Related papers: Statistics of High-Throughput Characterization of …
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
Species interactions (ranging from direct predator prey relationships to indirect effects mediated by the environment) are central to ecosystem balance and biodiversity. While empirical methods for measuring these interactions exist, their…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the…
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
During the last decades macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full…
Dynamical behaviors of complex interacting systems, including brain activities, financial price movements, and physical collective phenomena, are associated with underlying interactions between the system's components. The issue of…
Microfluidics, the study of fluids in microscopic channels, has led to important advances in fields as diverse as microelectronics, biotechnology and chemistry. Microfluidic research is primarily based on the use of microfluidic chips,…
Percolation theory has been widely used to study phase transitions in complex networked systems. It has also successfully explained several macroscopic phenomena across different fields. Yet, the existent theoretical framework for…
Droplet microfluidics, in which micro-droplets serve as individual reactors, has enabled a wide range of high-throughput biochemical processes. Unlike solid wells typically used in current biochemical assays, droplets are subject to…
We present current methods for estimating treatment effects and spillover effects under "interference", a term which covers a broad class of situations in which a unit's outcome depends not only on treatments received by that unit, but also…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
Effective mixing is essential for biochemical reactions. In droplet-based microfluidics, immediate mixing of substances upon contact in the droplet formation stage can greatly enhance the uniformity of chemical reactions. Furthermore, it…
Microdrop impact and spreading phenomena are explored as an interface formation process using a recently developed computational framework. The accuracy of the results obtained from this framework for the simulation of high deformation…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
We present a mesoscale representation of near-contact interactions between colliding droplets which permits to reach up to the scale of full microfluidic devices, where such droplets are produced. The method is demonstrated for the case of…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…
Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated…