Francesco Oteri

Multi-dimensional optimization of a lysin towards a ribolysin against life-threatening S. aureus infections: Fc-LysM-CHAP and its strong synergy with standard of care antibiotics

Adriana Badarau, Benedikt Bauer, Zehra Visram, Renping Qiao et autres

Abstract Bacterial lysins are promising novel antimicrobials but are limited by poor pharmacokinetics and challenging manufacturability. We developed a lysin discovery platform tailored for lysin delivery via mRNA: staphylococcal LysM-CHAP (cysteine, histidine-dependent amidohydrolases/peptidase) autolysin was selected and its serum half-life extended via …

at, us, fr (code pays fourni par la source)

Designing AI-programmable therapeutics with the EDEN family of foundation models

Geraldene Munsamy, Gavin Ayres, Carla Greco, Keith Kam et autres

Abstract The ability to interpret, modify, and design DNA has driven many of the most significant advances in modern medicine, from diagnostics, biologics, and vaccines to cell and gene therapies. However, the inherent complexity of biological systems means that most modern medicines …

gb, us, es, fi, in (code pays fourni par la source)

CAMP: a modular metagenomics analysis system for integrated multistep data exploration

Lauren Mak, Braden Tierney, Wei Wei, Cynthia Ronkowski et autres

Abstract Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click …

us, pl, br, ch, gb, kz, ee, ua, se, ro (code pays fourni par la source)

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza‐Revilla, Nicolás López Carranza et autres

The prediction of molecular phenotypes from DNA sequences remains a longstanding challenge in genomics, often driven by limited annotated data and the inability to transfer learnings between tasks. Here, we present an extensive study of foundation models pre-trained on DNA sequences, named …

us, de (code pays fourni par la source)

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Marie Lopez, Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza‐Revilla et autres

gb (code pays fourni par la source)

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza‐Revilla, Nicolás López Carranza et autres

Closing the gap between measurable genetic information and observable traits is a longstanding challenge in genomics. Yet, the prediction of molecular phenotypes from DNA sequences alone remains limited and inaccurate, often driven by the scarcity of annotated data and the inability to …

gb (code pays fourni par la source)

iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families

Francesco Oteri, Edoardo Sarti, Francesca Nadalin, Alessandra Carbone

Residue coevolution within and between proteins is used as a marker of physical interaction and/or residue functional cooperation. Pairs or groups of coevolving residues are extracted from multiple sequence alignments based on a variety of computational approaches. However, coevolution signals emerging in …

fr, at, gb (code pays fourni par la source)

A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study

Staëlle Makamte, Aurélien Thureau, Amira Jabrani, Annick Paquelin et autres

Hedgehog (Hh) pathway inhibition by the conserved protein Suppressor of Fused (SuFu) is crucial to vertebrate development. By constrast, SuFu loss-of-function mutant has little effect in drosophila. Previous publications showed that the crystal structures of human and drosophila SuFu consist of two …

fr (code pays fourni par la source)

A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study

Staëlle Makamte, Amira Jabrani, Annick Paquelin, Anne Plessis et autres

Abstract Hedgehog (Hh) pathway inhibition by the conserved protein Suppressor of Fused (SuFu) is crucial to vertebrate development. By constrast, SuFu removal has little effect in drosophila. Previous publications showed that the crystal structures of human and drosophila SuFu consist of two …

fr (code pays fourni par la source)

A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko, Daniela Bezdan, Evan E. Afshin, Sofia Ahsanuddin et autres

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial …

us, de, sg, es, ch, Kenya, in, cl, it, ru, fr, br, no, se, ua, gb, uy, kr, pl, cn, hk, pt, Nigéria, tr, Égypte, vn, jp, bg, co (code pays fourni par la source)

MyCLADE: a multi-source domain annotation server for sequence functional exploration

Riccardo Vicedomini, Clémence Blachon, Francesco Oteri, Alessandra Carbone

The ever-increasing number of genomic and metagenomic sequences accumulating in our databases requires accurate approaches to explore their content against specific domain targets. MyCLADE is a user-friendly webserver designed for targeted functional profiling of genomic and metagenomic sequences based on a database …

fr (code pays fourni par la source)

Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Guénola Drillon, Raphaël Champeimont, Francesco Oteri, Gilles Fischer et autres

Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with …

fr (code pays fourni par la source)