Long-term support projects

Click on a project for further details and links to publications, analysis tools and data.

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  • 1000 ancient genomes PI: Anders Götherström (SU)
    Application round: May 2019
    Subject: Evolutionary Biology/Genetics

    Co-applicants: Love Dalén (NRM)
  • A new diagnostic test for rheumatoid arthritis PI: Rikard Holmdahl (KI)
    Application round: Oct 2018
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Inger Gjertsson (GU)
  • Acquisition of lymphatic endothelial cell fate during zebrafish development PI: Kaska Koltowska (UU)
    Application round: Feb 2019
    Subject: Cell and Developmental Biology

    Co-applicants: Hannah Stanforth (UU)
  • Adaptive deregulation of miRNA genes by genomic rearrangements PI: Carlos Rovira (LU)
    Application round: Feb 2019
    Subject: Cancer Biology
  • B cell receptor diversity and convergence after COVID-19 vaccination PI: Karin Loré (KI)
    Application round: Jan 2021
    Subject: Molecular Medicine & Biomarkers
  • Baltic sea CRISPR dynamics PI: Anders Andersson (KTH)
    Application round: Feb 2016
    Subject: Biodiversity
  • Barcode-linked reads technology for genome sequencing and haplotyping PI: Afshin Ahmadian (KTH)
    Application round: Feb 2019
    Subject: New Technology Development
  • Cellular heterogeneity and differentiation during salamander regeneration PI: Andras Simon (KI)
    Application round: Jan 2020
    Subject: Cell and Developmental Biology
  • Chromatin dynamics and inheritance PI: Simon Elsässer (KI)
    Application round: May 2017
    Subject: Cell and Developmental Biology
  • Chromatin-associated RNAs and their roles in chromatin regulation PI: Neus Visa (SU)
    Application round: Feb 2019
    Subject: Cell and Developmental Biology

    Co-applicants: Jordi Planells (SU), Vincent Pelechano (KI)
  • Clonal evolution from diagnosis to relapse in acute lymphoblastic leukemia PI: Ann-Christine Syvänen (UU)
    Application round: Oct 2016
    Subject: Cancer Biology
  • Correlation between patient-derived CAR-T cells and treatment outcome PI: Magnus Essand (UU)
    Application round: Jan 2021
    Subject: Molecular Medicine & Biomarkers
  • Data integration for molecular classification of multiple sclerosis patients PI: Maja Jagodic (KI)
    Application round: Feb 2019
    Subject: Molecular Medicine & Biomarkers
    Publications:
    Zheleznyakova et al. Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology. Proc Natl Acad Sci USA 118:e2011574118 (2021)
    Data: ncRNA counts
  • Decoding the birth of hair follicles by single-cell RNA-seq PI: Maria Kasper (KI)
    Application round: Sep 2017
    Subject: Cell and Developmental Biology
  • Defining cell heterogeneity and therapy resistance in neuroblastoma PI: Per Kogner (KI)
    Application round: Oct 2018
    Subject: Cancer Biology

    Co-applicants: Ninib Baryawno (KI)
  • Delineating the genetics in severe scoliosis PI: Paul Gerdhem (KI)
    Application round: Oct 2020
    Subject: Human Genetics

    Co-applicants: Elisabet Einarsdottir (KTH), Juha Kere (KI)
  • Dissection of cell-fate decisions in early B lymphocyte activation PI: Taras Kreslavskiy (KI)
    Application round: Oct 2019
    Subject: Cell and Developmental Biology
  • Environmental genomics in the Northern krill PI: Andreas Wallberg (UU)
    Application round: Oct 2018
    Subject: Evolutionary Biology/Genetics
  • Epigenetic regulation of human skin wound healing PI: Ning Xu Landén (KI)
    Application round: Oct 2020
    Subject: Molecular Medicine & Biomarkers
  • Epigenetics of acute myeloid leukemia PI: Karl Ekwall (KI)
    Application round: Nov 2014
    Subject: Cancer Biology
  • Establishment of epigenomic landscapes in the Drosophila embryo PI: Mattias Mannervik (SU)
    Application round: May 2019
    Subject: Cell and Developmental Biology
  • Evolution of human skeletal muscle metabolism PI: Ola Hansson (LU)
    Application round: Sep 2017
    Subject: Evolutionary Biology/Genetics
  • Evolution of sex chromosomes PI: Bengt Hansson (LU)
    Application round: Oct 2016
    Subject: Evolutionary Biology/Genetics
  • Evolutionary genomics of Darwin's finches PI: Leif Andersson (UU)
    Application round: Feb 2019
    Subject: Evolutionary Biology/Genetics

    Co-applicants: Mats Pettersson (UU)
  • Evolutionary genomics of the Motacilla (wagtails) radiation PI: Per Alström (UU)
    Application round: May 2020
    Subject: Evolutionary Biology/Genetics

    Co-applicants: Erik Enbody (UU), Leif Andersson (UU)
  • Fat heterogeneity PI: Kirsty Spalding (KI)
    Application round: Jun 2016
    Subject: Cell and Developmental Biology
  • Fate mapping of human cells PI: Jonas Frisén (KI)
    Application round: Feb 2016
    Subject: New Technology Development
    Publications:
    Hård et al. Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing. Genome Biol 20:68 (2019)
  • From single nuclei genomes to the arbuscular mycorrhizal tree of life PI: Anna Rosling Larsson (UU)
    Application round: May 2018
    Subject: Evolutionary Biology/Genetics
  • Genome and metagenome of the deep-sea Swedish sponge Geodia barretti PI: Paco Cárdenas (UU)
    Application round: Jan 2020
    Subject: Biodiversity
  • Genome-wide consequences of population declines in endangered species PI: Love Dalén (NRM)
    Application round: Sep 2017
    Subject: Evolutionary Biology/Genetics

    Co-applicants: Johanna von Seth (SU), Nicolas Dussex (NRM)
    Publications:
    Larsson et al. Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox. Philos Trans R Soc Lond B Biol Sci 374:20190212 (2019) Lord et al. Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros. Curr Biol 30:3871-3879.e7 (2020) von Seth et al. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations. Nat Commun 12:2393 (2021)
  • Genome-wide screen for inhibitors of lysosomal damage-induced cell death PI: Sonja Aits (LU)
    Application round: Oct 2018
    Subject: Cell and Developmental Biology
  • Genomic analysis of adaptation to climate change in two bumblebee species PI: Matthew Webster (UU)
    Application round: Sep 2017
    Subject: Evolutionary Biology/Genetics
    Publications:
    Christmas et al. Genetic barriers to historical gene flow between cryptic species of alpine bumblebees revealed by comparative population genomics. Mol Biol Evol advance online publication (2021)
    Data: WGS reads
  • Genomic analysis of pediatric solid tumors PI: Monica Nistér (KI)
    Application round: May 2017
    Subject: Cancer Biology

    Co-applicants: Teresita Diaz de Ståhl (KI), Johanna Sandgren (KI), Maxime Garcia (KI), Gustaf Ljungman (UU)
    Publications:
    Garcia et al. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res 9:63 (2020)
    Tools and scripts:
    Sarek – Complete open source pipeline to detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data.
  • Genomic and transcriptome profiling of MDS cells PI: Eva Hellström-Lindberg (KI)
    Application round: May 2019
    Subject: Cancer Biology

    Co-applicants: Seishi Ogawa (Kyoto Univ. and KI)
  • Genomic dynamics over space and time in salmonid metapopulations PI: Linda Laikre (SU)
    Application round: May 2018
    Subject: Evolutionary Biology/Genetics
    Publications:
    Kurland et al. Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species. Ecol Evol 9:11448-11463 (2019)
  • Identification of functionally perturbing non-coding mutations PI: Robert Måsson (KI)
    Application round: Jan 2017
    Subject: Cancer Biology
  • Impact of spaceflight on mouse heart spatial gene expression PI: Stefania Giacomello (KTH)
    Application round: May 2020
    Subject: Cell and Developmental Biology
  • Improved gene-finding annotation in complex genomes PI: Anders Blomberg (GU)
    Application round: May 2019
    Subject: Evolutionary Biology/Genetics
  • Imputing genetic variants in a high kinship human cohort PI: Åsa Johansson (UU)
    Application round: Jun 2015
    Subject: Human Genetics
    Publications:
    Höglund et al. Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers. Sci Rep 9:16844 (2019)
  • Insect aging omics PI: Christopher Wheat (SU)
    Application round: Jun 2016
    Subject: Evolutionary Biology/Genetics
    Publications:
    Lehmann et al. Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases. J Exp Biol 221:jeb169508 (2018)
    Data: Cold tolerance and metabolome data
  • Integrate multiple omics in 9000 Swedish individuals PI: Marju Orho-Melander (LU)
    Application round: Jan 2020
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Louise Brunkwall (LU)
  • Interneuronal populations in locomotor networks PI: Ole Kiehn (KI)
    Application round: Feb 2014
    Subject: Cell and Developmental Biology
  • Intragenomic conflict PI: Hanna Johannesson (UU)
    Application round: Jan 2017
    Subject: Evolutionary Biology/Genetics
    Publications:
    Hosseini et al. Comparative analysis of genome-wide DNA methylation in Neurospora. Epigenetics 15:972-987 (2020)
  • Is DNA methylation heritable in clonal water fleas? PI: Tobias Uller (LU)
    Application round: Jan 2018
    Subject: Evolutionary Biology/Genetics

    Co-applicants: Reinder Radersma (LU)
  • Long-term evolution of germline-restricted chromosomes in songbirds PI: Alexander Suh (UU)
    Application round: Jan 2020
    Subject: Evolutionary Biology/Genetics

    Co-applicants: Francisco Ruiz-Ruano (UU)
  • Longitudinal proteomic profiling in blood and airways of COVID-19 patients PI: Anna Smed Sörensen (KI)
    Application round: Oct 2020
    Subject: Molecular Medicine & Biomarkers
  • Machine learning approach to spatially resolved sequencing in brain tissue PI: Tomas Björklund (LU)
    Application round: Feb 2019
    Subject: New Technology Development
  • Massive and parallel single-cell sequencing of eukaryotic plankton PI: Anders Andersson (KTH)
    Application round: Oct 2020
    Subject: New Technology Development

    Co-applicants: Rachel Foster (SU)
  • Microbes in the deep PI: Mark Dopson (LNU)
    Application round: Jan 2017
    Subject: Biodiversity
    Tools and scripts:
    Metagenomics pipeline – a Snakemake workflow for processing and analysis of metagenomic sequence reads
  • Mitochondrial dysfunction in Parkinson's disease PI: Nils-Göran Larsson (KI)
    Application round: May 2017
    Subject: Molecular Medicine & Biomarkers
  • Molecular pathogenesis of liver lipotoxicity PI: Margit Mahlapuu (GU)
    Application round: May 2020
    Subject: Molecular Medicine & Biomarkers
  • Multiomics analysis of response to epigenetic treatments in multiple myeloma PI: Helena Jernberg Wiklund (UU)
    Application round: Jan 2020
    Subject: Cancer Biology

    Co-applicants: Jan Komorowski (UU)
  • Mutation calling to enable sensitive proteogenomics for cancer immunotherapy PI: Janne Lehtiö (KI)
    Application round: Oct 2018
    Subject: New Technology Development

    Co-applicants: Rui Branca (KI)
  • Non-coding regulatory RNAs in the transition from uni- to multicellularity PI: Fredrik Söderbom (UU)
    Application round: May 2020
    Subject: Cell and Developmental Biology
  • Novel regulatory patterns of biofilm formation in Candida parapsilosis PI: Ute Römling (KI)
    Application round: May 2018
    Subject: Cell and Developmental Biology
  • Omics of sleep loss PI: Christian Benedict (UU)
    Application round: Oct 2016
    Subject: Cell and Developmental Biology

    Co-applicants: Jonathan Cedernaes (UU)
    Publications:
    Cedernaes et al. Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans. Sci Adv 4:eaar8590 (2018)
    Tools and scripts:
    RNA-seq and DNA methylation analysis – R scripts and output
    Data: RNA-seq data DNA methylation data
  • Oral microbiota and immune dynamics in early cancer protection PI: Margaret Sällberg Chen (KI)
    Application round: Oct 2019
    Subject: Cancer Biology
    Publications:
    Morgell et al. Metabolic characterization of plasma and cyst fluid from cystic precursors to pancreatic cancer patients reveal metabolic signatures of bacterial infection. J Proteome Res 20:2725-2738 (2021)
  • Organ-specific features of the lymphatic vasculature in the gastrointestinal tract PI: Taija Mäkinen (UU)
    Application round: May 2020
    Subject: Cell and Developmental Biology
  • Pericyte fibrosis PI: Christian Göritz (KI)
    Application round: Jun 2016
    Subject: Cell and Developmental Biology
    Tools and scripts:
    Single-cell RNA-seq pipeline – a Snakemake workflow for quality control and basic analysis of single-cell RNA-seq data (under development)
  • Pneumonial metagenomics, metatranscriptomics and metabolomics PI: Birgitta Henriques-Normark (KI)
    Application round: Jun 2016
    Subject: Molecular Medicine & Biomarkers
    Tools and scripts:
    Metagenomics pipeline – a Snakemake workflow for processing and analysis of metagenomic sequence reads
  • Preimplantation stress: programming our future generations PI: Sophie Petropoulos (KI)
    Application round: Jan 2017
    Subject: Cell and Developmental Biology
  • Profiling of drug treatments on sarcoma and coronavirus-infected cell lines PI: Ola Spjuth (UU)
    Application round: May 2020
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Sven Nelander (UU), Jordi Carreras-Puigvert (KI)
  • Prophylactic probiotics to extremely low birth weight preterm infants PI: Thomas Abrahamsson (LiU)
    Application round: Oct 2018
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Maria Jenmalm (LiU)
    Tools and scripts:
    Metagenomics pipeline – a Snakemake workflow for processing and analysis of metagenomic sequence reads
  • Proteogenomics of radiotherapy resistance in locally recurring breast cancer PI: Emma Niméus (LU)
    Application round: Jan 2020
    Subject: Cancer Biology

    Co-applicants: Lars Malmström (Univ. of Zurich)
  • Quantifying the dynamics of the blood plasma proteome during acute HIV PI: Joakim Esbjörnsson (LU)
    Application round: Jan 2021
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Jamirah Nazziwa (LU)
  • Redefining the molecular landscape of triple-negative breast cancer PI: Johan Staaf (LU)
    Application round: Oct 2018
    Subject: Cancer Biology
  • Reproductive isolation and the evolution of key innovations PI: Charlie Cornwallis (LU)
    Application round: Feb 2015
    Subject: Evolutionary Biology/Genetics
  • Respiratory genomics in flies and mammals PI: Christos Samakovlis (SU)
    Application round: Nov 2014
    Subject: Cell and Developmental Biology
  • Seqitope - a novel tool for mapping antibody epitopes PI: Mats Persson (KI)
    Application round: Oct 2020
    Subject: New Technology Development

    Co-applicants: Anders Andersson (KTH)
  • Sex-biased gene expression and its dependence on condition PI: Urban Friberg (LiU)
    Application round: May 2018
    Subject: Evolutionary Biology/Genetics
  • Sex-limited experimental evolution of novel sex chromosomes PI: Jessica Abbott (LU)
    Application round: May 2018
    Subject: Evolutionary Biology/Genetics
  • Single cell profiling of cell types and lineages in the mouse brain PI: Jonas Frisén (KI)
    Application round: Jan 2018
    Subject: New Technology Development
  • Single-cell analysis of SARS-CoV-2 infection in a 3D primary cell lung PI: Johan Henriksson (UmU)
    Application round: Jan 2021
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Anna Överby Wernstedt (UmU), Annasara Lenman (UmU)
  • Single-cell gene expression analysis of limb regeneration PI: Andras Simon (KI)
    Application round: Jun 2015
    Subject: Cell and Developmental Biology
  • Somatic mutations and its implications for age-related disease PI: Maria Eriksson (KI)
    Application round: Oct 2020
    Subject: Human Genetics
  • SuperGenE - supergene evolution in a classic plant system PI: Tanja Slotte (SU)
    Application round: Feb 2019
    Subject: Evolutionary Biology/Genetics
  • Symbiont-induced host speciation in insects PI: Lisa Klasson (UU)
    Application round: Jan 2017
    Subject: Evolutionary Biology/Genetics
  • Systems biology dynamics of liver regeneration in humans PI: Niklas Björkström (KI)
    Application round: Oct 2019
    Subject: Cell and Developmental Biology

    Co-applicants: Martin Cornillet (KI)
  • Targeting topoisomerase regulation as a mean to control transcription in cancer cells PI: Laura Baranello (KI)
    Application round: Oct 2019
    Subject: Cancer Biology
  • The basis of inherited migratory directions in the Australian bogong moth PI: Eric Warrant (LU)
    Application round: May 2018
    Subject: Evolutionary Biology/Genetics
  • The epigenetic landscape in MLL-rearranged leukemia PI: Anna Andersson (LU)
    Application round: Feb 2016
    Subject: Cancer Biology
  • The genomics and transcriptomics behind Nature's high performance material PI: Anna Rising (KI)
    Application round: Oct 2018
    Subject: Cell and Developmental Biology
  • The molecular basis of recombination rate variation in butterflies PI: Niclas Backström (UU)
    Application round: Oct 2019
    Subject: Evolutionary Biology/Genetics
  • The role for gene repression in maintaining differentiated identity PI: Johan Holmberg (KI)
    Application round: May 2019
    Subject: Cell and Developmental Biology
  • The transcriptional landscape of mucosal healing PI: Eduardo Villablanca (KI)
    Application round: May 2020
    Subject: Molecular Medicine & Biomarkers
  • Towards tailored treatments in multiple sclerosis PI: Joachim Burman (UU)
    Application round: Oct 2019
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Kim Kultima (UU)
  • Tracing human history in southern Africa using ancient proteomics PI: Carina Schlebusch (UU)
    Application round: Jan 2021
    Subject: Evolutionary Biology/Genetics

    Co-applicants: Imke Lankheet (UU)
  • Transcriptional and immune receptor profiling of influenza-specific B cells PI: Davide Angeletti (GU)
    Application round: Oct 2019
    Subject: Cell and Developmental Biology
    Publications:
    Matthew et al. Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells. Cell Rep 35:109286 (2021)
    Tools and scripts:
    Data analysis scripts – Code and supporting files for reproducing the analyses reported in the publication
    Data: VDJ data Gene expression data
  • Transcriptional profiling of mononuclear phagocytes in sarcoidosis patients PI: Anna Smed Sörensen (KI)
    Application round: May 2018
    Subject: Molecular Medicine & Biomarkers
    Publications:
    Lepzien et al. Monocytes in sarcoidosis are potent TNF producers and predict disease outcome. Eur Respir J 2003468 (2021)
  • Transcriptome analysis of memory T cells during influenza virus challenge PI: Nils Lycke (GU)
    Application round: Jan 2018
    Subject: Cell and Developmental Biology
  • Transcriptome analysis of the response to mechanical stimulation in cereals PI: Olivier van Aken (LU)
    Application round: Jan 2020
    Subject: Biodiversity

    Co-applicants: Nick Sirijovski (LU), Essam Darwish (LU)
  • Understanding epigenetics of type 2 diabetes by WGBS PI: Charlotte Ling (LU)
    Application round: Jan 2018
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Alexander Perfilyev (LU)
  • Understanding the tissue-material interface during wound healing PI: Molly Stevens (KI)
    Application round: Jan 2018
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Alessondra Speidel (KI), Annina Steinbach (KI)
  • WGS and RNA-seq in chronic lymphocytic leukemia subsets PI: Richard Rosenquist (UU)
    Application round: Jun 2016
    Subject: Cancer Biology
  • Whole genome sequencing to identify genetic causes of adverse drug reactions PI: Mia Wadelius (UU)
    Application round: Sep 2017
    Subject: Human Genetics
  • Whole-genome sequencing of 1000 colorectal cancers PI: Tobias Sjöblom (UU)
    Application round: Oct 2018
    Subject: Cancer Biology

    Co-applicants: Mathias Uhlén (KTH)
  • Why such high genetic diversity in songbird immunity? PI: Helena Westerdahl (LU)
    Application round: Jun 2016
    Subject: Evolutionary Biology/Genetics
  • scRNA-seq analysis of B cells in patients with Sjögren's Syndrome PI: Ann-Christine Syvänen (UU)
    Application round: Jan 2021
    Subject: Molecular Medicine & Biomarkers

    Co-applicants: Gunnel Nordmark (UU), Gustav Arvidsson (UU), Amanda Raine (UU)

Click on a project for further details and links to publications, analysis tools and data.

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