Alexej S. Abyzov

This study characterizes somatic mutations in urine-derived iPSCs, showing they reflect age-related genomic changes and can trace developmental lineages non-invasively.

The paper uses single-cell DNA sequencing to analyze somatic mosaicism in postmortem lung and colon tissues, revealing mutation heterogeneity, chromosomal abnormalities, and cellular ancestry.

This study uses single-cell whole genome amplification to link somatic mutations to cell identity and ancestry in a live donor.

This study corrects a pathogenic ATAD3A variant in iPSCs using CRISPR-Cas9-induced gene conversion without donor templates, showing high efficiency and dependence on HR proteins.

The paper benchmarks somatic mutation detection methods using short-read and long-read sequencing across multiple samples, showing improved accuracy with donor-specific assemblies and highlighting the complementary value of bulk, single-cell, and duplex analyses.

The paper traces germline origin in humans using post-zygotic mutations, finding a balanced 50:50 lineage allocation from the first two blastomeres across generations.

The paper processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

This study uses morphogen gradients in organoids to generate human brain neuronal lineages and identifies interindividual variability in response to these signals.

This study uses single-cell transcriptomics to show reduced interneurons and microglia activation in TS basal ganglia, linking gene expression changes to impaired striatal function.

The paper uses MPRA in forebrain organoids to validate enhancer activity in early human neurodevelopment, identifying over 2,300 enhancers with temporal-specific activity.

The paper constructs an enhancer-driven gene regulatory network from human forebrain organoids with ASD and neurotypical controls, identifying key regulators of excitatory neuron specification in macrocephalic ASD.

The paper shows that clonally selected CRISPR-edited cell lines acquire many culture-specific mutations, making them non-isogenic, and recommends comparing multiple edited and unedited line mixes.

This study identifies 69 mutated genes in malformations of cortical development using multiomic profiling of 317 brain resections and single-cell sequencing.

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

All2 filters mosaic mutations from multi-cell comparisons by classifying variants as germline, mosaic, or false positive, improving sensitivity and reducing false positives in whole genome and exome analysis.

The paper evaluates brain somatic mosaicism in the adult human to identify rules governing cellular distribution during embryogenesis.

The paper models ASD in organoids and finds transcriptomic imbalances in excitatory cortical neuron subtypes during early neurogenesis in ASD probands.

The paper identifies prenatal mutational processes in schizophrenia brains linked to transcription factor binding sites and proposes a new term 'skiagenesis' for these mutations.

CNVpytor is a Python-based tool for detecting and analyzing CNVs/CNAs from whole genome sequencing data, offering improved speed, functionality, and visualization compared to CNVnator.

This study identifies somatic SNVs in non-cancerous human brain tissues and establishes best practices for detecting low-frequency variants.

The paper tracks cell lineages in humans using post-zygotic mutations and finds lineage imbalance and correlations with developmental axes.

The paper introduces a machine learning method to detect somatic L1 insertions in human brain tissue, revealing their widespread distribution in neurons and glia and potential role in neuropsychiatric diseases.

The paper provides a comprehensive whole-genome analysis of K562, identifying genomic structural features and their impact on functional genomics data.

This paper provides a haplotype-resolved genome analysis of the HepG2 cell line, identifying genomic features and allele-specific regulation to support functional genomics studies.

CompStor Novos provides fast and precise variant calling for personal genomes using assembly-based methods on standard hardware, outperforming existing algorithms in speed and accuracy.