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Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Related publications (39)

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Phylogenetic correlations can suffice to infer protein partners from sequences

Anne-Florence Raphaëlle Bitbol

Author summary Many biologically important protein-protein interactions are conserved over evolutionary time scales. This leads to two different signals that can be used to computationally predict interactions between protein families and to identify speci ...

2019

IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback

James Richard Larus, Sahand Kashani, Stuart Anthony Byma

Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This pape ...

2019

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

ASSOC COMPUTING MACHINERY2019

Functional characterization of 3D protein structures informed by human genetic diversity

Amalio Telenti, Istvan Bartha, Julia di Iulio

Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homolog ...

PNAS2019

Database 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 Press2019

Identity Switching remains one of the main difficulties Multiple Object Tracking (MOT) algorithms have to deal with. Many state-of-the-art approaches now use sequence models to solve this problem but their training can be affected by biases that decrease t ...

IEEE2019

Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between proteins result in ...

2018

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

Learning to Predict Human Behavior in Crowded Scenes

Alexandre Massoud Alahi, Vignesh Ramanathan

Pedestrians follow different trajectories to avoid obstacles and accommodate fellow pedestrians. Any autonomous vehicle navigating such a scene should be able to foresee the future positions of pedestrians and accordingly adjust its path to avoid collision ...

Elsevier2017

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