Related papers: Reevaluating Assembly Evaluations with Feature Res…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
Deploying Large Language Model (LLM) applications, particularly those relying on Retrieval-Augmented Generation (RAG), remains challenging due to high computational demands, outdated knowledge bases, and the need to manually select optimal…
Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
Retrieval-Augmented Generation (RAG) systems rely critically on the retriever module to surface relevant context for large language models. Although numerous retrievers have recently been proposed, each built on different ranking principles…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
While the prominent quantum computing architectures are based on superconducting technology, new quantum hardware technologies are emerging, such as Trapped Ions, Neutral Atoms (or FPQAs), Silicon Spin Qubits, etc. This diverse set of…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Retrieval-Augmented Generation (RAG) is increasingly employed in generative AI-driven scientific workflows to integrate rapidly evolving scientific knowledge bases, yet its reliability is frequently compromised by non-determinism in their…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
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…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…