相关论文: META-pipe - Pipeline Annotation, Analysis and Visu…
Our view of the microbial world and its impact on human health is changing radically with the ability to sequence uncultured or unculturable microbes sampled directly from their habitats, ability made possible by fast and cheap next…
Identifying threats in a network traffic flow which is encrypted is uniquely challenging. On one hand it is extremely difficult to simply decrypt the traffic due to modern encryption algorithms. On the other hand, passing such an encrypted…
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
The availability of both structured and unstructured databases, such as electronic health data, social media data, patent data, and surveys that are often updated in real time, among others, has grown rapidly over the past decade. With this…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…
In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…
The simulation and parameter optimization of coupled ocean circulation and ecosystem models in three space dimensions is one of the most challenging tasks in numerical climate research. Here we present a scientific toolkit that aims at…
Over the past decade, data science and machine learning has grown from a mysterious art form to a staple tool across a variety of fields in academia, business, and government. In this paper, we introduce the concept of tree-based pipeline…
Monitoring plankton populations in situ is fundamental to preserve the aquatic ecosystem. Plankton microorganisms are in fact susceptible of minor environmental perturbations, that can reflect into consequent morphological and dynamical…
Metabarcoding on amplicons is rapidly expanding as a method to produce molecular based inventories of microbial communities. Here, we work on freshwater diatoms, which are microalgae possibly inventoried both on a morphological and a…
Optimization methods are playing an increasingly important role in all facets of photonics engineering, from integrated photonics to free space diffractive optics. However, efforts in the photonics community to develop optimization…
Metagenomics has led to significant advancements in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large…
Increasing interest in the acquisition of biotic and abiotic resources from within the deep sea (e.g. fisheries, oil-gas extraction, and mining) urgently imposes the development of novel monitoring technologies, beyond the traditional…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
Meta-graph is currently the most powerful tool for similarity search on heterogeneous information networks,where a meta-graph is a composition of meta-paths that captures the complex structural information. However, current relevance…
The effectiveness of the machine learning methods for real-world tasks depends on the proper structure of the modeling pipeline. The proposed approach is aimed to automate the design of composite machine learning pipelines, which is…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…