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Genomics & transcriptomics data

Published Data

Data available on the European COVID-19 Data Portal

Published raw and assembled sequences related to the COVID-19 outbreak, including outbreak isolates and records relating to coronavirus biology:

Data available from research groups in Sweden

The list of available data on this Portal was curated manually until February 2022. After February 2022, we instead began to use a script to query the Europe PMC database (making use of their API) in order to locate relevant publications. We only include data from publications about COVID-19/SARS-CoV-2 that BOTH involve at least one author affiliated with a Swedish research institution AND openly share reusable data and/or code. The code used for the query is written in Python and, as with all of our code, it is openly available in GitHub. We welcome others to reuse it and to repurpose it for other pathogens.

The lists of available data may not be exhaustive as the script used to generate it does not search for every possible database/repository. If you find that a dataset is missing, or that the information related to it is incorrect, please get in touch with us

Last updated: 2022-09-23

Publication Available dataset and code
Gao Y., Cai C., Wullimann D., Niessl J., et al (2022)
Elsevier BV
DOI: 10.1016/j.immuni.2022.07.005
Lentini A., Pereira A., Winqvist O., Reinius B. (2022)
Elsevier BV
DOI: 10.1016/j.medj.2022.07.007
Barturen G., Carnero-Montoro E., Martínez-Bueno M., Rojo-Rello S., et al (2022)
Springer Science and Business Media LLC
DOI: 10.1038/s41467-022-32357-2
Siddhuraj P., Jönsson J., Alyamani M., Prabhala P., et al (2022)
Frontiers Media SA
DOI: 10.3389/fimmu.2022.924244
Brandão P. E., Berg M., Leite B. A., Silva S. O., et al (2022)
FapUNIFESP (SciELO)
DOI: 10.1590/1678-4685-gmb-2022-0034
Fadista J., Kraven L. M., Karjalainen J., Andrews S. J., et al (2022)
Elsevier BV
DOI: 10.1016/j.ebiom.2021.103277
Dahlgren M. W., Plumb A. W., Niss K., Lahl K., et al (2022)
Frontiers Media SA
DOI: 10.3389/fimmu.2022.932388
Rosendal E., Mihai I. S., Becker M., Das D., et al (2022)
American Society for Microbiology
DOI: 10.1128/mbio.00892-22
Noske G., Nakamura A., Gawriljuk V., Fernandes R., et al (2022)
Elsevier BV
DOI: 10.1016/j.jmb.2021.167118
Zhu K., Wang Y., Sarlus H., Geng K., et al (2022)
EMBO
DOI: 10.15252/embr.202154499
Martin D. P., Weaver S., Tegally H., San J. E., et al (2022)
Elsevier BV
DOI: 10.1016/j.cell.2021.09.003
Albrich W. C., Ghosh T. S., Ahearn-Ford S., Mikaeloff F., et al (2022)
Informa UK Limited
DOI: 10.1080/19490976.2022.2073131
Zuo F., Abolhassani H., Du L., Piralla A., et al (2022)
Springer Science and Business Media LLC
DOI: 10.1038/s41467-022-30340-5
Bai X., Narayanan A., Skagerberg M., Ceña-Diez R., et al (2022)
MDPI AG
DOI: 10.3390/biomedicines10050982
Tsitsiklis A., Osborne C. M., Kamm J., Williamson K., et al (2022)
Elsevier BV
DOI: 10.1016/s2666-5247(21)00304-9
Hanke L., Sheward D. J., Pankow A., Vidakovics L. P., et al (2022)
American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciadv.abm0220
Bryant P., Pozzati G., Elofsson A. (2022)
Springer Science and Business Media LLC
DOI: 10.1038/s41467-022-28865-w
Zeberg H. (2022)
Proceedings of the National Academy of Sciences
DOI: 10.1073/pnas.2116435119
Sanchez-Burgos L., Gómez-López G., Al-Shahrour F., Fernandez-Capetillo O. (2022)
Springer Science and Business Media LLC
DOI: 10.1038/s41598-022-05597-x
Carapito R., Li R., Helms J., Carapito C., et al (2022)
American Association for the Advancement of Science (AAAS)
DOI: 10.1126/scitranslmed.abj7521
Huffman J. E., Butler-Laporte G., Khan A., Pairo-Castineira E., et al (2022)
Springer Science and Business Media LLC
DOI: 10.1038/s41588-021-00996-8
Huffman J. E., Butler-Laporte G., Khan A., Pairo-Castineira E., et al (2022)
Springer Science and Business Media LLC
DOI: 10.1038/s41588-021-00996-8
Hellman U., Karlsson M. G., Engström-Laurent A., Cajander S., et al (2021)
Elsevier BV
DOI: 10.1074/jbc.AC120.015967
Nakanishi T., Pigazzini S., Degenhardt F., Cordioli M., et al (2021)
American Society for Clinical Investigation
DOI: 10.1172/jci152386
Simnica D., Schultheiß C., Mohme M., Paschold L., et al (2021)
Wiley
DOI: 10.1002/cti2.1340
O'Toole Á., Hill V., Pybus O. G., Watts A., et al (2021)
F1000 Research Ltd
DOI: 10.12688/wellcomeopenres.16661.2
Das J., Idh N., Sikkeland L. I. B., Paues J., et al (2021)
Informa UK Limited
DOI: 10.1080/15592294.2021.1969499
Ringlander J., Olausson J., Nyström K., Härnqvist T., et al (2021)
Informa UK Limited
DOI: 10.1080/23744235.2021.1957143
Niemi M. E. K., Karjalainen J., Liao R. G., Neale B. M., et al (2021)
Springer Science and Business Media LLC
DOI: 10.1038/s41586-021-03767-x
Razzaq M., Iglesias M. J., Ibrahim-Kosta M., Goumidi L., et al (2021)
Springer Science and Business Media LLC
DOI: 10.1038/s41598-021-93390-7
Galien S., Hultström M., Lipcsey M., Stattin K., et al (2021)
Springer Science and Business Media LLC
DOI: 10.1186/s12959-021-00272-z
Fyles M., Fearon E., Overton C., Wingfield T., et al (2021)
The Royal Society
DOI: 10.1098/rstb.2020.0267
Yelagandula R., Bykov A., Vogt A., Heinen R., et al (2021)
Springer Science and Business Media LLC
DOI: 10.1038/s41467-021-22664-5
Funk T., Pharris A., Spiteri G., Bundle N., et al (2021)
European Centre for Disease Control and Prevention (ECDC)
DOI: 10.2807/1560-7917.ES.2021.26.16.2100348
Sheward D. J., Mandolesi M., Urgard E., Kim C., et al (2021)
Cold Spring Harbor Laboratory
DOI: 10.1101/2021.04.03.438330
Ganna A. (2021)
Cold Spring Harbor Laboratory
DOI: 10.1101/2021.03.10.21252820
Alekseenko A., Barrett D., Pareja-Sanchez Y., Howard R. J., et al (2021)
Springer Science and Business Media LLC
DOI: 10.1038/s41598-020-80352-8
Maricic T., Nickel O., Aximu-Petri A., Essel E., et al (2020)
Public Library of Science (PLoS)
DOI: 10.1371/journal.pone.0244824
Zeberg H., Pääbo S. (2020)
Cold Spring Harbor Laboratory
DOI: 10.1101/2020.12.11.422139
Hemati M., Soosanabadi M., Ghorashi T., Ghaffari H., et al (2020)
Wiley
DOI: 10.1002/jcp.30206
Tampere M., Pettke A., Salata C., Wallner O., et al (2020)
MDPI AG
DOI: 10.3390/v12121423
Delavari S., Abolhassani H., Abolnezhadian F., Babaha F., et al (2020)
Springer Science and Business Media LLC
DOI: 10.1007/s10875-020-00928-x
Duchene S., Featherstone L., de Blasio B. F., Holmes E. C., et al (2020)
Cold Spring Harbor Laboratory
DOI: 10.1101/2020.11.18.20233767
Zeng H., Dichio V., Rodríguez Horta E., Thorell K., et al (2020)
Proceedings of the National Academy of Sciences
DOI: 10.1073/pnas.2012331117
Böhmer M. M., Buchholz U., Corman V. M., Hoch M., et al (2020)
Elsevier BV
DOI: 10.1016/S1473-3099(20)30314-5
Bastard P., Rosen L. B., Zhang Q., Michailidis E., et al (2020)
American Association for the Advancement of Science (AAAS)
DOI: 10.1126/science.abd4585
Zhang Q., Bastard P., Liu Z., Le Pen J., et al (2020)
American Association for the Advancement of Science (AAAS)
DOI: 10.1126/science.abd4570
Bryant P., Elofsson A. (2020)
Cold Spring Harbor Laboratory
DOI: 10.1101/2020.10.19.20215046
Sekine T., Perez-Potti A., Rivera-Ballesteros O., Strålin K., et al (2020)
Elsevier BV
DOI: 10.1016/j.cell.2020.08.017
Edén A., Kanberg N., Gostner J., Fuchs D., et al (2020)
Ovid Technologies (Wolters Kluwer Health)
DOI: 10.1212/WNL.0000000000010977
Zeberg H., Pääbo S. (2020)
Springer Science and Business Media LLC
DOI: 10.1038/s41586-020-2818-3
Smyrlaki I., Ekman M., Lentini A., Rufino de Sousa N., et al (2020)
Springer Science and Business Media LLC
DOI: 10.1038/s41467-020-18611-5
Parrot T., Gorin J., Ponzetta A., Maleki K. T., et al (2020)
American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciimmunol.abe1670
Ling J., Hickman R. A., Li J., Lu X., et al (2020)
MDPI AG
DOI: 10.3390/v12091026
Hanke L., Vidakovics Perez L., Sheward D. J., Das H., et al (2020)
Springer Science and Business Media LLC
DOI: 10.1038/s41467-020-18174-5
Maucourant C., Filipovic I., Ponzetta A., Aleman S., et al (2020)
American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciimmunol.abd6832
Ying K., Zhai R., Pyrkov T. V., Mariotti M., et al (2020)
Cold Spring Harbor Laboratory
DOI: 10.1101/2020.08.06.20169854
Su Y., Chen D., Lausted C., Yuan D., et al (2020)
Cold Spring Harbor Laboratory
DOI: 10.1101/2020.07.27.224063
Petrazzuolo A., Le Naour J., Vacchelli E., Gaussem P., et al (2020)
Informa UK Limited
DOI: 10.1080/2162402X.2020.1857112