Rahul Siddharthan

The paper identifies two groups of transcription factors that show intra-group attraction and inter-group repulsion in both genomic and spatial contexts across human cell lines.

The paper identifies centromere structures and evolutionary changes in Candida auris and related species, revealing clade-specific karyotype innovations.

The paper identifies centromere regions in Malassezia species and shows that centromere loss drives karyotype evolution by causing chromosome breakage and fusion.

This study shows Orc4 stabilizes centromeric chromatin by interacting with CENPA and Mcm2, and its spatiotemporal localization is crucial for kinetochore stability in C. albicans.

ChIPulate evaluates how biological and experimental factors affect ChIP-seq outcomes, finding that replicate numbers and extraction efficiency significantly impact binding strength inference.

The paper introduces CPI-EM, a method using ChIP-seq peak intensities and expectation maximization to detect cooperative TF pairs, showing improved performance over distance-based and sequence-based methods.

THiCweed detects sequence features in ChIP-seq data by clustering bound regions based on sequence similarity, outperforming existing methods on synthetic and real data.