Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres

K Guin, Y Chen, R Mishra, SRBM Muzaki… - Elife, 2020 - elifesciences.org
Centromeres of Candida albicans form on unique and different DNA sequences but a
closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR) …

CDK4 and CDK6 upregulation promotes DNA replication stress, genomic instability and resistance to EGFR targeted therapy in lung cancer

B Gini, P Gui, W Wu, DL Kerr, L Tan, D Barbosa… - bioRxiv, 2024 - biorxiv.org
Genetic interactions impact both normal human physiology and human diseases, such as
cancer. Here, we study genetic interactions through the lens of human lung cancers driven …

Simulating Tumor Evolution from scDNA-Seq as an Accumulation of both SNVs and CNAs

Z Tayebi, A Juyal, A Zelikovsky, M Patterson - International Symposium on …, 2023 - Springer
Ever since single-cell sequencing (scDNA-seq) was coined 'method of the year'in 2013, it
has provided many insights into the evolution of tumors, viewed as a branching process of …

Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines

AIS Khalil, SRBM Muzaki, A Chattopadhyay… - BMC …, 2020 - Springer
Background Hi-C and its variant techniques have been developed to capture the spatial
organization of chromatin. Normalization of Hi-C contact map is essential for accurate …

Clustering, Classification, and Simulation of Evolutionarily Related Sequences in the Context of Cancer and Viral Spread

Z Tayebi - 2024 - scholarworks.gsu.edu
Molecular sequence analysis is vital for understanding the functions, structures, and
behaviors of organisms, including viruses, playing a key role in disease prevention and …

Evolution of RNA Viruses and Cancer Clones: Insights from Sequencing Data

A Juyal - 2024 - scholarworks.gsu.edu
The utilization of extensive sequencing data is essential for exploration of computational
challenges, particularly resolving clustering problems and simulating single-cell tumor …

Population Genomics of Aneuploidy in Yeast

ESF da Costa - 2022 - search.proquest.com
Aneuploidy is the gain or loss of chromosomes in a cell, has major effects in eukaryotes and
is linked to cancer and genetic diseases in humans. Aneuploidy is common in the wine …

Analysis of Aneuploidy Spectrum From Whole-Genome Sequencing Provides Rapid Assessment of Clonal Variation Within Established Cancer Cell Lines

AIS Khalil, A Chattopadhyay, A Sanyal - Cancer Informatics, 2021 - journals.sagepub.com
Background: The revolution in next-generation sequencing (NGS) technology has allowed
easy access and sharing of high-throughput sequencing datasets of cancer cell lines and …

Enhanced Bayesian detection for copy number alterations from next-generation sequencing data

Z Yu, F Du - 2021 IEEE International Conference on …, 2021 - ieeexplore.ieee.org
Next-generation sequencing (NGS) promises highresolution landscapes of cancer
genomes, especially the genomewide copy number alterations (CNAs). Detecting CNAs …

Cytogenomic Changes in Sporadic Colorectal Cancer and Surrounding Nonneoplastic Tissues: The Relevance of Subtelomeric Copy Number Variations

M Rocha, EA Zanardo, AT Dias, FAR Madia… - 2021 - researchsquare.com
The purpose of this study was to investigate the relevance of subtelomeric cytogenomic
changes in patients with sporadic colorectal cancer (CRC) using multiplex ligation …