Per Stenberg
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View article: Airborne eDNA captures three decades of ecosystem biodiversity
Airborne eDNA captures three decades of ecosystem biodiversity Open
Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. La…
View article: Rapid shifts in bryophyte phenology revealed by airborne <scp>eDNA</scp>
Rapid shifts in bryophyte phenology revealed by airborne <span>eDNA</span> Open
Bryophytes constitute a diverse plant group with important roles in ecosystem functioning, in particular in arctic and subarctic environments. As they are physiologically strongly dependent on climatic conditions bryophytes could serve as …
View article: Airborne eDNA captures three decades of ecosystem biodiversity
Airborne eDNA captures three decades of ecosystem biodiversity Open
Conserving biodiversity is a global imperative, yet our capacity to quantify and understand species occurrences has been limited. To help address this challenge, we develop a novel monitoring approach based on deep sequencing of airborne e…
View article: Mapping the semi-nested community structure of 3D chromosome contact networks
Mapping the semi-nested community structure of 3D chromosome contact networks Open
Mammalian DNA folds into 3D structures that facilitate and regulate genetic processes such as transcription, DNA repair, and epigenetics. Several insights derive from chromosome capture methods, such as Hi-C, which allow researchers to con…
View article: The path to immortalization of cells starts by managing stress through gene duplications
The path to immortalization of cells starts by managing stress through gene duplications Open
The genomes of immortalized cell lines (and cancer cells) are characterized by multiple types of aberrations, ranging from single nucleotide polymorphisms (SNPs) to structural rearrangements that have accumulated over time. Consequently, i…
View article: Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities
Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities Open
Background Surface raw water used as a source for drinking water production is a critical resource, sensitive to contamination. We conducted a study on Swedish raw water sources, aiming to identify mutually co‐occurring metacommunities of …
View article: Mapping the semi-nested community structure of 3D chromosome contact networks
Mapping the semi-nested community structure of 3D chromosome contact networks Open
Mammalian DNA folds into 3D structures that facilitate and regulate genetic processes such as transcription, DNA repair, and epigenetics. Several insights derive from chromosome capture methods, such as Hi-C, which allow researchers to con…
View article: Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line
Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line Open
Background Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used…
View article: Additional file 5 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line
Additional file 5 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line Open
Additional file 5. Multiple tables containing data used to generate figures.
View article: Additional file 3 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line
Additional file 3 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line Open
Additional file 3. Public datasets used.
View article: Additional file 2 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line
Additional file 2 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line Open
Additional file 2. GO-terms with p-values for DAVID functional clusters of disrupted/gained genes.
View article: Additional file 6 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line
Additional file 6 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line Open
Additional file 6. Gene copy-number and disrupted genes in S2-DRSC.
View article: Additional file 4 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line
Additional file 4 of Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line Open
Additional file 4. Assembly QUAST statistics.
View article: FlexTaxD: flexible modification of taxonomy databases for improved sequence classification
FlexTaxD: flexible modification of taxonomy databases for improved sequence classification Open
Summary The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing met…
View article: Airborne microbial biodiversity and seasonality in Northern and Southern Sweden
Airborne microbial biodiversity and seasonality in Northern and Southern Sweden Open
Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors sh…
View article: Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins
Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins Open
In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Captu…
View article: The gut microbiome participates in transgenerational inheritance of low‐temperature responses in <i>Drosophila melanogaster</i>
The gut microbiome participates in transgenerational inheritance of low‐temperature responses in <i>Drosophila melanogaster</i> Open
Environmental perturbations induce transcriptional changes, some of which may be inherited even in the absence of the initial stimulus. Previous studies have focused on transfers through the germline although microbiota is also passed on t…
View article: Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking
Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking Open
Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify contaminants based on operational taxonomic …
View article: Dataset for: The gut microbiome participates in transgenerational inheritance of low temperature responses in <i>Drosophila melanogaster</i>
Dataset for: The gut microbiome participates in transgenerational inheritance of low temperature responses in <i>Drosophila melanogaster</i> Open
Environmental perturbations induce transcriptional changes, some of which may be inherited even in the absence of the initial stimulus. Previous studies have focused on transfers through the germ-line although microbiota is also passed on …
View article: PTE, a novel module to target Polycomb Repressive Complex 1 to the<i>Cyclin D2</i>oncogene
PTE, a novel module to target Polycomb Repressive Complex 1 to the<i>Cyclin D2</i>oncogene Open
Polycomb Group proteins are essential epigenetic repressors. They form multiple protein complexes of which two kinds, PRC1 and PRC2, are indispensable for repression. Although much is known about their biochemical properties, how PRC1 and …
View article: Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps
Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps Open
Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they …
View article: Atrophin controls developmental signaling pathways via interactions with Trithorax-like
Atrophin controls developmental signaling pathways via interactions with Trithorax-like Open
Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, pa…
View article: Erratum to: CBP binding outside of promoters and enhancers in Drosophila melanogaster
Erratum to: CBP binding outside of promoters and enhancers in Drosophila melanogaster Open
[This corrects the article DOI: 10.1186/s13072-015-0042-4.].
View article: Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements
Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements Open
Polycomb Group (PcG) proteins are epigenetic repressors essential for control of development and cell differentiation. They form multiple complexes of which PRC1 and PRC2 are evolutionary conserved and obligatory for repression. The target…