Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

Statistical and integrative system-level analysis of DNA methylation data

AE Teschendorff, CL Relton - Nature Reviews Genetics, 2018 - nature.com
Epigenetics plays a key role in cellular development and function. Alterations to the
epigenome are thought to capture and mediate the effects of genetic and environmental risk …

Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling

LA Salas, Z Zhang, DC Koestler, RA Butler… - Nature …, 2022 - nature.com
DNA methylation microarrays can be employed to interrogate cell-type composition in
complex tissues. Here, we expand reference-based deconvolution of blood DNA …

An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray

LA Salas, DC Koestler, RA Butler, HM Hansen… - Genome biology, 2018 - Springer
Genome-wide methylation arrays are powerful tools for assessing cell composition of
complex mixtures. We compare three approaches to select reference libraries for …

A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

AE Teschendorff, CE Breeze, SC Zheng, S Beck - BMC bioinformatics, 2017 - Springer
Background Intra-sample cellular heterogeneity presents numerous challenges to the
identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While a …

Epigenetics and allergy: from basic mechanisms to clinical applications

DP Potaczek, H Harb, S Michel, BA Alhamwe… - …, 2017 - Taylor & Francis
Allergic diseases are on the rise in the Western world and well-known allergy-protecting and-
driving factors such as microbial and dietary exposure, pollution and smoking mediate their …

Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease

NT Ventham, NA Kennedy, AT Adams, R Kalla… - Nature …, 2016 - nature.com
Epigenetic alterations may provide important insights into gene-environment interaction in
inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation …

Cell-type deconvolution from DNA methylation: a review of recent applications

AJ Titus, RM Gallimore, LA Salas… - Human molecular …, 2017 - academic.oup.com
Recent advances in cell-type deconvolution approaches are adding to our understanding of
the biology underlying disease development and progression. DNA methylation (DNAm) …

Cell-type deconvolution in epigenome-wide association studies: a review and recommendations

AE Teschendorff, SC Zheng - Epigenomics, 2017 - Taylor & Francis
A major challenge faced by epigenome-wide association studies (EWAS) is cell-type
heterogeneity. As many EWAS have already demonstrated, adjusting for changes in cell …

Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology

E Rahmani, R Schweiger, B Rhead, LA Criswell… - Nature …, 2019 - nature.com
High costs and technical limitations of cell sorting and single-cell techniques currently
restrict the collection of large-scale, cell-type-specific DNA methylation data. This, in turn …