User profiles for Hakan Ozadam
Hakan ÖzadamBioinformatician, University of Texas at Austin Verified email at utexas.edu Cited by 2713 |
Integrative detection and analysis of structural variation in cancer genomes
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms.
Despite their importance, the identification of SVs in cancer genomes remains challenging. …
Despite their importance, the identification of SVs in cancer genomes remains challenging. …
[HTML][HTML] Systematic evaluation of chromosome conformation capture assays
Chromosome conformation capture (3C) assays are used to map chromatin interactions
genome-wide. Chromatin interaction maps provide insights into the spatial organization of …
genome-wide. Chromatin interaction maps provide insights into the spatial organization of …
The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes
…, I El-Idrissi, THN Huynh, H Ozadam… - Genes & …, 2017 - genesdev.cshlp.org
The mammalian HoxD cluster lies between two topologically associating domains (TADs)
matching distinct enhancer-rich regulatory landscapes. During limb development, the …
matching distinct enhancer-rich regulatory landscapes. During limb development, the …
[HTML][HTML] Single-cell quantification of ribosome occupancy in early mouse development
Translation regulation is critical for early mammalian embryonic development 1 . However,
previous studies had been restricted to bulk measurements 2 , precluding precise …
previous studies had been restricted to bulk measurements 2 , precluding precise …
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase
Chromosome folding is modulated as cells progress through the cell cycle. During mitosis,
condensins fold chromosomes into helical loop arrays. In interphase, the cohesin complex …
condensins fold chromosomes into helical loop arrays. In interphase, the cohesin complex …
[HTML][HTML] Measuring the reproducibility and quality of Hi-C data
Background Hi-C is currently the most widely used assay to investigate the 3D organization
of the genome and to study its role in gene regulation, DNA replication, and disease. …
of the genome and to study its role in gene regulation, DNA replication, and disease. …
[PDF][PDF] Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts
A major challenge in biology is to understand how complex gene expression patterns are
encoded in the genome. While transcriptional enhancers have been studied extensively, few …
encoded in the genome. While transcriptional enhancers have been studied extensively, few …
[HTML][HTML] The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome
The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin
structure, manifested as a global loss of local topologically associated domains (TADs), A/…
structure, manifested as a global loss of local topologically associated domains (TADs), A/…
[PDF][PDF] Measuring the reproducibility and quality of Hi-C data
Background: Hi-C is currently the most widely used assay to investigate the 3D organization
of the genome and to study its role in gene regulation, DNA replication, and disease. …
of the genome and to study its role in gene regulation, DNA replication, and disease. …
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling
In light of the numerous studies identifying post-transcriptional regulators on the surface of
the endoplasmic reticulum (ER), we asked whether there are factors that regulate …
the endoplasmic reticulum (ER), we asked whether there are factors that regulate …