相关论文: Matching reads to many genomes with the $r$-index

To work at scale, a complete image indexing system comprises two components: An inverted file index to restrict the actual search to only a subset that should contain most of the items relevant to the query; An approximate distance…

Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a…

Algorithms that create recommendations based on observed data have significant commercial value for online retailers and many other industries. Recommender systems have a significant research community, and studying such systems is part of…

Cross-fitting is a key ingredient in many semiparametric estimation procedures, such as double/debiased machine learning (DML), enabling valid estimation of low-dimensional targets in the presence of high-dimensional nuisance functions by…

Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…

Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…

RKappa is a framework for the development, simulation and analysis of rule-base models within the mature statistically empowered R environment. It is designed for model editing, parameter identification, simulation, sensitivity analysis and…

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…

We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection,…

metasnf is an R package that enables users to apply meta clustering, a method for efficiently searching a broad space of cluster solutions by clustering the solutions themselves, to clustering workflows based on similarity network fusion…

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…

Computing time is becoming a key issue for tracking algorithms both online and off-line. Programming using adequate data structures can largely improve the efficiency of the reconstruction in terms of time response. We propose using one…

We investigate a prototype application for machine-readable literature. The program is called "pyDataRecognition" and serves as an example of a data-driven literature search, where the literature search query is an experimental data-set…

The recursive model index (RMI) has recently been introduced as a machine-learned replacement for traditional indexes over sorted data, achieving remarkably fast lookups. Follow-up work focused on explaining RMI's performance and…

This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…

Although various forms of linkage map construction software are widely available, there is a distinct lack of packages for use in the R statistical computing environment. This article introduces the ASMap linkage map construction R package…

DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…

We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…