Martin Vingron

A knowledge graph-guided framework for multitask single-cell analysis

scKNIFE integrates gene expression with functional annotations to identify tumor programs and treatment-related functional variation in breast cancer.

A draft atlas of the human plasma proteome at isoform resolution

The paper creates a proteoform-resolved atlas of the human plasma proteome, revealing extensive proteoform diversity and highlighting discrepancies between proteomic platforms.

Context-aware sequence-to-function model of human gene regulation

The paper introduces Corgi, a context-aware sequence-to-function model that predicts gene expression and epigenetic signals across unseen cell types using DNA sequence and trans-regulator expression.

TandemTwister: Scalable genotyping and advanced visualization of tandem repeats

TandemTwister is a tool for tandem repeat genotyping and visualization, showing high accuracy and speed across sequencing technologies and datasets.

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development

The paper compares bat and mouse limb development using single-cell analyses to show how a conserved gene program is repurposed in bat wing formation.

Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances

The paper identifies functionally conserved regulatory elements across distantly related vertebrates despite sequence divergence using a synteny-based method.

Accurate detection of pathogenic structural variants guided by multi-platform comparison

The paper introduces dicast, a machine-learning method that improves the detection of pathogenic structural variants from short-read sequencing by leveraging genomic context and alignment features.

CAdir: Fast Clustering and Visualization of Single-Cell Transcriptomics Data by Direction in CA Space

CAdir improves single-cell clustering by inferring cluster numbers, identifying marker genes, and providing diagnostic plots using correspondence analysis geometry.

Transfer learning and DNA language models enhance transcription factor binding predictions

This paper improves TF binding site prediction using DNA language models and transfer learning, achieving state-of-the-art performance across TFs, cell types, and chromosomes.

Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus

The paper uses CRISPR screens to identify transcription factors regulating Xist expression and their interactions with cis-regulatory elements during X-chromosome inactivation.

scATAcat: Cell-type annotation for scATAC-seq data

scATAcat annotates scATAC-seq data using bulk ATAC-seq prototypes and pseudobulk aggregation to overcome sparsity, showing improved performance on benchmark datasets.

Hepatocyte differentiation requires anisotropic expansion of bile canaliculi

This study shows that hepatocyte differentiation requires anisotropic expansion of bile canaliculi, with loss of polarity leading to cholangiocyte-like gene expression.

CENTRE: A gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction

CENTRE predicts cell-type-specific enhancer-target interactions using gene expression and ChIP-seq data, outperforming methods requiring extensive experimental data.

Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries

This paper introduces HIBF, a fast and space-efficient data structure for approximate sequence queries, showing significant improvements in speed and resource usage over existing tools.

CAbiNet: Joint visualization of cells and genes based on a gene-cell graph

CAbiNet jointly visualizes cells and genes using a gene-cell graph and biMAP embedding for interactive exploration and biclustering.

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

TADA - a Machine Learning Tool for Functional Annotation based Prioritisation of Putative Pathogenic CNVs

TADA prioritizes pathogenic CNVs using functional annotations and machine learning, achieving high AUC scores for deletions and duplications.

Effect of imputation on gene network reconstruction from single-cell RNA-seq data

This study evaluates how imputation methods affect gene regulatory network reconstruction from single-cell RNA-seq data, finding that imputation can inflate gene-gene correlations and alter network structures.

A RIF1/KAP1-based toggle switch stabilises the identities of the inactive and active X chromosomes during X inactivation

The paper identifies RIF1 and KAP1 as key factors in establishing an asymmetric state during X inactivation by coordinating Tsix and Xist expression.

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

The paper quantifies enhancer activity dynamics in mESCs during differentiation using FAIRE-STARR-seq, identifying features that predict enhancer activity and reveal regulatory insights.

Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs

The paper shows that divergent gene expression within TADs is resolved through TAD restructuring and DNA methylation, not enhancer-promoter compatibility or position.

Quantifying the Tissue-Specific Regulatory Information within Enhancer DNA Sequences

The paper uses epigenetic data to identify sequence patterns in enhancers that predict cell type-specific regulatory activity and finds that some patterns correspond to transcription factor footprints.

Long-read transcriptome sequencing analysis with IsoTools

The paper introduces IsoTools, a Python package for analyzing long-read transcriptome data, showing it improves alternative and differential splicing analysis compared to short-read RNA-Seq.

Trans control of cardiac mRNA translation in a protein length-dependent fashion

The paper identifies a trans locus in rats that causes a protein length-dependent shift in translational efficiency, affecting cardiac hypertrophy and sarcomere protein stoichiometry.

SVIM-asm: Structural variant detection from haploid and diploid genome assemblies

SVIM-asm detects and genotypes six classes of structural variants from haploid and diploid genome assemblies, outperforming existing tools in sensitivity and F1 scores for insertions and deletions.

Association Plots: Visualizing associations in high-dimensional correspondence analysis biplots

The paper introduces Association Plots to visualize cluster-specific measurements in high-dimensional data using Correspondence Analysis, demonstrating their effectiveness on genomic data.

SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing

CRUP: A comprehensive framework to predict condition-specific regulatory units

CRUP predicts condition-specific regulatory units by analyzing histone modification ChIP-seq data and linking enhancers to target genes in rheumatoid arthritis.

Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb Development

The paper shows that preformed chromatin topology supports robust Shh transcription during limb development, with CTCF and ZRS alleles influencing enhancer-promoter communication.

Functional dissection of TADs reveals non-essential and instructive roles in regulating gene expression

The paper investigates TAD function in mice by editing TAD organization, finding that TADs provide robustness but are not essential for gene regulation, and that disease phenotypes arise from re-direction of regulatory contacts.