Concept
Biological database
Related publications (43)
Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods
Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...
Washington2024Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...
Berlin2024Impact of phylogeny on structural contact inference from protein sequence data
Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Umberto Lupo
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...
ROYAL SOC2023Protein language models trained on multiple sequence alignments learn phylogenetic relationships
Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo
Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...
NATURE PORTFOLIO2022Metadata standards and tools in Life Sciences – an overview
Eliane Ninfa Blumer, Sitthida Samath
In 2020, EPFL Library conducted a study about Tools and Metadata Standards practice in EPFL School of Life Sciences. By standard, we mean: - terminological resources (vocabularies, terminologies, classifications, thesauri), - formats and data models / sche ...
2020Parallel and Scalable Bioinformatics
The field of genomics is likely to become the largest producer of data as a consequence of the large-scale application of next-generation sequencing technology for biological research and personalized medical treatments. The raw sequence data produced by t ...
EPFL2020Database Alignment with Gaussian Features
Negar Kiyavash, Osman Emre Dai
We consider the problem of aligning a pair of databases with jointly Gaussian features. We consider two algorithms, complete database alignment via MAP estimation among all possible database alignments, and partial alignment via a thresholding approach of ...
MLR Press2019Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones
Recent advances in DNA sequencing technologies led to the accumulation of enormous quantities of genetic information available in public databases. This rapid growth of available biological datasets calls for quantitative analysis tools and concomitantly o ...
EPFL2018Comparison of computational methods for the identification of topologically associating domains
Elisa Oricchio, Daniele Tavernari, Giovanni Ciriello
BackgroundChromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiati ...
BMC2018