Frank Alber

Decoding single-cell replication states from imaging data reveals locus-specific subnuclear position dependencies of replication initiation

The paper introduces RepTile, a framework to infer single-cell replication states from imaging data, revealing locus-specific dependencies of replication initiation on subnuclear position.

Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes

The paper identifies a nuclear subcompartment in mouse cerebellum formed by long enhancers and genes, and shows Etv1's role in their compartmentalization and expression.

map3C: a computational tool for processing multiomic single-cell Hi-C data

map3C improves the quality of multiomic single-cell Hi-C data and aids in identifying structural variant locations.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Prediction of single-cell chromatin compartments from single-cell chromosome structures by MaxComp

This paper introduces MaxComp, an unsupervised method to predict single-cell chromatin compartments from 3D chromosome structures, showing that compartment annotations can be derived from geometric considerations alone.

Conformational analysis of chromosome structures reveals vital role of chromosome morphology in gene function

The paper introduces a dimensionality reduction method to classify single-cell chromosome structures into conformational clusters, revealing that distinct morphologies influence gene function through subnuclear positioning.

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

This paper introduces CTCC, a method using cryomilling to map chromatin interactions, showing it can generate global contact maps similar to Hi-C but with enhanced signal for stable inter-chromosomal contacts.

Population-based structure modeling reveals key roles of nuclear microenvironment in gene functions

The paper uses population-based modeling of Hi-C data to analyze the nuclear microenvironment's role in gene function, revealing structural variability and functional heterogeneity.

Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis

This paper introduces cfSNV, a somatic SNV caller for cfDNA that outperforms existing tools in detecting low-frequency mutations and applies it to immunotherapy prognosis in non-small-cell lung cancer.

Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography

This study evaluates 15 scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography, identifying two robust methods that work across varying signal-to-noise ratios.

PGS: a dynamic and automated population-based genome structure software

PGS generates a population of 3D genome structures from Hi-C data to better understand genome organization and provides analysis tools.

The 3D genome organization of Drosophila melanogaster through data integration

This paper integrates Hi-C and lamina-DamID data to compute 3D genome structures for Drosophila melanogaster, revealing structural features and functional insights.

Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture

The paper uses Tethered Chromosome Conformation Capture to analyze adenovirus-host genome interactions in human lung fibroblasts, finding specific and non-random interactions enriched in active chromatin regions.

Comprehensive characterization of neutrophil genome topology

This study characterizes the genome topology of neutrophils, revealing super-contraction and chromatin reorganization during differentiation.