Natural Sciences

Accelerating Physics-based Models with Generative Neural Networks

Over the past few years, the potential of machine learning methods that can generate text and images has expanded significantly.…

INSERM

The project aims to understand the functional role of heterochromatin regulation during early embryogenesis. Using a combination of…

Math Encoding In The Human Brain

I am analyzing a large dataset of intracranial electrophysiological recordings in humans, who…

How Animals Keep Time Annually: Molecular Mechanisms of The Seasonal Rhythm

In nature, it is common to see seasonal changes in animal morphology and behavior. For example,

Population Genetics of Cancer Evolution

Cancer develops when evolutionary forces act on mutated cells. When mutations and natural selection repeat over time, cancerous cell…

The Constitution of Individuals and Groups in the Biological Sciences: Implications of an Ecological Framework for Understanding Cancer

Recent biological and biomedical research has featured the idea that living things are not “individuals” but collectives. …

Spatially Modeling the Earthworm Contribution to California's Mercury Cycle

California’s mining and industrial history have led to an excessive build-up of mercury in the Bay Area. As one of the top ten pollutants of the world, this…

Undergraduate Internship - Study of Copy Number Variation in ancient genomes of Homo sapiens, Neanderthals and Denisovans

Climate Variability and Global Food Security, With an Eye on France

Large variations in seasonal temperature and rainfall threaten crop production, food prices, and food security at local to global scales. This project focuses on the impacts…

Energy Transfers for Les of MHD Turbulence: Implication for Realistic Simulations of the Sun

The goal of the Stanford Solar Observatories Group is to study the origin of solar variability, characterize and understand the Sun's interior and the various components of…

Diagnosis of Lower Back Pain From CT Images by Combining Computational Topology

In developed countries about 80% of the total population suffers from acute and 5–10% from permanent lower back pain (LBP). An early diagnosis is crucial to reduce patient…

Molecular Basis of Cytoplasmic Incompatibility Induced by Wolbachia in the Culex Pipiens Mosquito Complex: Role of Transposable Elements?

Symbiosis is a close interaction between different species. The bacteria Wolbachia is the most common endosymbiont (a symbiont living within host cells) described to date.…

Innovative DNA Building Blocks as Biohybrid Catalysts

The need for chiral compounds has escalated tremendously in recent years as many biological activities, flavors or fragrances are associated with their absolute molecular…

Geostatistical Methods for Remote Sensing Data

With the widespread use of satellite imaging, a wealth of information is available to help in the understanding and modeling of earth system processes. In particular, these…

Inference of Demographic History Using Joint Genetic and Linguistic Analyses in Cape Verde

Major human migrations during the last several hundred years have generated new populations of mixed European and African ancestry. The Cape Verde archipelago, located near…

Accelerating Physics-based Models with Generative Neural Networks

Over the past few years, the potential of machine learning methods that can generate text and images has expanded significantly. This project seeks to explore the implications of these advanced techniques for simulating and characterizing chemical and biological systems computationally. While physics-based models of biomolecular systems have been studied extensively, the computational burden of conducting simulations can be prohibitively high, hindering progress on important questions, e.g. small molecule drug design.

INSERM

The project aims to understand the functional role of heterochromatin regulation during early embryogenesis. Using a combination of epigenome editing tools and microscopy, the student will investigate the consequence of DNA repeated derepression on genome integrity in embryonic stem cells.

Math Encoding In The Human Brain

I am analyzing a large dataset of intracranial electrophysiological recordings in humans, who performed a variety of mathematical cognitive tasks, from basic number identification to mental calculation. The recordings were performed on patients with refractory epilepsy during their presurgical evaluation at Stanford University Medical Center. The database includes 100 subjects implanted with grids of electrodes or with penetrating depth electrode arrays.

How Animals Keep Time Annually: Molecular Mechanisms of The Seasonal Rhythm

In nature, it is common to see seasonal changes in animal morphology and behavior. For example, squirrels and bears hibernate in winter; many birds migrate seasonally; and a wide range of animals from frogs to sheep mate and reproduce only during a fixed breeding season. These seasonal rhythms are adaptations of the animals to seasonally changing environment and are vital for animal survival.

Population Genetics of Cancer Evolution

Cancer develops when evolutionary forces act on mutated cells. When mutations and natural selection repeat over time, cancerous cell populations grow and spread. The resulting cancer cell population displays extensive genetic and functional heterogeneity within and across tumors. This diversity presents challenges to our understanding of tumor biology and ability to treat cancer, especially because the evolutionary dynamics and variables underlying the heterogeneity are often poorly understood.

The Constitution of Individuals and Groups in the Biological Sciences: Implications of an Ecological Framework for Understanding Cancer

Recent biological and biomedical research has featured the idea that living things are not “individuals” but collectives.  Gordon and Pradeu examine this question, combining the perspectives of a biologist who studies collective behavior in ant colonies and other natural systems and a philosopher of science who studies the immune system and the microbiome.  They offer a philosophical and scientific examination of the conditions under which something can be said to be an “individual” in the living world, and how, in certain circumstances, i

Spatially Modeling the Earthworm Contribution to California's Mercury Cycle

California’s mining and industrial history have led to an excessive build-up of mercury in the Bay Area. As one of the top ten pollutants of the world, this toxic heavy metal has troubling implications for human and environmental health. Although mercury is relatively well studied in aquatic ecosystems, less work has focused on terrestrial animals. However, we know that soil organisms, such as earthworms, accumulate mercury by consuming decaying plant and animal materials in the ground.

Climate Variability and Global Food Security, With an Eye on France

Large variations in seasonal temperature and rainfall threaten crop production, food prices, and food security at local to global scales. This project focuses on the impacts of climate variability on Europe’s agricultural regions, with an emphasis on wheat in France. Although France has a relatively small agricultural area, it has among the highest wheat yields in the world. Climateinduced shocks to crop production thus influence global prices for wheat and other commodities linked to wheat through markets.

Energy Transfers for Les of MHD Turbulence: Implication for Realistic Simulations of the Sun

The goal of the Stanford Solar Observatories Group is to study the origin of solar variability, characterize and understand the Sun's interior and the various components of magnetic activity. To achieve this goal, data analysis is performed from space missions. For a better understanding of the Sun and predictive capabilities for solar activity and space weather, these observations have to be accompanied by realistic numerical simulations of the subsurface flows and magnetic structures of the Sun.