Molecular Precision Medicine

Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

Arvidsson, Gustav; Czarnewski, Paulo; Johansson, Alina; Raine, Amanda et al.

Part of Arthritis & Rheumatology, p. 255-267, 2024

• DOI for Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.
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An endothelial regulatory module links blood pressure regulation with elite athletic performance

Fegraeus, Kim; Rosengren, Maria K.; Naboulsi, Rakan; Orlando, Ludovic et al.

Part of PLOS Genetics, 2024

• DOI for An endothelial regulatory module links blood pressure regulation with elite athletic performance
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Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Gezelius, Henrik; Enblad, Anna Pia; Lundmark, Anders; Åberg, Martin et al.

Part of NAR Genomics and Bioinformatics, 2024

• DOI for Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening
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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Lysenkova, Mariya; Arvidsson, Gustav; Bunikis, Ignas; Lundmark, Anders et al.

Part of Life Science Alliance, 2024

• DOI for A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling

Orgueira, Adrian Mosquera; Krali, Olga; Miguez, Carlos Perez; Raindo, Andres Peleteiro et al.

Part of Clinical Epigenetics, 2024

• DOI for Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling
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Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia

Fehr, André; Arvidsson, Gustav; Nordlund, Jessica; Lönnerholm, Gudmar et al.

Part of Genes, Chromosomes and Cancer, p. 597-606, 2023

• DOI for Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia
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Long-read whole-genome analysis of human single cells

Hård, Joanna; Mold, Jeff E; Eisfeldt, Jesper; Tellgren-Roth, Christian et al.

Part of Nature Communications, 2023

• DOI for Long-read whole-genome analysis of human single cells
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Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Krali, Olga; Marincevic-Zuniga, Yanara; Arvidsson, Gustav; Enblad, Anna Pia et al.

Part of npj Precision Oncology, 2023

• DOI for Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia
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Distinct HLA associations with autoantibody-defined subgroups in idiopathic inflammatory myopathies

Leclair, Valerie; Galindo-Feria, Angeles S.; Rothwell, Simon; Krystufkova, Olga et al.

Part of EBioMedicine, 2023

• DOI for Distinct HLA associations with autoantibody-defined subgroups in idiopathic inflammatory myopathies
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Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

Lysenkova Wiklander, Mariya; Övernäs, Elin; Lagensjö, Johanna; Raine, Amanda et al.

Part of BMC Research Notes, 2023

• DOI for Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

Ren, Luyao; Duan, Xiaoke; Dong, Lianhua; Zhang, Rui et al.

Part of Genome Biology, 2023

• DOI for Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
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Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

Rezayee, Fatemah; Eisfeldt, Jesper; Skaftason, Aron; Ofverholm, Ingegerd et al.

Part of Frontiers in Oncology, 2023

• DOI for Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia
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Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.

Riihimäki, Miia; Fegraeus, K. Jaderkvist; Nordlund, Jessica; Waern, Ida et al.

Part of Scientific Reports, p. 16261, 2023

• DOI for Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.
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Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative

Butler-Laporte, Guillaume; Povysil, Gundula; Kosmicki, Jack A; Cirulli, Elizabeth T et al.

Part of PLOS Genetics, 2022

• DOI for Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative
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Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases

Lundtoft, Christian; Pucholt, Pascal; Martin, Myriam; Bianchi, Matteo et al.

Part of Arthritis & Rheumatology, p. 1440-1450, 2022

• DOI for Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases
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Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report

Oldoni, Emanuela; Saunders, Gary; Bietrix, Florence; Garcia Bermejo, Maria Laura et al.

Part of Frontiers in Molecular Biosciences, 2022

• DOI for Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report
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scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

Raine, Amanda; Lundmark, Anders; Annett, Alva; Wiman, Ann-Christin et al.

Part of Scientific Reports, 2022

• DOI for scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
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Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology

Skaftason, Aron; Qu, Ying; Abdulla, Maysaa; Nordlund, Jessica et al.

Part of Genes, Chromosomes and Cancer, p. 27-36, 2022

• DOI for Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology
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Variants in BANK1 are associated with lupus nephritis of European ancestry.

Bolin, Karin; Imgenberg-Kreuz, Juliana; Leonard, Dag; Sandling, Johanna K. et al.

Part of Genes and Immunity, p. 194-202, 2021

• DOI for Variants in BANK1 are associated with lupus nephritis of European ancestry.
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Contributions of de novo variants to systemic lupus erythematosus

Carlsson Almlöf, Jonas; Nystedt, Sara; Mechtidou, Aikaterini; Leonard, Dag et al.

Part of European Journal of Human Genetics, p. 184-193, 2021

• DOI for Contributions of de novo variants to systemic lupus erythematosus
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RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children

Chen, Dongfeng; Camponeschi, Alessandro; Nordlund, Jessica; Marincevic-Zuniga, Yanara et al.

Part of Cancer Medicine, p. 3997-4003, 2021

• DOI for RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children
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Single nucleus transcriptomics data integration recapitulates the major cell types in human liver

Diamanti, Klev; Inda Díaz, Juan Salvador; Raine, Amanda; Pan, Gang et al.

Part of Hepatology Research, p. 233-238, 2021

• DOI for Single nucleus transcriptomics data integration recapitulates the major cell types in human liver
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Immune cells lacking Y chromosome show dysregulation of autosomal gene expression

Dumanski, Jan P.; Halvardson, Jonatan; Davies, Hanna; Rychlicka-Buniowska, Edyta et al.

Part of Cellular and Molecular Life Sciences (CMLS), p. 4019-4033, 2021

• DOI for Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Fang, Li Tai; Zhu, Bin; Zhao, Yongmei; Chen, Wanqiu et al.

Part of Nature Biotechnology, p. 1151-1160, 2021

• DOI for Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

The SEQC2 epigenomics quality control (EpiQC) study

Foox, Jonathan; Nordlund, Jessica; Lalancette, Claudia; Gong, Ting et al.

Part of Genome Biology, 2021

• DOI for The SEQC2 epigenomics quality control (EpiQC) study
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DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome

Imgenberg-Kreuz, Juliana; Sandling, Johanna K.; Norheim, Katrine Braekke; Johnsen, Svein Joar Auglaend et al.

Part of Frontiers in Immunology, 2021

• DOI for DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome
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DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML)

Krali, Olga; Palle, J; Bäcklin, Christofer; Abrahamsson, Jonas et al.

Part of Genes, 2021

• DOI for DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML)
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Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99

Mattisson, Jonas; Danielsson, Marcus; Hammond, Maria; Davies, Hanna et al.

Part of Scientific Reports, 2021

• DOI for Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99
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Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis

Mäkinen, Artturi; Nikkilä, Atte; Mehtonen, Juha; Teppo, Susanna et al.

Part of Pathology, p. 875-882, 2021

• DOI for Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis
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Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing

Sandling, Johanna K.; Pucholt, Pascal; Hultin-Rosenberg, Lina; Farias, Fabiana H. G. et al.

Part of Annals of the Rheumatic Diseases, p. 109-117, 2021

• DOI for Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing
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Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia

Sayyab, Shumaila; Lundmark, Anders; Larsson, Malin; Ringner, Markus et al.

Part of Scientific Reports, 2021

• DOI for Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Xiao, Wenming; Ren, Luyao; Chen, Zhong; Fang, Li Tai et al.

Part of Nature Biotechnology, p. 1141-1150, 2021

• DOI for Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study

Zhao, Yongmei; Fang, Li Tai; Shen, Tsai-wei; Choudhari, Sulbha et al.

Part of Scientific Data, 2021

• DOI for Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study
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Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

Almeida, Pedro; Proux-Wera, Estelle; Churcher, Allison; Soler, Lucile et al.

Part of BMC Biology, 2020

• DOI for Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion
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Recent advances in single-molecule fluorescence microscopy render structural biology dynamic

Bacic, Luka; Sabantsev, Anton; Deindl, Sebastian

Part of Current opinion in structural biology, p. 61-68, 2020

• DOI for Recent advances in single-molecule fluorescence microscopy render structural biology dynamic
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Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome

Björk, Albin; Andersson, Elina Richardsdotter; Imgenberg-Kreuz, Juliana; Thorlacius, Gudny Ella et al.

Part of RMD Open, 2020

• DOI for Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome
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The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Duran-Ferrer, Marti; Clot, Guillem; Nadeu, Ferran; Beekman, Renee et al.

Part of NATURE CANCER, p. 1066-1081, 2020

• DOI for The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia

Gronroos, Toni; Makinen, Artturi; Laukkanen, Saara; Mehtonen, Juha et al.

Part of Scientific Reports, 2020

• DOI for Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia
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Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia

Ivanov Öfverholm, I.; Zachariadis, V.; Taylan, F.; Marincevic-Zuniga, Yanara et al.

Part of Leukemia and Lymphoma, p. 604-613, 2020

• DOI for Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia
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Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling

Lundtoft, Christian; Pucholt, Pascal; Imgenberg-Kreuz, Juliana; Carlsson Almlöf, Jonas et al.

Part of PLOS Genetics, 2020

• DOI for Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling
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Chapter Eleven: Advances in whole genome methylomic sequencing

Nordlund, Jessica

Part of Epigenetics Methods, p. 213-233, 2020

• DOI for Chapter Eleven: Advances in whole genome methylomic sequencing

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

Nordlund, Jessica; Marincevic-Zuniga, Yanara; Cavelier, Lucia; Raine, Amanda et al.

Part of Scientific Reports, 2020

• DOI for Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing
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High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus

Reid, Sarah; Alexsson, Andrei; Frodlund, Martina; Morris, David et al.

Part of Annals of the Rheumatic Diseases, p. 363-369, 2020

• DOI for High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus
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Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL

Watanabe, A.; Miyake, K.; Nordlund, Jessica; Syvänen, Ann-Christine et al.

Part of Blood, p. 2319-2333, 2020

• DOI for Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL

Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus

Almlöf, Jonas Carlsson; Nystedt, Sara; Leonard, Dag; Eloranta, Maija-Leena et al.

Part of Human Genetics, p. 141-150, 2019

• DOI for Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus
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CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia

Chen, Dongfeng; Camponeschi, Alessandro; Wu, Qingqing; Gerasimcik, Natalija et al.

Part of British Journal of Haematology, p. 418-423, 2019

• DOI for CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia

Arteria: An automation system for a sequencing core facility

Dahlberg, Johan; Hermansson, Johan; Sturlaugsson, Steinar; Lysenkova, Mariya et al.

Part of GigaScience, 2019

• DOI for Arteria: An automation system for a sequencing core facility
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A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts

Farias, Fabiana H. G.; Dahlqvist, Johanna; Kozyrev, Sergey V.; Leonard, Dag et al.

Part of European Journal of Human Genetics, p. 432-441, 2019

• DOI for A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts
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Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients.

Idborg, Helena; Zandian, Arash; Ossipova, Elena; Wigren, Edvard et al.

Part of Frontiers in Immunology, 2019

• DOI for Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients.
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Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjogren's Syndrome

Imgenberg-Kreuz, Juliana; Carlsson Almlöf, Jonas; Leonard, Dag; Sjöwall, Christopher et al.

Part of Frontiers in Immunology, 2019

• DOI for Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjogren's Syndrome
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