Efficient sequence alignment against millions of prokaryotic genomes with LexicMap
Probe generation Probes, also referred to as ‘masks’ in the LexicHash paper, consist of a fixed number (m = 20,000…
Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation
Nonparametric baselines We design two nonparametric baselines that we refer to as perturbed mean and matching mean. Perturbed…
The genetic history of Portugal over the past 5,000 years | Genome Biology
Gómez-Carballa, A., Olivieri, A., Behar, D.M., Achilli, A., Torroni, A., and Salas, A. . Genetic Continuity in the…
GeneRiskCalc: a web-based tool for genetic risk association analysis in case–control studies | BMC Bioinformatics
Hardy–Weinberg equilibrium The HWE is a key principle in population genetics, stating that allele and genotype frequencies remain…
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants | BMC Bioinformatics
GenMasterTable is a standalone, cross-platform desktop application developed in Python to facilitate scalable genomic data analysis. It integrates…
Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden | Genome Biology
Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of Population Structure using Dense Haplotype Data. Copenhaver GP,…
Morphological map of under- and overexpression of genes in human cells
Mattiazzi Usaj, M. et al. High-content screening for quantitative cell biology. Trends Cell Biol. 26, 598–611 (2016). CAS …
The Platinum Pedigree: a long-read benchmark for genetic variants
Gonzaga-Jauregui, C., Lupski, J. R. & Gibbs, R. A. Human genome sequencing in health and disease. Annu. Rev.…
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines
The success of large language models in knowledge representation has spawned efforts to apply the foundation model concept…
GeneAgent: self-verification language agent for gene-set analysis using domain databases
Model setting and data collection In this work, we utilized GPT-4 (version 20230613) as the backend model via…
Healthy Life: Ancient viruses in our DNA may hold clues to what makes us human | Healthy Life
Fragments of ancient viral DNA once dismissed as “junk” may play a role in controlling our genes, according…