An online copy number variant detection method for short sequencing reads

A Yiğiter, J Chen, L An… - Journal of Applied Statistics, 2015 - Taylor & Francis
The availability of the next generation sequencing (NGS) technology in today's biomedical
research has provided new opportunities in scientific discovery of genetic information. The …

Modeling the next generation sequencing read count data for DNA copy number variant study

T Ji, J Chen - Statistical applications in genetics and molecular …, 2015 - degruyter.com
As one of the most recent advanced technologies developed for biomedical research, the
next generation sequencing (NGS) technology has opened more opportunities for scientific …

SeqBBS: a change-point model based algorithm and R package for searching CNV regions via the ratio of sequencing reads

H Li, J Vallandingham, J Chen - 2013 IEEE International …, 2013 - ieeexplore.ieee.org
Following the breakthrough of the microarray technology, the next generation sequencing
(NGS) technology further advanced approaches in modern biomedical research. The high …

Statistical models for DNA copy number variation detection using read‐depth data from next generation sequencing experiments

T Ji, J Chen - Australian & New Zealand Journal of Statistics, 2016 - Wiley Online Library
Summary In this 'Big Data'era, statisticians inevitably encounter data generated from various
disciplines. In particular, advances in bio‐technology have enabled scientists to produce …

A penalized regression approach for DNA copy number study using the sequencing data

J Lee, J Chen - Statistical Applications in Genetics and Molecular …, 2019 - degruyter.com
Modeling the high-throughput next generation sequencing (NGS) data, resulting from
experiments with the goal of profiling tumor and control samples for the study of DNA copy …

Combinatorial detection algorithm for copy number variations using high-throughput sequencing reads

H Yang, D Zhu - International Journal of Pattern Recognition and …, 2019 - World Scientific
Copy number variation (CNV) is a prevalent kind of genetic structural variation which leads
to an abnormal number of copies of large genomic regions, such as gain or loss of DNA …

Detection of copy number variation from next generation sequencing data with total variation penalized least square optimization

J Duan, JG Zhang, J Lefante, HW Deng… - … on Bioinformatics and …, 2011 - ieeexplore.ieee.org
The detection of copy number variation is important to understand complex diseases such
as autism, schizophrenia, cancer, etc. In this paper we propose a method to detect copy …

[HTML][HTML] The screening and ranking algorithm for change-points detection in multiple samples

C Song, X Min, H Zhang - The annals of applied statistics, 2016 - ncbi.nlm.nih.gov
The chromosome copy number variation (CNV) is the deviation of genomic regions from
their normal copy number states, which may associate with many human diseases. Current …

A backward procedure for change‐point detection with applications to copy number variation detection

S Jun Shin, Y Wu, N Hao - Canadian Journal of Statistics, 2020 - Wiley Online Library
Change‐point detection regains much attention recently for analyzing array or sequencing
data for copy number variation (CNV) detection. In such applications, the true signals are …

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

R Xi, AG Hadjipanayis, LJ Luquette… - Proceedings of the …, 2011 - National Acad Sciences
DNA copy number variations (CNVs) play an important role in the pathogenesis and
progression of cancer and confer susceptibility to a variety of human disorders. Array …