Hamed Shateri Najafabadi

The paper introduces ecCLIP for high-resolution RBP binding maps and Pythia for structure-aware RNA-protein interaction modeling, improving RNA half-life prediction and variant effect assessment.

The paper maps regulatory connections between RBPs and miRNAs in cancer, showing RBP-driven regulation contributes to miRNA activity heterogeneity and identifies DDX55 as a key regulator of miR-29-3p.

This study identifies TACC3 as a coordinator of translation and epitranscriptomic reprogramming that determines cancer cell sensitivity or tolerance to mitotic stress induced by microtubule targeting agents.

This study identifies TCF4 as a downstream effector of PHF6 in neural stem cell regulation, showing its role in restricting self-renewal and rescuing BFLS phenotypes.

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

This study identifies LOX as a driver of ccRCC progression by sustaining HIF-2α transcription and modulating the tumor microenvironment.

The paper investigates ribosome clusters in neuronal RNA granules, finding they contain stalled ribosomes and unique 3D structures that avoid quality-control mechanisms.

This study identifies 59 gene expression programs in RCC that reveal subtype identity and metastatic trajectories, including a metastatic signature linked to poor clinical outcomes.

The paper introduces LEAF-1, a fragment-level foundation model for genomics data analysis, showing it can classify cell types and detect cancer from sparse datasets and cell-free DNA.

The paper identifies intra-genic mutational robustness through alternative splicing in cancer, showing it can complement inter-genic robustness and is associated with worse disease outcomes.

This paper introduces scLSD, a thermodynamics-inspired model for cell differentiation that reconstructs differentiation trajectories and predicts fate commitment, outperforming existing methods.

This study identifies cancer-driven suppression of muscle stem cell differentiation in cachectic mice through GDF15 and MMP9, revealing a new mechanism of muscle wasting.

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

Decoy-seq enables single-cell perturbation screening of small noncoding RNAs by using TuD decoys to inhibit smRNAs, revealing their regulatory roles in cancer.

The paper identifies genomic binding sites of 166 poorly characterized human transcription factors, revealing that some bind to dark matter DNA and others to regulatory regions.

This paper improves power to detect gene-environment interactions by adapting SharePro to account for genetic effect heterogeneity in fine-mapping.

The paper introduces Mach-1, an RNA foundation model that predicts transcriptome architecture from DNA sequence, validated through experimental perturbations and CRISPR editing.

This paper introduces GEDI, a generative model that unifies multi-sample, multi-condition single-cell analysis tasks, enabling cross-sample cell state mapping, differential gene expression, and pathway activity projection.

This paper introduces MPAQT, a framework that improves isoform quantification in bulk and single-cell RNA-seq by integrating short- and long-read data and using sequence-to-expression models.

SharePro improves genetic colocalization analysis by handling multiple causal signals, showing increased power and efficiency in simulations and real data.

SparsePro improves fine-mapping of GWAS results by integrating summary statistics and functional annotations, achieving higher power and faster computation than existing methods.

This study shows that the niche environment significantly influences skeletal muscle stem cell transcriptional activity, with some age-related changes being reversible through exposure to a young niche.

The paper analyzes mRNA stability across 7760 cancer samples to identify stability changes and factors driving them in tumour development.

The paper introduces JAMS models to analyze how cytosine methylation affects TF binding in vivo, finding that 45% of TFs are inhibited by methylation while only 6% prefer it.

This study shows that Myf6/MRF4 regulates myokine production and maintains the muscle stem cell pool by controlling signaling pathways like EGFR and STAT3.

The paper identifies DNA-binding zinc finger domains in 209 human multi-ZF proteins and shows their mutations affect gene expression in cancer.

The paper introduces a probabilistic model to estimate and correct sample index hopping in single-cell RNA-seq data, reducing phantom molecules by up to 85%.

This paper develops smfRNA-Seq to analyze the whole transcriptome of individual myofibers and finds aging causes significant changes in metabolic and structural gene expression.

The paper shows that PKM inhibits translation of 7% of the transcriptome under high glucose and pyruvate conditions by stalling ribosome elongation, linking glycolysis to protein synthesis and cell cycle regulation.