Long-Term Support Projects

Long-Term support projects

Active projects
Past projects

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

1000 ancient genomes PI: Anders Götherström (SU)

Application round: May 2019
Subject: Evolutionary Biology/Genetics

Co-applicants: Love Dalén (NRM)
A first dog brain atlas to study genome regulation and disease PI: Kerstin Lindblad-Toh (UU)

Application round: Oct 2021
Subject: Cell and Developmental Biology
AI-guided phenomics screening for combination treatments PI: Ola Spjuth (UU)

Application round: Jan 2022
Subject: New Technology Development

Co-applicants: Päivi Östling (KI)
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

Publications:
Hafstað et al. Regulatory networks and 5′ partner usage of miRNA host gene fusions in breast cancer. Int J Cancer 151:95-106 (2022)
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
Biodiversity of the Central Arctic Ocean analyzed by metagenomic eDNA PI: Pauline Snoeijs-Leijonmalm (SU)

Application round: May 2022
Subject: Biodiversity

Co-applicants: Stefan Bertilsson (SLU)
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)
Circadian rhythms in human metabolic tissues - impact of diet PI: Jonathan Cedernaes (UU)

Application round: May 2021
Subject: Molecular Medicine & Biomarkers
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
Deciphering sex differences in the human immune system PI: Nils Landegren (UU)

Application round: Jan 2022
Subject: Molecular Medicine & Biomarkers
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

Publications:
Glaros et al. Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response. Immunity 54:2005-2023.e10 (2021)
Effects of polyploidy on genome evolution and adaptation PI: Pär Ingvarsson (SLU)

Application round: Oct 2021
Subject: Evolutionary Biology/Genetics

Co-applicants: Girma Bedada (SLU)
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
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

Publications:
Oskolkov et al. High-throughput muscle fiber typing from RNA sequencing data. Skelet Muscle 12:16 (2022)
Evolution of sex chromosomes PI: Bengt Hansson (LU)

Application round: Oct 2016
Subject: Evolutionary Biology/Genetics

Publications:
Sigeman et al. Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration. Mol Biol Evol 38:5275-5291 (2021) Sigeman et al. Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data. BMC Genomics 23:328 (2022)
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
From single nuclei genomes to the arbuscular mycorrhizal tree of life PI: Anna Rosling Larsson (UU)

Application round: May 2018
Subject: Evolutionary Biology/Genetics

Publications:
Montoliu-Nerin et al. In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies. Front Fungal Biol 2:716385 (2021)
Genetic resources for extreme weather resilience PI: Jenny Hagenblad (LiU)

Application round: May 2021
Subject: Evolutionary Biology/Genetics

Co-applicants: Matti Leino (SU)
Genetics of songbird migration PI: Staffan Bensch (LU)

Application round: May 2022
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-scale classification of ancient and modern metagenomic data PI: Tom van der Valk (NRM)

Application round: May 2022
Subject: Biodiversity

Co-applicants: Peter Heintzman (SU), Anna Linderholm (SU)
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 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) Saha et al. Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes. Mol Ecol 31:498-511 (2021) Kurland et al. Genomic dynamics of brown trout populations released to a novel environment. Ecol Evol 12:e9050 (2022)
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
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
Insect biome atlas PI: Fredrik Ronquist (NRM)

Application round: Oct 2021
Subject: Biodiversity

Co-applicants: Tomas Roslin (SLU), Ayco Tack (SU), Piotr Lukasik (Jagiellonian Uni.), Anders Andersson (KTH)
Inspiration at birth: Inflammation & perturbation of perinatal breathing PI: Eric Herlenius (KI)

Application round: May 2022
Subject: Cell and Developmental Biology

Co-applicants: Wiktor Phillips (Massachusetts Institute of Technology)
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)
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) Nguyen et al. Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies. Fungal Genetics Reports 66:1 (2022) Meunier et al. Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma. Proc Biol Sci 289:20220971 (2022)
Large national study of COVID-19 symptoms, exposures, and risk factors PI: Paul Franks (LU)

Application round: May 2021
Subject: Molecular Medicine & Biomarkers

Co-applicants: Maria Gomez (LU)

Publications:
Kennedy et al. App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden. Nat Commun 13:2110 (2022)
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
Loss of Y in leukocytes may predispose to severe COVID-19 in males PI: Jan Dumanski (UU)

Application round: May 2021
Subject: Molecular Medicine & Biomarkers

Co-applicants: Daniil Sarkisyan (UU)
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

Publications:
Mehrshad et al. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nat Commun 12:4253 (2021)

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 GI tract PI: Taija Mäkinen (UU)

Application round: May 2020
Subject: Cell and Developmental Biology
Paediatric medulloblastoma and effects of radiotherapy PI: Klas Blomgren (KI)

Application round: Oct 2021
Subject: Cancer Biology
Pneumonial metagenomics, metatranscriptomics and metabolomics PI: Birgitta Henriques-Normark (KI)

Application round: Jun 2016
Subject: Molecular Medicine & Biomarkers

Publications:
Nannapaneni et al. Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health. Am J Respir Crit Care Med advance online publication (2022)

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

Publications:
Zhao et al. Single-cell multi-omics of human preimplantation embryos demonstrates susceptibility to glucocorticoids. Genome Res 32:1627-1641 (2022)
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

Publications:
Malacrinò et al. Ageing desexualizes the Drosophila brain transcriptome. Proc R Soc B 289:20221115 (2022)
Sex-limited experimental evolution of novel sex chromosomes PI: Jessica Abbott (LU)

Application round: May 2018
Subject: Evolutionary Biology/Genetics
Single cell characterization of pathogenic immune cells in MS PI: Maja Jagodic (KI)

Application round: May 2022
Subject: Molecular Medicine & Biomarkers
Single cell profiling of cell types and lineages in the mouse brain PI: Jonas Frisén (KI)

Application round: Jan 2018
Subject: New Technology Development

Publications:
Ratz et al. Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nat Neurosci 25:285-294 (2022)
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
Single-nucleus profiling of humidity and temperature sensing neurons PI: Anders Enjin (LU)

Application round: May 2021
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

Publications:
Gutiérrez-Valencia et al. Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level. Curr Biol advance online publication (2022)
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 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

Publications:
Boman et al. The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes. Genome Biol Evol 13:evab064 (2021)
The role for gene repression in maintaining differentiated identity PI: Johan Holmberg (KI)

Application round: May 2019
Subject: Cell and Developmental Biology

Publications:
Toskas et al. PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons. Sci Adv 8:eabo1543 (2022)
The transcriptional landscape of mucosal healing PI: Eduardo Villablanca (KI)

Application round: May 2020
Subject: Molecular Medicine & Biomarkers
The tumour immune microenvironment in mantle cell lymphoma PI: Sara Ek (LU)

Application round: May 2021
Subject: Cancer Biology

Co-applicants: Anna Gerdtsson (LU), Mats Jerkeman (LU)
Towards tailored treatments in multiple sclerosis PI: Joachim Burman (UU)

Application round: Oct 2019
Subject: Molecular Medicine & Biomarkers

Co-applicants: Kim Kultima (UU)

Publications:
Carlsson et al. Evaluation of polarity switching for untargeted lipidomics using liquid chromatography coupled to high resolution mass spectrometry. Journal of Chromatography B 1195:123200 (2022)
Tracing human history in southern Africa using ancient proteomics PI: Carina Schlebusch (UU)

Application round: May 2021
Subject: Evolutionary Biology/Genetics

Co-applicants: Imke Lankheet (UU)
Transcription factor networks underlying dendritic cell reprogramming PI: Filipe Pereira (LU)

Application round: Oct 2021
Subject: Cell and Developmental Biology
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 tumour necrosis factor producers and predict disease outcome. Eur Respir J 58:2003468 (2021) Lepzien et al. Pulmonary and blood dendritic cells from sarcoidosis patients more potently induce IFNγ-producing Th1 cells compared with monocytes. J Leukoc Biol 111:857-866 (2021)
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)
Tumor evolution and metastasis: finding drivers among neutral mutation PI: Mattias Höglund (LU)

Application round: Jan 2022
Subject: Cancer Biology

Co-applicants: Carina Bernardo (LU)
Ultra-fast and accurate alignment with a novel fuzzy seeding technique PI: Kristoffer Sahlin (SU)

Application round: Jan 2022
Subject: New Technology Development
Understanding ageing through the lens of the transcriptome PI: Urban Friberg (LiU)

Application round: May 2022
Subject: Evolutionary Biology/Genetics
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)
Unraveling the mechanism of nuclear small RNA mediated gene silencing PI: Aishe Sarshad (GU)

Application round: May 2022
Subject: Cell and Developmental Biology

Co-applicants: Daniel Benhalevy (University of Tel Aviv)
Using transcriptomics for closed-loop model improvement PI: Ross King (CTH)

Application round: May 2021
Subject: New Technology Development
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)
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)

  Organization,No of projects
  CTH, 1
  GU, 4
  KI, 34
  KTH, 4
  LNU, 1
  LU, 21
  LiU, 4
  NRM, 2
  SLU, 1
  SU, 9
  UU, 26
  UmU, 1

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

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A new diagnostic test for rheumatoid arthritis PI: Rikard Holmdahl (KI)

Application round: Oct 2018
Subject: Molecular Medicine & Biomarkers

Co-applicants: Inger Gjertsson (GU)
Acoelomorph genomes PI: Ulf Jondelius (NRM)

Application round: Jun 2015
Subject: Evolutionary Biology/Genetics
Analysis of the nuclear and cytosolic transcriptomes in human brain PI: Lars Feuk (UU)

Application round: Feb 2015
Subject: New Technology Development

Publications:
Zaghlool et al. Expression profiling and in situ screening of circular RNAs in human tissues. Sci Rep 8:16953 (2018) Zaghlool et al. Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts. Sci Rep 11:4076 (2021)
Ancient DNA metagenome PI: Barbara Wohlfarth (SU)

Application round: Jun 2016
Subject: Biodiversity

Publications:
Ahmed et al. Archaeal community changes in lateglacial lake sediments: Evidence from ancient DNA. Quat Sci Rev 181:19-29 (2018) Parducci et al. Shotgun environmental DNA, pollen, and macrofossil analysis of lateglacial lake sediments from southern Sweden. Front Ecol Evol 7:189 (2019)
Data: DNA sequence reads
Antibody repertoires PI: Gunilla Karlsson Hedestam (KI)

Application round: May 2014
Subject: New Technology Development

Publications:
Corcoran et al. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity. Nat Commun 7:13642 (2016)

Tools and scripts:
IgDiscover – Software for antibody repertoire analysis and V gene discovery from high-throughput sequencing reads
Bacterial regulatory RNAs PI: Emmanuelle Charpentier (UmU)

Application round: Oct 2013
Subject: Evolutionary Biology/Genetics

Publications:
Le Rhun et al. RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. RNA Biol 13:177-195 (2015) Le Rhun et al. Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes. Nucleic Acids Res gkw1316 (2017)
Data: RNA-seq data set 1 RNA-seq data set 2
Beetle genome assembly and annotation PI: Göran Arnqvist (UU)

Application round: May 2013
Subject: Evolutionary Biology/Genetics

Publications:
Sayadi et al. The evolution of dark matter in the mitogenome of seed beetles. Genome Biol Evol 9:2697-2706 (2017) Sayadi et al. The genomic footprint of sexual conflict. Nat Ecol Evol 3:1725-1730 (2019)
Biodiversity in air PI: Per Stenberg (UmU)

Application round: Jun 2016
Subject: Biodiversity

Tools and scripts:
Metagenomics pipeline – a snakemake workflow for processing and analysis of metagenomic sequence reads
Body weight sensor PI: Claes Ohlsson (GU)

Application round: Oct 2016
Subject: Cell and Developmental Biology
Cancer proteogenomics PI: Janne Lehtiö (KI)

Application round: Nov 2014
Subject: Cancer Biology

Publications:
Zhu et al. Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nat Commun 9:903 (2018) Johansson et al. Breast cancer quantitative proteome and proteogenomic landscape. Nat Commun 10:1600 (2019)
Data: Proteomics data for A431 cells and tissues Proteomics data for breast tumors Proteomics data for tumor and matched normal tissue RNA-seq data for A431 cells RNA-seq data for tissues
Clonal evolution from diagnosis to relapse in acute lymphoblastic leukemia PI: Ann-Christine Syvänen (UU)

Application round: Oct 2016
Subject: Cancer Biology

Publications:
Sayyab et al. Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia. Sci Rep 11:15988 (2021)
Colon cancer genes PI: Erik Johansson (UmU)

Application round: Feb 2014
Subject: Cancer Biology

Publications:
Rentoft et al. A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis. PLoS One 14:e0213350 (2019)
DACP rat genome sequencing PI: Ulrika Norin (KI)

Application round: Jan 2013
Subject: Molecular Medicine & Biomarkers

Publications:
Norin et al. Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation. Nat Commun 12:610 (2021)
Development and diversity of midbrain dopamine neurons PI: Thomas Perlmann (KI)

Application round: Feb 2014
Subject: Cell and Developmental Biology

Publications:
Kee et al. Single-cell analysis reveals a close relationship between differentiating dopamine and subthalamic nucleus neuronal lineages. Cell Stem Cell 20:29-40 (2017) Tiklová et al. Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development. Nat Commun 10:581 (2019)
Data: RNA-seq data set 1 RNA-seq data set 2
Diabetogenic perturbations of the fetal methylome PI: Paul Franks (LU)

Application round: Jan 2017
Subject: New Technology Development
Diseases in human history PI: Kristian Kristiansen (GU)

Application round: Oct 2015
Subject: Biodiversity

Tools and scripts:
Metagenomics pipeline – a snakemake workflow for processing and analysis of metagenomic sequence reads
Endurance training and gene expression in human muscle PI: Carl-Johan Sundberg (KI)

Application round: Jan 2013
Subject: Cell and Developmental Biology

Publications:
Lindholm et al. The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing. FASEB J 28:4571-4581 (2014) Lindskog et al. The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling. BMC Genomics 16:475 (2015) Lindholm et al. The impact of endurance training on human skeletal muscle memory, global isoform expression and novel transcripts. PLoS Genet 12:e1006294 (2016)
Data: RNA-seq data set 1 RNA-seq data set 2 RNA-seq data set 3 RNA-seq data set 4
Epigenetic states of oligodendrocyte lineage cells PI: Gonçalo Castelo-Branco (KI)

Application round: Feb 2016
Subject: Cell and Developmental Biology

Publications:
Marques et al. Transcriptional convergence of oligodendrocyte lineage progenitors during development. Dev Cell 46:504-517 (2018) Falcão et al. Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis. Nat Med 24:1837-1844 (2018)

Tools and scripts:
OPCs throughout mouse development – Web resource for exploring gene expression data from Marques et al. Oligodendrocyte lineage in a mouse model of multiple sclerosis – Web resource for exploring gene expression data from Falcão et al.
Data: Bulk RNA-seq data Single-cell RNA-seq data 1 Single-cell RNA-seq data 2
Epigenetics of acute myeloid leukemia PI: Karl Ekwall (KI)

Application round: Nov 2014
Subject: Cancer Biology
Evolution of gene regulation in plants PI: Tanja Slotte (UU)

Application round: Jan 2013
Subject: Evolutionary Biology/Genetics

Publications:
Steige et al. Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Mol Biol Evol 32:2501-2514 (2015) Steige et al. The role of transposable elements for gene expression in Capsella hybrids and allopolyploids. bioRxiv 44016 (2016) Steige et al. Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora. Proc Natl Acad Sci USA 114:1087-1092 (2017)
Examination of embryonic and adult stem cell characteristics PI: Jonas Muhr (KI)

Application round: May 2014
Subject: Cell and Developmental Biology

Publications:
Hagey et al. Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells. Genome Res 26:908-917 (2016) Klum et al. Sequentially acting SOX proteins orchestrate astrocyte‐ and oligodendrocyte‐specific gene expression. EMBO Rep e46635 (2018)
Exercise-regulated mechanisms in mouse organs PI: Pontus Boström (KI)

Application round: Feb 2014
Subject: Cell and Developmental Biology
Exploring sex-biased gene expression in willows PI: Sofia Berlin Kolm (SLU)

Application round: Oct 2015
Subject: Evolutionary Biology/Genetics

Publications:
Almeida et al. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 18:78 (2020) Hallingbäck et al. Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis. BMC Genomics 22:710 (2021)
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)
Finding causal variants within schizophrenia risk loci PI: Patrick Sullivan (KI)

Application round: Oct 2016
Subject: Human Genetics

Publications:
Halvorsen et al. Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia. Nat Commun 11:1842 (2020)
Finding new treatments for type 2 diabetes PI: Nils Wierup (LU)

Application round: Feb 2015
Subject: Molecular Medicine & Biomarkers
Flycatcher genomics PI: Hans Ellegren (UU)

Application round: Jan 2013
Subject: Evolutionary Biology/Genetics

Publications:
Burri et al. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Res 25:1656-1665 (2015)
Data: Reference genome assembly Genotypes for linkage analysis Resequencing data
Fungal genome annotation through proteogenomics PI: Annika Scheynius (KI)

Application round: May 2013
Subject: New Technology Development

Publications:
Zhu et al. Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. Nucleic Acids Res 45:2629-2643 (2017)
Data: DNA sequence reads, genome assemblies and gene annotation RNA-seq data Proteomics data
Gene regulatory networks in β-cells PI: Olov Andersson (KI)

Application round: Sep 2017
Subject: Cell and Developmental Biology

Publications:
Charbord et al. In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR. Nat Metab 3:682-700 (2021)

Tools and scripts:
Data exploration – Web resource for exploring gene expression data from Charbord et al.
Data: RNA-seq data
Genetic associations of serum lipidome in a prospective cohort PI: Olle Melander (LU)

Application round: May 2014
Subject: Molecular Medicine & Biomarkers

Publications:
Kjellqvist et al. Identification of shared and unique serum lipid profiles in diabetes mellitus and myocardial infarction. J Am Heart Assoc 5:e004503 (2016) Fernandez et al. Plasma lipidome and prediction of type 2 diabetes in the population-based Malmö diet and cancer cohort. Dia Care 43:366-373 (2020) Ottosson et al. A plasma lipid signature predicts incident coronary artery disease. Int J Cardiol 331:249-254 (2021)
Genetic risk factors for ANCA-associated vasculitides PI: Kerstin Lindblad-Toh (UU)

Application round: Feb 2015
Subject: Human Genetics

Publications:
Dahlqvist et al. Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA. Rheumatology 61:3461-3470 (2022)
Genetic variation of European aspen PI: Pär Ingvarsson (UmU)

Application round: Oct 2013
Subject: Evolutionary Biology/Genetics

Publications:
Wang et al. A major locus controls local adaptation and adaptive life history variation in a perennial plant. Genome Biol 19:72 (2018) Lin et al. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proc Natl Acad Sci USA 115:E10970-E10978 (2018)
Genetics of heart stress recovery PI: Jan Borén (GU)

Application round: Oct 2013
Subject: Human Genetics
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) Dussex et al. Population genomics of the critically endangered kakapo. Cell Genomics 1:100002 (2021) Kutschera et al. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 23: (2022)

Tools and scripts:
GenErode – A pipeline for analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
Genome-wide epigenetic variation in type 2 diabetes PI: Charlotte Ling (LU)

Application round: Nov 2014
Subject: Human Genetics

Publications:
Bysani et al. ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes. Sci Rep 9:7785 (2019)
Data: Gene expression data ATAC-seq data
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 38:3126-3143 (2021) Christmas et al. A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component. Mol Ecol 31:1111-1127 (2021)
Data: WGS reads
Hemostatic regulation in human liver PI: Christina Jern (GU)

Application round: May 2014
Subject: Human Genetics

Publications:
Olsson Lindvall et al. Hemostatic genes exhibit a high degree of allele-specific regulation in liver. Thromb Haemost 119:1072-1083 (2019) Olsson Lindvall et al. A comprehensive sequencing-based analysis of allelic methylation patterns in hemostatic genes in human liver. Thromb Haemost 120:229-242 (2020) Olsson Lindvall et al. Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals. Thromb Haemost 121:573-583 (2021)
Human structural genetic variation PI: Magnus Nordenskjöld (KI)

Application round: Nov 2014
Subject: Human Genetics

Publications:
Eisfeldt et al. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res 6:664 (2017) Lindstrand et al. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. Genome Med 11:68 (2019)

Tools and scripts:
vcf2cytosure – Convert structural variants from VCF format to the format used in CytoSure Interpret
Impacts of nitrogen fertilisation on forest belowground fungal communities PI: Nathaniel Street (UmU)

Application round: Jan 2018
Subject: Biodiversity

Co-applicants: Vaughan Hurry (SLU)

Publications:
Schneider et al. Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce. mSystems 6:e00884-20 (2021) Law et al. Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. Proc Natl Acad Sci USA 119:e2118852119 (2022)
Improving transcriptome reconstruction PI: Olof Emanuelsson (KTH)

Application round: May 2013
Subject: Evolutionary Biology/Genetics

Publications:
Reimegård et al. Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. Nucleic Acids Res 45:3253-3265 (2017)
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) Kierczak et al. Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability. Nat Commun 13:2532 (2022)
Integrated multiomics analysis of pediatric acute myeloid leukemia PI: Linda Holmfeldt (UU)

Application round: Jan 2018
Subject: Cancer Biology

Publications:
Stratmann et al. Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets. Blood Adv 5:900-912 (2021) Stratmann et al. Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression. Blood Adv 6:152-164 (2022)
Interneuronal populations in locomotor networks PI: Ole Kiehn (KI)

Application round: Feb 2014
Subject: Cell and Developmental Biology
Iron metabolism and inflammation PI: Anna-Lena Spetz (SU)

Application round: Oct 2015
Subject: Human Genetics
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)

Publications:
Feiner et al. Environmentally-induced DNA methylation is inherited across generations in an aquatic keystone species. iScience 25:104303 (2022)
Leptidea butterfly genomics PI: Niclas Backström (UU)

Application round: Feb 2015
Subject: Evolutionary Biology/Genetics

Publications:
Talla et al. Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species. Mol Ecol 28:3756-3770 (2019)
Data: Leptidea DNA sequence reads, genome assembly and variant calls
Marine genomics of barnacle PI: Anders Blomberg (GU)

Application round: Jan 2013
Subject: Biodiversity

Publications:
Alm Rosenblad et al. Genomic characterization of the barnacle Balanus improvisus reveals extreme nucleotide diversity in coding regions. Mar Biotechnol 23:402-416 (2021)
Data: Pilot genome assembly
Melanoma genetics PI: Veronica Höiom (KI)

Application round: Jan 2013
Subject: Human Genetics

Publications:
Tuominen et al. The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility. Genes Chromosomes Cancer 55:601-611 (2016) Yang et al. Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma. Genet Med 24:157-169 (2021)
Methods for multiplex protein analysis PI: Ulf Landegren (UU)

Application round: May 2017
Subject: New Technology Development

Co-applicants: Caroline Gallant (UU)

Publications:
Reimegård et al. A combined approach for single-cell mRNA and intracellular protein expression analysis. Commun Biol 4:624 (2021)

Tools and scripts:
Scripts and data files – to generate figures and tables from the article
Methylation QTL analysis in the chicken PI: Dominic Wright (LiU)

Application round: Jun 2015
Subject: Evolutionary Biology/Genetics

Publications:
Höglund et al. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat Ecol Evol 4:1713-1724 (2020)
MicroRNA in muscle dystrophy PI: Madeleine Durbeej-Hjalt (LU)

Application round: Nov 2014
Subject: Molecular Medicine & Biomarkers
MicroRNA networks in Parkinson's disease PI: Johan Jakobsson (LU)

Application round: Oct 2015
Subject: Cell and Developmental Biology
Multi-level omics profiling of the yeast cell cycle PI: Jens Nielsen (CTH)

Application round: Jun 2016
Subject: Cell and Developmental Biology

Publications:
Campbell et al. Building blocks are synthesized on demand during the yeast cell cycle. Proc Natl Acad Sci USA 117:7575-7583 (2020)
Multi-omics analysis of human neuronal cells in health and disease PI: Niklas Dahl (UU)

Application round: Feb 2016
Subject: Cell and Developmental Biology

Publications:
Sobol et al. Transcriptome and proteome profiling of neural induced pluripotent stem cells from individuals with Down syndrome disclose dynamic dysregulations of key pathways and cellular functions. Mol Neurobiol 56:7113-7127 (2019) Schuster et al. Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment. Neurobiol Dis 132:104583 (2019) Laan et al. DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors. Clin Epigenetics 12:9 (2020)
Mutations in childhood acute lymphoblastic leukemia PI: Ann-Christine Syvänen (UU)

Application round: May 2013
Subject: Cancer Biology

Publications:
Lindqvist et al. The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing. Hum Mutat 36:118-128 (2015) Lindqvist et al. Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. Oncotarget 7:64071-64088 (2016)
Neo-antigens in melanoma PI: Göran Jönsson (LU)

Application round: Oct 2015
Subject: Cancer Biology

Publications:
Lauss et al. Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma. Nat Commun 8:1738 (2017)
Neuronal identity PI: Johan Holmberg (KI)

Application round: Jun 2015
Subject: Cell and Developmental Biology

Publications:
Södersten et al. A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons. Nat Commun 9:1226 (2018)
Data: RNA-seq, ChIP-seq and TRAP-seq data
New mutations in dilated cardiomyopathy PI: Martin Bergö (GU)

Application round: May 2013
Subject: Human Genetics

Publications:
Dalin et al. Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy. Int J Cardiol 228:742-748 (2017)
Next-gen plant phylogenetics PI: Alexandre Antonelli (GU)

Application round: Feb 2014
Subject: Evolutionary Biology/Genetics

Publications:
Andermann et al. SECAPR - a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments. PeerJ 6:e5175 (2018)

Tools and scripts:
SECAPR – pipeline for processing of sequence capture data
Novel subpopulations in the brain reward-aversion system PI: Åsa Mackenzie (UU)

Application round: Oct 2015
Subject: Cell and Developmental Biology

Publications:
Wallén-Mackenzie et al. Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures. Commun Biol 3:338 (2020)
Omics interplay in cardiometabolic disease PI: Marju Orho-Melander (LU)

Application round: Jan 2017
Subject: Molecular Medicine & Biomarkers
Origin and heterogeneity of the most primitive nervous system PI: Igor Adameyko (KI)

Application round: Jun 2016
Subject: Evolutionary Biology/Genetics

Publications:
Klimovich et al. Prototypical pacemaker neurons interact with the resident microbiota. Proc Natl Acad Sci USA 117:17854-17863 (2020)

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)
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)
Personalized profiling of adaptive immune genes PI: Gunilla Karlsson Hedestam (KI)

Application round: May 2017
Subject: New Technology Development

Publications:
Vázquez Bernat et al. High-quality library preparation for NGS-based immunoglobulin germline gene inference and repertoire expression analysis. Front Immunol 10:660 (2019) Phad et al. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. J Exp Med 217:e20191155 (2020)

Tools and scripts:
IgDiscover – Software for antibody repertoire analysis and V gene discovery from high-throughput sequencing reads
Plant spatial transcriptomics PI: Nathaniel Street (UmU)

Application round: Feb 2016
Subject: New Technology Development

Publications:
Giacomello et al. Spatially resolved transcriptome profiling in model plant species. Nat Plants 3:17061 (2017)
SCAPIS human wellness profiling PI: Mathias Uhlén (KTH)

Application round: Feb 2016
Subject: Cell and Developmental Biology

Publications:
Tebani et al. Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat Commun 11:4487 (2020)
Sequencing the missing link in land plant evolution PI: Hans Ronne (SLU)

Application round: Oct 2013
Subject: Evolutionary Biology/Genetics
Single nuclei sequencing of arbuscular mycorrhizal fungi PI: Anna Rosling (UU)

Application round: May 2017
Subject: Biodiversity

Publications:
Montoliu-Nerin et al. Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei. Sci Rep 10:1303 (2020)
Somatic genetic variation in the aging brain and Alzheimer's disease PI: Maria Eriksson (KI)

Application round: Oct 2015
Subject: Human Genetics

Publications:
Helgadottir et al. Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient. Hum Mol Genet 28:2675–2685 (2019)
Somatic mutations in tissue stem cells during human aging PI: Maria Eriksson (KI)

Application round: Jun 2015
Subject: Human Genetics

Publications:
Franco et al. Somatic mutagenesis in satellite cells associates with human skeletal muscle aging. Nat Commun 9:800 (2018)
Spatial transcripts PI: Jonas Frisén (KI)

Application round: Feb 2014
Subject: New Technology Development

Publications:
Ståhl et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353:78-82 (2016) Vickovic et al. Massive and parallel expression profiling using microarrayed single-cell sequencing. Nat Commun 7:13182 (2016)
Spatially resolved gene expression analysis in human developing heart tissue PI: Matthias Corbascio (KI)

Application round: Oct 2016
Subject: Cell and Developmental Biology

Publications:
Asp et al. A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart. Cell 179:1647-1660.e19 (2019)
Speciation genomics in crows PI: Jochen Wolf (UU)

Application round: Jan 2013
Subject: Evolutionary Biology/Genetics

Publications:
Poelstra et al. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 344:1410-1414 (2014)
Stem cell mutational signatures PI: Maria Eriksson (KI)

Application round: Sep 2017
Subject: Human Genetics

Publications:
Franco et al. Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type. Genome Biol 20:285 (2019)
The Swedish reference database of genetic variants PI: Ulf Gyllensten (UU)

Application round: Oct 2015
Subject: Human Genetics

Publications:
Ameur et al. SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population. Eur J Hum Genet 25:1253-1260 (2017) Ameur et al. De novo assembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data. Genes 9:486 (2018)

Tools and scripts:
Structural variation pipeline – A workflow for standardized calling and filtering of structural variants, designed for whole genome sequencing projects
Data: Genetic variant frequencies
The herring genome PI: Leif Andersson (UU)

Application round: Jan 2013
Subject: Evolutionary Biology/Genetics

Publications:
Martinez Barrio et al. The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. Elife 5:e12081 (2016)
Data: Genome assembly Gene annotation and genetic variants Population sequencing reads, set 1 Population sequencing reads, set 2 Population sequencing reads, set 3
The transcriptional heterogeneity of human intestinal innate lymphoid cells PI: Jenny Mjösberg (KI)

Application round: Sep 2017
Subject: Cell and Developmental Biology

Publications:
Mazzurana et al. Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing. Cell Res 31:554-568 (2021)

Tools and scripts:
Analysis scripts – to reproduce the analyses reported in the publication
Data: Gene expression data
Transcriptome analysis of memory T cells during influenza virus challenge PI: Nils Lycke (GU)

Application round: Jan 2018
Subject: Cell and Developmental Biology

Publications:
Omokanye et al. Clonotypic analysis of protective influenza M2e-specific lung resident Th17 memory cells reveals extensive functional diversity. Mucosal Immunol 15:717-729 (2022)
Transcriptomics of plant-insect coevolution PI: Niklas Janz (SU)

Application round: Oct 2013
Subject: Evolutionary Biology/Genetics

Publications:
Celorio-Mancera et al. Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly. BMC Evol Biol 16:59 (2016)

Tools and scripts:
Gene expression analysis – R and python scripts
Data: RNA-seq data
Travel and antibiotic resistance PI: Joakim Larsson (GU)

Application round: Jan 2013
Subject: Biodiversity

Publications:
Bengtsson-Palme et al. The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrob Agents Chemother 59:6551-6560 (2015)
Tumorgan single cell sequencing PI: Kristian Pietras (LU)

Application round: Feb 2016
Subject: Cancer Biology

Publications:
Bartoschek et al. Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing. Nat Commun 9:5150 (2018)
WGS and RNA-seq in chronic lymphocytic leukemia subsets PI: Richard Rosenquist (UU)

Application round: Jun 2016
Subject: Cancer Biology
Whole genome sequencing of neuroblastoma PI: Tommy Martinsson (GU)

Application round: Oct 2015
Subject: Cancer Biology

Tools and scripts:
Sarek – Complete open source pipeline to detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data.
Why such high genetic diversity in songbird immunity? PI: Helena Westerdahl (LU)

Application round: Jun 2016
Subject: Evolutionary Biology/Genetics

Publications:
Sigeman et al. Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration. Mol Biol Evol 38:5275-5291 (2021) Westerdahl et al. The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes. Mol Ecol Resour 22:2379-2395 (2022)
Zebrafish mutation identification PI: Olov Andersson (KI)

Application round: Feb 2014
Subject: Cell and Developmental Biology

Publications:
Reischauer et al. Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification. Nature 535:294-298 (2016)
Data: Whole-genome sequencing of zebrafish on PacBio Assembly of the Cloche/npas4l locus