Eliminating Exposure Bias and Metric Mismatch in Multiple Object Tracking

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

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

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

David Atienza Alonso, Marina Zapater Sancho, Yasir Mahmood Qureshi, José Manuel Herruzo Ruiz

Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As ...

2020

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

Kalpani Anuradha Welivita

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

Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

Marco Mattavelli, Claudio Paolo Alberti, Ana Angelica Hernandez Lopez

The intrinsic high entropy metadata, known as quality scores, are largely the cause of the substantial size of sequence data files. Yet, there is no consensus on a viable reduction of the resolution of the quality score scale, arguably because of collatera ...

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

Persona: A High-Performance Bioinformatics Framework

James Richard Larus, Edouard Bugnion, Christos Kozyrakis, Stuart Anthony Byma, Sam David Whitlock

Next-generation genome sequencing technology has reached a point at which it is becoming cost-effective to sequence all patients. Biobanks and researchers are faced with an oncoming deluge of genomic data, whose processing requires new and scalable bioinfo ...

2017

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Matteo Dal Peraro, Christophe Bovigny, Luciano Andres Abriata

Background: Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting d ...

2016

Eliminating Exposure Bias and Metric Mismatch in Multiple Object Tracking

Generative power of a protein language model trained on multiple sequence alignments

Impact of phylogeny on structural contact inference from protein sequence data

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

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

Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

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

On the relevance of quality score metadata in genomic sequence data for omics applications

Persona: A High-Performance Bioinformatics Framework

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Graph Chatbot

Generative power of a protein language model trained on multiple sequence alignments

Impact of phylogeny on structural contact inference from protein sequence data

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

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

Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

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

On the relevance of quality score metadata in genomic sequence data for omics applications

Persona: A High-Performance Bioinformatics Framework

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server