Methods for copy number aberration detection from single-cell DNA-sequencing data

XF Mallory, M Edrisi, N Navin, L Nakhleh - Genome biology, 2020 - Springer
Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs),
play an important role in the initiation and progression of cancer. Single-cell DNA …

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning

JB Lugagne, H Lin, MJ Dunlop - PLoS computational biology, 2020 - journals.plos.org
Microscopy image analysis is a major bottleneck in quantification of single-cell microscopy
data, typically requiring human oversight and curation, which limit both accuracy and …

Graph-based change-point analysis

H Chen, L Chu - Annual Review of Statistics and Its Application, 2023 - annualreviews.org
Recent technological advances allow for the collection of massive data in the study of
complex phenomena over time and/or space in various fields. Many of these data involve …

High dimensional change point estimation via sparse projection

T Wang, RJ Samworth - Journal of the Royal Statistical Society …, 2018 - academic.oup.com
Change points are a very common feature of 'big data'that arrive in the form of a data stream.
We study high dimensional time series in which, at certain time points, the mean structure …

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

G Nilsen, K Liestøl, P Van Loo, HK Moen Vollan… - BMC genomics, 2012 - Springer
Background Cancer progression is associated with genomic instability and an accumulation
of gains and losses of DNA. The growing variety of tools for measuring genomic copy …

On optimal multiple changepoint algorithms for large data

R Maidstone, T Hocking, G Rigaill, P Fearnhead - Statistics and computing, 2017 - Springer
Many common approaches to detecting changepoints, for example based on statistical
criteria such as penalised likelihood or minimum description length, can be formulated in …

Graph-based change-point detection

H Chen, N Zhang - 2015 - projecteuclid.org
Supplement to “Graph-based change-point detection”. Supplement A: Proofs for lemmas,
propositions and theorems. We provide the proofs to the lemmas, propositions and …

CODEX: a normalization and copy number variation detection method for whole exome sequencing

Y Jiang, DA Oldridge, SJ Diskin… - Nucleic acids …, 2015 - academic.oup.com
High-throughput sequencing of DNA coding regions has become a common way of
assaying genomic variation in the study of human diseases. Copy number variation (CNV) is …

Change-point detection in panel data via double CUSUM statistic

H Cho - 2016 - projecteuclid.org
Supplement to “Change-point detection in panel data via double CUSUM statistic”. We
provide the detailed description of the Local Bootstrap and proof of some auxillary results. In …

The group fused lasso for multiple change-point detection

K Bleakley, JP Vert - arXiv preprint arXiv:1106.4199, 2011 - arxiv.org
We present the group fused Lasso for detection of multiple change-points shared by a set of
co-occurring one-dimensional signals. Change-points are detected by approximating the …