Syed Murtuza Baker

DeepPathway predicts pathway expression from H&E images using contrastive learning, validated on prostate cancer and brain tumor datasets.

This study presents a transcriptomic atlas of the developing human outflow tract and its adult aortic valve derivatives, revealing persistent embryonic signatures and key regulatory factors in valve development.

Spartan identifies spatial domains and variable genes by integrating spatial topology and activation signals in spatial transcriptomics data.

This study uses a multi-omics approach to analyze regional differences in cardiac responses to radiation, identifying distinct molecular and structural changes in different heart regions.

This study identifies gene regulatory networks driving periderm formation in early skin development using single-cell multiome and spatial transcriptomics data.

This paper uses spatial transcriptomics and hypergraph analysis to identify distinct transcriptomic signatures in acute versus chronic wounds, revealing pathway differences and entropy patterns.

The paper integrates scRNA-seq data to create an AML single-cell atlas, revealing age-related gene regulatory networks in t(8;21) AML and identifying BCLAF1 as a prognostic indicator.

The paper identifies a metaplastic precursor state in Barrett's oesophagus as a reversion to a fetal epithelial cell state, revealing HNF4A's role and GWAS SNPs in regulatory regions.

The paper identifies CD82 as a marker of the endothelium-to-hematopoietic transition in human blood specification using single-cell analysis.

The paper maps the spatial transcriptional changes in human liver cirrhosis, identifying gene signatures and cell state transitions linked to disease progression.

The paper investigates how acetylation dynamics affect gene activation, finding two distinct gene classes with opposing requirements for acetylation levels in their transcriptional response.

This study identifies Foxm1 as a critical transcription factor for spinal cord regeneration in axolotls by regulating neuronal differentiation rather than proliferation.

The paper investigates how HOX paralogs interact with TALE TFs to generate tissue-specific enhancer activation patterns in mouse embryos.

This study identifies ZIC3 as a key regulator of the transition from naïve to primed pluripotency in mouse ESCs by analyzing open chromatin changes and transcriptional networks.

The paper introduces Scasat, a pipeline for analyzing single-cell ATAC-seq data, and shows it can identify cell types by analyzing open chromatin regions.