News

Gallery of cell shapes from Ewing sarcoma xenografts

September, 2022

Different Places, Different Shapes

Segal et al. determines environmental cell shape adaptation of human Ewing sarcoma xenografts in zebrafish embryos.

View Article
functional redundancy

August, 2022

Mixed signals driving oncogenesis: clues from cell morphology

Dr. Gabriel Muhire Gihana awarded the highly competitive HHMI Hanna Gray Fellowship to study how cell morphology regulates RAS oncogenic signaling.

View Article
functional redundancy

June, 2022

Econometrics meets molecular cell biology

How can we study molecular processes that are regulated by multiple components and functionally connected to one another through feedbacks?

View Article
filament dynamics in a keratinocyte

March, 2022

Dr. Benjamin Nanes awarded a Physician Scientist Career Development Award

The Dermatology Foundation, which funds innovative research in skin biology with the potential to lead to new treatments and cures, has awarded Benjamin Nanes a Physician Scientist Career Development Award. Dr. Nanes is a practicing dermatologist and joined the Danuser laboratory in 2019 to conduct research into the mechanics behind skin remodeling during wound repair or in diseases.

View Article
Zebrafish embryo

November, 2021

Danuser Lab takes the lead in launching an innovative metastasis imaging Center

The National Cancer Institute (NCI) at NIH funds innovative research directions in cancer biology. The Cellular Cancer Biology Imaging Research (CCBIR) is one such program that brings together diverse scientists from academic and clinical backgrounds to establish interdisciplinary Centers.

View Article
Zebrafish embryo

July, 2021

Mechanism for interpreting complex cell image features driving deep learning classifiers

Deep learning has emerged as the technique of choice for identifying subtle patterns in biomedical data sets, which are meaningful for the classification of the data content.

View Article
Cell systems cover

July, 2021

Mechanism for interpreting complex cell image features driving deep learning classifiers

Deep learning has emerged as the technique of choice for identifying subtle patterns in biomedical data sets, which are meaningful for the classification of the data content.

View Article
SH3BP4

April, 2021

SH3BP4 -- the link between adhesion and Akt signaling

In a paper published in the April issue of Developmental Cell, Christoph Burckhardt describes his discovery of the mechanism by which SH3BP4 mediated in an Akt-dependent fashion endocytosis of α5-integrin and neuroplin-1.

View Article

January, 2021

Welf et al. discover the necessity of membrane-actin bond release for cell protrusion initiation

In a collaborative effort, Welf et al. discovered that separation of the cell membrane from an existing actin network is required to initiate the molecular events that lead to cell shape change.

View Article
Gabriel

December, 2020

Gabriel Muhire Gihana Receives the Damon Runyon Fellowship

The Damon Runyon Cancer Research Foundation awards competitive fellowships to selected researchers and physician scientists.

View Article
Jin Suk Park

May, 2020

Jin Suk Park 2020 Nominata Award Recipient

Danuser Lab alum and recent graduate from the UTSW Cancer Biology Graduate Program is the 2020 recipient of the Nominata Award, the highest honor for academic and research accomplishment bestowed by the graduate school to an advanced graduate student.

View Article
model of mechanically regulated glycolysis

February, 2020

Jin Suk Park et. al. discovered a mechanism by which epithelial cells adjust glucose metabolism to extracellular matrix stiffness

Recently published work by Park, Burkhardt, Isogai, Minna, DeBerardinis and Danuser was featured as a Nature News and Views article on February 12, 2020 and as a Research Highlight in Nature Reviews Molecular Cell Biology on February 14, 2020.

View Article

December, 2019

Assaf Zaritsky et. al. deep learning program featured in The Scientist

Recently published work by Zaritsky, Jamieson, Cillay, Nevarez, Welf and Danuser was featured as the "Image of the Day" in an article on December 9, 2019 in The Scientist. The article covers a presentation, Live cell histology for classification of melanoma cell population based on single cell actions (Abstract MS98, page 342), which was given on December 10, 2019 at the combined American Society of Cell Biology and European Molecular Biology Organization 2019 Meeting.

View Article
Automatic detection of morphological motifs

October, 2019

Automatic detection of morphological motifs

Driscoll et al. published an article in the October issue of Nature Methods describing u-shape3D, a suite of computational tools to investigate how 3D cellular morphology governs intracellular signaling. In this article, we introduce a generic morphological motif detector that uses machine learning to find morphological structures, such as lamillipodia, blebs, and filopodia, given user provided examples of these structures. Combining this detector with tools to measure signaling near the cell surface, boundary motion, and other metrics, we measure how Kras and PIP2, two central signaling molecules, associate with blebs, a type of morphological motif. A Behind the Paper blog post details our motivation for building an automated analysis framework for 3D images.

View Article

August, 2019

Discrete events of microtubule depolymerization correlate with continuous activity of GEF-H1, as shown by Poisson point process theory

Azoitei, Noh et al. published a paper in the August issue of the Journal of Cell Biology determines how local changes in microtubule (MT) cytoskeleton regulate the activity of guanine nucleotide exchange factor H1 (GEF-H1),

View Article

May, 2019

The hyperactivating Rac1P29S mutation drives drug tolerance and metastasis in melanoma

A lab team orchestrated by Ashwathi (Abbee) Mohan discovered that the molecular infrastructure that allows a cell to control its shape and migrate can also be engaged in cancer cells to increase signals that promote growth.

View Article

March, 2019

Assaf Zaritsky et. al. deep learning program featured in The Jerusalem Post

Recently published work by Zaritsky, Jamieson, Cillay, Nevarez, Welf and Danuser was the feature of an article on February 25, 2019 in The Jerusalem Post. The article covers a presentation, Live cell histology for classification of melanoma cell population based on single cell actions (Abstract P1894, page 699), which was given on December 10, 2018 at the combined American Society of Cell Biology and European Molecular Biology Organization 2018 Meeting.

View Article

February, 2019

Release of Growth Cone Analyzer: A new method to quantify morphological variation among complex cellular architectures.

Growth cones are complex, motile structures at the tip of an outgrowing neurite. They often exhibit a high density of filopodia (thin actin bundles), which complicates the unbiased quantification of their morphologies by software. Contemporary image processing methods require extensive tuning of segmentation parameters and are often not sufficiently adaptable to capture morphology changes associated with switches in regulatory signals.

In a study recently published in the Journal of Cell Biology, Bagonis et al. devise a method to overcome such limitations. The robustness of this new tool enabled the study of morphological variation and its relation to motility in both an unperturbed system and in the context of modified Rho GTPase signaling.

The project was initiated jointly with the lab of Dr. Olivier Pertz at the University of Bern.

The Journal of Cell Biology, published by The Rockefeller University Press, is the leading peer-reviewed journal for cell biology.

View Article

January, 2019

EMBO Long-Term Research Fellowship awarded to Dagan Segal

Dagan Segal has become an EMBO Long-Term Research Fellow starting January 2019. The EMBO fellowship is a prestigious European 2-year fellowship, with a strong emphasis on international exchange.

Dagan’s work focuses on development of zebrafish and in vitro models to study interactions of cells with their complex surroundings. Joining UT Southwestern in February 2018, Dagan is a joint postdoctoral fellow with the Amatruda and Danuser labs and is combining imaging, genomics, molecular biology, and analytical tools to gain mechanistic understanding of the responses of cells to their environment, particularly in pediatric cancer.
In a study recently published in the Journal of Cell Biology, Bagonis et al. devise a method to overcome such limitations. The robustness of this new tool enabled the study of morphological variation and its relation to motility in both an unperturbed system and in the context of modified Rho GTPase signaling.

The project was initiated jointly with the lab of Dr. Olivier Pertz at the University of Bern.

The Journal of Cell Biology, published by The Rockefeller University Press, is the leading peer-reviewed journal for cell biology.

Patient-derived melanoma cells

December, 2018

Assaf Zaritsky et. al. deep learning program featured in The Scientist

A recent presentation of work by Zaritsky, Jamieson, Cillay, Nevarez, Welf and Danuser was highlighted on December 12, 2018 as the Image of the Day in The Scientist magazine. The presentation, Live cell histology for classification of melanoma cell population based on single cell actions (Abstract P1894, page 699), was given on December 10, 2018 at the combined American Society of Cell Biology and European Molecular Biology Organization 2018 Meeting.
Dagan’s work focuses on development of zebrafish and in vitro models to study interactions of cells with their complex surroundings. Joining UT Southwestern in February 2018, Dagan is a joint postdoctoral fellow with the Amatruda and Danuser labs and is combining imaging, genomics, molecular biology, and analytical tools to gain mechanistic understanding of the responses of cells to their environment, particularly in pediatric cancer.
In a study recently published in the Journal of Cell Biology, Bagonis et al. devise a method to overcome such limitations. The robustness of this new tool enabled the study of morphological variation and its relation to motility in both an unperturbed system and in the context of modified Rho GTPase signaling.

The project was initiated jointly with the lab of Dr. Olivier Pertz at the University of Bern.

The Journal of Cell Biology, published by The Rockefeller University Press, is the leading peer-reviewed journal for cell biology.

Fibroblast-like cells with different

October, 2018

Xiao Ma et. al. PLOS Computational Biology article featured in Science Trends

A paper by postdoctoral fellow Xiao Ma recently published in PLOS Computational Biology, Profiling cellular morphodynamics by spatiotemporal spectrum decomposition (Xiao Ma, Onur Dagliyan, Klaus M. Hahn, and Gaudenz Danuser,) was selected for highlighting in the form of a perspective article by Science Trends, which reports and shares the up-to-date outstanding scientific research progress for a large and global audience.Dagan’s work focuses on development of zebrafish and in vitro models to study interactions of cells with their complex surroundings. Joining UT Southwestern in February 2018, Dagan is a joint postdoctoral fellow with the Amatruda and Danuser labs and is combining imaging, genomics, molecular biology, and analytical tools to gain mechanistic understanding of the responses of cells to their environment, particularly in pediatric cancer.
In a study recently published in the Journal of Cell Biology, Bagonis et al. devise a method to overcome such limitations. The robustness of this new tool enabled the study of morphological variation and its relation to motility in both an unperturbed system and in the context of modified Rho GTPase signaling.

The project was initiated jointly with the lab of Dr. Olivier Pertz at the University of Bern.

The Journal of Cell Biology, published by The Rockefeller University Press, is the leading peer-reviewed journal for cell biology.

View Article

May, 2018

Jane Coffin Childs Memorial Fund Fellowship Award

Andrew Weems was recently selected as a Fellow of the Jane Coffin Childs Memorial Fund for Medical Research. One of the most prestigious fellowships available to postdoctoral biomedical researchers, the fund provides three years of support for the brightest young cancer researchers at a critical stage of career growth. Several past Fellows have gone on to become Nobel laureates in physiology, medicine and chemistry.

View Article

April, 2018

Human Frontier Science Program Fellowship Award

Jaewon Huh joined the Danuser lab as a postdoctoral fellow in January 2017. This month he was awarded a three-year postdoctoral fellowship from the Human Frontier Science Program (HFSP). The award will provide over $160,000 to support Huh's research that applies financial mathematics to molecular cell biology, creating new frameworks to decipher signal transduction.

View Article

March, 2018

NIH Pathway to Independence Award

Postdoctoral researcher Meghan Driscoll has been awarded a Pathway to Independence Award (K99/R00) from the National Institutes of Health. The grant is designed to facilitate the transition of outstanding researchers from mentored, postdoctoral research positions to independent, tenure-track or equivalent faculty positions. The award will provide over $900,000 over a five-year period to support Driscoll's research program that focuses on how cells migrate through and interact with complex 3D environments.

View Article

October, 2017

Outstanding Educator Award

Gaudenz Danuser, Ph.D. is one of two professors who received 2016-17 Outstanding Educator Awards from the UT Southwestern Academy of Teachers (SWAT) this week in recognition of their teaching excellence in the Graduate School of Biomedical Sciences. The announcement was made, with congratulations, by Dr. Andrew Zinn, Dean of the Graduate School. Dr. Danuser is Professor and Chair of Bioinformatics and member of the faculty of the Cancer Biology and Cell and Molecular Biology graduate programs. A leading researcher in the field of computational and quantitative cell biology, he co-chairs the Computational and Systems Biology track, leads a MatLab programming bootcamp he created for incoming graduate students, has innovated a suite of bioinformatics nanocourses for students and postdocs, and teaches a medical school elective, Mathematical Methods in Medicine.

heterogeneous particle

October, 2017

A new model for tracking heterogeneous particle movement in dense environments

A major challenge in the tracking of multiple particle is the capture of heterogeneous movements in crowded scenes. Current models for motion prediction, adapted from aerospatial, are challenged by rapid and unpredictable changes in the nature of the dynamics of objects in motion in a dense intracellular environment. In a study recently published in IEEE Transactions on Image Processing, Roudot et al. propose a piecewise-stationary motion model tailored for intracellular dynamics and a new estimator that exploits multiple tracking rounds within an iterative multiple model smoother (PMMS). This method identifies meaningful dynamical switches in trajectories but also confers an increased robustness toward speed variation and lower acquisition speeds. These results indicate that PMMS is a potent solution to the problem of heterogeneous motion tracking in crowded particle fields which has been a notorious obstacle to high-fidelity analysis of object dynamics, especially in bioimaging applications.

The IEEE Transactions on Image Processing is a leading journal for imaging processing and computer vision. It covers novel theory, algorithms, and architectures for the formation, capture, processing, communication, analysis, and display of images, video, and multidimensional signals in a wide variety of applications.

RHOA GEFs

May, 2017

RHOA GEFs regulate long-range intercellular communication during collective cell migration

Effective collective cell migration depends on delicate tuning of cell motility forces and cell–cell communication. Coordination between these processes is regulated, among several pathways, by a family of proteins called the Rho family GTPases. By design of quantitative measures that encode the dynamics of collectively migrating cells in space and time, Assaf Zaritsky, Yun-Yu Tseng, and colleagues identified a surprising role of the Rho GTPases RhoA, RhoC, and their upstream activators in mediating long-range transmission of guidance cues. Their results were published this month in the Journal of Cell Biology.

The project was initiated jointly with Alan Hall, the founder of the Rho GTPase signaling field who tragically died in 2015.

The Journal of Cell Biology, published by The Rockefeller University Press, is the leading peer-reviewed journal for cell biology.
The IEEE Transactions on Image Processing is a leading journal for imaging processing and computer vision. It covers novel theory, algorithms, and architectures for the formation, capture, processing, communication, analysis, and display of images, video, and multidimensional signals in a wide variety of applications.

RHOA GEFs

March, 2017

DeBias: generalized framework for analysis of coupled cell biological variables

Assaf Zaritsky and colleagues introduced DeBias, software for the analysis of complex relations between coupled cellular variables, published this month in eLife.

View Article
Schafer et. al, 2016, Figure 4b

January, 2017

Schafer article journal's most downloaded last year

Congratulations to Claudia Schafer whose article in Convergent Science Physical Oncology (CSPO) was the journal's most downloaded paper for 2015-2016!

View Article

December, 2016

Ning Zhang receives GSO travel award

Congratulations to Ning Zhang, who was selected by the UTSW Graduate Student Organization as one of five Fall Travel Award recipients. Zhang joined the Danuser lab in 2014 as a graduate student in the Cancer Biology program with emphasis in the Computational and Systems Biology track. His research interest is to develop imaging analysis tools for high-throughput 3D spots quantification, which is combined with the fluorescent in situ hybridization (FISH) to analyze genes that can be regulated by telomeres with different lengths. Congratulations Ning!

October, 2016

Danuser Website is Online

Danuser lab website goes online, 3.5 years after the first members opened lab at UTSW and others moved from Harvard Medical School. Over the past few years we have assembled a great team of 20+ researchers with a broad range of scientific backgrounds.