Nature Search

A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects

Kathiriya et al. identify a cardiac progenitor lineage with expression of Tbx5 and anterior heart field-specific expression of Mef2c that bisects the intraventricular septum during development and show that alterations in this lineage lead to congenital heart defects in mice.

Irfan S. Kathiriya
Martin H. Dominguez
Benoit G. Bruneau
ResearchOpen Access29 Dec 2025
Nature Cardiovascular Research

Volume: 5, P: 67-83
Mechano-induced patterned domain formation by monocytes

Human primary monocytes reversibly phase separate into regular, multicellular, multilayered domains on soft matrices with physiological stiffness due to local activation and global inhibition processes that occur during random cell migration.

Wenxuan Du
Jingyi Zhu
Denis Wirtz
Research05 Nov 2025
Nature Materials

P: 1-14
InterpolAI: deep learning-based optical flow interpolation and restoration of biomedical images for improved 3D tissue mapping

InterpolAI leverages optimal flow-based artificial intelligence to produce synthetic images between pairs of images for diverse three-dimensional image types. InterpolAI is more robust and accurate than existing methods, improving data quality for downstream analysis.

Saurabh Joshi
André Forjaz
Denis Wirtz
ResearchOpen Access28 May 2025
Nature Methods

Volume: 22, P: 1556-1567
Selecting the optimal cell migration assay: fundamentals and practical guidelines

This Review introduces ten cell migration assays, offers practical guidance toward selecting the best assay for a specific biological question and describes how future advances can reveal important insights into dynamic cellular behaviors.

Wenxuan Du
Praful R. Nair
Denis Wirtz
Reviews18 Dec 2025
Nature Methods

Volume: 23, P: 30-42
Methods to analyze cell migration data: fundamentals and practical guidelines

This Review describes the principles of data analysis for extracting quantitative data from cell migration assays. It also highlights advanced image analysis tools and offers practical guidance for interested users.

Pei-Hsun Wu
Jude M. Phillip
Denis Wirtz
Reviews18 Dec 2025
Nature Methods

Volume: 23, P: 43-55
A physical sciences network characterization of non-tumorigenic and metastatic cells

David B. Agus
Jenolyn F. Alexander
Pei-Hsun Wu
ResearchOpen Access26 Apr 2013
Scientific Reports

Volume: 3, P: 1-12
3D genomic mapping reveals multifocality of human pancreatic precancers

Quantitative multimodal 3D reconstruction of human pancreatic tissue at single-cell resolution reveals a high burden of multifocal, genetically heterogeneous pancreatic intraepithelial neoplasias in the normal adult pancreas.

Alicia M. Braxton
Ashley L. Kiemen
Laura D. Wood
Research01 May 2024
Nature

Volume: 629, P: 679-687
Hypoxia and the extracellular matrix: drivers of tumour metastasis

Emerging data indicate that hypoxia and the extracellular matrix (ECM) together might have a crucial role in metastasis. In this Opinion article the authors suggest a model in which multiple microenvironmental signals might converge to synergistically influence metastatic outcome.

Daniele M. Gilkes
Gregg L. Semenza
Denis Wirtz
Reviews15 May 2014
Nature Reviews Cancer

Volume: 14, P: 430-439
Programmed subcellular release for studying the dynamics of cell detachment

As cells move over a substrate, they need to first sever their contact with the matrix by detaching focal adhesions. A setup that allows spatially and temporally controlled release of focal adhesions now facilitates the quantitative measurement of cell movement across a substrate.

Bridget Wildt
Denis Wirtz
Peter C Searson
Research01 Feb 2009
Nature Methods

Volume: 6, P: 211-213
Dynamics of individual flexible polymers in a shear flow

Philip LeDuc
Charbel Haber
Denis Wirtz
Research10 Jun 1999
Nature

Volume: 399, P: 564-566
CODA: quantitative 3D reconstruction of large tissues at cellular resolution

CODA: a method for 3D reconstruction of large serially sectioned tissues.

Ashley L. Kiemen
Alicia M. Braxton
Pei-Hsun Wu
Research24 Oct 2022
Nature Methods

Volume: 19, P: 1490-1499
Tumour mechanopathology: Cutting the stress out

Solid stress within tumours can be quantified by measuring their deformation after cutting, slicing or taking a needle biopsy of them.

Daniele M. Gilkes
Denis Wirtz
News & Views10 Jan 2017
Nature Biomedical Engineering

Volume: 1, P: 1-2
Bundles from boundaries

Using a micropatterning technique, the architecture of actin networks is revealed to be influenced by the spatial organization of actin filament nucleation. Considering the geometric boundaries within live cells, implications in the realm of actin-induced cell functions are vast.

Denis Wirtz
Shyam B. Khatau
News & Views23 Sept 2010
Nature Materials

Volume: 9, P: 788-790
Author Correction: Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology

Jeong-Ki Kim
Arghavan Louhghalam
Dong-Hwee Kim
Amendments and CorrectionsOpen Access13 Mar 2018
Nature Communications

Volume: 9, P: 1
Dimensional and temporal controls of three-dimensional cell migration by zyxin and binding partners

Molecular and oscillations are common in biology, but periodic cell migrations have not been observed. Fraleyet al. report regular, periodic migrations of cells along tracks generated inside 3D matrices, and show that these 1D oscillations are controlled by zyxin and its binding partners α-actinin and p130Cas.

Stephanie I. Fraley
Yunfeng Feng
Denis Wirtz
Research06 Mar 2012
Nature Communications

Volume: 3, P: 1-13
Biophysical and biomolecular determination of cellular age in humans

The biophysical properties of cells can be used to predict the cellular age of humans with higher accuracy than conventional biomolecular markers.

Jude M. Phillip
Pei-Hsun Wu
Denis Wirtz
Research11 Jul 2017
Nature Biomedical Engineering

Volume: 1, P: 1-12
Synergistic IL-6 and IL-8 paracrine signalling pathway infers a strategy to inhibit tumour cell migration

Tumor cell proliferation and migration, key drivers of metastasis, can be mechanistically coupled in matrix embedded human sarcoma and carcinoma cells through cell density via a synergistic, paracrine signaling mechanism between Interleukins 6/8. Inhibition of this mechanism significantly decreases metastasis in mouse xenograft models.

Hasini Jayatilaka
Pranay Tyle
Denis Wirtz
ResearchOpen Access26 May 2017
Nature Communications

Volume: 8, P: 1-12
A 'hot-spot' mutation alters the mechanical properties of keratin filament networks

Linglei Ma
Soichiro Yamada
Pierre A. Coulombe
Research12 Apr 2001
Nature Cell Biology

Volume: 3, P: 503-506
Inactivation of Arid1a in the endometrium is associated with endometrioid tumorigenesis through transcriptional reprogramming

ARID1A, which is often mutated in human endometrial cancer, is a component of the SWI/SNF chromatin remodelling complex. Here, the authors show that Arid1a mutations in the mouse endometrium and primary human endometrial epithelial cells cause widespread reprogramming of gene transcription and result in a loss of response to TGFβ.

Yohan Suryo Rahmanto
Wenjing Shen
Ie-Ming Shih
ResearchOpen Access01 Jun 2020
Nature Communications

Volume: 11, P: 1-14
Extracellular vesicles in immunomodulation and tumor progression

Extracellular vesicles (EVs) can exert potent immunomodulatory effects. Wirtz and colleagues review the types of EV and their influence on tumor responses.

Carolyn Marar
Bartholomew Starich
Denis Wirtz
Reviews22 Mar 2021
Nature Immunology

Volume: 22, P: 560-570
Dynamic organelle distribution initiates actin-based spindle migration in mouse oocytes

Mammalian oocytes divide asymmetrically during meiotic maturation. Here, the authors show that spindle movement away from oocyte center depends on actin filaments nucleated from the spindle periphery pushing against surrounding mitochondria, which polarizes spontaneously to produce directional spindle motion.

Xing Duan
Yizeng Li
Rong Li
ResearchOpen Access14 Jan 2020
Nature Communications

Volume: 11, P: 1-15
Correction: E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer

Gabriella C. Russo
Ashleigh J. Crawford
Denis Wirtz
Amendments and Corrections05 Apr 2024
Oncogene

Volume: 43, P: 1488
Circulating extracellular vesicles predict outcome in patient undergoing transjugular intrahepatic portosystemic shunt (TIPS) placement

Sven H. Loosen
Frederik J. Hansen
Christoph Roderburg
ResearchOpen Access07 Oct 2025
Scientific Reports

Volume: 15, P: 1-10
A distinctive role for focal adhesion proteins in three-dimensional cell motility

Focal adhesion proteins promote cell adhesion and migration in both two-dimensional and three-dimensional environments. When cells are embedded in a 3D matrix, focal adhesion proteins modulate the speed and persistence of migration by regulating protrusion activity.

Stephanie I. Fraley
Yunfeng Feng
Denis Wirtz
Research16 May 2010
Nature Cell Biology

Volume: 12, P: 598-604
The physics of cancer: the role of physical interactions and mechanical forces in metastasis

This article describes the importance of key physical and mechanical processes at each step of the metastatic cascade. The emerging insight into these physical interactions may lead to new approaches to developing cancer diagnostics and therapies.

Denis Wirtz
Konstantinos Konstantopoulos
Peter C. Searson
Reviews24 Jun 2011
Nature Reviews Cancer

Volume: 11, P: 512-522
Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology

An actin cap protects the morphology of the nucleus during cellular mechanical stress. Here, the authors show that the nuclear lamina protein lamin A/C mediates the formation of the actin cap in response to stress, and model the distribution of forces in the presence and absence of the actin cap.

Jeong-Ki Kim
Arghavan Louhghalam
Dong-Hwee Kim
ResearchOpen Access14 Dec 2017
Nature Communications

Volume: 8, P: 1-13
A comparison of methods to assess cell mechanical properties

This Analysis compares and contrasts methods for measuring the mechanical properties of cells by applying the different approaches to the same breast cancer cell line.

Pei-Hsun Wu
Dikla Raz-Ben Aroush
Denis Wirtz
Research18 Jun 2018
Nature Methods

Volume: 15, P: 491-498
Reply: reducing background fluorescence reveals adhesions in 3D matrices

Stephanie I. Fraley
Yunfeng Feng
Gregory D. Longmore
Correspondence21 Dec 2010
Nature Cell Biology

Volume: 13, P: 5-7
E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer

Gabriella C. Russo
Ashleigh J. Crawford
Denis Wirtz
Research20 Mar 2024
Oncogene

Volume: 43, P: 1445-1462
Use of the p-values as a size-dependent function to address practical differences when analyzing large datasets

Estibaliz Gómez-de-Mariscal
Vanesa Guerrero
Arrate Muñoz-Barrutia
ResearchOpen Access22 Oct 2021
Scientific Reports

Volume: 11, P: 1-13
Triggering cell detachment from patterned electrode arrays by programmed subcellular release

Bridget Wildt
Denis Wirtz
Peter C Searson
Protocols17 Jun 2010
Nature Protocols

Volume: 5, P: 1273-1280
Unifying fragmented perspectives with additive deep learning for high-dimensional models from partial faceted datasets

Yufei Wu
Pei-Hsun Wu
Sean X. Sun
ResearchOpen Access24 Feb 2025
npj Biological Physics and Mechanics

Volume: 2, P: 1-10
High-throughput ballistic injection nanorheology to measure cell mechanics

Pei-Hsun Wu
Christopher M Hale
Denis Wirtz
Protocols05 Jan 2012
Nature Protocols

Volume: 7, P: 155-170
A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei

This protocol describes VAMPIRE, an unsupervised machine-learning approach that can be used to quantify and categorize cellular morphology from fluorescence or bright-field images of cells grown in 2D, 3D and tissue slices.

Jude M. Phillip
Kyu-Sang Han
Pei-Hsun Wu
Protocols11 Jan 2021
Nature Protocols

Volume: 16, P: 754-774
Statistical analysis of cell migration in 3D using the anisotropic persistent random walk model

This protocol enables the statistical analysis of cell motility in 2D and 3D microenvironments using the anisotropic persistent random walk model, providing a new tool to characterize 3D cell migration.

Pei-Hsun Wu
Anjil Giri
Denis Wirtz
Protocols26 Feb 2015
Nature Protocols

Volume: 10, P: 517-527
Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions

Stephanie I. Fraley
Pei-hsun Wu
Denis Wirtz
ResearchOpen Access01 Oct 2015
Scientific Reports

Volume: 5, P: 1-13
Evolution of cellular morpho-phenotypes in cancer metastasis

Pei-Hsun Wu
Jude M. Phillip
Denis Wirtz
ResearchOpen Access17 Dec 2015
Scientific Reports

Volume: 5, P: 1-10
Actin cap associated focal adhesions and their distinct role in cellular mechanosensing

Dong-Hwee Kim
Shyam B. Khatau
Denis Wirtz
ResearchOpen Access03 Aug 2012
Scientific Reports

Volume: 2, P: 1-13
The distinct roles of the nucleus and nucleus-cytoskeleton connections in three-dimensional cell migration

Shyam B. Khatau
Ryan J. Bloom
Denis Wirtz
ResearchOpen Access03 Jul 2012
Scientific Reports

Volume: 2, P: 1-11
Adhesion and fusion efficiencies of human immunodeficiency virus type 1 (HIV-1) surface proteins

Terrence M. Dobrowsky
S. Alireza Rabi
Denis Wirtz
ResearchOpen Access22 Oct 2013
Scientific Reports

Volume: 3, P: 1-9
The LINC-anchored actin cap connects the extracellular milieu to the nucleus for ultrafast mechanotransduction

Allison B. Chambliss
Shyam B. Khatau
Denis Wirtz
ResearchOpen Access18 Jan 2013
Scientific Reports

Volume: 3, P: 1-9
Fractional re-distribution among cell motility states during ageing

Phillip and colleagues use dermal fibroblasts from a range of donors to quantify cell motility in ageing cells. They show that the age-dependent decrease in cell motility is not due to the reduced motility of all cells, but results from the fractional redistribution among motility states.

Jude M. Phillip
Nahuel Zamponi
Denis Wirtz
ResearchOpen Access19 Jan 2021
Communications Biology

Volume: 4, P: 1-9
Multi-nucleated cells use ROS to induce breast cancer chemo-resistance in vitro and in vivo

Aditya Parekh
Subhayan Das
Mahitosh Mandal
Research10 May 2018
Oncogene

Volume: 37, P: 4546-4561
Three-dimensional visualization of cleared human pancreas cancer reveals that sustained epithelial-to-mesenchymal transition is not required for venous invasion

Seung-Mo Hong
DongJun Jung
Laura D. Wood
Research07 Nov 2019
Modern Pathology

Volume: 33, P: 639-647
Inhibition of ovarian tumor cell invasiveness by targeting SYK in the tyrosine kinase signaling pathway

Yu Yu
Yohan Suryo Rahmanto
Tian-Li Wang
Research11 Apr 2018
Oncogene

Volume: 37, P: 3778-3789
Multiple scale model for cell migration in monolayers: Elastic mismatch between cells enhances motility

Benoit Palmieri
Yony Bresler
Martin Grant
ResearchOpen Access02 Jul 2015
Scientific Reports

Volume: 5, P: 1-13
A robust nonlinear tissue-component discrimination method for computational pathology

Jacob S Sarnecki
Kathleen H Burns
Pei-Hsun Wu
Research18 Jan 2016
Laboratory Investigation

Volume: 96, P: 450-458

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