Christoph Bock

The paper uses plasma immunopeptidomics guided by mutanomes to detect neoepitopes in solid tumors, finding that cfDNA variant calling sensitivity and MS detection limits constrain plasma-based detection.

This study uses scRNA-seq and immunophenotyping to analyze immune changes in RA patients on MTX, showing early restoration of naive T/B cells and reduced memory T cells, with plasmablasts as a potential biomarker.

This study investigates the role of Mtor/Rptor in cortical development, finding that its loss causes microcephaly through tissue-wide effects, while cell-autonomous Rptor function is critical for postnatal neuron survival in a cell-type-specific manner.

The paper benchmarks DNA methylation sequencing workflows against an experimental gold-standard, identifying superior workflows and developing a sustainable benchmarking platform.

This study creates a comprehensive single-cell transcriptomic atlas of human endothelial cells across adult life, identifying age-related transcriptional changes and a p21-linked senescence program.

This study identifies purine nucleobases as immunometabolites that enhance CD8+ T cell effector function by enabling a metabolic switch from de novo synthesis to salvage pathway.

SpotWhisperer links histopathology images to spatial gene expression and text annotations using natural language AI, outperforming existing models on a new benchmark dataset.

This study shows HDAC1 is essential for generating and maintaining CX3CR1+ effector-like T cells during chronic viral infection, which helps control viral load.

The paper shows that centrosomes in non-dividing cells can fracture under mechanical stress during cell navigation, and Dyrk3 prevents this fracturing to maintain cellular function.

This study reveals that PHLPP2 is a pseudophosphatase with no catalytic activity, challenges its role as a tumor suppressor, and identifies its non-catalytic functions in Akt signaling.

This study uses scRNA-seq to identify two distinct subsets of pathogenic Th2 cells in allergic asthma and establishes an in vitro model to study their regulation.

This study examines how altering Atlantic salmon spawning seasons affects offspring gene expression and DNA methylation, influencing lipid metabolism and cell cycle regulation.

The paper evaluates four organoid protocols to recreate human brain cell diversity, identifies factors affecting variability, and introduces a scoring system to assess differentiation propensities.

CellWhisperer enables chat-based exploration of single-cell RNA-seq data using natural language by connecting transcriptomes with text through multimodal learning.

This paper introduces SimulateGPT, a text-based simulator using large language models to predict biomedical outcomes without domain knowledge or manual tuning.

The paper examines how one-carbon metabolism nutrients affect DNA methylation and gene expression in Atlantic salmon liver, showing their impact on protein synthesis pathways.

This study analyzes the epigenetic evolution of IDH1-mutant and IDH1-wildtype gliomas under treatment, showing IDHmut tumors undergo epigenomic changes resembling IDHwt tumors, with implications for treatment strategies.

This study identifies multipotent progenitors in the superior colliculus that generate all excitatory and inhibitory neuron types without extrinsic input.

This study uses scRNA-seq to analyze early hyperglycaemia responses in multiple organs of a mouse model, identifying conserved and organ-specific transcriptional changes linked to diabetes complications.

The paper maps DNA methylation in 580 animal species, revealing conserved and evolving patterns across vertebrates and invertebrates.

This study identifies TBXT's role in early posterior regionalisation of human neural crest cells through chromatin remodelling and WNT signalling.

The paper identifies a stress signature in brain organoid scRNA-seq data and introduces Gruffi to remove stressed cells, improving developmental accuracy.

The paper identifies molecular and metabolic signatures of cardiometabolic syndrome using extreme phenotype groups and shows changes after bariatric surgery.

This paper introduces scifi-RNA-seq, a high-throughput single-cell RNA sequencing method that increases throughput by 15-fold through combinatorial fluidic indexing and enables large-scale experiments.

The paper identifies an enhancer element that amplifies Fgf5 expression by accumulating paused RNA Polymerase II, revealing a new mechanism of enhancer collaboration during differentiation.

The paper identifies novel imprinted genes in mouse blastocysts and shows that their expression is mostly independent of DNA methylation but associated with H3K27me3 marks.

This paper introduces knowledge-primed neural networks (KPNNs) for interpretable deep learning on single-cell RNA-seq data, demonstrating their ability to predict T cell receptor stimulation and infer cell types.

This study infers tumor cell-specific transcription factor binding from cell-free DNA to predict tumor subtypes and detect cancer early.

The paper identifies functional enhancers in human embryonic stem cells using a combination of chromatin immunoprecipitation and a massively parallel reporter assay, revealing novel enhancer classes and activity patterns.

The paper predicts tissue-specific gene expression across species using epigenome data from reference organisms.