Publications related to Consensus sequence

Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems

Melanie Blokesch, David William Adams, Alexandre Lemopoulos, Grazia Vizzarro

In response to predation by bacteriophages and invasion by other mobile genetic elements such as plasmids, bacteria have evolved specialised defence systems that are often clustered together on genomic islands. The O1 El Tor strains of Vibrio cholerae resp ...

2024

Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance

Sebastian Maerkl, Shiyu Cheng, Ivan Istomin, Maria Lopez Malo, Amir Shahein, Evan James Olson

Binding to binding site clusters has yet to be characterized in depth, and the functional relevance of low-affinity clusters remains uncertain. We characterized transcription factor binding to low-affinity clusters in vitro and found that transcription fac ...

NATURE PORTFOLIO2022

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

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

Automatic Content Curation of Visual Heritage

Mathieu Salzmann, Frédéric Kaplan, Delphine Ribes Lemay, Nicolas Henchoz, Valentine Bernasconi

Digitization and preservation of large heritage induce high maintenance costs to keep up with the technical standards and ensure sustainable access. Creating impactful usage is instrumental to justify the resources for long-term preservation. The Museum fü ...

2021

A Rosetta-based protein design protocol converging to natural sequences

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Stéphane Rosset, Giulia Sormani

Computational protein design has emerged as a powerful tool capable of identifying sequences compatible with pre-defined protein structures. The sequence design protocols, implemented in the Rosetta suite, have become widely used in the protein engineering ...

AMER INST PHYSICS2021

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Philipp Bucher, René Dreos

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

PUBLIC LIBRARY SCIENCE2021

Modulating the properties of DNA-SWCNT sensors using chemically modified DNA

Ardemis Anoush Boghossian, Benjamin Paul Johanès Gabriel Lambert, Alice Judith Gillen, Alessandra Antonucci, Daniel Molina Romero

Properties of SWCNT-based sensors such as brightness and detection capabilities strongly depend on the characteristics of the wrapping used to suspend the nanotubes. In this study, we explore ways to modify the properties of DNA-SWCNT sensors by us- ing ch ...

2021

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Consensus sequence

Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems

Outlier-free spline spaces for isogeometric discretizations of biharmonic and polyharmonic eigenvalue problems

Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Dynamic Chromatin Invasion and Remodeling by the Transcription Factor Rap1

Automatic Content Curation of Visual Heritage

A Rosetta-based protein design protocol converging to natural sequences

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Modulating the properties of DNA-SWCNT sensors using chemically modified DNA

Graph Chatbot

Chat with Graph Search

Outlier-free spline spaces for isogeometric discretizations of biharmonic and polyharmonic eigenvalue problems

Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

A Rosetta-based protein design protocol converging to natural sequences

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Dynamic Chromatin Invasion and Remodeling by the Transcription Factor Rap1

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Automatic Content Curation of Visual Heritage

Modulating the properties of DNA-SWCNT sensors using chemically modified DNA

Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance