HMS

danuser lab

harvard medical school :: department of cell biology :: laboratory for computational cell biology

Essex Bay, May 3, 2011

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lab members

Gaudenz Danuser

Principal Investigator

LHRRB building, room 301B

...@hms.harvard.edu

Before moving to Harvard Medical School in fall 2009, Gaudenz directed research groups at ETH Zurich and at The Scripps Research Institute in La Jolla. He entered the field of cell biology as a postdoctoral fellow in the Program for Architectural Dynamics of Living Cells at the MBL in Woods Hole. Since then, he has been fascinated by the complex interface between chemical and mechanical signaling and structural adaptation that dictates the regulation of cell function. His teaching activities focus on computational cell biology, molecular biomechanics and measurement theory applied to cell biological analyses.
Karen Easley

Lab manager

LHRRB building, room 301

(617) 432-7947

...@hms.harvard.edu

Karen has over 20 years of experience as a lab manager, beginning her career at Harvard Medical School in the laboratory of Dr. Howard Green. She received her BS in Zoology from the University of Massachusetts/Amherst. She joined the Danuser lab in November 2009.
Sebastien Besson

Software Engineer

LHRRB building, room 302

(617) 432-7942

...@hms.harvard.edu

Sebastien is converting image analysis tools developed in the lab into turn-key software packages for the cell biology community. Since March 2012, he is working on a joint project with the Open Microscopy Environment Consortium to integrate the tracking tools into the OMERO platform. He received his PhD degree in Physics from the Université Pierre et Marie Curie in Paris, France and joined the lab in March 2011.
François Aguet

Postdoctoral Fellow

LHRRB building, room 303D

(617) 432-7942

...@hms.harvard.edu

François's research interests include mathematical modeling of cell-biological processes measured by high-resolution light microscopy. Currently, he is studying mechanisms of clathrin-mediated endocytosis. He obtained his Ph.D. at the Swiss Federal Institute of Technology, Lausanne (EPFL) with a thesis on super-resolution fluorescence microscopy, and holds an M.Sc. in computer science from the same institution.
Christoph Burckhardt

Postdoctoral Fellow

LHRRB building, room 303C

(617) 432-7943

...@hms.harvard.edu

Christoph is interested in how cells take up cargo by endocytosis. He studies the maturation process of clathrin coated pits using live cell microscopy and quantitative image analysis. Christoph obtained his PhD from the University of Zürich where he studied early steps of virus infection.
Deepak Chittajallu

Postdoctoral Fellow

LHRRB building, room 303B

(617) 432-7942

...@hms.harvard.edu

Deepak's research interests are in the areas of image analysis, computer vision, machine learning, and pattern recognition. His research in the Danuser Lab focuses on the development of algorithms for segmentation, tracking, and clustering problems in microscopic imagery. Prior to joining the Danuser lab, he received a Ph.D. and an M.Sc. in Computer Science from University of Houston under the supervision of Prof. Ioannis A. Kakadiaris, where he worked on cardiovascular image analysis and computer-aided breast reconstructive surgery.
Nancy Costigliola

Postdoctoral Fellow

LHRRB building, room 312

(617) 432-7943

...@hms.harvard.edu

Nancy's research focuses on the dynamic spatial regulation of vimentin networks during cell migration. She obtained her PhD in Cell Biology and Biophysics under the supervision of Ken Jacobson at the University of North Carolina, Chapel Hill and her undergraduate degree in Biology from Cornell University. She joined the Danuser lab in February 2012.
Liya Ding

Postdoctoral Fellow

LHRRB building, room 303C

(617) 432-7942

...@hms.harvard.edu

Liya's research focuses on computational analysis of cytoskeleton dynamics. Liya got her Ph.D. degree from Ohio State University in 2009, majoring in Computer Vision. She then worked as a post-doc researcher in the same institute working on biomedical image processing. She joined LCCB in December 2011.
Nadia Halidi

Postdoctoral Fellow

LHRRB building, room 312

(617) 432-7943

...@hms.harvard.edu

Nadia's research is focused on the intersection between Rho GTPase and calcium signaling in the regulation of cell migration. She studied physics and chemistry at the University of Pécs, Hungary and received her Ph.D. from the Swiss Federal Institute of Technology, Lausanne (EPFL). She joined the Danuser lab in June 2011.
Sangyoon Han

Postdoctoral Fellow

LHRRB building, room 303D

(617) 432-7942

...@hms.harvard.edu

Sangyoon's research interests center around how mechanics affect cell biology. He will study the coordination between intracellular forces, traction forces, biochemical signaling and adhesion dynamics in migrating cells. He received his Ph.D. in Mechanical Engineering from University of Washington under the supervision of Dr. Nathan Sniadecki with a thesis on cell mechanics during single cell spreading and migration. He joined LCCB in October 2012.
Kwonmoo Lee

Postdoctoral Fellow

LHRRB building, room 312

(617) 432-7943

...@hms.harvard.edu

Kwonmoo's research focuses on understanding the roles of interactions between biochemistry and mechanics in cell migration. Currently, he studies the coordination of multiple actin nucleation modules in protrusive force generation of migrating epithelial cells using experimental and computational approaches. In 2010, he received his Ph.D. in physics from MIT under the supervision of Marc Kirschner at Harvard, and joined LCCB in June 2010.
Alexis Lomakin

Postdoctoral Fellow

LHRRB building, room 312

(617) 432-7943

...@hms.harvard.edu

Alexis's research focuses on how distinct cytoskeletal polymer machines are integrated with one another to orchestrate directional cell migration, and on the mechanochemical pathways that control spatio-temporal organization of the cytoskeletal network in migrating cells. He conducted his doctoral research on the role of microtubule dynamics in membrane trafficking in Vladimir Rodionov's lab at the University of Connecticut, USA, collaborating with Anna Akhmanova from Erasmus University, the Netherlands. Alexis recently obtained the Ph.D. degree in Molecular and Cellular Biology from Moscow State University, Russia.
Marco Vilela

Postdoctoral Fellow

LHRRB building, room 303D

(617) 432-7942

...@hms.harvard.edu

Marco's research is focused on the development of methods to reconstruct signal transduction pathways from image fluctuations. He received his PhD degree in Biomathematics from ITQB/New University of Lisbon, Portugal.
Maria Bagonis

Graduate Student

LHRRB building, room 303B

(617) 432-7942

...@fas.harvard.edu

Maria currently develops stochastic computational models to explore how multiple kinesin and dynein motor proteins coordinate to regulate vesicle transport in vivo. Such microscopic models can be used to help interpret experimental measurements corresponding to vesicle transport dynamics and guide future experimental work. She also presently works with the Reck-Peterson lab, where she uses in vitro single molecule microscopy to elucidate the molecular stepping mechanism of cytoplasmic dynein. She holds an MSc in Theoretical Chemistry from the University of Oxford and a B.S. in Biochemistry from the State University of New York at Binghamton.
Pei-hsin Hsu

Graduate Student

LHRRB building, room 303C

(617) 432-7942

...@hms.harvard.edu

Pei-hsin joined the Laboratory for Computational Cell Biology at The Scripps Research Institute in 2008 to conduct his doctoral thesis research. By using the time series analysis tool to unravel the stochastic behavior of kinetochore microtubules (kMT), he hopes the study will lead to the construction of an explicit, mechanistic model that can reconstitute kinetochore-kMT interactions. Pei-hsin graduated from National Taiwan University and received two M.S. degrees (Biological Sciences and Mathematics) from Stanford University.
Daniel Nunez

Graduate Student

LHRRB building, room 303B

(617) 432-7942

...@hms.harvard.edu

Daniel is working on elucidating the mechanisms that lead to the spatial organization of endocytosis by using and developing novel computational microscopy tools. He also studies the role that endocytic protein stoichiometry has in determining endocytic pit behavior. He is currently a PhD candidate from the Bioengineering Department at the University of California, San Diego, and he obtained his bachelors degree in Mechanical Engineering from MIT.
Youbean Oak

Graduate Student

LHRRB building, room 303B

(617) 432-7942

...@fas.harvard.edu

Youbean's research centers around the role of the actin-bundling protein fascin on cell motility. She is currently a graduate student in the Department of Molecular and Cellular Biology at Harvard University. She completed her undergraduate studies at Cornell University where she majored in biology and mathematics.

affiliates

Michelle Mendoza

Postdoctoral Fellow

Department of Cell Biology

Harvard Medical School

...@hms.harvard.edu

Michelle is interested in how oncogenic signal transduction pathways regulate cell motility. She is currently focusing on the ERK-MAPK pathway and how it regulates actin polymerization to impact protrusion dynamics. She uses a combination of quantitative imaging, including qFSM, and biochemical strategies in epithelial cells. She received her Ph.D. in Biomedical Sciences in 2005 from UCSD and was a postdoctoral fellow in the Blenis lab within the Department of Cell Biology at HMS. She began collaborating with the Danuser lab when they moved here in 2009 and formally joined the lab in 2012.

alumni

Sylvain Berlemont

Postdoctoral Fellow

...@hms.harvard.edu

During his postdoctoral experience in the lab, Sylvain pushed forward the development of Quantitative Fluorescent Speckle Microscopy to study intermediate filament regulation in living cells. He also contributed to the development of new approaches to study focal adhesion dynamics and its role in mediating other cytoskeleton components. Back in France, Sylvain has now set up his own company in Paris as an independent consultant, providing consulting services to biotech and biomedical companies.
Achim Besser

Postdoctoral Fellow

10/2009-09/2011

...@hms.harvard.edu

Worked on: Achim developed new tools for reconstructing cellular forces in multicellular systems. In close collaboration with the Brugge Lab, these tools have been applied to quantify the mechanical interactions between cells in small clusters. The work revealed new insights into the mechanical communication between cells and in their collective mechanosensitive responses.
Left for: Now back in Germany, Achim joined BASF as a research scientist in the polymer physics division. His new task is to support the development of advanced materials by modeling and simulation techniques.
Anindya Chanda

Postdoctoral Fellow

04/2010-07/2012

...@hms.harvard.edu

Anindya joined the lab in April 2010, and studied the role of CD36 receptor in endothelial cell apoptosis and anti-angiogenic signaling with Dr. Khuloud Jaqaman (Systems Biology, HMS). He received his M.Tech degree in Food Technology and Biochemical Engineering from Jadavpur University, India in 2002. In 2009, he obtained his Ph.D. in Food Science and Environmental Toxicology from Michigan State University where he studied the regulation of fungal secondary metabolism at molecular and cellular levels.

Christian Dittrich

Postdoctoral Fellow

05/2010–06/2011

...@hms.harvard.edu

Worked on: Christian applied a unique peptide-based nanoparticle system for the intracellular delivery of cargo, targeted by a corona of transferrin.
Left for: Merck Millipore, Switzerland. In his new position, Chris is responsible for the global marketing of lipids as drug delivery compounds.
Hunter Elliott

Graduate Student

LHRRB building, room 303D

(617) 432-7942

...@hms.harvard.edu

As a graduate student, Hunter studied the dynamics of Rho GTPase signaling in cell migration in 2D environments, and the contribution of actomyosin organization and contractility to endothelial cell shape and migration in 3D environments. He developed software for processing raw 2D FRET microscopy data into quantitative biosensor activation maps, and for the analysis of correlations between these biosensor signals and cell morphodynamics. For the analysis of cell migration in 3D environments, he developed software to extract and quantify cell shape, motion and subcellular protein localization from 3D fluorescence microscopy data.
In October of 2012, Hunter left the Danuser lab to become co-leader of the new Image and Data Analysis Core (IDAC) facility at HMS.
Khuloud Jaqaman

Postdoctoral fellow &

Instructor in Systems Biology

2003-2012

...@UTSouthwestern.edu

Khuloud was a postdoctoral fellow in the Danuser lab at TSRI (2003-2009), after which she became an Instructor in the Department of Systems Biology at HMS closely affiliated with the lab (2009-2012). Her work focused on using quantitative single molecule imaging approaches to link cell surface receptor dynamics and organization to downstream cell signaling. She primarily studied the receptor CD36, first in macrophages where it internalizes oxLDL, and then in endothelial cells where it transduces the anti-angiogenic signal of the extracellular matrix protein thrombospondin-1.
In January 2013, Khuloud joined the Department of Biophysics at UT Southwestern, where she continues to develop quantitative single molecule imaging approaches to study cell surface receptor dynamics, organization and signaling, with particular focus on angiogenesis signaling.
http://www.utsouthwestern.edu/labs/jaqaman/
Allen Liu

Postdoctoral Fellow

10/2007-12/2011

...@umich.edu

Worked on: Allen worked on two projects in the Danuser/Schmid labs where he used live cell TIRF microscopy and computational image analysis to examine the heterogeneity of clathrin-coated pit (CCP) dynamics on the plasma membrane. Using micro-contact printed substrates, he showed that CCP lifetime was prolonged in regions of presumably high cortical tension. Using a unique method for manipulating receptor organization, he showed that clustering of receptors increases CCP initiation and demonstrated cargo-specific effects on CCP lifetime and size.
Left for: Allen has joined the Mechanical Engineering Department at the University of Michigan as part of the cluster hire in cell mechanics. He is now working on the role of chemokine receptor endocytosis in migration, receptor dynamics, and cellular reconstitution.
Laura Anne Lowery

Postdoctoral Fellow

Department of Cell Biology

Harvard Medical School

...@hms.harvard.edu

After receiving her Ph.D. in Biology from MIT, Laura Anne joined the Danuser lab in November 2010 (in addition to being a member of the Van Vactor lab within the Department of Cell Biology at Harvard Medical School since July 2008). During her time in the lab, she focused on using quantitative imaging analysis tools in order to investigate the regulation of microtubule plus-end-tracking protein (+TIP) localization and function in cultured Xenopus laevis neurons. In July 2013, Laura Anne joined the Department of Biology at Boston College as an Assistant Professor, where she continues to study the regulation of cytoskeletal dynamics in neuronal growth cones.
Andressa Mota

Lab technician

11/2011-07/2013

...@hms.harvard.edu

Andressa joined the lab in November 2011 as a lab technician. She contributed to various projects in endocytosis, cell migration, and cytoskeleton dynamics. She completed her undergraduate studies at Bridgewater State University where she majored in Biology. In September 2013, Andressa entered Boston University’s Ph.D program in Molecular Biology, Cell Biology & Biochemistry.
Ulrich Schmidt

Postdoctoral Fellow

06/2010-02/2013

(617) 432-7942

...@hms.harvard.edu

Uli is now working as a research manager at TWT Science and Innovation near Stuttgart, Germany. There, he is managing, coordinating and supporting industrial research projects from various areas including automotive, aerospace, and medical engineering.
Jessica Tytell

Lab director

10/2009-06/2013

(617) 432-7942

...@hms.harvard.edu

Jessica joined the Danuser lab as Lab Director in 2009 when it moved to Harvard Medical School. After building the wet lab, she spearheaded two migration project teams: one investigating the small GTPases RhoA and Rac1 in migration in collaboration with Klaus Hahn's lab at UNC and another designing imaging and image analysis methods to study the dynamics of the intermediate filament protein vimentin as part of a multi-lab NIH-funded Program Project Grant lead by Robert Goldman at Northwestern. In July of 2013, Jessica moved on to become the Sr. Director for Life Science Innovation at Firefly BioWorks, Inc. (www.fireflybio.com), an exciting biotechnology startup in Cambridge, MA that develops novel integrated assays and analytical tools based on the FireplexTM platform.