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

Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states

Joana Raquel Pinto Vieira

Systems biology is a multidisciplinary field that weaves together all the basic sciences through the use of computational and bioinformatics tools, to provide a more integrative view of the complex molecular interactions taking place within and among cells ...

EPFL2017

On Computing Breakpoint Distances for Genomes with Duplicate Genes

Bernard Moret, Mingfu Shao

A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or syntenic blocks). For two genomes without duplicate genes, we can easily define (and almost always eff ...

Mary Ann Liebert, Inc2017

PROPER: global protein interaction network alignment through percolation matching

Matthias Grossglauser, Seyed Hamed Hassani, Ehsan Kazemi, Hasan Pezeshgi Modarres

Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological know ...

2016

Flow boiling and frictional pressure gradients in plate heat exchangers. Part 1: Review and experimental database

John Richard Thome, Raffaele Luca Amalfi, Farzad Vakili Farahani

This two-part paper presents an overview of evaporation heat transfer mechanisms, a review of the experimental and prediction methods and a creation of a consolidated multi-lab database of 3601 data points and provides a detailed comparison of all the pred ...

Elsevier Sci Ltd2016

The Resource Identification Initiative: A cultural shift in publishing

Sean Lewis Hill

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insuff ...

2015

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Philipp Bucher, Jacques Rougemont, Olivier Michielin, Mauro Delorenzi, Heinz Stockinger, Ioannis Xenarios, Amos Bairoch

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRI ...

Oxford University Press2014

Learning by Imitation with the STIFF-FLOP Surgical Robot: A Biomimetic Approach Inspired by Octopus Movements

Sylvain Calinon

Transferring skills from a biological organism to a hyper-redundant system is a challenging task, especially when the two agents have very different structure/embodiment and evolve in different environments. In this article we propose to address this probl ...

2014

Biologically active secondary metabolites from cyanobacteria

Cyril Portmann

For millennia, nature was the only source of medicine for mankind. Even today natural products represent a large proportion of the drugs in use. In some areas, like cancer or infectious diseases, about 50 % of the compounds used are of natural origin. Cyan ...

EPFL2010

Leveraging User-Generated Content for Information Discovery on the Web

Adriana Budura

The large-scale adoption of the Web 2.0 paradigm has revolutionized the way we interact with the Web today. End-users, so far mainly passive consumers of information are now becoming active information producers, creating, uploading, and commenting on all ...

EPFL2010

The Microbe browser for comparative genomics

Jacques Rougemont, Alexandre Gattiker, Marco Pagni, Ioannis Xenarios

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene pr ...

Oxford University Press2009