Related papers: Apollo: A Sequencing-Technology-Independent, Scala…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
The implementation of a new final-state parton-shower algorithm in the Pythia event generator is described. The shower algorithm, dubbed Apollo, combines central aspects of the Vincia antenna shower with the global transverse-recoil scheme…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
Producing images from interferometer data requires accurate modeling of the sources in the field of view, which is typically done using the CLEAN algorithm. Given the large number of degrees of freedom in interferometeric images, one…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
Long-form numerical reasoning in financial analysis aims to generate a reasoning program to calculate the correct answer for a given question. Previous work followed a retriever-generator framework, where the retriever selects key facts…
Low-Rank Adaptation (LoRA) is a widely used finetuning method for large models. Its small memory footprint allows practitioners to adapt large models to specific tasks at a fraction of the cost of full finetuning. Different modifications…
Optical Pooled Screening (OPS) is a powerful tool combining high-content microscopy with genetic engineering to investigate gene function in disease. The characterization of high-content images remains an active area of research and is…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
The optimal robot assembly planning problem is challenging due to the necessity of finding the optimal solution amongst an exponentially vast number of possible plans, all while satisfying a selection of constraints. Traditionally, robotic…
In recent years, the advancement of AI technologies has accelerated the development of smart factories. In particular, the automatic monitoring of product assembly progress is crucial for improving operational efficiency, minimizing the…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…
High-throughput computational screening of polymers offers a powerful way to address the imbalance between the vast number of polymers synthesised for diverse applications and the relatively small subset that can be studied using atomistic…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Long-read sequencing has enabled the de novo assembly of several mammalian genomes, but with high cost in computing. Here, we demonstrated de novo assembly of mammalian genome using long reads in an efficient and inexpensive workstation.