Oleh Krupa
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View article: Massively parallel assessment of gene regulatory activity at human cortical structure associated variants
Massively parallel assessment of gene regulatory activity at human cortical structure associated variants Open
Genetic association studies have identified hundreds of largely non-coding loci associated with inter-individual differences in the structure of the human cortex, though the specific genetic variants that impact regulatory activity are unk…
View article: Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis
Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis Open
View article: SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images Open
Image-based cell counting is a fundamental yet challenging task with wide applications in biological research. In this paper, we propose a novel unified deep network framework designed to solve this problem for various cell types in both 2…
View article: Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy.
Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy. Open
Tissue clearing followed by light-sheet microscopy (LSFM) enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of structural changes caused by genetic or environmental perturbations. Whole-brain ima…
View article: Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants Open
Genome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel r…
View article: Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis
Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis Open
Summary The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk post-mortem adult brain tissue. However, many br…
View article: Systematic investigation of allelic regulatory activity of schizophrenia-associated common variant
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variant Open
README for SCZ MPRA created by [email protected] 08/07/2023 BEFORE RUNNING SCRIPTS Download files files from GEO (GSE211045) Git clone or download our files and scripts to your local/virtual environment. Modify config_scz.yml
View article: MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size
MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size Open
Expression quantitative trait loci (eQTL) data have proven important for linking non-coding loci to protein-coding genes. But eQTL studies rarely measure microRNAs (miRNAs), small non-coding RNAs known to play a role in human brain develop…
View article: MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size
MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size Open
Expression quantitative trait loci (eQTL) data have proven important for linking non-coding loci to protein-coding genes. But eQTL studies rarely measure microRNAs (miRNAs), small non-coding RNAs known to play a role in human brain develop…
View article: Author response: MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size
Author response: MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size Open
View article: Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants Open
Genome-wide association studies (GWAS) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium (LD) makes it challenging to discern causal variants. Computational finemapping prior…
View article: Focus on your locus with a massively parallel reporter assay
Focus on your locus with a massively parallel reporter assay Open
A growing number of variants associated with risk for neurodevelopmental disorders have been identified by genome-wide association and whole genome sequencing studies. As common risk variants often fall within large haplotype blocks coveri…
View article: Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy
Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy Open
Tissue clearing followed by light-sheet microscopy (LSFM) enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of structural changes caused by genetic or environmental perturbations. Whole-brain ima…
View article: MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size
MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size Open
Expression quantitative trait loci (eQTL) data have proven important for linking non-coding loci to protein-coding genes. But eQTL studies rarely measure microRNAs (miRNAs), small non-coding RNAs known to play a role in human brain develop…
View article: NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images
NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images Open
Tissue-clearing methods allow every cell in the mouse brain to be imaged without physical sectioning. However, the computational tools currently available for cell quantification in cleared tissue images have been limited to counting spars…
View article: Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis
Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis Open
View article: SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images Open
Image-based cell counting is a fundamental yet challenging task with wide applications in biological research. In this paper, we propose a novel unified deep network framework designed to solve this problem for various cell types in both 2…
View article: Segmentor: a tool for manual refinement of 3D microscopy annotations
Segmentor: a tool for manual refinement of 3D microscopy annotations Open
View article: Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation
Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation Open
View article: Segmentor: A tool for manual refinement of 3D microscopy annotations
Segmentor: A tool for manual refinement of 3D microscopy annotations Open
Background Recent advances in tissue clearing techniques, combined with high-speed image acquisition through light sheet microscopy, enable rapid three-dimensional (3D) imaging of biological specimens, such as whole mouse brains, in a matt…
View article: Genetic effects on brain traits impact cell-type specific gene regulation during neurogenesis
Genetic effects on brain traits impact cell-type specific gene regulation during neurogenesis Open
Interpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing is generally performed in bulk post-mortem adult tissue. However, genetic risk loc…
View article: NuMorph: tools for cellular phenotyping in tissue cleared whole brain images
NuMorph: tools for cellular phenotyping in tissue cleared whole brain images Open
Tissue clearing methods allow every cell in the mouse brain to be imaged without physical sectioning. However, the computational tools currently available for cell quantification in cleared tissue images have been limited to counting spars…
View article: Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation
Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation Open
Summary Common genetic risk for neuropsychiatric disorders is enriched in regulatory elements active during cortical neurogenesis. However, the mechanisms mediating the effects of genetic variants on gene regulation are poorly understood. …
View article: Memo1-Mediated Tiling of Radial Glial Cells Facilitates Cerebral Cortical Development
Memo1-Mediated Tiling of Radial Glial Cells Facilitates Cerebral Cortical Development Open
View article: Cross Modality Microscopy Segmentation via Adversarial Adaptation
Cross Modality Microscopy Segmentation via Adversarial Adaptation Open
View article: Initiation of Behavioral Response to Antidepressants by Cholecystokinin Neurons of the Dentate Gyrus
Initiation of Behavioral Response to Antidepressants by Cholecystokinin Neurons of the Dentate Gyrus Open