Amanda Raine

Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

Fegraeus, Kim; Riihimäki, Miia; Nordlund, Jessica; Akula, Srinivas et al.

Part of PLOS ONE, 2025

• DOI for Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells
• Download full text (pdf) of Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

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.
• Download full text (pdf) of Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

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
• Download full text (pdf) of A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

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
• Download full text (pdf) of An endothelial regulatory module links blood pressure regulation with elite athletic performance

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
• Download full text (pdf) of Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

Fegraeus, Kim; Riihimäki, Miia; Nordlund, Jessica; Akula, Srinivas et al.

Part of PLOS ONE, 2025

• DOI for Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells
• Download full text (pdf) of Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

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.
• Download full text (pdf) of Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

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
• Download full text (pdf) of A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

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
• Download full text (pdf) of An endothelial regulatory module links blood pressure regulation with elite athletic performance

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
• Download full text (pdf) of Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

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
• Download full text (pdf) of Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

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.
• Download full text (pdf) of Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.

Comparison of EM-seq and PBAT methylome library methods for low-input DNA

Han, Yanan; Zheleznyakova, Galina Yurevna; Marincevic-Zuniga, Yanara; Kakhki, Majid Pahlevan et al.

Part of Epigenetics, p. 1195-1204, 2022

• DOI for Comparison of EM-seq and PBAT methylome library methods for low-input DNA
• Download full text (pdf) of Comparison of EM-seq and PBAT methylome library methods for low-input DNA

Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species

Feiner, Nathalie; Radersma, Reinder; Vasquez, Louella; Ringner, Markus et al.

Part of iScience, 2022

• DOI for Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species
• Download full text (pdf) of Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species

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
• Download full text (pdf) of scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

Quantitative Transcriptome Analysis of Purified Equine Mast Cells Identifies a Dominant Mucosal Mast Cell Population with Possible Inflammatory Functions in Airways of Asthmatic Horses

Akula, Srinivas; Riihimaki, Miia; Waern, Ida; Abrink, Magnus et al.

Part of International Journal of Molecular Sciences, 2022

• DOI for Quantitative Transcriptome Analysis of Purified Equine Mast Cells Identifies a Dominant Mucosal Mast Cell Population with Possible Inflammatory Functions in Airways of Asthmatic Horses
• Download full text (pdf) of Quantitative Transcriptome Analysis of Purified Equine Mast Cells Identifies a Dominant Mucosal Mast Cell Population with Possible Inflammatory Functions in Airways of Asthmatic Horses

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
• Download full text (pdf) of Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99

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
• Download full text (pdf) of The SEQC2 epigenomics quality control (EpiQC) study

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
• Download full text (pdf) of Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

Data quality of whole genome bisulfite sequencing on Illumina platforms

Raine, Amanda; Liljedahl, Ulrika; Nordlund, Jessica

Part of PLOS ONE, 2018

• DOI for Data quality of whole genome bisulfite sequencing on Illumina platforms
• Download full text (pdf) of Data quality of whole genome bisulfite sequencing on Illumina platforms

Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles

Marincevic-Zuniga, Yanara; Dahlberg, Johan; Nilsson, Sara; Raine, Amanda et al.

Part of Journal of Hematology & Oncology, 2017

• DOI for Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles
• Download full text (pdf) of Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

Raine, Amanda; Manlig, Erika; Wahlberg, Per; Syvänen, Ann-Christine et al.

Part of Nucleic Acids Research, 2017

• DOI for SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing
• Download full text (pdf) of SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands

Wahlberg, Per; Lundmark, Anders; Nordlund, Jessica; Busche, Stephan et al.

Part of Epigenomics, p. 1367-1387, 2016

• DOI for DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands
• Download full text (pdf) of DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands

Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes

Lindqvist, C. Mårten; Lundmark, Anders; Nordlund, Jessica; Freyhult, Eva et al.

Part of Oncotarget, p. 64071-64088, 2016

• DOI for Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes

Histological characterization of orphan transporter MCT14 (SLC16A14) shows abundant expression in mouse CNS and kidney

Roshanbin, Sahar; Lindberg, Frida; Lekholm, Emilia; Perland, Emelie et al.

Part of BMC Neuroscience, 2016

• DOI for Histological characterization of orphan transporter MCT14 (SLC16A14) shows abundant expression in mouse CNS and kidney
• Download full text (pdf) of Histological characterization of orphan transporter MCT14 (SLC16A14) shows abundant expression in mouse CNS and kidney

The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing

Lindqvist, C Mårten; Nordlund, Jessica; Ekman, Diana; Johansson, Anna et al.

Part of Human Mutation, p. 118-128, 2015

• DOI for The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing

PAT4 is abundantly expressed in excitatory and inhibitory neurons as well as epithelial cells

Roshanbin, Sahar; Hellsten, Sofie V; Tafreshiha, Atieh; Zhu, Yinan et al.

Part of Brain Research, p. 12-25, 2014

• DOI for PAT4 is abundantly expressed in excitatory and inhibitory neurons as well as epithelial cells
• Download full text (pdf) of PAT4 is abundantly expressed in excitatory and inhibitory neurons as well as epithelial cells

Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome.

Raine, Amanda; Ivanova, Natalia; Wikberg, Jarl E S; Ehrenberg, Måns

Part of Biochimie, p. 495-500, 2004

Targeting and insertion of heterologous membrane proteins in E. coli

Raine, A; Ullers, R; Pavlov, M; Luirink, J et al.

Part of Biochimie, p. 659-668, 2003

Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome

Ullers, R S; Houben, E N G; Raine, A; ten Hagen-Jongman, C M et al.

Part of J. Cell Biology, p. 679-684, 2003

Computational and Statistical Analysis of Array-Based DNA Methylation Data

Nordlund, Jessica; Backlin, Carin; Raine, Amanda

Part of Cancer Bioinformatics, p. 173-191, Springer, 2019

• DOI for Computational and Statistical Analysis of Array-Based DNA Methylation Data

Identification of somatic single nucleotide variants inleukemia by targeted sequencing of non-indexed overlapping pools

Lindqvist, Carl Mårten; Dahlberg, Johan; Raine, Amanda; Övernäs, Elin et al.

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

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