CREPAS is a Nextflow pipeline for analyzing nascent chromatin sequencing data, improving scalability, reproducibility, and compatibility across multiple chromatin assays.

bioRxiv · Jun 25, 2026 · PreprintBioinformatics

The single-molecule accessibility landscape of newly replicated mammalian chromatin

Megan S Ostrowski, Marty G. Yang, Colin P McNally, Nour J. Abdulhay, Simai Wang, Keerthi Renduchintala, Iryna Irkliyenko, Alva Biran, Brandon T.L. Chew, Ayush D. Midha, Emily V. Wong, Jonathan Sandoval, Isha H. Jain, Anja Groth, Elphège Pierre Nora, , Vijay Ramani

This study introduces RASAM, a method to analyze nascent chromatin structure, finding that newly replicated chromatin is hyperaccessible and has unique organization features.

Cell · Nov 15, 2024Peer-reviewedGenomics

CloneSeq: A Highly Sensitive Single-cell Analysis Platform for Comprehensive Characterization of Cells from 3D Culture

Danny Bavli, Xue Sun, Chen Kozulin, Dena Ennis, Alex Motzik, Alva Biran, Shlomi Brielle, Adi Alajem, Eran Meshorer, Amnon Buxboim, Oren Ram

CloneSeq identifies rare cell subpopulations by combining clonal expansion with single-cell RNA-seq, revealing cancer stem-like cells and improved stemness in embryonic cells.

bioRxiv · Nov 24, 2020 · PreprintMolecular Biology