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.

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Analysis of the nuclear and cytosolic transcriptomes in human brain PI: Lars Feuk (UU)

Application round: Feb 2015
Subject: New Technology Development
Baltic sea CRISPR dynamics PI: Anders Andersson (KTH)

Application round: Feb 2016
Subject: Biodiversity
Chromatin dynamics and inheritance PI: Simon Elsässer (KI)

Application round: May 2017
Subject: Cell and Developmental Biology
Clonal evolution from diagnosis to relapse in acute lymphoblastic leukemia PI: Ann-Christine Syvänen (UU)

Application round: Oct 2016
Subject: Cancer Biology
Decoding the birth of hair follicles by single-cell RNA-seq PI: Maria Kasper (KI)

Application round: Sep 2017
Subject: Cell and Developmental Biology
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
Epigenetics of acute myeloid leukemia PI: Karl Ekwall (KI)

Application round: Nov 2014
Subject: Cancer 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
Exploring sex-biased gene expression in willows PI: Sofia Berlin Kolm (SLU)

Application round: Oct 2015
Subject: Evolutionary Biology/Genetics
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
Finding causal variants within schizophrenia risk loci PI: Patrick Sullivan (KI)

Application round: Oct 2016
Subject: Human Genetics
Gene regulatory networks in β-cells PI: Olov Andersson (KI)

Application round: Sep 2017
Subject: Cell and Developmental Biology
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)
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)
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)

Tools and scripts:
Sarek – Complete open source pipeline to detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data.
Genomic dynamics over space and time in salmonid metapopulations PI: Linda Laikre (SU)

Application round: May 2018
Subject: Evolutionary Biology/Genetics
Hemostatic regulation in human liver PI: Christina Jern (GU)

Application round: May 2014
Subject: Human Genetics
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)

Tools and scripts:
vcf2cytosure – Convert structural variants from VCF format to the format used in CytoSure Interpret
Identification of functionally perturbing non-coding mutations PI: Robert Måsson (KI)

Application round: Jan 2017
Subject: Cancer Biology
Impacts of nitrogen fertilisation on forest belowground fungal communities PI: Nathaniel Street (UmU)

Application round: Jan 2018
Subject: Biodiversity

Co-applicants: Vaughan Hurry (SLU)
Imputing genetic variants in a high kinship human cohort PI: Åsa Johansson (UU)

Application round: Jun 2015
Subject: Human 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
Integrated multiomics analysis of pediatric acute myeloid leukemia PI: Linda Holmfeldt (UU)

Application round: Jan 2018
Subject: Cancer Biology
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
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)
Leptidea butterfly genomics PI: Niclas Backström (UU)

Application round: Feb 2015
Subject: Evolutionary Biology/Genetics
Methods for multiplex protein analysis PI: Ulf Landegren (UU)

Application round: May 2017
Subject: New Technology Development

Co-applicants: Caroline Gallant (UU)
MicroRNA in muscle dystrophy PI: Madeleine Durbeej-Hjalt (LU)

Application round: Nov 2014
Subject: Molecular Medicine & Biomarkers
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
Multi-level omics profiling of the yeast cell cycle PI: Jens Nielsen (CTH)

Application round: Jun 2016
Subject: Cell and Developmental Biology
Multi-omics analysis of human neuronal cells in health and disease PI: Niklas Dahl (UU)

Application round: Feb 2016
Subject: Cell and Developmental Biology
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)
Omics interplay in cardiometabolic disease PI: Marju Orho-Melander (LU)

Application round: Jan 2017
Subject: Molecular Medicine & Biomarkers
Omics of sleep loss PI: Christian Benedict (UU)

Application round: Oct 2016
Subject: Cell and Developmental Biology

Co-applicants: Jonathan Cedernaes (UU)
Origin and heterogeneity of the most primitive nervous system PI: Igor Adameyko (KI)

Application round: Jun 2016
Subject: Evolutionary Biology/Genetics

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
Pneumonial metagenomics, metatranscriptomics and metabolomics PI: Birgitta Henriques-Normark (KI)

Application round: Jun 2016
Subject: Biodiversity

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
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
SCAPIS human wellness profiling PI: Mattias Uhlén (KTH)

Application round: Feb 2016
Subject: Cell and Developmental Biology
Sequencing the missing link in land plant evolution PI: Hans Ronne (SLU)

Application round: Oct 2013
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 nuclei sequencing of arbuscular mycorrhizal fungi PI: Anna Rosling (UU)

Application round: May 2017
Subject: Biodiversity
Single-cell gene expression analysis of limb regeneration PI: Andras Simon (KI)

Application round: Jun 2015
Subject: Cell and Developmental Biology
Somatic genetic variation in the aging brain and Alzheimer's disease PI: Maria Eriksson (KI)

Application round: Oct 2015
Subject: Human Genetics
Spatially resolved gene expression analysis in human developing heart tissue PI: Matthias Corbascio (KI)

Application round: Oct 2016
Subject: Cell and Developmental Biology
Stem cell mutational signatures PI: Maria Eriksson (KI)

Application round: Sep 2017
Subject: Human Genetics
Symbiont-induced host speciation in insects PI: Lisa Klasson (UU)

Application round: Jan 2017
Subject: Evolutionary Biology/Genetics
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)

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 epigenetic landscape in MLL-rearranged leukemia PI: Anna Andersson (LU)

Application round: Feb 2016
Subject: Cancer Biology
The transcriptional heterogeneity of human intestinal innate lymphoid cells PI: Jenny Mjösberg (KI)

Application round: Sep 2017
Subject: Cell and Developmental Biology
Transcriptome analysis of memory T cells during influenza virus challenge PI: Nils Lycke (GU)

Application round: Jan 2018
Subject: Cell and Developmental Biology
Tumorgan single cell sequencing PI: Kristian Pietras (LU)

Application round: Feb 2016
Subject: Cancer Biology
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 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

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

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Acoelomorph genomes PI: Ulf Jondelius (NRM)

Application round: Jun 2015
Subject: Evolutionary Biology/Genetics
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)
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)
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)
Data: Proteomics data RNA-seq data for A431 cells RNA-seq data for tissues
Colon cancer genes PI: Erik Johansson (UmU)

Application round: Feb 2014
Subject: Cancer Biology
DACP rat genome sequencing PI: Ulrika Norin (KI)

Application round: Jan 2013
Subject: Molecular Medicine & Biomarkers
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)
Data: RNA-seq data
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 advance online publication (2018)

Tools and scripts:
OPCs throughout mouse development – Web resource for exploring gene expression data from this study
Data: Single-cell RNA-seq data Bulk RNA-seq data
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)
Exercise-regulated mechanisms in mouse organs PI: Pontus Boström (KI)

Application round: Feb 2014
Subject: Cell and Developmental Biology
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
Genetic risk factors for ANCA-associated vasculitides PI: Kerstin Lindblad-Toh (UU)

Application round: Feb 2015
Subject: Human Genetics
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)
Genetics of heart stress recovery PI: Jan Borén (GU)

Application round: Oct 2013
Subject: Human Genetics
Genome-wide epigenetic variation in type 2 diabetes PI: Charlotte Ling (LU)

Application round: Nov 2014
Subject: Human Genetics
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)
Iron metabolism and inflammation PI: Anna-Lena Spetz (SU)

Application round: Oct 2015
Subject: Human Genetics
Marine genomics of barnacle PI: Anders Blomberg (GU)

Application round: Jan 2013
Subject: Biodiversity
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)
Methylation QTL analysis in the chicken PI: Dominic Wright (LiU)

Application round: Jun 2015
Subject: Evolutionary Biology/Genetics
MicroRNA networks in Parkinson's disease PI: Johan Jakobsson (LU)

Application round: Oct 2015
Subject: Cell and Developmental Biology
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)
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
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)
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)
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)
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: (2016)
Data: Genome assembly Gene annotation and genetic variants Population sequencing reads, set 1 Population sequencing reads, set 2 Population sequencing reads, set 3
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)
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