1205 papers
Bioinformatics sits at the exciting intersection where biology meets data science, using powerful computer tools to decode the vast complexity of living systems. From mapping the human genome to tracking how viruses evolve, this field transforms raw biological information into actionable insights that drive modern medicine and research forward without requiring a supercomputer to understand the basics.
On Gist.Science, we ensure you never miss a breakthrough by processing every new preprint in this category directly from bioRxiv. Our team provides both plain-language explanations and detailed technical summaries for each paper, making cutting-edge discoveries accessible to everyone regardless of their background.
Below are the latest bioinformatics papers added from bioRxiv, ready for you to explore with clarity and depth.
This paper introduces a novel method for comparing pangenome diversity by interpolating and extrapolating node counts in colored compacted de Bruijn graphs, utilizing Hill numbers to adjust for varying genome numbers and mitigate the disproportionate influence of rare genomic sequences.
SpeciefAI is a transformer-based model that generates multi-species, mRNA-level antibody framework regions tailored to specific host species and input CDRs, ensuring both high sequence similarity to natural repertoires and optimized codon adaptation for in vivo therapeutic expression.
This paper introduces homology-based metrics to evaluate and compare pangenome graphs (specifically variation graphs and whole genome alignments), proposes transformations between these models, and provides a software package to implement these methods.
This paper introduces faster, space-efficient subset rank data structures requiring less than 3 bits per k-mer, which enable new Pareto-optimal k-mer lookup structures for genomic analysis at the low-memory end of the space-time spectrum.
This paper introduces 10-minimizers, a new class of constant-space sampling schemes that provably achieve lower density than random minimizers in the non-asymptotic regime and offer competitive k-mer retrieval speeds through a specific variant called "spacers."
The paper introduces scTimeBench, a modular benchmarking platform that evaluates nine state-of-the-art single-cell time-series methods across multiple datasets and tasks, revealing that while many achieve high forecast accuracy, they often fail to preserve biological signals and lineage fidelity compared to simple baselines.
MosaicTR is a computational tool that leverages haplotype-tagged long-read sequencing to accurately quantify per-locus somatic instability of tandem repeats, overcoming the limitations of short-read methods to serve as a biomarker for mismatch repair deficiency and a monitor of disease progression in repeat expansion disorders.
This paper introduces MutationNetwork, a graph-based framework that integrates long-range intrachromosomal interactions with local genomic overlaps to construct mutation-centric networks, enabling the effective clustering of breast cancer subtypes and the prioritization of non-coding driver mutations through network-level impact analysis.
VICAST is an integrated software toolkit designed to streamline viral passage studies by combining semi-automated genome annotation with manual curation and optimized low-frequency variant calling, offering superior speed and accuracy compared to existing tools for diverse viral families.
This paper introduces SLAB, an efficient sweep line algorithm based on PBWT that identifies width-maximal haplotype block cores to reveal population genetic insights and selection signals complementary to traditional IBD rate analyses.