A5057052779- Single-cell and spatial transcriptomics
- Advanced biosensing and bioanalysis techniques
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- Genomic variations and chromosomal abnormalities
- RNA and protein synthesis mechanisms
- Advanced Fluorescence Microscopy Techniques
- Chromosomal and Genetic Variations
- RNA Research and Splicing
- Environmental DNA in Biodiversity Studies
- Genomics and Phylogenetic Studies
- Cell Image Analysis Techniques
- Gene expression and cancer classification
- MicroRNA in disease regulation
- Chronic Myeloid Leukemia Treatments
- Mast cells and histamine
- Cancer-related molecular mechanisms research
- PARP inhibition in cancer therapy
- Prostate Cancer Diagnosis and Treatment
- Prostate Cancer Treatment and Research
- Eosinophilic Disorders and Syndromes
Karolinska Institutet
2017-2024
Science for Life Laboratory
2017-2020
Karolinska University Hospital
2017
Abstract Emerging data demonstrate homologous recombination (HR) defects in castration-resistant prostate cancers, rendering these tumours sensitive to PARP inhibition. Here we a direct requirement for the androgen receptor (AR) maintain HR gene expression and activity cancer. We show that PARP-mediated repair pathways are upregulated cancer following androgen-deprivation therapy (ADT). Furthermore, upregulation of is essential survival cells synthetic lethality between ADT inhibition vivo....
Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting amount of extractable biological information. To overcome limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution widefield fluorescence microscopy images, which efficiently runs laptop computers. Deconwolf enables accurate quantification...
DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization single cells. At present, there lack of free resources FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 targeting multiple loci on the human autosomes chromosome X, as well genome-wide database optimally designed oligonucleotides freely accessible web interface ( http://ifish4u.org ) that used...
Abstract Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation cell cycle. We apply a tailored experimental design that eliminates these confounders, report thousands intrinsically covarying pairs in mouse embryonic stem cells. These covariations form network with biological properties, outlining known novel interactions. provide first evidence...
Tyrosine kinase inhibitors targeting the BCR-ABL oncoprotein in chronic myeloid leukemia (CML) are remarkably effective inducing deep molecular remission most patients. However, they less to eradicate leukemic stem cells (LSC), resulting disease persistence. Therefore, there is great need develop novel therapeutic strategies specifically target LSC. In an experimental mouse CML model system, leukotriene pathway, and specifically, expression ALOX5, encoding 5-lipoxygenase (5-LO), has been...
<title>Abstract</title> Microscopy-based spatially resolved omic methods are transforming biology and medicine. Currently, these rely on high magnification objectives cannot resolve crowded molecular targets, which limits the amount of biological information that can be extracted from a sample. To overcome limitations, we developed Deconwolf (DW), an open-source software enabling high-performance deconvolution widefield fluorescence microscopy image stacks large tissue scans laptop computer....
Abstract With the exception of lamina-associated domains, radial organization chromatin in mammalian cells remains largely unexplored. Here, we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to nuclear lamina all along radius that works gradual enzymatic restriction from towards nucleus center, followed generated cut sites. Using GPSeq, mapped human genome at 100 kb resolution, which revealed patterns and epigenomic features, gene...
DNA uorescence in situ hybridization \(DNA FISH) is a powerful method to study chromosomal organization single cells.At present, there lack of free resources FISH probes and probe design tools, which can be readily applied.Here, we describe iFISH, an open-source repository currently comprising 380 targeting multiple loci on the human autosomes chromosome X, as well genome-wide database optimally designed oligonucleotides freely accessible web interface \(http://i sh4u.org) that used...
Abstract Single-cell RNA sequencing studies into gene co-expression patterns could yield important new regulatory and functional insights, but have so far been limited by the confounding effects of cell differentiation cycle. We apply a tailored experimental design that eliminates these confounders, report >80,000 intrinsically covarying pairs in mouse embryonic stem cells. These covariances form network with biological properties, outlining known novel interactions. provide first...