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Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation

Elior Rahmani
Noah Zaitlen
Eran Halperin
Correspondence28 Feb 2017
Nature Methods

Volume: 14, P: 218-219
Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissue

This multiomic study, including single-nucleus DNA methylation and chromatin conformation matched with single-nuclei RNA sequencing, provides insights into the epigenomic landscape of human subcutaneous adipose tissue.

Zeyuan Johnson Chen
Sankha Subhra Das
Päivi Pajukanta
ResearchOpen Access20 Aug 2025
Nature Genetics

Volume: 57, P: 2238-2249
Publisher Correction: Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

Brandon Jew
Marcus Alvarez
Eran Halperin
Amendments and CorrectionsOpen Access03 Jun 2020
Nature Communications

Volume: 11, P: 1
Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology

Compared to bulk data, cell-type-specific DNA methylation data provide higher resolution of epigenetic variation. Here, the authors introduce Tensor Composition Analysis, a novel computational approach for learning cell-type-specific DNA methylation from tissue-level bulk data, and show its application in epigenome-wide association studies.

Elior Rahmani
Regev Schweiger
Eran Halperin
ResearchOpen Access31 Jul 2019
Nature Communications

Volume: 10, P: 1-11
Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

Wells et al. profile RNA and surface protein expression to describe dominant tissue-specific effects on immune cell composition and function across lineages in the human tissues across age.

Steven B. Wells
Daniel B. Rainbow
Nir Yosef
ResearchOpen Access13 Aug 2025
Nature Immunology

Volume: 26, P: 1612-1625
Genetic association analysis of human median voice pitch identifies a common locus for tonal and non-tonal languages

A GWAS finds genetic link in ABCC9 gene affecting vocal pitch in both Mandarin and Icelandic speakers, suggesting a shared genetic influence on human vocal systems across populations.

Yazheng Di
Joel Mefford
Jonathan Flint
ResearchOpen Access07 May 2024
Communications Biology

Volume: 7, P: 1-7
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies

Principal component analysis on a subset of differentially methylated regions in a mixture of cell types is the basis of ReFACTor, a program to account for heterogeneity in epigenome-wide association studies (EWAS).

Elior Rahmani
Noah Zaitlen
Eran Halperin
Research28 Mar 2016
Nature Methods

Volume: 13, P: 443-445
Accurate prediction of disease-risk factors from volumetric medical scans by a deep vision model pre-trained with 2D scans

A deep-learning model pre-trained on readily available 2D scans outperforms domain-specific state-of-the-art models in the prediction of disease-risk factors from 3D medical-scan modalities.

Oren Avram
Berkin Durmus
Eran Halperin
Research01 Oct 2024
Nature Biomedical Engineering

Volume: 9, P: 507-520
Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM

Marcus Alvarez
Elior Rahmani
Päivi Pajukanta
ResearchOpen Access03 Jul 2020
Scientific Reports

Volume: 10, P: 1-16
Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

Traditional methods for determining cell type composition lack scalability, while single-cell technologies remain costly and noisy compared to bulk RNA-seq. Here, the authors present a highly efficient tool to measure cellular heterogeneity in bulk expression through robust integration of single-cell information.

Brandon Jew
Marcus Alvarez
Eran Halperin
ResearchOpen Access24 Apr 2020
Nature Communications

Volume: 11, P: 1-11
Detecting heritable phenotypes without a model using fast permutation testing for heritability and set-tests

Standard approaches for heritability and set testing in statistical genetics rely on parametric models that might not hold in reality and give inflated p-values. Here, the authors develop a fast method for permutation-based testing of marker sets and of heritability that does not suffer from model misspecification.

Regev Schweiger
Eyal Fisher
Eran Halperin
ResearchOpen Access21 Nov 2018
Nature Communications

Volume: 9, P: 1-9
Unraveling the associations between voice pitch and major depressive disorder: a multisite genetic study

Yazheng Di
Elior Rahmani
Jonathan Flint
ResearchOpen Access31 Dec 2024
Molecular Psychiatry

Volume: 30, P: 2686-2695
Genome wide association study and genomic risk prediction of age related macular degeneration in Israel

Michelle Grunin
Daria Triffon
Itay Chowers
ResearchOpen Access06 Jun 2024
Scientific Reports

Volume: 14, P: 1-9

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