Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time

J Feichtinger, I Hernández, C Fischer… - Biotechnology and …, 2016 - Wiley Online Library
The most striking characteristic of CHO cells is their adaptability, which enables efficient
production of proteins as well as growth under a variety of culture conditions, but also results …

DNA methylation changes induced by long and short photoperiods in Nasonia

M Pegoraro, A Bafna, NJ Davies, DM Shuker… - Genome …, 2016 - genome.cshlp.org
Many organisms monitor the annual change in day length and use this information for the
timing of their seasonal response. However, the molecular mechanisms underlying …

Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments

Q Giai Gianetto, F Combes, C Ramus, C Bruley… - …, 2016 - Wiley Online Library
In MS‐based quantitative proteomics, the FDR control (ie the limitation of the number of
proteins that are wrongly claimed as differentially abundant between several conditions) is a …

HMM-DM: identifying differentially methylated regions using a hidden Markov model

X Yu, S Sun - Statistical applications in genetics and molecular …, 2016 - degruyter.com
DNA methylation is an epigenetic modification involved in organism development and
cellular differentiation. Identifying differential methylations can help to study genomic regions …

The CD4+ T cell methylome contributes to a distinct CD4+ T cell transcriptional signature in Mycobacterium bovis-infected cattle

R Doherty, R Whiston, P Cormican, EK Finlay… - Scientific reports, 2016 - nature.com
We hypothesised that epigenetic regulation of CD4+ T lymphocytes contributes to a shift
toward a dysfunctional T cell phenotype which may impact on their ability to clear …

Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive'hypothesis

A Chatterjee, M Lagisz, EJ Rodger, L Zhen… - Gene, 2016 - Elsevier
The sex drive hypothesis predicts that stronger selection on male traits has resulted in
masculinization of the genome. Here we test whether such masculinizing effects can be …

From the cover: sperm molecular biomarkers are sensitive indicators of testicular injury following subchronic model toxicant exposure

E Dere, SK Wilson, LM Anderson… - Toxicological …, 2016 - academic.oup.com
Traditional testis histopathology endpoints remain the gold standard for evaluating testicular
insult and injury in a non-clinical setting, but are invasive and unfeasible for monitoring …

Comparing five statistical methods of differential methylation identification using bisulfite sequencing data

X Yu, S Sun - Statistical applications in genetics and molecular …, 2016 - degruyter.com
We are presenting a comprehensive comparative analysis of five differential methylation
(DM) identification methods: methylKit, BSmooth, BiSeq, HMM-DM, and HMM-Fisher, which …

[HTML][HTML] Distinct epigenetic signatures elucidate enhancer-gene relationships that delineate CIMP and non-CIMP colorectal cancers

A Chong, JX Teo, KHK Ban - Oncotarget, 2016 - ncbi.nlm.nih.gov
Epigenetic changes, like DNA methylation, affect gene expression and in colorectal cancer
(CRC), a distinct phenotype called the CpG island methylator phenotype (“CIMP”) has …

[HTML][HTML] DNA methylation signature of post-injury neointimal cells during vascular remodeling in the rat balloon injury model

J Richards, HA Ogoe, W Li, O Babayewa… - … biology (Los Angeles …, 2016 - ncbi.nlm.nih.gov
Vascular smooth muscle cell (VSMC) accumulation in the neointimal is a common feature in
vascular diseases such as atherosclerosis, transplant arteriosclerosis and restenosis. In this …