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Showing results for joakim wide
Your search for Joakim Widén retrieved no results
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J. Asp M, et al. Cell. 2019 Dec 12;179(7):1647-1660.e19. doi: 10.1016/j.cell.2019.11.025. Cell. 2019. PMID: 31835037 Free article.
Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. ...
Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial r …
Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson A, He M, Berglund E, Marklund M, Mirzazadeh R, Schultz N, Kvastad L, Andersson A, Bergenstråhle L, Bergenstråhle J, Larsson L, Alonso Galicia L, Shamikh A, Basmaci E, Díaz De Ståhl T, Rajakumar T, Doultsinos D, Thrane K, Ji AL, Khavari PA, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy FC, Woodcock DJ, Helleday T, Mills IG, Lamb AD, Lundeberg J. Erickson A, et al. Nature. 2022 Aug;608(7922):360-367. doi: 10.1038/s41586-022-05023-2. Epub 2022 Aug 10. Nature. 2022. PMID: 35948708 Free PMC article.
We used spatially resolved transcriptomics(2) to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and i …
We used spatially resolved transcriptomics(2) to infer spatial copy number variations in >120,000 regions across multiple organs, in beni …
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.
Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmén F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J. Berglund E, et al. Nat Commun. 2018 Jun 20;9(1):2419. doi: 10.1038/s41467-018-04724-5. Nat Commun. 2018. PMID: 29925878 Free PMC article.
Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. ...
Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression …
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.
Mirzazadeh R, Andrusivova Z, Larsson L, Newton PT, Galicia LA, Abalo XM, Avijgan M, Kvastad L, Denadai-Souza A, Stakenborg N, Firsova AB, Shamikh A, Jurek A, Schultz N, Nistér M, Samakovlis C, Boeckxstaens G, Lundeberg J. Mirzazadeh R, et al. Nat Commun. 2023 Jan 31;14(1):509. doi: 10.1038/s41467-023-36071-5. Nat Commun. 2023. PMID: 36720873 Free PMC article.
Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. ...
Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance …
Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.
Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J. Thrane K, et al. Cancer Res. 2018 Oct 15;78(20):5970-5979. doi: 10.1158/0008-5472.CAN-18-0747. Epub 2018 Aug 28. Cancer Res. 2018. PMID: 30154148
Deconvolution combined with traditional approaches for dimensional reduction of transcriptome-wide data enabled us to both visualize the transcriptional landscape within the tissue and identify gene expression profiles linked to specific histologic entities. ...
Deconvolution combined with traditional approaches for dimensional reduction of transcriptome-wide data enabled us to both visualize …
Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.
Marklund M, Schultz N, Friedrich S, Berglund E, Tarish F, Tanoglidi A, Liu Y, Bergenstråhle L, Erickson A, Helleday T, Lamb AD, Sonnhammer E, Lundeberg J. Marklund M, et al. Nat Commun. 2022 Sep 17;13(1):5475. doi: 10.1038/s41467-022-33069-3. Nat Commun. 2022. PMID: 36115838 Free PMC article.
By doing so, we are able to couple clinical responsiveness and morphological information such as Gleason score to transcriptome-wide data. Our data-driven analysis of transcriptomes identifies several distinct intratumoral cell populations, characterized by their unique ge …
By doing so, we are able to couple clinical responsiveness and morphological information such as Gleason score to transcriptome-wide
Towards MR contrast independent synthetic CT generation.
Simkó A, Bylund M, Jönsson G, Löfstedt T, Garpebring A, Nyholm T, Jonsson J. Simkó A, et al. Z Med Phys. 2023 Aug 1:S0939-3889(23)00083-1. doi: 10.1016/j.zemedi.2023.07.001. Online ahead of print. Z Med Phys. 2023. PMID: 37537099 Free article.
On T2w images acquired with the same settings as the training dataset, there was no significant difference between the performance of the models. However, when evaluated on T1w images, and a wide range of other contrasts and scanners from both public and private datasets, …
On T2w images acquired with the same settings as the training dataset, there was no significant difference between the performance of the mo …
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality.
Kvastad L, Carlberg K, Larsson L, Villacampa EG, Stuckey A, Stenbeck L, Mollbrink A, Zamboni M, Magnusson JP, Basmaci E, Shamikh A, Prochazka G, Schaupp AL, Borg Å, Fugger L, Nistér M, Lundeberg J. Kvastad L, et al. Commun Biol. 2021 Jan 8;4(1):57. doi: 10.1038/s42003-020-01573-1. Commun Biol. 2021. PMID: 33420318 Free PMC article.
Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transc …
Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at ce …
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography.
Andersson A, Bergenstråhle J, Asp M, Bergenstråhle L, Jurek A, Fernández Navarro J, Lundeberg J. Andersson A, et al. Commun Biol. 2020 Oct 9;3(1):565. doi: 10.1038/s42003-020-01247-y. Commun Biol. 2020. PMID: 33037292 Free PMC article.
The field of spatial transcriptomics is rapidly expanding, and with it the repertoire of available technologies. However, several of the transcriptome-wide spatial assays do not operate on a single cell level, but rather produce data comprised of contributions from a - pot …
The field of spatial transcriptomics is rapidly expanding, and with it the repertoire of available technologies. However, several of the tra …
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