Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas

D Hübschmann, K Kleinheinz, R Wagener… - Leukemia, 2021 - nature.com
B cells have the unique property to somatically alter their immunoglobulin (IG) genes by V
(D) J recombination, somatic hypermutation (SHM) and class-switch recombination (CSR) …

Deciphering the emerging complexities of molecular mechanisms at GWAS loci

ME Cannon, KL Mohlke - The American Journal of Human Genetics, 2018 - cell.com
Genome-wide association studies (GWASs) have identified thousands of loci associated
with hundreds of complex diseases and traits, and progress is being made toward …

Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate

TJ Peters, MJ Buckley, Y Chen, GK Smyth… - Nucleic acids …, 2021 - academic.oup.com
Whole genome bisulphite sequencing (WGBS) permits the genome-wide study of single
molecule methylation patterns. One of the key goals of mammalian cell-type identity studies …

Regulatory variants: from detection to predicting impact

E Rojano, P Seoane, JAG Ranea… - Briefings in …, 2019 - academic.oup.com
Variants within non-coding genomic regions can greatly affect disease. In recent years,
increasing focus has been given to these variants, and how they can alter regulatory …

An ATAC-seq atlas of chromatin accessibility in mouse tissues

C Liu, M Wang, X Wei, L Wu, J Xu, X Dai, J Xia… - Scientific data, 2019 - nature.com
Abstract The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is
a fundamental epigenomics approach and has been widely used in profiling the chromatin …

Genomic data imputation with variational auto-encoders

YL Qiu, H Zheng, O Gevaert - GigaScience, 2020 - academic.oup.com
Background As missing values are frequently present in genomic data, practical methods to
handle missing data are necessary for downstream analyses that require complete data …

A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes

Q Luo, VB Dwaraka, Q Chen, H Tong, T Zhu, K Seale… - Genome Medicine, 2023 - Springer
Background Changes in cell-type composition of tissues are associated with a wide range of
diseases and environmental risk factors and may be causally implicated in disease …

Epigenetics in eating disorders: a systematic review

C Hübel, SJ Marzi, G Breen, CM Bulik - Molecular psychiatry, 2019 - nature.com
Eating disorders are complex heritable conditions influenced by both genetic and
environmental factors. Given the progress of genomic discovery in anorexia nervosa, with …

Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients

JK de Kanter, F Peci, E Bertrums, AR Huber… - Cell stem cell, 2021 - cell.com
Genetic instability is a major concern for successful application of stem cells in regenerative
medicine. However, the mutational consequences of the most applied stem cell therapy in …

Cell-type heterogeneity: Why we should adjust for it in epigenome and biomarker studies

L Qi, AE Teschendorff - Clinical Epigenetics, 2022 - Springer
Most studies aiming to identify epigenetic biomarkers do so from complex tissues that are
composed of many different cell-types. By definition, these cell-types vary substantially in …