Alexander Eckehart Urban

Peripheral Complement C4 Protein in Schizophrenia: Association with Gene Copy Number and Immune Cell Subtypes

This study identifies C4 protein expression in neutrophils and monocytes in schizophrenia, linking it to C4A gene copy number only in patients.

Single cell whole genome and transcriptome sequencing links somatic mutations to cell identity and ancestry

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

Multi-platform framework for mapping somatic retrotransposition in human tissues

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

Effect of cortisol on cortical organoids: Building a "stress in a dish" model system

This study develops a 'Stress-in-a-dish' model using cortical organoids to investigate the molecular effects of cortisol on gene expression and potential PTSD-related mechanisms.

Prioritizing disease-related rare variants by integrating gene expression data

This paper introduces a statistical framework to prioritize disease-related rare variants by integrating gene expression data, showing improved sensitivity in small sample sizes and identifying 16 rare variants in Alzheimer's disease.

Automatic detection of complex structural genome variation across world populations

The paper develops a method to detect complex structural variants across human genomes and finds they are associated with phenotypic hotspots and evolutionary changes.

DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks

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.

Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development

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

Direct induction of human neurons from fibroblasts carrying the neuropsychiatric 22q11.2 microdeletion reveals transcriptome- and epigenome-wide alterations

This paper develops a method to generate neuronal cells from adult fibroblasts and uses it to study gene expression and epigenetic changes in 22q11.2 deletion syndrome.

Cross-Platform Validation of Neurotransmitter Release Impairments in Schizophrenia Patient-Derived NRXN1-Mutant Neurons

This study validates that heterozygous NRXN1 deletions impair neurotransmitter release in human neurons across multiple labs, suggesting a human-specific synaptic dysfunction relevant for schizophrenia drug discovery.

Comprehensive identification of somatic nucleotide variants in human brain tissue

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

Network effects of the neuropsychiatric 15q13.3 microdeletion on the transcriptome and epigenome in human induced neurons

This study examines the transcriptome and epigenome effects of the 15q13.3 microdeletion in human induced neurons, identifying gene expression and pathway changes linked to neuropsychiatric disorders.

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

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.

Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

The paper introduces CTLR-Seq, a method to resolve complex genomic regions with high accuracy, and applies it to study CNVs associated with schizophrenia and autism.

Haplotype-phased common marmoset embryonic stem cells for genome editing using CRISPR/Cas9

This study provides haplotype-resolved genome characterization of a marmoset ESC line and demonstrates CRISPR/Cas9 targeting and neuronal differentiation capabilities.

Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

A 343-primer-pair multiplex PCR assay enables electrophoretic detection and full-genome sequencing of SARS-CoV-2 across 8 to half a million viral copies from 13 clinical specimens.

Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model

The paper investigates the molecular effects of 16p11.2 CNVs on gene expression and DNA methylation using an iPSC-to-iN model and identifies potential contributing genes.

Full-length LINE-1s with functional ORFs are favoured by host-level selection in human genomes

The paper shows that full-length LINE-1s with functional ORFs are under stronger host-level selection in human genomes, as indicated by higher selection coefficients and SNP depletion in ORFs.

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

The paper introduces BEAPR, a computational method to detect allele-specific binding of RNA-binding proteins, showing it outperforms existing methods and identifies disease-relevant variants.

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

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

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

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.

Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools

The paper generates deep re-sequencing datasets for the Venter/HuRef genome to develop and benchmark genome analysis tools using Illumina sequencing.

Local and global chromatin interactions are altered by large genomic deletions associated with human brain development

The paper investigates how large genomic deletions affect chromatin interactions and states in human brain development using Hi-C and ChIP-Seq analyses.

Whole-genome sequencing analysis of copy number variation (CNV) using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis

The paper compares low-coverage whole-genome sequencing strategies to array-based methods for detecting copy number variations, finding WGS more efficient and accurate.