{"entity": "researcher", "timestamp": "2026-08-20T20:26:47.497Z", "family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "affiliations": ["Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, Box 337, SE-75105, Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134"}}, "publications": [{"entity": "publication", "iuid": "265b7e96c4b0486d8b82f61266b9af90", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/265b7e96c4b0486d8b82f61266b9af90.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/265b7e96c4b0486d8b82f61266b9af90"}}, "title": "Dimensionality reduction of genetic data using contrastive learning.", "authors": [{"family": "Thor", "given": "Filip", "initials": "F", "orcid": "0009-0008-5041-3256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0529b14435b641aca02e5d387b45245a.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "journal article", "published": "2026-01-07", "journal": {"title": "Genetics", "issn": "1943-2631", "volume": "232", "issue": "1", "issn-l": "0016-6731"}, "abstract": "We introduce a framework for using contrastive learning for dimensionality reduction on genetic datasets to create principal component analysis (PCA)-like population visualizations. Contrastive learning is a self-supervised deep learning method that uses similarities between samples to train the neural network to discriminate between samples. Many of the advances in these types of models have been made for computer vision, but some common methodology does not translate well from image to genetic data. We define a loss function that outperforms loss functions commonly used in contrastive learning, and a data augmentation scheme tailored specifically towards SNP genotype datasets. We compare the performance of our method to PCA and contemporary nonlinear methods with respect to how well they preserve local and global structure, and how well they generalize to new data. Our method displays good preservation of global structure and has improved generalization properties over t-distributed stochastic neighbor embedding, Uniform Manifold Approximation and Projection, and popvae, while preserving relative distances between individuals to a high extent. A strength of the deep learning framework is the possibility of projecting new samples and fine-tuning to new datasets using a pretrained model without access to the original training data, and the ability to incorporate more domain-specific information in the model. We show examples of population classification on two datasets of dog and human genotypes.", "doi": "10.1093/genetics/iyaf068", "pmid": "40194517", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12774828"}, {"db": "pii", "key": "8107861"}], "notes": [], "created": "2026-08-20T09:41:28.977Z", "modified": "2026-08-20T09:41:29.075Z"}, {"entity": "publication", "iuid": "af66cb1019c54909a606f289f5a4b74a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/af66cb1019c54909a606f289f5a4b74a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/af66cb1019c54909a606f289f5a4b74a"}}, "title": "Dimensionality Reduction of Genetic Data using Contrastive Learning", "authors": [{"family": "Thor", "given": "Filip", "initials": "F", "orcid": "0009-0008-5041-3256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0529b14435b641aca02e5d387b45245a.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "posted-content", "published": "2024-10-02", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.09.30.615901", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:58:42.079Z", "modified": "2026-08-20T10:58:42.112Z"}, {"entity": "publication", "iuid": "3cbddbb141294cffa470d8b4f017e95e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3cbddbb141294cffa470d8b4f017e95e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3cbddbb141294cffa470d8b4f017e95e"}}, "title": "Observation of a single protein by ultrafast X-ray diffraction.", "authors": [{"family": "Ekeberg", "given": "Tomas", "initials": "T"}, {"family": "Assalauova", "given": "Dameli", "initials": "D"}, {"family": "Bielecki", "given": "Johan", "initials": "J", "orcid": "0000-0002-3012-603X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb981ea4fae1468fbf068f2b4b509c75.json"}}, {"family": "Boll", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-6286-4064", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11394aae9c824504bd45759deb2a7a76.json"}}, {"family": "Daurer", "given": "Benedikt J", "initials": "BJ", "orcid": "0000-0002-1887-7551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22e1c4b4b7fc427f9069efa4b1486d47.json"}}, {"family": "Eichacker", "given": "Lutz A", "initials": "LA"}, {"family": "Franken", "given": "Linda E", "initials": "LE", "orcid": "0000-0002-3040-8192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31a6b4279ad742e2b2078fb4b81b0967.json"}}, {"family": "Galli", "given": "Davide E", "initials": "DE", "orcid": "0000-0002-1312-1181", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70c549226f6d4264850608b3250dd0ba.json"}}, {"family": "Gelisio", "given": "Luca", "initials": "L"}, {"family": "Gumprecht", "given": "Lars", "initials": "L"}, {"family": "Gunn", "given": "Laura H", "initials": "LH"}, {"family": "Hajdu", "given": "Janos", "initials": "J"}, {"family": "Hartmann", "given": "Robert", "initials": "R", "orcid": "0000-0003-1839-5365", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11ce7ef4cc4f4c9f93d775dca73b40df.json"}}, {"family": "Hasse", "given": "Dirk", "initials": "D"}, {"family": "Ignatenko", "given": "Alexandr", "initials": "A"}, {"family": "Koliyadu", "given": "Jayanath", "initials": "J", "orcid": "0000-0002-0245-3842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbd250665f634af0a3643eb5ec8d1f87.json"}}, {"family": "Kulyk", "given": "Olena", "initials": "O"}, {"family": "Kurta", "given": "Ruslan", "initials": "R"}, {"family": "Kuster", "given": "Markus", "initials": "M", "orcid": "0000-0002-4361-7102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe962434b1de4f538c4752079e817360.json"}}, {"family": "Lugmayr", "given": "Wolfgang", "initials": "W", "orcid": "0000-0001-8501-8637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82a88df5177d400e969989f8f41b42bc.json"}}, {"family": "L\u00fcbke", "given": "Jannik", "initials": "J"}, {"family": "Mancuso", "given": "Adrian P", "initials": "AP"}, {"family": "Mazza", "given": "Tommaso", "initials": "T"}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}, {"family": "Ovcharenko", "given": "Yevheniy", "initials": "Y"}, {"family": "Rivas", "given": "Daniel E", "initials": "DE", "orcid": "0000-0002-7540-4902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e69eed8791a54c81a57a810a258cb787.json"}}, {"family": "Rose", "given": "Max", "initials": "M", "orcid": "0000-0001-5723-0884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc0508385e946bba69d99a356a04f28.json"}}, {"family": "Samanta", "given": "Amit K", "initials": "AK"}, {"family": "Schmidt", "given": "Philipp", "initials": "P", "orcid": "0000-0003-1980-6998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32ad7c99f9004741a7347fab1a0909f7.json"}}, {"family": "Sobolev", "given": "Egor", "initials": "E", "orcid": "0000-0003-2478-5685", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d276c61bf24456f90c0c4a4890c3dd6.json"}}, {"family": "Timneanu", "given": "Nicusor", "initials": "N"}, {"family": "Usenko", "given": "Sergey", "initials": "S", "orcid": "0000-0001-5202-5267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7752b794dac4a2ead20312996e4ae87.json"}}, {"family": "Westphal", "given": "Daniel", "initials": "D"}, {"family": "Wollweber", "given": "Tamme", "initials": "T"}, {"family": "Worbs", "given": "Lena", "initials": "L"}, {"family": "Xavier", "given": "Paul Lourdu", "initials": "PL", "orcid": "0000-0001-5132-2999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4541dbeb59ad44f6aaa167fb4d4a1e89.json"}}, {"family": "Yousef", "given": "Hazem", "initials": "H"}, {"family": "Ayyer", "given": "Kartik", "initials": "K", "orcid": "0000-0002-6881-564X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed596a62143046adb46e0484fcd454da.json"}}, {"family": "Chapman", "given": "Henry N", "initials": "HN", "orcid": "0000-0002-4655-1743", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c661cbe64a6143ac8c44594ce69931a5.json"}}, {"family": "Sellberg", "given": "Jonas A", "initials": "JA", "orcid": "0000-0003-2793-5052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86c7efd806b5436296298d6243778574.json"}}, {"family": "Seuring", "given": "Carolin", "initials": "C", "orcid": "0000-0003-1000-0859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f355ad3b6894b11896335c578ec956c.json"}}, {"family": "Vartanyants", "given": "Ivan A", "initials": "IA", "orcid": "0000-0002-0340-8234", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3828d7e3b604adc92e8d9b74b47896d.json"}}, {"family": "K\u00fcpper", "given": "Jochen", "initials": "J", "orcid": "0000-0003-4395-9345", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4418443871e14f17ada6b50ac02f1232.json"}}, {"family": "Meyer", "given": "Michael", "initials": "M", "orcid": "0000-0002-1444-6770", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fdcd87f28ccc40d19b0345fc1a41c08a.json"}}, {"family": "Maia", "given": "Filipe R N C", "initials": "FRNC"}], "type": "journal article", "published": "2024-01-12", "journal": {"title": "Light Sci Appl", "issn": "2047-7538", "volume": "13", "issue": "1", "pages": "15", "issn-l": null}, "abstract": "The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.", "doi": "10.1038/s41377-023-01352-7", "pmid": "38216563", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10786860"}, {"db": "pii", "key": "10.1038/s41377-023-01352-7"}], "notes": [], "created": "2026-08-20T08:47:31.976Z", "modified": "2026-08-20T08:47:56.394Z"}, {"entity": "publication", "iuid": "58bee921d50c42609ba4d471ad61cc42", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/58bee921d50c42609ba4d471ad61cc42.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/58bee921d50c42609ba4d471ad61cc42"}}, "title": "Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost", "authors": [{"family": "Clouard", "given": "Camille", "initials": "C", "orcid": "0009-0006-3654-6525", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1276f8e61854d5b8d72b48de487056f.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "posted-content", "published": "2023-12-12", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.12.571203", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:50:58.025Z", "modified": "2026-08-20T10:50:58.115Z"}, {"entity": "publication", "iuid": "7279b78cb89a4a7eaae3fafbd1ddc965", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7279b78cb89a4a7eaae3fafbd1ddc965.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7279b78cb89a4a7eaae3fafbd1ddc965"}}, "title": "A deep learning framework for characterization of genotype data.", "authors": [{"family": "Ausmees", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-6212-539X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e920010123044c6a82869061862607ad.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "journal article", "published": "2022-03-04", "journal": {"title": "G3", "issn": "2160-1836", "volume": "12", "issue": "3", "issn-l": "2160-1836"}, "abstract": "Dimensionality reduction is a data transformation technique widely used in various fields of genomics research. The application of dimensionality reduction to genotype data is known to capture genetic similarity between individuals, and is used for visualization of genetic variation, identification of population structure as well as ancestry mapping. Among frequently used methods are principal component analysis, which is a linear transform that often misses more fine-scale structures, and neighbor-graph based methods which focus on local relationships rather than large-scale patterns. Deep learning models are a type of nonlinear machine learning method in which the features used in data transformation are decided by the model in a data-driven manner, rather than by the researcher, and have been shown to present a promising alternative to traditional statistical methods for various applications in omics research. In this study, we propose a deep learning model based on a convolutional autoencoder architecture for dimensionality reduction of genotype data. Using a highly diverse cohort of human samples, we demonstrate that the model can identify population clusters and provide richer visual information in comparison to principal component analysis, while preserving global geometry to a higher extent than t-SNE and UMAP, yielding results that are comparable to an alternative deep learning approach based on variational autoencoders. We also discuss the use of the methodology for more general characterization of genotype data, showing that it preserves spatial properties in the form of decay of linkage disequilibrium with distance along the genome and demonstrating its use as a genetic clustering method, comparing results to the ADMIXTURE software frequently used in population genetic studies.", "doi": "10.1093/g3journal/jkac020", "pmid": "35078229", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8896001"}, {"db": "pii", "key": "6515290"}], "notes": [], "created": "2026-08-20T09:41:12.898Z", "modified": "2026-08-20T09:41:13.026Z"}, {"entity": "publication", "iuid": "cc8129c7431c4f4abe00e0d50be63b5f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cc8129c7431c4f4abe00e0d50be63b5f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cc8129c7431c4f4abe00e0d50be63b5f"}}, "title": "The presence and impact of reference bias on population genomic studies of prehistoric human populations.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "15", "issue": "7", "pages": "e1008302", "issn-l": "1553-7390"}, "abstract": "Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.", "doi": "10.1371/journal.pgen.1008302", "pmid": "31348818", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6685638"}, {"db": "pii", "key": "PGENETICS-D-19-00061"}], "notes": [], "created": "2026-08-20T12:43:40.040Z", "modified": "2026-08-20T12:43:40.126Z"}, {"entity": "publication", "iuid": "1ef676ebcdfa4f6fa76bbdcc96a8f6ea", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ef676ebcdfa4f6fa76bbdcc96a8f6ea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ef676ebcdfa4f6fa76bbdcc96a8f6ea"}}, "title": "Erratum: Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. Corrigendum.", "authors": [{"family": "Daurer", "given": "Benedikt J", "initials": "BJ", "orcid": "0000-0002-1887-7551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22e1c4b4b7fc427f9069efa4b1486d47.json"}}, {"family": "Okamoto", "given": "Kenta", "initials": "K"}, {"family": "Bielecki", "given": "Johan", "initials": "J"}, {"family": "Maia", "given": "Filipe R N C", "initials": "FRNC"}, {"family": "M\u00fchlig", "given": "Kerstin", "initials": "K"}, {"family": "Seibert", "given": "M Marvin", "initials": "MM"}, {"family": "Hantke", "given": "Max F", "initials": "MF"}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}, {"family": "Benner", "given": "W Henry", "initials": "WH"}, {"family": "Svenda", "given": "Martin", "initials": "M"}, {"family": "T\u00eemneanu", "given": "Nicu\u015for", "initials": "N", "orcid": "0000-0001-7328-0400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2a9165954da4b14b334d1d7151efb9e.json"}}, {"family": "Ekeberg", "given": "Tomas", "initials": "T"}, {"family": "Loh", "given": "N Duane", "initials": "ND"}, {"family": "Pietrini", "given": "Alberto", "initials": "A", "orcid": "0000-0002-1171-6683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c36ada5fa2c64f85ade5c5ff616d5c6d.json"}}, {"family": "Zani", "given": "Alessandro", "initials": "A"}, {"family": "Rath", "given": "Asawari D", "initials": "AD"}, {"family": "Westphal", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8735-0369", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b65c15572f045bebbd2b3e54d3361ca.json"}}, {"family": "Kirian", "given": "Richard A", "initials": "RA"}, {"family": "Awel", "given": "Salah", "initials": "S", "orcid": "0000-0002-9470-5911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16d6587f34eb44469144a76e97afcd1e.json"}}, {"family": "Wiedorn", "given": "Max O", "initials": "MO", "orcid": "0000-0002-0856-2695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d3b5568bd774edfb9ff83bd4bbafc7a.json"}}, {"family": "van der Schot", "given": "Gijs", "initials": "G"}, {"family": "Carlsson", "given": "Gunilla H", "initials": "GH"}, {"family": "Hasse", "given": "Dirk", "initials": "D", "orcid": "0000-0001-8710-327X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4395deedd98b4a82867e6034fc11ad79.json"}}, {"family": "Sellberg", "given": "Jonas A", "initials": "JA", "orcid": "0000-0003-2793-5052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86c7efd806b5436296298d6243778574.json"}}, {"family": "Barty", "given": "Anton", "initials": "A"}, {"family": "Andreasson", "given": "Jakob", "initials": "J", "orcid": "0000-0001-8951-0530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b97bebb109fd43dc89e36bcc9cdceca1.json"}}, {"family": "Boutet", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0003-3928-1244", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87ca2ff0de224bb98dc1d16755f0c340.json"}}, {"family": "Williams", "given": "Garth", "initials": "G"}, {"family": "Koglin", "given": "Jason", "initials": "J"}, {"family": "Andersson", "given": "Inger", "initials": "I", "orcid": "0000-0002-2729-0787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d190a3ec37394343b3b27fab0f2ed5bc.json"}}, {"family": "Hajdu", "given": "Janos", "initials": "J"}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7f10a849faa444ab45f565e86abac5a.json"}}], "type": "journal article", "published": "2019-05-01", "journal": {"title": "IUCrJ", "issn": "2052-2525", "volume": "6", "issue": "Pt 3", "pages": "500", "issn-l": "2052-2525"}, "abstract": "[This corrects the article DOI: 10.1107/S2052252517003591.].", "doi": "10.1107/S2052252519004317", "pmid": "31098030", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6503930"}, {"db": "pii", "key": "it9021"}], "notes": [], "created": "2026-08-20T11:16:04.037Z", "modified": "2026-08-20T11:16:04.376Z"}, {"entity": "publication", "iuid": "e6fb98199d6545378b4d0dd55ff791e1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e6fb98199d6545378b4d0dd55ff791e1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e6fb98199d6545378b4d0dd55ff791e1"}}, "title": "Electrospray sample injection for single-particle imaging with x-ray lasers.", "authors": [{"family": "Bielecki", "given": "Johan", "initials": "J", "orcid": "0000-0002-3012-603X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb981ea4fae1468fbf068f2b4b509c75.json"}}, {"family": "Hantke", "given": "Max F", "initials": "MF", "orcid": "0000-0003-1251-0465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/803e4afe61af49fc8a37f3b5b0522ea7.json"}}, {"family": "Daurer", "given": "Benedikt J", "initials": "BJ", "orcid": "0000-0002-1887-7551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22e1c4b4b7fc427f9069efa4b1486d47.json"}}, {"family": "Reddy", "given": "Hemanth K N", "initials": "HKN"}, {"family": "Hasse", "given": "Dirk", "initials": "D", "orcid": "0000-0001-8710-327X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4395deedd98b4a82867e6034fc11ad79.json"}}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7f10a849faa444ab45f565e86abac5a.json"}}, {"family": "Gunn", "given": "Laura H", "initials": "LH", "orcid": "0000-0003-2072-0884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35fd1150a0f64d7db5b81ace81bb7f4f.json"}}, {"family": "Svenda", "given": "Martin", "initials": "M"}, {"family": "Munke", "given": "Anna", "initials": "A", "orcid": "0000-0002-5510-2245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3b83fcda1004315a30e61c7c2c678f7.json"}}, {"family": "Sellberg", "given": "Jonas A", "initials": "JA", "orcid": "0000-0003-2793-5052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86c7efd806b5436296298d6243778574.json"}}, {"family": "Flueckiger", "given": "Leonie", "initials": "L"}, {"family": "Pietrini", "given": "Alberto", "initials": "A", "orcid": "0000-0002-1171-6683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c36ada5fa2c64f85ade5c5ff616d5c6d.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}, {"family": "Lundholm", "given": "Ida", "initials": "I"}, {"family": "Carlsson", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-7565-0177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7409d72a83104ceebf22dfe6e19e756b.json"}}, {"family": "Okamoto", "given": "Kenta", "initials": "K"}, {"family": "Timneanu", "given": "Nicusor", "initials": "N", "orcid": "0000-0001-7328-0400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2a9165954da4b14b334d1d7151efb9e.json"}}, {"family": "Westphal", "given": "Daniel", "initials": "D"}, {"family": "Kulyk", "given": "Olena", "initials": "O"}, {"family": "Higashiura", "given": "Akifumi", "initials": "A", "orcid": "0000-0001-8448-9349", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/848a654049a84a81b6d88bb2603fb82b.json"}}, {"family": "van der Schot", "given": "Gijs", "initials": "G", "orcid": "0000-0002-6128-4196", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79d5acb7b94846aa9819e92a99dae0b9.json"}}, {"family": "Loh", "given": "Ne-Te Duane", "initials": "ND", "orcid": "0000-0002-8886-510X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1051c98d2c724698bcc25803a0404457.json"}}, {"family": "Wysong", "given": "Taylor E", "initials": "TE"}, {"family": "Bostedt", "given": "Christoph", "initials": "C"}, {"family": "Gorkhover", "given": "Tais", "initials": "T"}, {"family": "Iwan", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4352-013X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2510f70c398449f8973ce5f145f6ac8b.json"}}, {"family": "Seibert", "given": "M Marvin", "initials": "MM"}, {"family": "Osipov", "given": "Timur", "initials": "T"}, {"family": "Walter", "given": "Peter", "initials": "P"}, {"family": "Hart", "given": "Philip", "initials": "P", "orcid": "0000-0002-4569-3926", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b247ceeca3644ec39cc8bcfe33180591.json"}}, {"family": "Bucher", "given": "Maximilian", "initials": "M", "orcid": "0000-0001-7896-473X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bff3b3f3e7504b5fba4e5ead46fc22be.json"}}, {"family": "Ulmer", "given": "Anatoli", "initials": "A"}, {"family": "Ray", "given": "Dipanwita", "initials": "D"}, {"family": "Carini", "given": "Gabriella", "initials": "G"}, {"family": "Ferguson", "given": "Ken R", "initials": "KR"}, {"family": "Andersson", "given": "Inger", "initials": "I", "orcid": "0000-0002-2729-0787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d190a3ec37394343b3b27fab0f2ed5bc.json"}}, {"family": "Andreasson", "given": "Jakob", "initials": "J", "orcid": "0000-0002-3202-2330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1d15aba5354347b283b16122bef977ca.json"}}, {"family": "Hajdu", "given": "Janos", "initials": "J", "orcid": "0000-0002-3747-2760", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef8aa893b7854bea83edb8993f453162.json"}}, {"family": "Maia", "given": "Filipe R N C", "initials": "FRNC", "orcid": "0000-0002-2141-438X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a305c750241840a19612dc53e34beacc.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "5", "issue": "5", "pages": "eaav8801", "issn-l": "2375-2548"}, "abstract": "The possibility of imaging single proteins constitutes an exciting challenge for x-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available x-ray lasers and, as we demonstrate here, contamination of the aerosolized molecules by nonvolatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet size during aerosolization. Here, we show that, with our electrospray injector, we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next-generation x-ray lasers, constitute an important stepping stone toward the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.", "doi": "10.1126/sciadv.aav8801", "pmid": "31058226", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6499549"}, {"db": "pii", "key": "aav8801"}], "notes": [], "created": "2026-08-20T11:58:27.408Z", "modified": "2026-08-20T11:58:28.536Z"}, {"entity": "publication", "iuid": "c1e44f49ff7b446d9cfdca6d131c06eb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c1e44f49ff7b446d9cfdca6d131c06eb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c1e44f49ff7b446d9cfdca6d131c06eb"}}, "title": "A statistical approach to detect protein complexes at X-ray free electron laser facilities", "authors": [{"family": "Pietrini", "given": "Alberto", "initials": "A", "orcid": "0000-0002-1171-6683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c36ada5fa2c64f85ade5c5ff616d5c6d.json"}}, {"family": "Bielecki", "given": "Johan", "initials": "J"}, {"family": "Timneanu", "given": "Nicusor", "initials": "N"}, {"family": "Hantke", "given": "Max F", "initials": "MF"}, {"family": "Andreasson", "given": "Jakob", "initials": "J"}, {"family": "Loh", "given": "N Duane", "initials": "ND"}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7f10a849faa444ab45f565e86abac5a.json"}}, {"family": "Boutet", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Hajdu", "given": "Janos", "initials": "J"}, {"family": "Maia", "given": "Filipe R N C", "initials": "FRNC", "orcid": "0000-0002-2141-438X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a305c750241840a19612dc53e34beacc.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "journal-article", "published": "2018-12-07", "journal": {"title": "Commun Phys", "issn": "2399-3650", "volume": "1", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1038/s42005-018-0092-6", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:25:48.991Z", "modified": "2026-08-20T09:25:49.175Z"}, {"entity": "publication", "iuid": "5ecd8803519d425c958b5f6b859bcb3e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ecd8803519d425c958b5f6b859bcb3e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ecd8803519d425c958b5f6b859bcb3e"}}, "title": "The presence and impact of reference bias on population genomic studies of prehistoric human populations", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "posted-content", "published": "2018-12-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/487983", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:11:43.455Z", "modified": "2026-08-20T11:11:43.478Z"}, {"entity": "publication", "iuid": "152218a1696c4fb6a084dd2b6c5e9574", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/152218a1696c4fb6a084dd2b6c5e9574.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/152218a1696c4fb6a084dd2b6c5e9574"}}, "title": "Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses.", "authors": [{"family": "Daurer", "given": "Benedikt J", "initials": "BJ", "orcid": "0000-0002-1887-7551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22e1c4b4b7fc427f9069efa4b1486d47.json"}}, {"family": "Okamoto", "given": "Kenta", "initials": "K"}, {"family": "Bielecki", "given": "Johan", "initials": "J"}, {"family": "Maia", "given": "Filipe R N C", "initials": "FRNC"}, {"family": "M\u00fchlig", "given": "Kerstin", "initials": "K"}, {"family": "Seibert", "given": "M Marvin", "initials": "MM"}, {"family": "Hantke", "given": "Max F", "initials": "MF"}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}, {"family": "Benner", "given": "W Henry", "initials": "WH"}, {"family": "Svenda", "given": "Martin", "initials": "M"}, {"family": "T\u00eemneanu", "given": "Nicu\u015for", "initials": "N", "orcid": "0000-0001-7328-0400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2a9165954da4b14b334d1d7151efb9e.json"}}, {"family": "Ekeberg", "given": "Tomas", "initials": "T"}, {"family": "Loh", "given": "N Duane", "initials": "ND"}, {"family": "Pietrini", "given": "Alberto", "initials": "A"}, {"family": "Zani", "given": "Alessandro", "initials": "A"}, {"family": "Rath", "given": "Asawari D", "initials": "AD"}, {"family": "Westphal", "given": "Daniel", "initials": "D"}, {"family": "Kirian", "given": "Richard A", "initials": "RA"}, {"family": "Awel", "given": "Salah", "initials": "S"}, {"family": "Wiedorn", "given": "Max O", "initials": "MO"}, {"family": "van der Schot", "given": "Gijs", "initials": "G"}, {"family": "Carlsson", "given": "Gunilla H", "initials": "GH"}, {"family": "Hasse", "given": "Dirk", "initials": "D"}, {"family": "Sellberg", "given": "Jonas A", "initials": "JA"}, {"family": "Barty", "given": "Anton", "initials": "A"}, {"family": "Andreasson", "given": "Jakob", "initials": "J"}, {"family": "Boutet", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Williams", "given": "Garth", "initials": "G"}, {"family": "Koglin", "given": "Jason", "initials": "J"}, {"family": "Andersson", "given": "Inger", "initials": "I", "orcid": "0000-0002-2729-0787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d190a3ec37394343b3b27fab0f2ed5bc.json"}}, {"family": "Hajdu", "given": "Janos", "initials": "J"}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD"}], "type": "journal article", "published": "2017-05-01", "journal": {"title": "IUCrJ", "issn": "2052-2525", "volume": "4", "issue": "Pt 3", "pages": "251-262", "issn-l": "2052-2525"}, "abstract": "This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of \u223c40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from \u223c35 to \u223c300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 \u00d7 1012 photons per \u00b5m2 per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.", "doi": "10.1107/S2052252517003591", "pmid": "28512572", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC5414399"}, {"db": "pii", "key": "it5009"}], "notes": [], "created": "2018-12-05T11:26:37.870Z", "modified": "2026-08-20T11:16:00.566Z"}]}