Judith B. Zaugg

The paper shows that replication stress from chemotherapy accelerates erythroid differentiation but blocks terminal maturation, leading to impaired red cell output.

This study links multiscale biological interactions to clinical outcomes in AML by analyzing single-cell data and developing an analytical framework.

This study identifies a specific leukemic stem cell (LSC) subtype that drives niche remodeling in AML by altering fibroblast states and suppressing osteolineage differentiation.

The paper quantifies enhancer activation frequency in response to TF perturbations and identifies H3K27Ac as a chromatin mark required for enhancer activation.

This study uses single-cell transplantation and mathematical modeling to show that lineage biases in hematopoiesis arise from extrinsic feedback and clonal competition, not intrinsic HSC properties.

The paper maps variant, enhancer, and gene function in primary human CD4+ T cells by combining Perturb-seq of regulatory elements and genes, identifying CRE-gene pairs and linking variants to disease-related programs.

CryoSiam is a self-supervised framework for cryo-ET data analysis that learns hierarchical representations and transfers to experimental data for denoising, segmentation, and macromolecular detection.

This study identifies CDK1 as a key regulator of CD4+ T cell effector function through integrative multi-omics analysis, showing its role in linking phosphorylation to gene regulation and immune traits.

SpliceUp detects SF3B1-mutant cells in scRNA-seq data by analyzing aberrant splicing signatures, improving detection from low-coverage datasets.

FootprintCharter detects and quantifies footprints in single molecule footprinting data without prior assumptions on genomic locations.

This study investigates ZIC2's role in neural development, showing it acts as a pioneer transcription factor during pluripotency exit and an enhancer activator during neural induction.

This study identifies treatment-resistant stem-like T-ALL cells that expand during relapse using single-cell RNA sequencing of pediatric T-ALL patient samples.

The paper uses single-cell CRISPRi screens to functionally assess schizophrenia-associated genes, revealing disruptions in neurodevelopmental timing and identifying key regulatory factors.

The paper identifies PROX1 as a safeguard repressor that maintains hepatocyte identity and prevents liver tumourigenesis by repressing alternate fate regulators.

This study shows that dermal macrophages can maintain functional diversity without monocyte replenishment, but require monocytes during bacterial infections.

HIPSD&R-seq profiles genomic copy number and transcriptomes in thousands of cells, enabling rare clone detection in human cell models and primary tissue.

The paper identifies genetic variants affecting TF binding during Drosophila embryogenesis and uses a CNN to predict functional variants.

This study shows that H3.3K9 and K27 modifications regulate repressive chromatin states at cis-regulatory elements and bivalent promoters in mESCs, affecting gene expression.

This paper introduces SDR-seq, a multiomic scDNA-scRNA-seq method to link genotypes with gene expression, showing variants affect expression in iPSCs and B-cell lymphoma.

This study shows Xist RNA modulates X-chromosome inactivation beyond early development, reversibly silencing escapee genes and altering topological domain structures in mouse embryos.

This study identifies TF binding sites on the Integrator complex that mediate gene-specific transcription regulation and inducible transcriptional responses.

This study shows glycolysis regulates the segmentation clock period in mouse embryos through a glycolysis-FBP-Wnt signaling axis, with FBP entraining Wnt oscillations.

The paper integrates genetic and epigenetic data to identify autoimmune-specific enhancer dysregulation in CD4+ T cells and its role in disease pathogenesis.

This paper introduces SUM-seq, a scalable multiomic method for single-cell chromatin and RNA sequencing, revealing gene regulatory dynamics in macrophage polarization linked to autoimmune diseases.

This study reveals that cellular differentiation drives intratumor heterogeneity in B-cell lymphomas, with distinct maturation states associated with different survival outcomes.

DeePiCt is a deep-learning framework for segmenting and localizing macromolecular complexes in cryo-electron tomograms, showing effectiveness in identifying low-abundance structures across species.

The paper shows that parts of the TCA cycle operate in the nucleus, challenging the canonical view of metabolic compartmentalization.

The paper introduces GRaNIE and GRaNPA, tools for inferring and evaluating enhancer-mediated gene regulatory networks in macrophages, identifying PURA as a regulator of pro-inflammatory polarization.

The paper investigates the role of Tal1, Lmo2, and Lyl1 in the Endothelial to Hematopoietic Transition using a mouse embryonic-stem cell model and multi-omics approaches, finding that Tal1 expression in endothelial cells is crucial for the transition.