A5012563352- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Evolution and Genetic Dynamics
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Genetic diversity and population structure
- Plant Pathogens and Fungal Diseases
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Acute Myeloid Leukemia Research
- Cancer Genomics and Diagnostics
- Metabolomics and Mass Spectrometry Studies
- Plant Disease Resistance and Genetics
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Forensic and Genetic Research
- Environmental DNA in Biodiversity Studies
- Molecular spectroscopy and chirality
- Coral and Marine Ecosystems Studies
- Plant Molecular Biology Research
- Fungal Biology and Applications
- Cleft Lip and Palate Research
- Genetic and phenotypic traits in livestock
- Mycorrhizal Fungi and Plant Interactions
Science for Life Laboratory
2013-2024
Uppsala University
2017-2024
Stockholm University
2013-2016
Karolinska Institutet
2010-2014
University of Helsinki
2013
Institut de Biologie Structurale
2007
Centre National de la Recherche Scientifique
2007
West Virginia University
2006
Umeå University
2004-2006
Oak Ridge National Laboratory
2006
We report the draft genome of black cottonwood tree, Populus trichocarpa . Integration shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction genome. More than 45,000 putative protein-coding genes were identified. Analysis assembled revealed a whole-genome duplication event; about 8000 pairs duplicated from that event survived in A second, older is indistinguishably coincident divergence and Arabidopsis lineages. Nucleotide substitution, tandem gene...
Crows of a feather flock together Closely related species with overlapping ranges typically evolve genetic barriers to prevent crossbreeding. Poelstra et al. sequenced genes from two central European crows: gray-bodied hooded crows and black carrion (see the Perspective by de Knijff). Although most genomes shared between species, one region that affected coat color vision differed. The authors suggest gray-coated prefer mate birds like themselves. Science , this issue p. 1410 ; see also 1345
Mutations in interferon regulatory factor 6 (IRF6) account for ∼70% of cases Van der Woude syndrome (VWS), the most common syndromic form cleft lip and palate. In 8 45 VWS-affected families lacking a mutation IRF6, we found coding mutations grainyhead-like 3 (GRHL3). According to zebrafish-based assay, disease-associated GRHL3 abrogated periderm development were consistent with dominant-negative effect, contrast haploinsufficiency seen VWS caused by IRF6 mutations. mouse, all embryos Grhl3...
Trees present a life form of paramount importance for terrestrial ecosystems and human societies because their ecological structure physiological function provision energy industrial materials. The genus Populus is the internationally accepted model molecular tree biology. We have analyzed 102,019 ESTs that clustered into 11,885 clusters 12,759 singletons. also provide >4,000 assembled full clone sequences to serve as basis upcoming annotation genome sequence. A public web-based EST database...
The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression, and the transcriptional events that underlie these processes have not yet been fully characterized. In this study RNA-Seq used compare transcription profiles four early developmental stages zebrafish (Danio rerio) on global scale.An average 79 M total reads were detected different stages. Out number 65% - 73% successfully mapped 36% 44% out those uniquely mapped. unique transcripts was...
The lake sediments of Hässeldala Port in south-east Sweden provide an archive local and regional environmental conditions ~14.5-9.5 ka BP (thousand years before present) allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun with plant micro- macrofossil analyses investigate dating the Allerød (14.1-12.7 BP), Younger Dryas (12.7-11.7 BP) Preboreal (<11.7 BP). Number reads taxa were not associated sample age or organic content. This suggests that,...
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been challenge in metagenomics, the availability computational frameworks that meet demands limited. Here, we propose aMeta, an accurate metagenomic profiling workflow DNA designed to minimize amount false discoveries computer memory requirements. Using simulated data, benchmark aMeta against current...
Abstract Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied impact T2D on open in human islets. used assay for transposase-accessible using sequencing (ATAC-seq) profile and non-diabetic donors. identified 57,105 53,284 ATAC-seq peaks representing regions diabetic donors, respectively. The majority mapped near transcription start sites. Additionally, were enriched enhancer...
Abstract We present Bioconda ( https://bioconda.github.io ), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, offers collection over 3000 packages, which is continuously maintained, updated, extended by growing global community more than 200 contributors. improves analysis reproducibility allowing users to define isolated environments with defined versions, all are easily installed managed without...
This article presents SOMCD, an improved method for the evaluation of protein secondary structure from circular dichroism spectra, based on Kohonen's self-organizing maps (SOM). Protein (CD) spectra are used to train a SOM, which arranges two-dimensional map. Location in map reflects composition protein. With prediction β-turn has been included. The number training set increased, and it now includes 39 6 reference spectra. Finally, SOM parameters have chosen minimize distortion make network...
Summary Refractory anaemia with ring sideroblasts ( RARS ) is distinguished by hyperplastic inefficient erythropoiesis, aberrant mitochondrial ferritin accumulation and anaemia. Heterozygous mutations in the spliceosome gene SF 3B1 are found a majority of cases. To explore link between anaemia, we studied mutated CD 34 + marrow cells regard to transcriptome sequencing, splice patterns mutational allele burden during erythroid differentiation. Transcriptome profiling early differentiation...
Infertility is a worldwide concern that can be treated with in vitro fertilization (IVF). Improvements IVF and infertility treatment depend largely on better understanding of the molecular mechanisms for human preimplantation development. Several large-scale studies have been conducted to identify gene expression patterns first five days development, many functional utilize mouse as model system. We identified genes possible importance this time period by analyzing microarray data available...
Abstract With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, population structures as shown by archaeological/zooarchaeological record, well stable isotope ancient DNA data. Here, we used metagenomic data analyse if transitions also impacted microbiome composition in 25 Mesolithic hunter-gatherers 13 farmers several Scandinavian Stone Age contexts. Salmonella enterica, a bacterium that...
Abstract Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill ( Meganyctiphanes norvegica ). We assemble characterize its large genome compare genome-scale variation among 74 specimens from colder Atlantic Ocean Mediterranean Sea. The 19 Gb likely evolved through proliferation of retrotransposons, now targeted inactivation extensive...
(1) To detect interferon regulatory factor 6 gene (IRF6) mutations in newly recruited Van der Woude syndrome (VWS) and popliteal pterygium (PPS) families. (2) test for association, nonsyndromic cleft lip and/or palate (NSCL/P) VWS/PPS families, the single nucleotide polymorphism (SNP) rs642961, from IRF6 enhancer AP-2α region, alone or as haplotype with rs2235371, a coding SNP (Val274Ile).IRF6 mutation screening was performed by direct sequencing genotyping of rs642961 rs2235371 TaqMan...
We applied a targeted sequencing approach to identify germline mutations conferring moderately highly increased risk of cutaneous and uveal melanoma. Ninety-two high-risk melanoma patients were screened for inherited variation in 120 candidate genes. Observed gene variants filtered based on frequency reference populations, cosegregation with families predicted functional effect. Several novel or rare genetic genes involved DNA damage response, cell-cycle regulation transcriptional control...
Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration sex-limited chromosome (e.g. W some birds Y mammals). However, in lineages, ancient escaped degeneration. Here, we study evolutionary maintenance sex ostrich (Struthio camelus), where remains 65% Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, show that population scaled recombination rate pseudoautosomal...
Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes transcription factories. This spatial proximity of actively transcribing could provide a means for RNA interaction at transcript level. We have screened public databases chimeric EST and mRNA sequences with intent mapping transcription-induced interchromosomal interactions. suggest transcripts may be result close encounters genes, either as functional products or "noise"...
Abstract Analysis of microbial data from archaeological samples is a rapidly growing field with great potential for understanding ancient environments, lifestyles and disease spread in the past. However, high error rates have been long-standing challenge metagenomics analysis. This also complicated by limited choice microbiome specific computational frameworks that meet demands field. Here, we propose aMeta, an accurate Metagenomic profiling workflow designed primarily to minimize amount...
Abstract Background Variant Call Format (VCF) is the standard file format for interchanging genetic variation data and associated quality control metrics. The usual row-wise encoding of VCF model (either as text or packed binary) emphasises efficient retrieval all a given variant, but accessing on field sample basis inefficient. Biobank scale datasets currently available consist hundreds thousands whole genomes terabytes compressed VCF. Row-wise storage fundamentally unsuitable more scalable...
Helminth infections and allergic diseases are associated with IgE hyperresponsiveness but the genetics of this phenotype remain to be defined. Susceptibility Ascaris lumbricoides infection antibody levels helminth polymorphisms in locus 13q33-34. We aimed explore other genomic regions identify genetic variants responsiveness humans. Forty-eight subjects from Cartagena, Colombia, extreme values specific ABA-1, a resistance marker nematode, were selected for targeted resequencing. Burden...