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Seminar

  • May 19, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    In Vitro Vascularized Models for Metastatic Cancer

    ROGER KAMM, MIT

    Over the past 10 years, our ability to realistically model the critical biological steps in disease have dramatically improved, due in part to the advances in microfluidic technologies. In particular, the capabilities to create realistic 3D microenvironments, including microvascular perfusion, have led to in vitro models for disease that offer considerable advantages over in vivo experiments. In this talk, Dr. Kamm will present some recent advances in modeling the successive stages of metastatic cancer, especially in the context of immunotherapies and organ-specific models of metastasis.

    May 19th, 2016 at 12:15 PM in Clark Center Seminar Room S360


    Hosted by:

    Alexander Dunn, Assistant Professor of Chemical Engineering

    Pre-Seminar May 17th, 2016 at 12:15 PM in Clark S361

  • April 07, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Optical Control of Protein Activity Using Engineered Photoreceptors

    CHANDRA TUCKER, UNIVERSITY OF COLORADO AT DENVER

    While chemical tools that allow control of protein activities and interactions have been in use for a number of decades, a recently emerging field centers on the use of light for protein control, allowing spatial, temporal, and reversible control of protein activity. Here Dr. Tucker will discuss different ways her group is engineering plant photoreceptor proteins as tools to directly control protein activity with light. In particular, she will focus on use of the Arabidopsis photoreceptor cryptochrome 2 (CRY2), which her lab has pioneered as an optogenetic module. Dr. Tucker will discuss recent work using CRY2 to regulate protein-protein interactions, alter protein localization, induce enzyme activity, or disrupt protein function using light.

    April 7th, 2016 at 12:15 PM in Clark Center Seminar Room S360


    Hosted by:

    Bianxiao Cui, Assistant Professor of Chemistry

    Pre-Seminar April 5th, 2016 at 12:15 PM in Clark S361

  • April 05, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S361
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Pre-Seminar for "Optical Control of Protein Activity Using Engineered Photoreceptors"

    BIANXIAO CUI, DEPARTMENT OF CHEMISTRY

    April 5th, 2016 at 12:15 PM in Clark Center Seminar Room S361

    Attend Dr. Cui's pre-seminar presentation to learn more about Dr. Chandra Tucker's seminar, "Optical Control of Protein Activity Using Engineered Photoreceptors", to be held Thursday, April 7th at 12:15 PM in Clark Center Seminar Room S360.

  • March 10, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Discerning Rare Disease Biomarkers by Micro- and Nanotechnologies

    JEFF TZA-HUEI WANG, JOHNS HOPKINS UNIVERSITY

    Genomic analysis of biomarkers, including genetic markers such as point mutations and epigenetic markers such as DNA methylation, has become a central theme in modern disease diagnosis and prognosis. Recently there is an increasing interest in using confocal single-molecule spectroscopy (SMS) for genomic detection. The driving force not only comes from its ultrahigh sensitivity that allows detection of low-abundance nucleic acids without the need for amplification but also from its potential in achieving high-accuracy quantification of rare targets via single-molecule sorting. Semiconductor quantum dots (QDs) also show a great promise for biomarker analysis. The unique photophysical properties of semiconductor quantum dots (QDs) such as high quantum yield and photostability make them ideal for use as spectral labels and luminescent probes. QDs also make excellent donors to pair with organic dyes in the fluorescence resonance energy transfer (FRET) process due to the features of narrow emission spectra and small Stokes shift. This enables FRET with minimal direct acceptor excitation and donor-acceptor crosstalk, thereby permitting the design of FRET molecular sensors with extremely low intrinsic fluorescence backgrounds necessary for detecting biomolecular targets at low abundance. On the other hand, microfluidic technologies offer an exciting opportunity to realize the use of biomarkers in routine clinical settings via the development of miniaturized diagnostic systems. These platforms may function as portable bench-top environments that dramatically shorten the transition of a bench-top assay into a point-of-care format. Dr. Wang’s group has developed highly sensitive, quantitative and clinically relevant technologies for analysis of genomic markers based on the convergence of SMS, microfluidic manipulations, and quantum dots. Extraordinary performances of these new technologies have been exemplified by analysis of a variety of biomarkers including point mutations, DNA integrity and DNA methylation in clinical samples.

    March 10th, 2016 at 12:15 PM in Clark Center Seminar Room S360


    Hosted by:

    Joseph Liao, Associate Professor of Urology

    Pre-Seminar March 8th, 2016 at 12:15 PM in Clark S361

  • April 26, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S361
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Pre-Seminar for "Move Over, Mice: How Integration of Systems Biology with Organs-on-Chips May Humanize Therapeutic Development"

    OVIJIT CHAUDHURI, DEPARTMENT OF MECHANICAL ENGINEERING

    April 5th, 2016 at 12:15 PM in Clark Center Seminar Room S361

    Attend Dr. Chaudhuri's pre-seminar presentation to learn more about Dr. Linda Griffith's seminar, "Move Over, Mice: How Integration of Systems Biology with Organs-on-Chips May Humanize Therapeutic Development", to be held Thursday, April 28th at 12:15 PM in Clark Center Seminar Room S360.

  • April 28, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Move Over, Mice: How Integration of Systems Biology with Organs-on-Chips May Humanize Therapeutic Development

    LINDA GRIFFITH, MIT

    “Mice are not little people” – a refrain becoming louder as the strengths and weaknesses of animal models of human disease become more apparent. At the same time, three emerging approaches are headed toward integration: powerful systems biology analysis of cell-cell and intracellular signaling networks in patient-derived samples; 3D tissue engineered models of human organ systems, often made from stem cells; and micro-fluidic and meso-fluidic devices that enable living systems to be sustained, perturbed and analyzed for weeks in culture. This talk will highlight the integration of these rapidly moving fields to understand difficult clinical problems, with an emphasis on translating academic discoveries into practical, widespread use. These technologies may have broad impact on regenerative medicine, as they may foster development of therapies that slow or halt progression of diseases that lead to organ or tissue failure.

    April 28th, 2016 at 12:15 PM in Clark Center Seminar Room S360


    Hosted by:

    Ovijit Chaudhuri, Assistant Professor of Mechanical Engineering

    Pre-Seminar April 26th, 2016 at 12:15 PM in Clark S361

  • January 14, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Mechanisms of Neuronal Morphogenesis - how does a neuron take its shape?

    KANG SHEN, DEPARTMENTS OF BIOLOGY AND PATHOLOGY

    The connectivity of a neuron (its unique constellation of synaptic inputs and outputs) is essential for its function. Neuronal connections are made with exquisite accuracy between specific types of neurons. How each neuron finds its synaptic partners has been a central question in developmental neurobiology.

    January 14th, 2016 at 12:15 PM in Clark Center Seminar Room S360


    Pre-Seminar January 12th, 2016 at 12:15 PM in Clark S361

  • February 11, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Novel Technologies to Investigate the Neural Stem Cell Niche

    DAVID SCHAFFER, UC BERKELEY

    Elucidating the mechanisms that regulate stem cell behavior is critical for understanding the roles these cells play in organismal development and function as well as for harnessing stem cells to repair tissues damaged by disease or injury. However, stem cell regulation is a complex process that involves intricate signaling interactions among diverse cell types in the niche that in turn activate multiple intracellular signaling pathways to ultimately control cell behavior. Improved techniques are needed to investigate these complex mechanisms in vitro and particular in vivo. For example, viral gene delivery vectors offer the potential for precise genetic perturbations in organisms at any age. In addition, vectors based on viruses such as adeno-associated virus (AAV) have been enjoying increasing human clinical trial success, and they therefore offer a translational path for any basic advances. However, evolution did not endow AAV or other viruses with the capacity for efficient and specific transduction of target cells such as stem cells. Over the past decade, Dr. Schaffer's group initially developed and has been implementing directed vector evolution as a high throughput approach to engineer AAV variants with novel properties, including enhanced biodistribution and spread, targeted delivery to specific cells such as stem cells or their neighbors, and gene editing within a cell. This talk will discuss directed evolution of novel and biomedically relevant AAV variants, as well as the application of gene delivery technologies to investigate cells and stem cells in the nervous system.

    February 11th, 2016 at 12:15 PM in Clark Center Seminar Room S360


    Hosted by:

    Michael Lin, Assistant Professor of Neurobiology and Bioengineering

    Pre-Seminar February 9th, 2016 at 12:15 PM in Clark S361

  • February 09, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S361
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Pre-Seminar for "Novel Technologies to Investigate the Neural Stem Cell Niche"

    MICHAEL LIN, DEPARTMENTS OF NEUROBIOLOGY AND BIOENGINEERING

    February 9th, 2016 at 12:15 PM in Clark Center Seminar Room S361

    Attend Dr. Lin's pre-seminar presentation to learn more about Dr. David Schaffer's seminar, "Novel Technologies to Investigate the Neural Stem Cell Niche", to be held Thursday, February 11th at 12:15 PM in Clark Center Seminar Room S360.

  • January 12, 2016 12:15 PM to 1:00 PM
    Clark Center Seminar Room S361
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Pre-Seminar for "Cell Survival Under Starvation"

    KANG SHEN, DEPARTMENTS OF BIOLOGY AND PATHOLOGY

    January 12th, 2016 at 12:15 PM in Clark Center Seminar Room S361

    Attend Dr. Shen's pre-seminar presentation to learn more about his seminar, "Mechanisms of Neuronal Morphogenesis - how does a neuron take its shape? ", to be held Thursday, January 14th at 12:15 PM in Clark Center Seminar Room S360.

  • January 14, 2016 2:00 PM to 3:00 PM
    Clark Center Auditorium
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Frontiers in Quantitative Biology Seminar

    NIKTA FAKHRI, MASSACHUSETTS INSTITUTE OF TECHNOLOGY

    The Fakhri research group focuses on combining concepts from physics, biology and engineering to decode non-equilibrium mechanisms in active living matter, to exploit these mechanisms for engineering functional active materials and to identify universal behavior in this broad class of internally driven systems.

    Nikta Fakhri has pioneered the use and development of fluorescent single-walled carbon nanotubes as probes in soft matter and biophysics.

    January 14th, 2016 at 2:00 PM in the Clark Center Auditorium

    Frontiers in Quantitative Biology 2015/2016 Seminar Series

    To sign up for the mailing list, please send a blank message to frontiers-qbio-join@lists.stanford.edu.

  • December 03, 2015 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Touring the Protein Folding Landscape: the View Depends on How and Where You Look

    SUSAN MARQUSEE, UC BERKELEY

    Understanding the structural and dynamic information encoded in the primary sequence of a protein is one of the most fundamental challenges in modern biology. The amino acid sequence of a protein encodes more than the native three-dimensional structure; it encodes the entire energy landscape – an ensemble of conformations whose energetics and dynamics are finely tuned for folding, binding and activity. Small variations in the sequence and environment modulate this landscape and can have effects that range from undetectable to pathological. Dr. Marqusee will present her laboratory's recent results probing these sequence and environmental effects using a combination of single-molecule and ensemble-based studies.

    Dr. Marqusee will address a fundamental question in protein folding of whether proteins fold through one or multiple trajectories. While most experiments indicate a single pathway, simulations suggest that proteins can fold through many parallel pathways. By using a combination of chemical denaturant, mechanical force and site-directed mutations, Dr. Marqusee's lab has resolved this apparent contradiction. They can detect the presence of multiple unfolding pathways in a simple, two-state folding protein; the dominant pathway can be altered by small changes in the sequence or environment. Dr. Marqusee will explore the implications of this result for 1) protein folding in complex environments, such as in the cell, or on the ribosome, and 2) the suggestion that evolution can modulate both the rates of folding and the specific pathway.

    December 3rd, 2015 at 12:15 PM in Clark Center Seminar Room S360


    Hosted by:

    Pehr Harbury, Associate Professor of Biochemistry

    Pre-Seminar December 1st, 2015 at 12:15 PM in Clark S361

  • December 01, 2015 12:15 PM to 1:00 PM
    Clark Center Seminar Room S361
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Pre-Seminar for "Touring the Protein Folding Landscape: the View Depends on How and Where You Look"

    PEHR HARBURY, DEPARTMENT OF BIOCHEMISTRY

    December 1st, 2015 at 12:15 PM in Clark Center Seminar Room S361

    Attend Dr. Harbury's pre-seminar presentation to learn more about Dr. Susan Marqusee's seminar, "Touring the Protein Folding Landscape: the View Depends on How and Where You Look", to be held Thursday, December 3rd at 12:15 PM in Clark Center Seminar Room S360.

  • October 29, 2015 12:15 PM to 1:00 PM
    Clark Center Seminar Room S360
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Nerve-Stem Cell Interactions During Organ Development and Regeneration

    SARAH KNOX, UCSF

    The Knox lab is concerned with analyzing the cellular and molecular events underlying the formation of epithelial organs (organogenesis) and their regeneration after injury.

    All epithelial organs receive a functional nerve supply from the parasympathetic branch of the autonomic nervous system. These nerves serve not only in promoting tissue function and homeostasis in the adult, but are also necessary for organ morphogenesis and regeneration after injury through the regulation of stem cells. Dr. Knox will describe her lab's recent findings on the mechanisms by which autonomic nerves regulate morphogenic and regenerative programs using the salivary gland as their model system.

    October 29th, 2015 at 12:15 PM in Clark Center Seminar Room S360


    Hosted by:

    Michelle Monje, Assistant Professor of Neurology, Stanford University

    Pre-Seminar October 27th, 2015 at 12:15 PM in Clark S361

  • April 07, 2016 2:00 PM to 3:00 PM
    Clark Center Auditorium
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Frontiers in Quantitative Biology Seminar

    MARK BRYNILDSEN, PRINCETON UNIVERSITY

    The Brynildsen research group uses both computational and experimental techniques in systems biology, synthetic biology, and metabolic engineering to understand and address threats to human health. They currently focus on the global public health crisis of antibiotic resistance, and are interested in the specific areas of antivirulence therapy and bacterial persistence.

    April 7th, 2016 at 2:00 PM in the Clark Center Auditorium

    Frontiers in Quantitative Biology 2015/2016 Seminar Series

    To sign up for the mailing list, please send a blank message to frontiers-qbio-join@lists.stanford.edu.

  • March 10, 2016 2:00 PM to 3:00 PM
    Clark Center Auditorium
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Frontiers in Quantitative Biology Seminar

    SOPHIE DUMONT, UC SAN FRANCISCO

    The Dumont Lab is interested in how cells coordinate mechanical and chemical activities to accurately segregate chromosomes during cell division. How do cells generate, detect and respond to mechanical force to equally distribute their genetic material when they divide? Errors in chromosome segregation can lead to birth defects and disease. While we know nearly all the molecules essential for chromosome segregation, we do not understand the underlying mechanical principles or how key cellular machines are designed to achieve such robustness and accuracy. New approaches are needed and the Dumont Lab is using new biophysical and molecular tools to address these questions.

    March 10th, 2016 at 2:00 PM in the Clark Center Auditorium

    Frontiers in Quantitative Biology 2015/2016 Seminar Series

    To sign up for the mailing list, please send a blank message to frontiers-qbio-join@lists.stanford.edu.

  • February 11, 2016 2:00 PM to 3:00 PM
    Clark Center Auditorium
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Frontiers in Quantitative Biology Seminar

    LONG CAI, CALTECH

    The main focus of the Cai group is single cell systems biology. They use super-resolution and live cell microscopy to study gene regulatory networks in cells and organisms.

    February 11th, 2016 at 2:00 PM in the Clark Center Auditorium

    Frontiers in Quantitative Biology 2015/2016 Seminar Series

    To sign up for the mailing list, please send a blank message to frontiers-qbio-join@lists.stanford.edu.

  • February 04, 2016 2:00 PM to 3:00 PM
    Clark Center Auditorium
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Frontiers in Quantitative Biology Seminar

    ARJUN RAJ, UNIVERSITY OF PENNSYLVANIA

    The Raj lab is interested in building a quantitative understanding of cellular function. They like to develop new tools for quantifying biological processes based on imaging and sequencing and then use those techniques to help us answer questions in molecular and cellular biology.

    February 4th, 2016 at 2:00 PM in the Clark Center Auditorium

    Frontiers in Quantitative Biology 2015/2016 Seminar Series

    To sign up for the mailing list, please send a blank message to frontiers-qbio-join@lists.stanford.edu.

  • January 21, 2016 2:00 PM to 3:00 PM
    Clark Center Auditorium
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Frontiers in Quantitative Biology Seminar

    IRENE CHEN, UC SANTA BARBARA

    How did chemistry give rise to life? The Chen lab studies principles of emergence and evolution of biomolecules by combining experiments and modeling.

    January 21st, 2016 at 2:00 PM in the Clark Center Auditorium

    Frontiers in Quantitative Biology 2015/2016 Seminar Series

    To sign up for the mailing list, please send a blank message to frontiers-qbio-join@lists.stanford.edu.

  • December 10, 2015 2:00 PM to 3:00 PM
    Clark Center Auditorium
    James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
    Event Type: 

    Frontiers in Quantitative Biology Seminar

    PETRA LEVIN, WASHINGTON UNIVERSITY

    The Levin lab's work seeks to understand the molecular mechanisms underlying the temporal and spatial control of cell division.

    All cells precisely control division to ensure that daughter cells are the correct size and shape and that each receives a complete genome. A short generation time—approximately 20 minutes under ideal growth conditions—coupled with the ease of genetic manipulation, make bacteria ideal model systems in which to study cytokinesis.

    The focus of the Levin lab's research is the highly conserved tubulin homolog FtsZ. In response to an unidentified cell cycle signal FtsZ assembles into a ring structure that serves as a framework for assembly of the division apparatus. The FtsZ ring remains in place until a second unidentified signal stimulates constriction of the ring at the leading edge of the invaginating septum.

    December 10th, 2015 at 2:00 PM in the Clark Center Auditorium

    Frontiers in Quantitative Biology 2015/2016 Seminar Series

    To sign up for the mailing list, please send a blank message to frontiers-qbio-join@lists.stanford.edu.

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