相关论文: CompostBin: A DNA composition-based algorithm for …
Bipartite networks are widely used to encode the ecological interactions. Being able to compare the organization of bipartite networks is a first step toward a better understanding of how environmental factors shape community structure and…
Continuous-time Bayesian Networks (CTBNs) represent a compact yet powerful framework for understanding multivariate time-series data. Given complete data, parameters and structure can be estimated efficiently in closed-form. However, if…
Semi-supervised clustering techniques have emerged as valuable tools for leveraging prior information in the form of constraints to improve the quality of clustering outcomes. Despite the proliferation of such methods, the ability to…
Microbiomes not only underpin Earth's biogeochemical cycles but also play crucial roles in both engineered and natural ecosystems, such as the soil, wastewater treatment, and the human gut. However, microbiome engineering faces significant…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
Reducing outcome variance is an essential task in deep learning based medical image analysis. Bootstrap aggregating, also known as bagging, is a canonical ensemble algorithm for aggregating weak learners to become a strong learner. Random…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Let a collection of networks represent interactions within several (social or ecological) systems. We pursue two objectives: identifying similarities in the topological structures that are held in common between the networks and clustering…
Inspired by the importance of diversity in biological system, we built an heterogeneous system that could achieve this goal. Our architecture could be summarized in two basic steps. First, we generate a diverse set of classification…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of…
Current advances in next generation sequencing techniques have allowed researchers to conduct comprehensive research on microbiome and human diseases, with recent studies identifying associations between human microbiome and health outcomes…
Discriminative pattern mining is an essential task of data mining. This task aims to discover patterns which occur more frequently in a class than other classes in a class-labeled dataset. This type of patterns is valuable in various…
Scientific practice typically involves repeatedly studying a system, each time trying to unravel a different perspective. In each study, the scientist may take measurements under different experimental conditions (interventions,…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
The human gut microbiota is known to contribute to numerous physiological functions of the body and also implicated in a myriad of pathological conditions. Prolific research work in the past few decades have yielded valuable information…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…