Related papers: Apollo: A Sequencing-Technology-Independent, Scala…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Large Language Model (LLM) agents have recently shown strong potential in domains such as automated coding, deep research, and graphical user interface manipulation. However, training them to succeed on long-horizon, domain-specialized…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
In this paper, we introduce Apollo, a quasi-Newton method for nonconvex stochastic optimization, which dynamically incorporates the curvature of the loss function by approximating the Hessian via a diagonal matrix. Importantly, the update…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…
Pooling specimens, a well-accepted sampling strategy in biomedical research, can be applied to reduce the cost of studying biomarkers. Even if the cost of a single assay is not a major restriction in evaluating biomarkers, pooling can be a…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
Computing haplotypes from sequencing data, i.e. haplotype assembly, is an important component of molecular and population genetics problems, including interpreting the effects of genetic variation on complex traits and reconstructing…
Molecular assembly offers a promising path to detect life beyond Earth, while minimizing assumptions based on terrestrial life. As mass spectrometers will be central to upcoming Solar System missions, predicting molecular assembly from…