Christoforos Nikolaou

The paper investigates the evolutionary origins of protein novelty in Saccharomycotina yeasts, identifying two distinct modes of de novo and divergent gene evolution and their structural implications.

This paper identifies senescence-induced CTCF clusters (SICCs) and shows they sustain the senescence splicing program by repurposing nuclear speckle components.

This study shows that SMC1A redistributes from nuclear speckles to the nuclear periphery during inflammation, affecting gene expression through changes in splicing and mRNA processing.

This study identifies Notch3 as a regulator of pericyte phenotypic plasticity in colorectal cancer, showing its role in promoting proliferation and altering contractile properties.

The paper uses machine learning to identify diverged orphan genes from similarity search outputs, finding that ~30% of simulated orphans are predicted to be divergent.

The paper investigates enhancer interactions in immune cell fate switching, finding synergistic and antagonistic effects of IRF8 and FOS enhancer pairs during transdifferentiation.

The paper measures DNA linking number differences restrained by nucleosomes in yeast, showing variation based on genomic location and demonstrating topological memory of nucleosomes.

This study uses a small molecule inhibitor to rapidly and synchronously induce senescence-like features in human cells, enabling analysis of its core regulatory program without paracrine effects.

This study shows that Wnt/TCF7L1 repression promotes primitive endoderm differentiation in mESCs by inhibiting naive and formative pluripotency factors.

The paper investigates TM-forming potential in intergenic regions of Saccharomycotina yeasts and finds it is pervasive but variable across species.

The paper identifies SATB1 as a tissue-specific genome organizer that regulates 3D enhancer networks in developing T cells, affecting immune system homeostasis and lineage specification.

The paper investigates positional preferences of gene duplicates in S. cerevisiae, finding SSD and WGD genes occupy distinct chromosomal niches with different structural and regulatory features.

The paper identifies Hes-regulated genes in Drosophila neural stem cell maintenance and tumorigenesis by combining transcriptomic and chromatin occupancy data.

This study identifies disease-associated alterations in gene co-regulation patterns in SLE, showing fragmentation and redistribution of co-expression domains correlate with disease activity and biological pathways.

The paper introduces a bipartite network approach to study gene expression by integrating topological and functional information, revealing two distinct phases of TNF-induced gene regulation in mouse fibroblasts.

The paper evaluates sequence representations and classification methods for predicting nucleosome positioning in yeast, finding that N-gram Graphs perform best.

The paper identifies 116 gene clusters in S. cerevisiae that respond to topological stress, showing distinct genomic locations and functional characteristics.