Publications associées à Base de données biologiques

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 ...

Amer Soc Microbiology2024

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic, Ziang Li

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 ...

Nature Portfolio2024

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

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 SOC2023

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

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 Portfolio2022

Parallel and Scalable Bioinformatics

Stuart Anthony Byma

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 ...

EPFL2020

Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity

Yimon Aye, Xuyu Liu

Here we discuss, how by applying chemical concepts to biological problems, methods have been developed to map spatiotemporal regulation of proteins and small-molecule modulation of proteome signaling responses. We outline why chemical-biology platforms are ...

2019

Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

Duccio Malinverni

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 ...

EPFL2018

Comparison of computational methods for the identification of topologically associating domains

Elisa Oricchio, Marie-Pierre Zufferey, 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 ...

2018

SCCER JA-RED - Description of the multi-energy demonstration system in the RE demo site - Deliverable 1.2.1

Luc Girardin, Nicolas Würsch, Lionel Benjamin Bloch, Jordan Holweger, Hervé Tommasi

In the optic of providing guidelines for the optimal integration of renewable energy in a connected multi-energy context, this report presents EPFL - IPESE and EPFL - PV-lab’s common work on the initial assessment of Romande Energie (RE) demonstration site ...

2017

Models and Algorithms in Biological Network Evolution with Modularity

Min Ye

Networks are commonly used to represent key processes in biology; examples include transcriptional regulatory networks, protein-protein interaction (PPI) networks, metabolic networks, etc. Databases store many such networks, as graphs, observed or inferred ...

EPFL2017