The Oomen Lab Department of Molecular, Cell and Cancer Biology - UMass Chan Medical School

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Publications

A full and up-to-date list of publications can also be found on PubMed or Google Scholar.

2026

Protocol for simultaneous profiling of transcription start sites and full-length transcripts from low-input samples using Smart-seq 5
Protocol for simultaneous profiling of transcription start sites and full-length transcripts from low-input samples using Smart-seq+5′
Diego Rodriguez-Terrones, Marlies E. Oomen, Maria-Elena Torres-Padilla
STAR Protocols  ·  01 Jun 2026  ·  doi:10.1016/j.xpro.2026.104583
TBP regulates transposable element expression in early mouse embryos
TBP regulates transposable element expression in early mouse embryos
Clara Hermant, Carlos Michel Mourra-Díaz, Marlies E Oomen, Natasha Jansz, Camille Noll, Antoine Canat, Mrinmoy Pal, Tsunetoshi Nakatani, Tamas Schauer, Maria-Elena Torres-Padilla
The EMBO Journal  ·  20 Mar 2026  ·  doi:10.1038/s44318-026-00736-w

2025

Pathway to Independence: a forecast for the future of developmental biology
Pathway to Independence: a forecast for the future of developmental biology
Chee Kiang Ewe, Max S. Farnworth, Anzy Miller, Joaquín Navajas Acedo, Marlies E. Oomen, Giulia Paci, Sonya A. Widen, Toshimichi Yamada
Development  ·  30 Sep 2025  ·  doi:10.1242/dev.205224
The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation
The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation
Clara Hermant, Carlos Michel Mourra-Díaz, Marlies E. Oomen, Luis Altamirano-Pacheco, Mrinmoy Pal, Tsunetoshi Nakatani, Maria-Elena Torres-Padilla
Genes & Development  ·  27 Feb 2025  ·  doi:10.1101/gad.352270.124
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development
Marlies E. Oomen, Diego Rodriguez-Terrones, Mayuko Kurome, Valeri Zakhartchenko, Lorenza Mottes, …, Pierre Savatier, Jonathan Göke, Eckhard Wolf, Henrik Kaessmann, Maria-Elena Torres-Padilla
Cell  ·  01 Feb 2025  ·  doi:10.1016/j.cell.2024.12.013

2024

Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo
Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo
Marlies E Oomen, Maria-Elena Torres-Padilla
EMBO Reports  ·  25 Mar 2024  ·  doi:10.1038/s44319-024-00118-5

2023

Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture
Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture
Marlies E. Oomen, A Nicole Fox, Inma Gonzalez, Amandine Molliex, Thaleia Papadopoulou, Pablo Navarro, Job Dekker
openRxiv  ·  09 Dec 2023  ·  doi:10.1101/2023.12.08.570796

2021

Systematic evaluation of chromosome conformation capture assays
Systematic evaluation of chromosome conformation capture assays
Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, …, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan H. Gibcus, Job Dekker
Nature Methods  ·  01 Sep 2021  ·  doi:10.1038/s41592-021-01248-7

2020

Histone Purification Combined with High Resolution Mass Spectrometry to Examine Histone Post Translational Modifications and Histone Variants in i Caenorhabditis elegans i
Histone Purification Combined with High‐Resolution Mass Spectrometry to Examine Histone Post‐Translational Modifications and Histone Variants in Caenorhabditis elegans
Lluís Millan‐Ariño, Zuo‐Fei Yuan, Marlies E. Oomen, Simone Brandenburg, Alexey Chernobrovkin, Jérôme Salignon, Lioba Körner, Roman A. Zubarev, Benjamin A. Garcia, Christian G. Riedel
Current Protocols in Protein Science  ·  30 Sep 2020  ·  doi:10.1002/cpps.114
Detecting chromatin interactions between and along sister chromatids with SisterC
Detecting chromatin interactions between and along sister chromatids with SisterC
Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker
Nature Methods  ·  23 Sep 2020  ·  doi:10.1038/s41592-020-0930-9

2019

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization
Elizabeth H. Finn, Gianluca Pegoraro, Hugo B. Brandão, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, Tom Misteli
Cell  ·  01 Mar 2019  ·  doi:10.1016/j.cell.2019.01.020
CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning
CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning
Marlies E. Oomen, Anders S. Hansen, Yu Liu, Xavier Darzacq, Job Dekker
Genome Research  ·  17 Jan 2019  ·  doi:10.1101/gr.241547.118

2018

Progress toward an amplifiable metabolic label for DNA: conversion of 4-thiothymidine 4sT to 5-methyl-2 -deoxycytidine and synthesis of a 4sT phosphorodiamidate prodrug
Progress toward an amplifiable metabolic label for DNA: conversion of 4-thiothymidine (4sT) to 5-methyl-2′-deoxycytidine and synthesis of a 4sT phosphorodiamidate prodrug
Adam K. Hedger, Marlies E. Oomen, Victor Liu, Michael P. Moazami, Nicholas Rhind, Job Dekker, Jonathan K. Watts
Canadian Journal of Chemistry  ·  01 Jul 2018  ·  doi:10.1139/cjc-2017-0732

2017

Epigenetic characteristics of the mitotic chromosome in 1D and 3D
Epigenetic characteristics of the mitotic chromosome in 1D and 3D
Marlies E. Oomen, Job Dekker
Critical Reviews in Biochemistry and Molecular Biology  ·  15 Feb 2017  ·  doi:10.1080/10409238.2017.1287160