Related papers: Bacterial Community Reconstruction Using A Single …
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
Synthetic aperture sonar (SAS) measures a scene from multiple views in order to increase the resolution of reconstructed imagery. Image reconstruction methods for SAS coherently combine measurements to focus acoustic energy onto the scene.…
Soil microbial communities are known to be robust against perturbations such as nutrition inputs, which appears as an obstacle for the soil improvement. On the other hand, its adaptable aspect has been also reported. Here we propose simple…
The dark sirens method combines gravitational waves and catalogs of galaxies to constrain the cosmological expansion history, merger rates and mass distributions of compact objects, and the laws of gravity. However, the incompleteness of…
We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using…
We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show…
Accurately establishing the state of large-scale quantum systems is an important tool in quantum information science; however, the large number of unknown parameters hinders the rapid characterisation of such states, and reconstruction…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a…
Compressed Sensing (CS) is an effective approach to reduce the required number of samples for reconstructing a sparse signal in an a priori basis, but may suffer severely from the issue of basis mismatch. In this paper we study the problem…
When working with large biological data sets, exploratory analysis is an important first step for understanding the latent structure and for generating hypotheses to be tested in subsequent analyses. However, when the number of variables is…
The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common…
We present an application of the well-known Mask R-CNN approach to the counting of different types of bacterial colony forming units that were cultured in Petri dishes. Our model was made available to lab technicians in a modern SPA…
We use the replica method of statistical mechanics to examine a typical performance of correctly reconstructing $N$-dimensional sparse vector $bx=(x_i)$ from its linear transformation $by=bF bx$ of $P$ dimensions on the basis of…
Sampling techniques such as Respondent-Driven Sampling (RDS) are widely used in epidemiology to sample "hidden" populations, such that properties of the network can be deduced from the sample. We consider how similar techniques can be…
Optimal reconstruction of a source sequence from multiple noisy traces corrupted by random insertions, deletions, and substitutions typically requires joint processing of all traces, leading to computational complexity that grows…
Networks often exhibit structure at disparate scales. We propose a method for identifying community structure at different scales based on multiresolution modularity and consensus clustering. Our contribution consists of two parts. First,…
We propose a permutation-based method for testing a large collection of hypotheses simultaneously. Our method provides lower bounds for the number of true discoveries in any selected subset of hypotheses. These bounds are simultaneously…