Concept

Sequence alignment

Related publications (32)

Sub-kHz-Linewidth External-Cavity Laser (ECL) With Si3N4 Resonator Used as a Tunable Pump for a Kerr Frequency Comb

Combining optical gain in direct-bandgap III-V materials with tunable optical feedback offered by advanced photonic integrated circuits is key to chip-scale external-cavity lasers (ECL), offering wideband tunability along with low optical linewidths. Exter ...

IEEE Institute of Electrical and Electronics Engineers2023

A new age in protein design empowered by deep learning

Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Casper Alexander Goverde, Arne Schneuing, Hamed Khakzad, Ilia Igashov

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Cell Press2023

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

Protein 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 Portfolio2022

Automatic pathological speech assessment

Parvaneh Janbakhshi

Many pathologies cause impairments in the speech production mechanism resulting in reduced speech intelligibility and communicative ability. To assist the clinical diagnosis, treatment and management of speech disorders, automatic pathological speech asses ...

EPFL2022

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

Nature Portfolio2022

fGOT: Graph Distances Based on Filters and Optimal Transport

Pascal Frossard, Mireille El Gheche, Hermina Petric Maretic

Graph comparison deals with identifying similarities and dissimilarities between graphs. A major obstacle is the unknown alignment of graphs, as well as the lack of accurate and inexpensive comparison metrics. In this work we introduce the filter graph dis ...

ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE2022

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

PUBLIC LIBRARY SCIENCE2022

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

Bart Deplancke

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs condi ...

Nature Portfolio2022

Scaffolding protein functional sites using deep learning

Bruno Emanuel Ferreira De Sousa Correia, Wayne Yang Wen Wei, Karla Montserrat Castro Gilabert

The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing ...

American Association for the Advancement of Science2022

Microscopic field theory for structure formation in systems of self-propelled particles with generic torques

Ignacio Pagonabarraga Mora, Elena Sesé Sansa

We derive a dynamical field theory for self-propelled particles subjected to generic torques and forces by explicitly coarse-graining their microscopic dynamics, described by a many-body Fokker-Planck equation. The model includes both intrinsic torques ind ...

AIP Publishing2022

Foot-Interfaces Control and Human-Robot Interaction in Four-Handed Manipulation

Jacob Hernandez Sanchez

Humans have a great capacity to perform complex manipulations. However, there are many tasks for which two hands are not enough, such as in surgery. For such tasks, a dyad of people is required. However, when not used to work together, a dyad collaboration ...

EPFL2022