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EMBL | Stanford Life Science Alliance

Creating synergies between EMBL and Stanford’s research communities

Members

At the core of the Alliance are our Members  – faculty from EMBL and the Stanford University School of Medicine.

Their combined expertise spans a broad spectrum of life science research from structural biology and bioinformatics, to chemistry, imaging and genomics. They are committed to the exchange of information to solve complex biomedical challenges together.

View their research interests and collaborations below.

Contact us

We are always open to accepting new members from EMBL and Stanford University. If our projects or interests match yours, contact us – we would love to hear from you.

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ncRNA annotation (with Mike Cherry)

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Dissecting NGLY1 deficiency (with Lars Steinmetz)

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Identification and in vitro functional characterization of human protective polymorphisms against severe malaria (with Elizabeth Egan)

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Developing global interaction networks of microbiome-encoded genes (with Peer Bork)

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Using and developing innovative methodologies to discover novel molecular mechanisms and therapies for kidney health.

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Molecular basis of chromatin-based silencing and cellular readout of cytosine methylation.

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Developing global interaction networks of microbiome-encoded genes (with Ami Bhatt)

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ncRNA annotation  (with Alex Bateman) 

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The development of cryo-EM methodology to determine 3D cellular structures. We also work on the EMDataResource which is an open access database for 3D EM for developing software, data standards and validation methods.

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Integrative model of human cell signalling (with Evangelia Petsalaki)

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Discovering new calcium-dependent signaling pathways in humans that are regulated by the calcineurin protein phosphatase.

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Personalizing dilated cardiomyopathy (with Lars Steinmetz & Utkan Demirci)

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Personalizing dilated cardiomyopathy (with Lars Steinmetz & Ron Davis)

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Developing novel molecular tools for advanced biological imaging by combining synthetic chemistry and protein engineering

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Understanding the response of roots to water-limiting conditions and across different organizational scales from the individual cell type to the whole plant.

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Assembly mechanisms and function of protein-RNA complexes at the single-molecule level

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Identification and in vitro functional characterization of human protective polymorphisms against severe malaria (with Maria Bernabeu)

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Advancing imaging technology (with Tobias Meyer)

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How oncogenes initiate and sustain tumorigenesis including: how oncogene activation causes tumor regression, and how tumors escape dependence on oncogenes.

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Regulation of self-renewal, proliferation and differentiation in adult stem cell lineages: including regulation of cell type specific transcription programs, cell-cell communication, and the role of differential mRNA processing and translational control in progression from one cell state to the next.

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Genome regulation and topology during embryonic development including: chromatin topology, chromatin remodelling during cell fate decisions, variation and plasticity in regulatory networks, developmental enhancers, and single cell genomics.

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Computational approaches to understand biological systems using genomic and proteomic data across populations. Most of our work is in cancer and neurodegenerative disease, but we love to hear about any interesting questions!

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Keith HodgsonDeciphering the molecular events responsible for touch, pain, and position sensation in C. elegans.

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Understanding the mechanistic interplay between genome regulation, chromatin and environmental cues (microbiome), with emphasis on intergenerational effects

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Using biochemical and systems-level approaches to investigate the connections between gene expression and cell metabolism, and their roles in human disease.

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Dissecting molecular mechanisms of epigenetic silencing (with Howard Chang)

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Integrated structural biology (with Matthias Wilmanns)

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Modern statistics for modern biology (with Wolfgang Huber)

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Modern statistics for modern biology (with Susann Holmes)

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How G protein-coupled receptors decode extracellular cues into dynamic and context-specific cellular signaling networks to elicit diverse physiologic responses

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Characterizing the structure and mechanism of G-Protein Coupled Receptors (GPCRs).

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TRNA editing. We are interested in ADAR-mediated RNA editing, for both its biological function in dsRNA-mediated innate immunity and its utility as a tool for transcriptome engineering. (with Anshul Kundaje)

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We employ state-of-the-art cellular cryo-electron tomography to study phase-separated assemblies in cell biology and to advance our understanding of the molecular organization of the cytoplasm.

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We develop methods and software for high-throughput, automated crystallography and use them to study the structure of sensing and signalling molecules.

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Advancing imaging technology (with Jan Ellenberg)

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Personalizing dilated cardiomyopathy (with Lars Steinmetz)

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Advanced optical techniques for deep tissue microscopy. In particular, we work in the fields of multi-photon microscopy, active wave-front shaping, photo-acoustics as well as computational imaging. Looking for collaboration in cell & developmental biology and neuroscience, where our novel imaging approaches can give new insights.

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Multiomics for pulmonary hypertension (with Judith Zaugg)

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Dissecting the cellular and molecular mechanisms of nervous system assembly and the underlying glia–neuron crosstalk, using advanced genetics, genomics and live imaging approaches.

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Studying the function of visual circuits using functional imaging, genetics, virology and behavioural assays

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Networks of subcellular compartments in health and disease (with Monther Abu-Remaileh)

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Developing a mechanistic understanding of signal translation at the cell membrane using structural biology, biochemistry and simulation methods

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Genetic regulation of chromatin (with Judith Zaugg)

Project:s

Personalizing dilated cardiomyopathy (with Ron Davis, Utkan Demirci, Euan Ashley, Victoria Parikh)

Dissecting NGLY1 deficiency (with Carolyn Bertozzi)

Co-translational nascent chain modifications and their adaptation to cellular stress (with Misha Savitski & Judith Frydman)

Unlocking the potential of image cell sorting for functional genomics and cell biology (with Anna Kreshuk)

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Somatic mosaicisms (with Jan Korbel)

Research Interests:

Gene expression and epigenetics: how DNA methylation, chromatin modifications, and RNA influence chromatin dynamics to affect gene regulation.

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Integrated structural biology (with Keith Hodgson)

Efficient in-cellulo X-ray data acquisition using advanced sample enrichment and delivery tool (with Tina Cohen & Mark Hunter)

Research Interest:

Developing bio-inspired biomaterials and platform technologies to engineer tissues and organs

Projects:

Using scMulti-omics to probe clinical outcome of child leukemia treatment (with Maya Kasowski)

Multiomics for pulmonary hypertension (with Marlene Rabinovitch)

Genetic regulation of chromatin (with Mike Snyder)

Research Interest:

By studying and comparing simple marine animals and their constituent cells, the Arendt group looks to understand the origin and evolution of the nervous system and of the entire animal body.

Research Interest:

We are an inter-disciplinary team of basic and clinical scientists with shared interests in using molecular genetics as a tool to uncover novel biology. We use a variety of different approaches to address important challenges in the field, which range from studies that work genome wide to those which are focused on specific genes and even precise nucleotide changes to understand their impact on pancreatic islet biology.

Research Interest:

Roles for microRNAs and circular RNAs during RNA virus infections.

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The Chen lab studies circuitry and molecular mechanisms underlying motivated behaviors, and how maladaptive changes in these circuits leads to neuropsychiatric disorders.

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The O’Brien lab studies spatial and temporal dynamics of stem cell lineages in vivo using cutting-edge live imaging approaches.

Research Interest:

Research in our lab is aimed at defining the structural correlates of broad and potent antibody-mediated neutralization of viruses. We combine biophysical and structural methods (e.g., cryo-EM), protein engineering, and in vivo approaches to understand how enveloped viruses infect host cells and elicit antigen-specific immune responses. 

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The Trivedi group aims to understand the self-organisation of cells, fundamental to metazoan development, through comparative study of embryos and organoids that generate a global coordinate system de novo.

Research Interest:

The Wang lab is a discovery-driven research group working at the interface between developmental biology, bioengineering, and statistical physics. We combine quantitative organism-wide fluorescence imaging, functional genomics, and physical modeling to understand the fundamental rules that control collective cell behaviors to optimize tissue regeneration, adaptation, and evolution.

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