a81cb729e1c42df987c6cc4b52e6bba"}}, "title": "The Quest for Orthologs orthology benchmark service in 2022.", "authors": [{"family": "Nevers", "given": "Yannis", "initials": "Y", "orcid": "0000-0002-8604-2943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e5e2aea9cc2433c880a3d650d4d0d5b.json"}}, {"family": "Jones", "given": "Tamsin E M", "initials": "TEM", "orcid": "0000-0002-0027-0858", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/966feebf7e9a43aea11edf9a4b531c90.json"}}, {"family": "Jyothi", "given": "Dushyanth", "initials": "D"}, {"family": "Yates", "given": "Bethan", "initials": "B", "orcid": "0000-0003-1658-1762", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/410431d70e2c41fea12f78f38aa58402.json"}}, {"family": "Ferret", "given": "Meritxell", "initials": "M"}, {"family": "Portell-Silva", "given": "Laura", "initials": "L"}, {"family": "Codo", "given": "Laia", "initials": "L", "orcid": "0000-0002-6797-8746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/878c386adc4a4384bdea1e9f7a999832.json"}}, {"family": "Cosentino", "given": "Salvatore", "initials": "S"}, {"family": "Marcet-Houben", "given": "Marina", "initials": "M"}, {"family": "Vlasova", "given": "Anna", "initials": "A"}, {"family": "Poidevin", "given": "Laetitia", "initials": "L"}, {"family": "Kress", "given": "Arnaud", "initials": "A"}, {"family": "Hickman", "given": "Mark", "initials": "M"}, {"family": "Persson", "given": "Emma", "initials": "E"}, {"family": "Pili\u017eota", "given": "Ivana", "initials": "I"}, {"family": "Guijarro-Clarke", "given": "Cristina", "initials": "C"}, {"family": "OpenEBench team the Quest for Orthologs Consortium", "given": "", "initials": ""}, {"family": "Iwasaki", "given": "Wataru", "initials": "W", "orcid": "0000-0002-9169-9245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77399cc41820467ba6e32dd3ee6eaaec.json"}}, {"family": "Lecompte", "given": "Odile", "initials": "O"}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}, {"family": "Roos", "given": "David S", "initials": "DS"}, {"family": "Gabald\u00f3n", "given": "Toni", "initials": "T"}, {"family": "Thybert", "given": "David", "initials": "D"}, {"family": "Thomas", "given": "Paul D", "initials": "PD", "orcid": "0000-0002-9074-3507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4af1f8a10ced487196829d162e22d314.json"}}, {"family": "Hu", "given": "Yanhui", "initials": "Y", "orcid": "0000-0003-1494-1402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d048ac84bf934c9d87774c6cab7430c6.json"}}, {"family": "Emms", "given": "David M", "initials": "DM"}, {"family": "Bruford", "given": "Elspeth", "initials": "E", "orcid": "0000-0002-8380-5247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3202468144774f85b3b80bd1cba9c84e.json"}}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S", "orcid": "0000-0002-0309-604X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c76a6ff4986b42f58a0be702993eef42.json"}}, {"family": "Martin", "given": "Maria J", "initials": "MJ"}, {"family": "Dessimoz", "given": "Christophe", "initials": "C", "orcid": "0000-0002-2170-853X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d9dc970f3da45a4a46ecfdf4ab0893f.json"}}, {"family": "Altenhoff", "given": "Adrian", "initials": "A"}], "type": "meta-analysis", "published": "2022-07-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "50", "issue": "W1", "pages": "W623-W632", "issn-l": "0305-1048"}, "abstract": "The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.", "doi": "10.1093/nar/gkac330", "pmid": "35552456", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9252809"}, {"db": "pii", "key": "6584783"}], "notes": [], "created": "2026-08-20T09:49:48.053Z", "modified": "2026-08-20T09:49:48.299Z"}, {"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": "8627f49ef46548189c1c8658fdface5e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8627f49ef46548189c1c8658fdface5e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8627f49ef46548189c1c8658fdface5e"}}, "title": "PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk.", "authors": [{"family": "Ogris", "given": "Christoph", "initials": "C"}, {"family": "Castresana-Aguirre", "given": "Miguel", "initials": "M"}, {"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": "2022-04-28", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "38", "issue": "9", "pages": "2659-2660", "issn-l": "1367-4803"}, "abstract": "Pathway annotation tools are indispensable for the interpretation of a wide range of experiments in life sciences. Network-based algorithms have recently been developed which are more sensitive than traditional overlap-based algorithms, but there is still a lack of good online tools for network-based pathway analysis.\n\nWe present PathwAX II-a pathway analysis web tool based on network crosstalk analysis using the BinoX algorithm. It offers several new features compared with the first version, including interactive graphical network visualization of the crosstalk between a query gene set and an enriched pathway, and the addition of Reactome pathways.\n\nPathwAX II is available at http://pathwax.sbc.su.se.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btac153", "pmid": "35266519", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9048662"}, {"db": "pii", "key": "6546284"}], "notes": [], "created": "2026-08-20T09:39:32.955Z", "modified": "2026-08-20T09:39:33.019Z"}, {"entity": "publication", "iuid": "629f30362a644ded8147411333833e1e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/629f30362a644ded8147411333833e1e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/629f30362a644ded8147411333833e1e"}}, "title": "Fast and accurate gene regulatory network inference by normalized least squares regression.", "authors": [{"family": "Hillerton", "given": "Thomas", "initials": "T", "orcid": "0000-0002-6362-0659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07f7f1ec854d4c309f77524357f64400.json"}}, {"family": "Se\u00e7ilmi\u015f", "given": "Deniz", "initials": "D", "orcid": "0000-0001-8284-356X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66278168a97a4e54a355f2514a9773c9.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"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": "2022-04-12", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "38", "issue": "8", "pages": "2263-2268", "issn-l": "1367-4803"}, "abstract": "Inferring an accurate gene regulatory network (GRN) has long been a key goal in the field of systems biology. To do this, it is important to find a suitable balance between the maximum number of true positive and the minimum number of false-positive interactions. Another key feature is that the inference method can handle the large size of modern experimental data, meaning the method needs to be both fast and accurate. The Least Squares Cut-Off (LSCO) method can fulfill both these criteria, however as it is based on least squares it is vulnerable to known issues of amplifying extreme values, small or large. In GRN this manifests itself with genes that are erroneously hyper-connected to a large fraction of all genes due to extremely low value fold changes.\n\nWe developed a GRN inference method called Least Squares Cut-Off with Normalization (LSCON) that tackles this problem. LSCON extends the LSCO algorithm by regularization to avoid hyper-connected genes and thereby reduce false positives. The regularization used is based on normalization, which removes effects of extreme values on the fit. We benchmarked LSCON and compared it to Genie3, LASSO, LSCO and Ridge regression, in terms of accuracy, speed and tendency to predict hyper-connected genes. The results show that LSCON achieves better or equal accuracy compared to LASSO, the best existing method, especially for data with extreme values. Thanks to the speed of least squares regression, LSCON does this an order of magnitude faster than LASSO.\n\nData: https://bitbucket.org/sonnhammergrni/lscon; Code: https://bitbucket.org/sonnhammergrni/genespider.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btac103", "pmid": "35176145", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9004640"}, {"db": "pii", "key": "6530276"}], "notes": [], "created": "2026-08-20T09:39:30.922Z", "modified": "2026-08-20T09:39:31.022Z"}, {"entity": "publication", "iuid": "701b3b45ae43486bad194db59c33d076", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/701b3b45ae43486bad194db59c33d076.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/701b3b45ae43486bad194db59c33d076"}}, "title": "DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life.", "authors": [{"family": "Acevedo", "given": "Nathalie", "initials": "N", "orcid": "0000-0002-5154-2964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be22f41f7e6a4daaa896400aecc03938.json"}}, {"family": "Scala", "given": "Giovanni", "initials": "G"}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK"}, {"family": "Frumento", "given": "Paolo", "initials": "P"}, {"family": "Bruhn", "given": "S\u00f6ren", "initials": "S"}, {"family": "Andersson", "given": "Anna", "initials": "A"}, {"family": "Ogris", "given": "Christoph", "initials": "C"}, {"family": "Bottai", "given": "Matteo", "initials": "M"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH", "orcid": "0000-0001-8567-3252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e9a287e31a64ec1a4a3cfc3dab53c6c.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}, {"family": "Alm", "given": "Johan", "initials": "J", "orcid": "0000-0002-9062-4479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8a4f5b121e34f6480dacab9f9fe8729.json"}}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Greco", "given": "Dario", "initials": "D", "orcid": "0000-0001-9195-9003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db0acb9d0db7478fbd9c6a3719511918.json"}}, {"family": "Scheynius", "given": "Annika", "initials": "A", "orcid": "0000-0001-5520-990X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c815af1a90f7440da03fbc06347fa9cd.json"}}], "type": "journal article", "published": "2021-01-14", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "2", "issn-l": null}, "abstract": "DNA methylation changes may predispose becoming IgE-sensitized to allergens. We analyzed whether DNA methylation in peripheral blood mononuclear cells (PBMC) is associated with IgE sensitization at 5 years of age (5Y). DNA methylation was measured in 288 PBMC samples from 74 mother/child pairs from the birth cohort ALADDIN (Assessment of Lifestyle and Allergic Disease During INfancy) using the HumanMethylation450BeadChip (Illumina). PBMCs were obtained from the mothers during pregnancy and from their children in cord blood, at 2 years and 5Y. DNA methylation levels at each time point were compared between children with and without IgE sensitization to allergens at 5Y. For replication, CpG sites associated with IgE sensitization in ALADDIN were evaluated in whole blood DNA of 256 children, 4 years old, from the BAMSE (Swedish abbreviation for Children, Allergy, Milieu, Stockholm, Epidemiology) cohort. We found 34 differentially methylated regions (DMRs) associated with IgE sensitization to airborne allergens and 38 DMRs associated with sensitization to food allergens in children at 5Y (Sidak p \u2264 0.05). Genes associated with airborne sensitization were enriched in the pathway of endocytosis, while genes associated with food sensitization were enriched in focal adhesion, the bacterial invasion of epithelial cells, and leukocyte migration. Furthermore, 25 DMRs in maternal PBMCs were associated with IgE sensitization to airborne allergens in their children at 5Y, which were functionally annotated to the mTOR (mammalian Target of Rapamycin) signaling pathway. This study supports that DNA methylation is associated with IgE sensitization early in life and revealed new candidate genes for atopy. Moreover, our study provides evidence that maternal DNA methylation levels are associated with IgE sensitization in the child supporting early in utero effects on atopy predisposition.", "doi": "10.3390/ijms22020801", "pmid": "33466918", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7830007"}, {"db": "pii", "key": "ijms22020801"}], "notes": [], "created": "2026-08-20T13:41:17.886Z", "modified": "2026-08-20T13:41:18.096Z"}, {"entity": "publication", "iuid": "96fba7af607f44b38a3a053ee3540397", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/96fba7af607f44b38a3a053ee3540397.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/96fba7af607f44b38a3a053ee3540397"}}, "title": "Drug repurposing improves disease targeting 11-fold on average. New insights from network module targeting and its application to COVID-19.", "authors": [{"family": "Rivero", "given": "In\u00e9s", "initials": "I"}, {"family": "Castresana", "given": "Miguel", "initials": "M"}, {"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", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}], "type": "posted-content", "published": "2020-11-13", "journal": {"issn-l": null}, "abstract": null, "doi": "10.31219/osf.io/4rvaz", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:04:15.573Z", "modified": "2026-08-20T13:04:15.608Z"}, {"entity": "publication", "iuid": "f21d910ecaca414e84e9ae52c1d0f35c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f21d910ecaca414e84e9ae52c1d0f35c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f21d910ecaca414e84e9ae52c1d0f35c"}}, "title": "Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data.", "authors": [{"family": "Se\u00e7ilmi\u015f", "given": "Deniz", "initials": "D", "orcid": "0000-0001-8284-356X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66278168a97a4e54a355f2514a9773c9.json"}}, {"family": "Hillerton", "given": "Thomas", "initials": "T"}, {"family": "Morgan", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8326-6178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae01d9b1d3c487eb66e5379b0faa35e.json"}}, {"family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0064-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4d51b0b08948cd8be856ec4c0a50b2.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Nordling", "given": "Torbj\u00f6rn E M", "initials": "TEM", "orcid": "0000-0003-4867-6707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ff2e55d28354900a39b69cb1de8c532.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": "2020-11-09", "journal": {"title": "NPJ Syst Biol Appl", "issn": "2056-7189", "volume": "6", "issue": "1", "pages": "37", "issn-l": "2056-7189"}, "abstract": "The interactions among the components of a living cell that constitute the gene regulatory network (GRN) can be inferred from perturbation-based gene expression data. Such networks are useful for providing mechanistic insights of a biological system. In order to explore the feasibility and quality of GRN inference at a large scale, we used the L1000 data where ~1000 genes have been perturbed and their expression levels have been quantified in 9 cancer cell lines. We found that these datasets have a very low signal-to-noise ratio (SNR) level causing them to be too uninformative to infer accurate GRNs. We developed a gene reduction pipeline in which we eliminate uninformative genes from the system using a selection criterion based on SNR, until reaching an informative subset. The results show that our pipeline can identify an informative subset in an overall uninformative dataset, allowing inference of accurate subset GRNs. The accurate GRNs were functionally characterized and potential novel cancer-related regulatory interactions were identified.", "doi": "10.1038/s41540-020-00154-6", "pmid": "33168813", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7652823"}, {"db": "pii", "key": "10.1038/s41540-020-00154-6"}], "notes": [], "created": "2026-08-20T08:54:42.056Z", "modified": "2026-08-20T08:54:42.243Z"}, {"entity": "publication", "iuid": "ca66623f75d44a9c91f1349be35a46a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ca66623f75d44a9c91f1349be35a46a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ca66623f75d44a9c91f1349be35a46a1"}}, "title": "Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms", "authors": [{"family": "Morgan", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8326-6178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae01d9b1d3c487eb66e5379b0faa35e.json"}}, {"family": "Studham", "given": "Matthew", "initials": "M", "orcid": "0000-0001-9147-4882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3686d0959484118916f9cd826b25d9a.json"}}, {"family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0064-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4d51b0b08948cd8be856ec4c0a50b2.json"}}, {"family": "Weishaupt", "given": "Holger", "initials": "H", "orcid": "0000-0002-0364-2709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ae643d4831f469c95c3d5b3955784ea.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e673fa8c86348fb8c1a2ae34ba7ba9a.json"}}, {"family": "Nordling", "given": "Torbj\u00f6rn E M", "initials": "TEM", "orcid": "0000-0003-4867-6707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ff2e55d28354900a39b69cb1de8c532.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": "2019-08-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/735514", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:14:40.679Z", "modified": "2026-08-20T11:14:40.832Z"}]}