Click on a project for further details and links to publications, analysis tools and data.
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Application round: May 2019
Subject: Evolutionary Biology/Genetics
Co-applicants: Love Dalén (NRM)
Application round: Oct 2018
Subject: Molecular Medicine & Biomarkers
Co-applicants: Inger Gjertsson (GU)
Application round: Feb 2019
Subject: Cell and Developmental Biology
Co-applicants: Hannah Stanforth (UU)
Application round: Feb 2019
Subject: Cancer Biology
Application round: Jan 2021
Subject: Molecular Medicine & Biomarkers
Application round: Feb 2016
Subject: Biodiversity
Application round: Feb 2019
Subject: New Technology Development
Application round: Jan 2020
Subject: Cell and Developmental Biology
Application round: May 2017
Subject: Cell and Developmental Biology
Application round: Feb 2019
Subject: Cell and Developmental Biology
Co-applicants: Jordi Planells (SU), Vincent Pelechano (KI)
Application round: Oct 2016
Subject: Cancer Biology
Application round: Jan 2021
Subject: Molecular Medicine & Biomarkers
Application round: Feb 2019
Subject: Molecular Medicine & Biomarkers
Publications:
Data: ncRNA counts
Application round: Sep 2017
Subject: Cell and Developmental Biology
Application round: Oct 2018
Subject: Cancer Biology
Co-applicants: Ninib Baryawno (KI)
Application round: Oct 2020
Subject: Human Genetics
Co-applicants: Elisabet Einarsdottir (KTH), Juha Kere (KI)
Application round: Oct 2019
Subject: Cell and Developmental Biology
Application round: Oct 2018
Subject: Evolutionary Biology/Genetics
Application round: Oct 2020
Subject: Molecular Medicine & Biomarkers
Application round: Nov 2014
Subject: Cancer Biology
Application round: May 2019
Subject: Cell and Developmental Biology
Application round: Sep 2017
Subject: Evolutionary Biology/Genetics
Application round: Oct 2016
Subject: Evolutionary Biology/Genetics
Application round: Feb 2019
Subject: Evolutionary Biology/Genetics
Co-applicants: Mats Pettersson (UU)
Application round: May 2020
Subject: Evolutionary Biology/Genetics
Co-applicants: Erik Enbody (UU), Leif Andersson (UU)
Application round: Jun 2016
Subject: Cell and Developmental Biology
Application round: Feb 2016
Subject: New Technology Development
Publications:
Application round: May 2018
Subject: Evolutionary Biology/Genetics
Application round: Jan 2020
Subject: Biodiversity
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 &aposs last remaining Sumatran rhinoceros populations. Nat Commun 12:2393 (2021)
Application round: Oct 2018
Subject: Cell and Developmental Biology
Application round: Sep 2017
Subject: Evolutionary Biology/Genetics
Publications:
Data: WGS reads
Application round: May 2017
Subject: Cancer Biology
Co-applicants: Teresita Diaz de Ståhl (KI), Johanna Sandgren (KI), Maxime Garcia (KI), Gustaf Ljungman (UU)
Publications:
Tools and scripts:
Application round: May 2019
Subject: Cancer Biology
Co-applicants: Seishi Ogawa (Kyoto Univ. and KI)
Application round: May 2018
Subject: Evolutionary Biology/Genetics
Publications:
Application round: Jan 2017
Subject: Cancer Biology
Application round: May 2020
Subject: Cell and Developmental Biology
Application round: May 2019
Subject: Evolutionary Biology/Genetics
Application round: Jun 2015
Subject: Human Genetics
Publications:
Application round: Jun 2016
Subject: Evolutionary Biology/Genetics
Publications:
Data: Cold tolerance and metabolome data
Application round: Jan 2020
Subject: Molecular Medicine & Biomarkers
Co-applicants: Louise Brunkwall (LU)
Application round: Feb 2014
Subject: Cell and Developmental Biology
Application round: Jan 2017
Subject: Evolutionary Biology/Genetics
Publications:
Application round: Jan 2018
Subject: Evolutionary Biology/Genetics
Co-applicants: Reinder Radersma (LU)
Application round: Jan 2020
Subject: Evolutionary Biology/Genetics
Co-applicants: Francisco Ruiz-Ruano (UU)
Application round: Oct 2020
Subject: Molecular Medicine & Biomarkers
Application round: Feb 2019
Subject: New Technology Development
Application round: Oct 2020
Subject: New Technology Development
Co-applicants: Rachel Foster (SU)
Application round: Jan 2017
Subject: Biodiversity
Tools and scripts:
Application round: May 2017
Subject: Molecular Medicine & Biomarkers
Application round: May 2020
Subject: Molecular Medicine & Biomarkers
Application round: Jan 2020
Subject: Cancer Biology
Co-applicants: Jan Komorowski (UU)
Application round: Oct 2018
Subject: New Technology Development
Co-applicants: Rui Branca (KI)
Application round: May 2020
Subject: Cell and Developmental Biology
Application round: May 2018
Subject: Cell and Developmental Biology
Application round: Oct 2016
Subject: Cell and Developmental Biology
Co-applicants: Jonathan Cedernaes (UU)
Publications:
Tools and scripts:
RNA-seq and DNA methylation analysis – R scripts and output
Data: RNA-seq data DNA methylation data
Application round: Oct 2019
Subject: Cancer Biology
Publications:
Application round: May 2020
Subject: Cell and Developmental Biology
Application round: Jun 2016
Subject: Cell and Developmental Biology
Tools and scripts:
Application round: Jun 2016
Subject: Molecular Medicine & Biomarkers
Tools and scripts:
Application round: Jan 2017
Subject: Cell and Developmental Biology
Application round: May 2020
Subject: Molecular Medicine & Biomarkers
Co-applicants: Sven Nelander (UU), Jordi Carreras-Puigvert (KI)
Application round: Oct 2018
Subject: Molecular Medicine & Biomarkers
Co-applicants: Maria Jenmalm (LiU)
Tools and scripts:
Application round: Jan 2020
Subject: Cancer Biology
Co-applicants: Lars Malmström (Univ. of Zurich)
Application round: Jan 2021
Subject: Molecular Medicine & Biomarkers
Co-applicants: Jamirah Nazziwa (LU)
Application round: Oct 2018
Subject: Cancer Biology
Application round: Feb 2015
Subject: Evolutionary Biology/Genetics
Application round: Nov 2014
Subject: Cell and Developmental Biology
Application round: Oct 2020
Subject: New Technology Development
Co-applicants: Anders Andersson (KTH)
Application round: May 2018
Subject: Evolutionary Biology/Genetics
Application round: May 2018
Subject: Evolutionary Biology/Genetics
Application round: Jan 2018
Subject: New Technology Development
Application round: Jan 2021
Subject: Molecular Medicine & Biomarkers
Co-applicants: Anna Överby Wernstedt (UmU), Annasara Lenman (UmU)
Application round: Jun 2015
Subject: Cell and Developmental Biology
Application round: Oct 2020
Subject: Human Genetics
Application round: Feb 2019
Subject: Evolutionary Biology/Genetics
Application round: Jan 2017
Subject: Evolutionary Biology/Genetics
Application round: Oct 2019
Subject: Cell and Developmental Biology
Co-applicants: Martin Cornillet (KI)
Application round: Oct 2019
Subject: Cancer Biology
Application round: May 2018
Subject: Evolutionary Biology/Genetics
Application round: Feb 2016
Subject: Cancer Biology
Application round: Oct 2018
Subject: Cell and Developmental Biology
Application round: Oct 2019
Subject: Evolutionary Biology/Genetics
Application round: May 2019
Subject: Cell and Developmental Biology
Application round: May 2020
Subject: Molecular Medicine & Biomarkers
Application round: Oct 2019
Subject: Molecular Medicine & Biomarkers
Co-applicants: Kim Kultima (UU)
Application round: Jan 2021
Subject: Evolutionary Biology/Genetics
Co-applicants: Imke Lankheet (UU)
Application round: Oct 2019
Subject: Cell and Developmental Biology
Publications:
Tools and scripts:
Data: VDJ data Gene expression data
Application round: May 2018
Subject: Molecular Medicine & Biomarkers
Publications:
Application round: Jan 2018
Subject: Cell and Developmental Biology
Application round: Jan 2020
Subject: Biodiversity
Co-applicants: Nick Sirijovski (LU), Essam Darwish (LU)
Application round: Jan 2018
Subject: Molecular Medicine & Biomarkers
Co-applicants: Alexander Perfilyev (LU)
Application round: Jan 2018
Subject: Molecular Medicine & Biomarkers
Co-applicants: Alessondra Speidel (KI), Annina Steinbach (KI)
Application round: Jun 2016
Subject: Cancer Biology
Application round: Sep 2017
Subject: Human Genetics
Application round: Oct 2018
Subject: Cancer Biology
Co-applicants: Mathias Uhlén (KTH)
Application round: Jun 2016
Subject: Evolutionary Biology/Genetics
Application round: Jan 2021
Subject: Molecular Medicine & Biomarkers
Co-applicants: Gunnel Nordmark (UU), Gustav Arvidsson (UU), Amanda Raine (UU)
Organization,No of projects
GU, 4
KI, 36
KTH, 4
LNU, 1
LU, 17
LiU, 2
NRM, 1
SU, 7
UU, 25
UmU, 1Click on a project for further details and links to publications, analysis tools and data.
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Application round: Jun 2015
Subject: Evolutionary Biology/Genetics
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)
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
Application round: May 2014
Subject: New Technology Development
Publications:
Tools and scripts:
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
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)
Application round: Jun 2016
Subject: Biodiversity
Tools and scripts:
Application round: Oct 2016
Subject: Cell and Developmental Biology
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
Application round: Feb 2014
Subject: Cancer Biology
Publications:
Application round: Jan 2013
Subject: Molecular Medicine & Biomarkers
Publications:
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
Application round: Jan 2017
Subject: New Technology Development
Application round: Oct 2015
Subject: Biodiversity
Tools and scripts:
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
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
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)
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)
Application round: Feb 2014
Subject: Cell and Developmental Biology
Application round: Oct 2015
Subject: Evolutionary Biology/Genetics
Publications:
Application round: Oct 2016
Subject: Human Genetics
Publications:
Application round: Feb 2015
Subject: Molecular Medicine & Biomarkers
Application round: Jan 2013
Subject: Evolutionary Biology/Genetics
Publications:
Data: Reference genome assembly Genotypes for linkage analysis Resequencing data
Application round: May 2013
Subject: New Technology Development
Publications:
Data: DNA sequence reads, genome assemblies and gene annotation RNA-seq data Proteomics data
Application round: Sep 2017
Subject: Cell and Developmental Biology
Publications:
Tools and scripts:
Data exploration – Web resource for exploring gene expression data from Charbord et al.
Data: RNA-seq data
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)
Application round: Feb 2015
Subject: Human Genetics
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)
Application round: Oct 2013
Subject: Human Genetics
Application round: Nov 2014
Subject: Human Genetics
Publications:
Data: Gene expression data ATAC-seq data
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)
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
Application round: Jan 2018
Subject: Biodiversity
Co-applicants: Vaughan Hurry (SLU)
Publications:
Application round: May 2013
Subject: Evolutionary Biology/Genetics
Publications:
Application round: Jan 2018
Subject: Cancer Biology
Publications:
Application round: Oct 2015
Subject: Human Genetics
Application round: Feb 2015
Subject: Evolutionary Biology/Genetics
Publications:
Data: Leptidea DNA sequence reads, genome assembly and variant calls
Application round: Jan 2013
Subject: Biodiversity
Publications:
Data: Pilot genome assembly
Application round: Jan 2013
Subject: Human Genetics
Publications:
Application round: May 2017
Subject: New Technology Development
Co-applicants: Caroline Gallant (UU)
Publications:
Tools and scripts:
Scripts and data files – to generate figures and tables from the article
Application round: Jun 2015
Subject: Evolutionary Biology/Genetics
Publications:
Application round: Nov 2014
Subject: Molecular Medicine & Biomarkers
Application round: Oct 2015
Subject: Cell and Developmental Biology
Application round: Jun 2016
Subject: Cell and Developmental Biology
Publications:
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)
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)
Application round: Oct 2015
Subject: Cancer Biology
Publications:
Application round: Jun 2015
Subject: Cell and Developmental Biology
Publications:
Data: RNA-seq, ChIP-seq and TRAP-seq data
Application round: May 2013
Subject: Human Genetics
Publications:
Application round: Feb 2014
Subject: Evolutionary Biology/Genetics
Publications:
Tools and scripts:
SECAPR – pipeline for processing of sequence capture data
Application round: Oct 2015
Subject: Cell and Developmental Biology
Publications:
Application round: Jan 2017
Subject: Molecular Medicine & Biomarkers
Application round: Jun 2016
Subject: Evolutionary Biology/Genetics
Publications:
Tools and scripts:
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:
Application round: Feb 2016
Subject: New Technology Development
Publications:
Application round: Feb 2016
Subject: Cell and Developmental Biology
Publications:
Application round: Oct 2013
Subject: Evolutionary Biology/Genetics
Application round: May 2017
Subject: Biodiversity
Publications:
Application round: Oct 2015
Subject: Human Genetics
Publications:
Application round: Jun 2015
Subject: Human Genetics
Publications:
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)
Application round: Oct 2016
Subject: Cell and Developmental Biology
Publications:
Application round: Jan 2013
Subject: Evolutionary Biology/Genetics
Publications:
Application round: Sep 2017
Subject: Human Genetics
Publications:
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:
Data: Genetic variant frequencies
Application round: Jan 2013
Subject: Evolutionary Biology/Genetics
Publications:
Data: Genome assembly Gene annotation and genetic variants Population sequencing reads, set 1 Population sequencing reads, set 2 Population sequencing reads, set 3
Application round: Sep 2017
Subject: Cell and Developmental Biology
Publications:
Tools and scripts:
Analysis scripts – to reproduce the analyses reported in the publication
Data: Gene expression data
Application round: Oct 2013
Subject: Evolutionary Biology/Genetics
Publications:
Tools and scripts:
Gene expression analysis – R and python scripts
Data: RNA-seq data
Application round: Jan 2013
Subject: Biodiversity
Publications:
Application round: Feb 2016
Subject: Cancer Biology
Publications:
Application round: Oct 2015
Subject: Cancer Biology
Tools and scripts:
Application round: Feb 2014
Subject: Cell and Developmental Biology
Publications:
Data: Whole-genome sequencing of zebrafish on PacBio Assembly of the Cloche/npas4l locus