The paper introduces a novel dual-spike-in normalization method for ChIP-seq, demonstrating its ability to clarify the relationship between RNA polymerase II activity and histone modifications.

Nature Genetics · Aug 25, 2026Peer-reviewedGenomics

Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

A B Anil Kumar, Yanning Zuo, Numaan Formoli, Daimeng Sun, Narayan Pokhrel, Carlos Guzman, Sven Heinz, Christopher Benner, Francesca Telese

This study maps transcription initiation in mouse astrocytes to define how inflammatory signals drive cell-type-specific gene regulation and links enhancer activity to human disease risk.

bioRxiv · May 28, 2026 · PreprintGenomics

Increased atherosclerosis and expression of inflammarafts in macrophage foam cells in AIBP-deficient mice

Shenglin Li, Nicolaus Nazarenkov, Elena A. Alekseeva, Soo-Ho Choi, Juliana Maria Navia Pelaez, Aakash V. Patel, Patrick Secrest, Philip L.S.M. Gordts, Sven Heinz, Yury I. Miller

This study shows that AIBP deficiency in mice leads to increased foam cell inflammation and atherosclerosis through enhanced inflammaraft expression and lipid accumulation.

Scientific Reports · Feb 7, 2026Peer-reviewedImmunology

Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq

Tianyao Xu, Jingyao Wang, Yoonju Shin, Yuwei Cao, Lingzhi Zhang, Eduardo Modolo, Tamar Dishon, Jeremy Fisher, Matthew Norton, Christopher J. Fry, Yossi Farjoun, Eric M. Mendenhall, Sven Heinz, Christopher W. Benner, Alon Goren

Prod&PQ-seq detects and quantifies protein-protein interactions and protein abundance across different cellular conditions, showing changes in PRC2 interactions with EZH2 inhibition and H3 variants.

bioRxiv · Jan 14, 2026 · PreprintGenomics

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations

Yuwei Cao, Lauren Patel, Lauren Alcoser, Eric M. Mendenhall, Christopher W. Benner, Sven Heinz, Alon Goren

The paper introduces spa-ChIP-seq, an automated ChIP-seq protocol, showing it achieves comparable signal-to-noise ratios to manual methods and identifies sensitivity of weak signals to antibody-to-cell-number ratio changes.

Genome Research · Dec 12, 2025Peer-reviewedGenomics

Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of multiple cardiovascular disease risk factors

Natalie DeForest, Babu Kavitha, Siqi Hu, Roi Isaac, Lynne Krohn, Minxian Wang, Xiaomi Du, Camila De Arruda Saldanha, Jenny Gylys, Edoardo Merli, Ruben A Abagyan, Laeya Abdoli Najmi, Viswanathan Mohan, Jason A. Flannick, Gina Marie Peloso, , Amit R. Majithia

Cell Genomics · May 30, 2023Peer-reviewedGenetic & Genomic Medicine

The epigenetic modifier DOT1L regulates gene regulatory networks necessary for cardiac patterning and cardiomyocyte cell cycle withdrawal

Paola Cattaneo, Michael G.B. Hayes, Nina Baumgarten, Dennis Hecker, Sofia Peruzzo, Galip Servet Aslan, Paolo Kunderfranco, Veronica Larcher, Lunfeng Zhang, Riccardo Contu, Gregory J. Fonseca, Simone Spinozzi, Ju Chen, Gianluigi Condorelli, Stefanie Dimmeler, , Sylvia Μ. Evans

This study shows that DOT1L regulates specific gene networks in cardiac development and cell cycle withdrawal through H3K79me2 modifications.

Nature Communications · Dec 2, 2022Peer-reviewedDevelopmental Biology