相关论文: CompostBin: A DNA composition-based algorithm for …

The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…

The compositionality and sparsity of high-throughput sequencing data poses a challenge for regression and classification. However, in microbiome research in particular, conditional modeling is an essential tool to investigate relationships…

We present a new algorithm, MULTIGRAIN, for modelling the dynamics of an entire population of small dust grains immersed in gas, typical of conditions that are found in molecular clouds and protoplanetary discs. The MULTIGRAIN method is…

In many high-throughput experimental design settings, such as those common in biochemical engineering, batched queries are more cost effective than one-by-one sequential queries. Furthermore, it is often not possible to directly choose…

Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…

Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…

The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic…

The in vitro clonogenic assay is a technique to study the ability of a cell to form a colony in a culture dish. By optical imaging, dishes with stained colonies can be scanned and assessed digitally. Identification, segmentation and…

Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…

DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…

In the field of transmission electron microscopy, data interpretation often lags behind acquisition methods, as image processing methods often have to be manually tailored to individual datasets. Machine learning offers a promising approach…

To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow.…

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…

Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…

Microbiome functions are encoded within the genes of the community-wide metagenome. A natural question is whether properties of a microbial community can be predicted just from knowing the raw DNA sequences of its members. In this work, we…

In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…

Clustering techniques have been the key drivers of data mining, machine learning and pattern recognition for decades. One of the most popular clustering algorithms is DBSCAN due to its high accuracy and noise tolerance. Many superior…

Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster, and with better coverage than…

Global climate change has reduced crop resilience and pesticide efficacy, making reliance on synthetic pesticides inevitable, even though their widespread use poses significant health and environmental risks. While these pesticides remain a…